My question is actually a bit more broad than what's in the title, but I don't know how to put it succinctly. When I was trying to find the answer to that question, I found that all known terrestrial vertebrates are ultimately descended from a species of lobe-finned fish that had 2 sets of bilaterally symmetric fins (which excludes the dorsal and ventral fins), which were the basis for the limbs of its tetrapodal descendants.
The best way I can think of to phrase the question is: Does paleontology has any evidence of a vertebrate that had 3 (or more) sets of bilaterally symmetric limbs or lobe-based fins? I'd like the focus to stay away from ray-finned fish, even though they're vertebrates and related.
This is not the common question, which is whether there is or can be a mammal/reptile species with more than four limbs. The essence of that question's answer is that mammals and reptiles both evolved from a common ancestor species that were tetrapods, and that it's extremely difficult to change the genetic floor plan in the necessary way without causing fatal problems (along with other evolutionary issues). By and large, this common question is so common that it chokes out the type of question that I have, making my amateur attempts at further research difficult to impossible.
I've not read it but this SE question Why don't mammals have more than 4 limbs? though not a duplicate (it asks about mammals not all vertebrates) may have some elements in its answers pertinent to your question.
And the question Why are there no vertebrates with more than four limbs? has been asked in Quora where it has 7 answers you may find useful.
Also this discussion thread Why can insects have 6+ limbs, but mammals only have 4? in reddit.
Does paleontology has any evidence of a vertebrate that had 3 (or more) sets of bilaterally symmetric limbs or lobe-based fins?
You sent me far down the rabbit hole with this one, for reasons that escape me my instant response was 'yes the Coelacanth' but as you correctly point out that has only 4 paired fins.
As seen from The origin of tetrapods our limbs came from fins, Coelacanth is a good example of the likely early beginnings of Tetrapod limbs, they occasionally use them to 'walk' on the seabed.
The image provided in this National Geographic article Coelacanth Rediscovered gives a much clearer picture of it's 'limb' structures.
Latimeria chalumnae, the coelacanth (SEE-lee-uh-kanth), thought extinct until a biologist identified one off the coast of South Africa in 1939.
I've trawled Google for early chordates looking for examples of more than two pairs of fins & haven't been able to find any, it seems the earliest paired fins appeared in (or shortly before) Ostracoderms & from there continued in an unbroken line to the tetrapods & our limbs.
Paired fins don't appear to have developed in chordates before then or to have ever developed into more than two pairs.
So to the best of my knowledge it appears that the answer to your question is no.
Other links. Yunnanozoon Myllokunmingia Haikouichthys Evolution of fish
Vertebrate with Extra Limbs
In Real Life, vertebrates have at most four functional limbs - legs, arms (which anatomically are really modified forelegs), or wings (which are modified arms) - and one tail. If it has more than that, like arthropods (insects, spiders, centipedes, etc), it's not a vertebrate. Some individuals have abnormal numbers due to injury or glitches during development, but additional limbs rarely function properly. Those with less, like snakes and whales, still evolved from four-limbed animals.
There's nothing intrinsically wrong with six or more legs - it's just that current large land animals originated from a species with a four limb body plan, and adding more requires all sorts of complicated skeleton and muscle changes that are much more complex than just making the ones the organism already has a little better. Or, if they're weighing the critter down. take them out. Just look at whales for a demo. This apparently happens a lot - evidence suggests that when the first fish crawled out of the water, it did so on seven-toed feet. (For more info on the topic, try the other wiki)
Of course the fact that there's one standard land vertebrate body plan doesn't stop fiction writers from subverting nature's tropes. This trope may be exactly as old as dirt, for a number of documentaries have suggested that many tales of fantastic creatures could have been inspired by early humans encountering bones of prehistoric creatures and misinterpreting the evidence. For reasons that should be obvious, in modern writing, vertebrates with five or more limbs is primarily a Speculative Fiction trope. They're often very useful in said fiction, in combat or for grabbing.
Sometimes justified because A Wizard Did It or because there's no obvious reason why aliens would always have exactly four limbs, but trying to determine the internal anatomy of such creatures may lead to Fridge Logic. While in most cases authors Hand Wave such things, it doesn't stop others from trying.
Note: as the subtropes get filled out with three or more examples, they can be TLP'd and moved into separate subtropes.
Contrast Four-Legged Insect, which provides examples of invertebrates with fewer limbs than in real life.
Tiktaalik provides insights on the features of the extinct closest relatives of the tetrapods. Unlike many previous, more fishlike transitional fossils, the "fins" of Tiktaalik have basic wrist bones and simple rays reminiscent of fingers. The homology of distal elements is uncertain there have been suggestions that they are homologous to digits, although this is incompatible with the digital arch developmental model because digits are supposed to be postaxial structures, and only three of the (reconstructed) eight rays of Tiktaalik are postaxial. 
However, the proximal series can be directly compared to the ulnare and intermedium of tetrapods. The fin was clearly weight bearing, being attached to a massive shoulder with expanded scapular and coracoid elements and attached to the body armor, large muscular scars on the ventral surface of the humerus, and highly mobile distal joints. The bones of the forefins show large muscle facets, suggesting that the fin was both muscular and had the ability to flex like a wrist joint. These wrist-like features would have helped anchor the creature to the bottom in fast moving current.  
Also notable are the spiracles on the top of the head, which suggest the creature had primitive lungs as well as gills. This attribute would have been useful in shallow water, where higher water temperature would lower oxygen content. This development may have led to the evolution of a more robust ribcage, a key evolutionary trait of land-living creatures.  The more robust ribcage of Tiktaalik would have helped support the animal's body any time it ventured outside a fully aquatic habitat. Tiktaalik also lacked a characteristic that most fishes have—bony plates in the gill area that restrict lateral head movement. This makes Tiktaalik the earliest known fish to have a neck, with the pectoral girdle separate from the skull. This would give the creature more freedom in hunting prey either on land or in the shallows. 
Tiktaalik is sometimes compared to gars (esp. Atractosteus spatula, the alligator gar) of the family Lepisosteidae, with whom it shares a number of characteristics: 
- diamond-shaped scale patterns common to the Crossopterygii class (in both species scales are rhombic, overlapping and tuberculated)
- teeth structured in two rows
- both internal and external nostrils
- tubular and streamlined body
- absence of anterior dorsal fin
- broad, dorsoventrally compressed skull
- paired frontal bones
- marginal nares
- subterminal mouth
- lung-like organ.
Tiktaalik generally had the characteristics of a lobe-finned fish, but with front fins featuring arm-like skeletal structures more akin to those of a crocodile, including a shoulder, elbow, and wrist. The fossil discovered in 2004 did not include the rear fins and tail. It had rows  of sharp teeth indicative of a predator fish, and its neck could move independently of its body, which is not common in other fish (Tarrasius, Mandageria, placoderms,   and extant seahorses being some exceptions see also Lepidogalaxias and Channallabes apus  ). The animal had a flat skull resembling a crocodile's eyes on top of its head a neck and ribs similar to those of tetrapods, with the ribs being used to support its body and aid in breathing via lungs well developed jaws suitable for catching prey and a small gill slit called a spiracle that, in more derived animals, became an ear. 
The fossils were found in the "Fram Formation", deposits of meandering stream systems near the Devonian equator, suggesting a benthic animal that lived on the bottom of shallow waters and perhaps even out of the water for short periods, with a skeleton indicating that it could support its body under the force of gravity whether in very shallow water or on land.  At that period, for the first time, deciduous plants were flourishing and annually shedding leaves into the water, attracting small prey into warm oxygen-poor shallows that were difficult for larger fish to swim in.  The discoverers said that in all likelihood, Tiktaalik flexed its proto-limbs primarily on the floor of streams and may have pulled itself onto the shore for brief periods.  In 2014, the discovery of the animal's pelvic girdle was announced it was strongly built, indicating the animal could have used them for moving in shallow water and across mudflats.  Neil Shubin and Daeschler, the leaders of the team, have been searching Ellesmere Island for fossils since 2000  
We're making the hypothesis that this animal was specialized for living in shallow stream systems, perhaps swampy habitats, perhaps even to some of the ponds. And maybe occasionally, using its very specialized fins, for moving up overland. And that's what is particularly important here. The animal is developing features which will eventually allow animals to exploit land. 
- Panderichthys, suited to muddy shallows
- Tiktaalik with limb-like fins that could take it onto land in weed-filled swamps, such as:
Tiktaalik roseae is the only species classified under the genus. Tiktaalik lived approximately 375 million years ago. It is representative of the transition between non-tetrapod vertebrates (fish) such as Panderichthys, known from fossils 380 million years old, and early tetrapods such as Acanthostega and Ichthyostega, known from fossils about 365 million years old. Its mixture of primitive fish and derived tetrapod characteristics led one of its discoverers, Neil Shubin, to characterize Tiktaalik as a "fishapod".  
Tiktaalik is a transitional fossil it is to tetrapods what Archaeopteryx is to birds, troodonts and dromaeosaurids. While it may be that neither is ancestor to any living animal, they serve as evidence that intermediates between very different types of vertebrates did once exist. The mixture of both fish and tetrapod characteristics found in Tiktaalik include these traits:
- fish gills
- fish scales
- fish fins
- half-fish, half-tetrapod limb bones and joints, including a functional wrist joint and radiating, fish-like fins instead of toes
- half-fish, half-tetrapod ear region
- tetrapod rib bones
- tetrapod mobile neck with separate pectoral girdle
- tetrapod lungs
2006 – 2010 Edit
The phylogenetic analysis by Daeschler et al. placed Tiktaalik as a sister taxon to Elpistostege and directly above Panderichthys preceded by Eusthenopteron. Tiktaalik was thus inserted below Acanthostega and Ichthyostega as a transitional form  and a true "missing link". 
Such order of the phylogenetic tree was initially adopted by other experts, most notably by Per Ahlberg and Jennifer Clack.  However, it was questioned in a 2008 paper by Boisvert et al., who noted that Panderichthys, due to its more derived distal portion, might be closer to tetrapods than Tiktaalik or even that it was convergent with tetrapods.  Ahlberg, co-author of the study, considered the possibility of Tiktaalik's fin having been "an evolutionary return to a more primitive form." 
2010 – now Edit
In January 2010, a group of paleontologists including Ahlberg published a paper  accompanied by extensive supplementary material  (discussed also in a Nature documentary   ) which showed that the first tetrapods appeared long before Tiktaalik and other elpistostegids. Their conclusions were based on numerous trackways (esp. Muz. PGI 1728.II.16) and individual footprints (esp. Muz. PGI 1728.II.1) discovered at the Zachełmie quarry in the Holy Cross Mountains (Poland). A tetrapod origin of those tracks was suggested based on:
- distinct digits and limb morphology
- trackways reflecting quadrupedal gait and diagonal walk
- no body or tail drag marks
- very wide stride in relation to body length (much beyond that of Tiktaalik or any other fish)
- various size footprints with some unusually big (up to 26 cm wide) indicating body lengths of over 2.5 m.
Track-bearing layers were assigned to the lower-middle Eifelian based on conodont index fossil samples (costatus Zone) and "previous biostratigraphic data obtained from the underlying and overlying strata"  with subsequent studies confirming this dating.   
Both Tiktaalik's discoverers were skeptical about the Zachelmie trackways. Daeschler said that trace evidence was not enough for him to modify the theory of tetrapod evolution,  while Shubin argued that Tiktaalik could have produced very similar footprints  (in a later study Shubin expressed a significantly modified opinion that some of the Zachelmie footprints, those which lacked digits, may have been made by walking fish  ). However, Ahlberg insisted that those tracks could not have possibly been formed either by natural processes or by transitional species such as Tiktaalik or Panderichthys.   Instead, the authors of the publication suggested ichthyostegalians as trackmakers, based on available pes morphology of those animals.  However, a paper published in 2015 that undertook a critical review of Devonian tetrapod footprints called into question the designation of the Zachelmie marks and instead suggested an origin as fish nests/feeding traces.  An earlier study in 2012 indicated that Zachelmie trackmakers were even more advanced than Ichthyostega in terms of quadrupedalism.  Grzegorz Niedźwiedzki's reconstruction of one of the trackmakers was identical to that of Tulerpeton.  
Narkiewicz, co-author of the article on the Zachelmie trackways, claimed that the Polish "discovery has disproved the theory that elpistostegids were the ancestors of tetrapods",  a notion partially shared by Philippe Janvier.  There have been a number of new hypotheses suggested as to a possible origin and phylogenetic position of the elpistostegids (including Tiktaalik):
- their phylogenetic position remains unchanged and the footprints found in the Holy Cross Mountains are attributed to tetrapods but as a result there are at least six long ghost lineages separating Zachelmie trackmakers from various elpistostegalian and ichthyostegalian species 
- they were "late-surviving relics rather than direct transitional forms" 
- they were "an evolutionary dead-end" 
- they were a result of convergent or parallel evolution so that apomorphies and striking anatomical similarities found in both digited tetrapods and elpistostegalians evolved at least twice. 
Convergency is considered responsible for uniquely tetrapod features found also in other non-elpistostegalian fish from the period like Sauripterus (finger-like jointed distal radial bones)   or Tarrasius (tetrapod-like spine with 5 axial regions). 
Estimates published after the discovery of Zachelmie tracks suggested that digited tetrapods may have appeared as early as 427.4 Ma ago and questioned attempts to read absolute timing of evolutionary events in early tetrapod evolution from stratigraphy. 
Until more data become available, the phylogenetic position of Tiktaalik and other elpistostegids remains uncertain.
In 2004, three fossilized Tiktaalik skeletons were discovered in the Late Devonian fluvial Fram Formation on Ellesmere Island, Nunavut, in northern Canada.   Estimated ages reported at 375 MYA, 379 MYA, and 383 MYA. At the time of the species' existence, Ellesmere Island was part of the continent Laurentia (modern eastern North America and Greenland),  which was centered on the equator and had a warm climate. When discovered, one of the skulls was found sticking out of a cliff. Upon further inspection, the fossil was found to be in excellent condition for a 375-million-year-old specimen.  
The discovery by Daeschler, Shubin, and Jenkins was published in the April 6, 2006, issue of Nature  and quickly recognized as a transitional form. Jennifer A. Clack, a Cambridge University expert on tetrapod evolution, said of Tiktaalik, "It's one of those things you can point to and say, 'I told you this would exist,' and there it is." 
After five years of digging on Ellesmere Island, in the far north of Nunavut, they hit pay dirt: a collection of several fish so beautifully preserved that their skeletons were still intact. As Shubin's team studied the species they saw to their excitement that it was exactly the missing intermediate they were looking for. 'We found something that really split the difference right down the middle,' says Daeschler.
The name Tiktaalik is an Inuktitut word meaning "large freshwater fish".  The "fishapod" genus received this name after a suggestion by Inuit elders of Canada's Nunavut Territory, where the fossil was discovered.  The specific name roseae cryptically honours an anonymous donor.  Taking a detailed look at the internal head skeleton of Tiktaalik roseae, in the October 16, 2008, issue of Nature,  researchers show how Tiktaalik was gaining structures that could allow it to support itself on solid ground and breathe air, a key intermediate step in the transformation of the skull that accompanied the shift to life on land by our distant ancestors. 
Other lobe-finned fish found in fossils from the Devonian Period:
- ^ abc Edward B. Daeschler, Neil H. Shubin and Farish A. Jenkins Jr. (6 April 2006). "A Devonian tetrapod-like fish and the evolution of the tetrapod body plan". Nature. 440 (7085): 757–763. Bibcode:2006Natur.440..757D. doi: 10.1038/nature04639 . PMID16598249.
- "What has the head of a crocodile and the gills of a fish?". evolution.berkeley.edu. Archived from the original on 2018-06-12 . Retrieved 2018-06-06 .
- ^ ab
- Shubin, Neil (2008). Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body. New York: University of Chicago Press. ISBN9780375424472 .
- Laurin M (2006). "Scanty evidence and changing opinions about evolving appendages". Zoologica Scripta. 35 (6): 667–668. doi:10.1111/zsc.2006.35.issue-6.
- ^ abcd
- Shubin, Neil (2008). Your Inner Fish. Pantheon. ISBN978-0-375-42447-2 .
- ^ abc
- Holmes, Bob (2007). "Meet Your ancestor, the Fish that crawled". New Scientist. Archived from the original on 2016-04-13 . Retrieved 2007-02-07 .
- ^ abJennifer A. Clack, Scientific American, Getting a Leg Up on LandArchived 2013-12-07 at the Wayback Machine November 21, 2005.
- Spitzer, Mark (2010). Season of the Gar: Adventures in Pursuit of America's Most Misunderstood Fish. University of Arkansas Press. pp. 65–66. ISBN978-1-55728-929-2 . Archived from the original on 2014-01-07 . Retrieved 2016-10-29 .
- "Fossil Suggests Missing Link From Fish to Land". NPR (National Public Radio). Archived from the original on 2006-10-13 . Retrieved 2006-11-27 .
- K. Trinajstic et al. (12 July 2013). "Fossil Musculature of the Most Primitive Jawed Vertebrates". Science. 341 (6142): 160–164. Bibcode:2013Sci. 341..160T. doi:10.1126/science.1237275. PMID23765280. S2CID39468073. CS1 maint: uses authors parameter (link)
- "Primitive fish could nod but not shake its head: Ancient fossils reveal surprises about early vertebrate necks, abdominal muscles". Science News. June 13, 2013. Archived from the original on December 15, 2013 . Retrieved December 14, 2013 .
- Sam Van Wassenbergh Anthony Herrel Dominique Adriaens Frank Huysentruyt Stijn Devaere & Peter Aerts (13 April 2006). "Evolution: A catfish that can strike its prey on land". Nature. 440 (7086): 881. Bibcode:2006Natur.440..881V. doi:10.1038/440881a. PMID16612372. S2CID4423295.
- Dalton, Rex (2006). "The fish that crawled out of the water". Nature: news060403–7. doi:10.1038/news060403-7. Archived from the original on 2006-04-11 . Retrieved 2006-04-06 .
- ^The Academy of Natural Sciences, Philadelphia, press release April 3, 2006. (doc)
- Neil H. Shubin, Edward B. Daeschler and Farish A. Jenkins Jr (6 April 2006). "The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb". Nature. 440 (7085): 764–771. Bibcode:2006Natur.440..764S. doi:10.1038/nature04637. PMID16598250. S2CID4412895.
- Shubin, N. H. Daeschler, E. B. Jenkins, F. A. (2014). "Pelvic girdle and fin of Tiktaalik roseae". Proceedings of the National Academy of Sciences. 111 (3): 893–899. Bibcode:2014PNAS..111..893S. doi:10.1073/pnas.1322559111. PMC3903263 . PMID24449831.
- ^ ab
- Peterson, Britt (April 5, 2006). "An Evolutionary Finding". Seed. Archived from the original on April 11, 2006 . Retrieved April 5, 2006 . CS1 maint: unfit URL (link)
- ^ NewsHour, Fossil DiscoveryArchived 2014-01-22 at the Wayback Machine, April 6, 2006.
- ^ John Noble Wilford, The New York Times, Scientists Call Fish Fossil the Missing LinkArchived 2017-11-15 at the Wayback Machine, Apr. 5, 2006.
- Daeschler, Edward B. Shubin, Neil H. Jenkins, Farish A. Jr (6 April 2006). "A Devonian tetrapod-like fish and the evolution of the tetrapod body plan" (PDF) . Nature. 440 (7085): 757–763. Bibcode:2006Natur.440..757D. doi: 10.1038/nature04639 . PMID16598249. S2CID4413217. Archived (PDF) from the original on 12 February 2015 . Retrieved 24 January 2015 .
- Rex Dalton (5 April 2006). "The fish that crawled out of the water". Nature. doi:10.1038/news060403-7. Archived from the original on 24 January 2015 . Retrieved 24 January 2015 .
- Ahlberg, Per Erik Clack, Jennifer A. (6 April 2006). "A firm step from water to land". Nature. 440 (7085): 747–749. Bibcode:2006Natur.440..747A. doi: 10.1038/440747a . PMID16598240. S2CID4392361.
- Boisvert, Catherine A. Mark-Kurik, Elga Ahlberg, Per E. (4 December 2008). "The pectoral fin of Panderichthys and the origin of digits". Nature. 456 (7222): 636–638. Bibcode:2008Natur.456..636B. doi:10.1038/nature07339. PMID18806778. S2CID2588617. Archived from the original on 4 January 2014 . Retrieved 24 January 2015 . Given that recent phylogenies consistently place Panderichthys below Tiktaalik in the tetrapod stem group, it is surprising to discover that its pectoral fin skeleton is more limb-like than that of its supposedly more derived relative. [. ] It is difficult to say whether this character distribution implies that Tiktaalik is autapomorphic, that Panderichthys and tetrapods are convergent, or that Panderichthys is closer to tetrapods than Tiktaalik.
- Ker Than (September 24, 2008). "Ancient Fish Had Primitive Fingers, Toes". National Geographic News. National Geographic Society. Archived from the original on September 27, 2008. Curiously, the radial bones of Panderichthys are more finger-like than those of Tiktaalik, a fish with stubby leg-like limbs that lived about five million years later. Many scientists regard Tiktaalik as a "missing link": the crucial transitional animal between fish and the first tetrapods. One possibility, Ahlberg said, is that finger development took a step backward with Tiktaalik, and that Tiktaalik's fins represented an evolutionary return to a more primitive form.
- ^ abcde
- Niedźwiedzki, Grzegorz Szrek, Piotr Narkiewicz, Katarzyna Narkiewicz, Marek Ahlberg, Per E. (7 January 2010). "Tetrapod trackways from the early Middle Devonian Period of Poland". Nature. 463 (7277): 43–48. Bibcode:2010Natur.463. 43N. doi:10.1038/nature08623. PMID20054388. S2CID4428903.
- Niedźwiedzki, Grzegorz Szrek, Piotr Narkiewicz, Katarzyna Narkiewicz, Marek Ahlberg, Per E. (2010). "Tetrapod trackways from the early Middle Devonian Period of Poland. Supplementary information". Nature. 463 (7277): 43–8. Bibcode:2010Natur.463. 43N. doi:10.1038/nature08623. PMID20054388. S2CID4428903.
- Walking with tetrapods. Nature. January 6, 2010. Archived from the original (FLV) on December 20, 2014.
- Jonathan Amos (6 January 2010). "Fossil tracks record 'oldest land-walkers ' ". BBC. Archived from the original on January 7, 2010.
- Narkiewicz, Katarzyna Narkiewicz, Marek (1 March 2010). "Mid Devonian carbonate platform development in the Holy Cross Mts. area (central Poland): new constraints from the conodont Bipennatus fauna". Neues Jahrbuch für Geologie und Paläontologie – Abhandlungen. 255 (3): 287–300. doi:10.1127/0077-7749/2009/0025.
- Niedźwiedzki, Grzegorz Narkiewicz, Marek Szrek, Piotr (2014). "The age of the oldest tetrapod tracks from Zachełmie, Poland". Bulletin of Geosciences. 89 (3): 593–606. Archived from the original on 2015-05-11 . Retrieved 2015-01-24 .
- Narkiewicz, Katarzyna Narkiewicz, Marek (January 2015). "Middle Devonian invertebrate trace fossils from the marginal marine carbonates of the Zachełmie tetrapod tracksite, Holy Cross Mountains, Poland". Lethaia. 48 (1): 10–12. doi:10.1111/let.12083.
- ^ "Trace evidence is not enough for me to change my mind about accepted theories on tetrapod evolution" – Daeschler as quoted in
- Rex Dalton (January 6, 2010). "Discovery pushes back date of first four-legged animal". Nature: news.2010.1. doi:10.1038/news.2010.1. Archived from the original on March 8, 2014. "I am not ready to discard the established paradigm for the fish-tetrapod transition" – Daeschler as quoted in
- Jef Akst (January 6, 2010). "Tetrapods' old age revealed". The Scientist. Archived from the original on March 4, 2016 . Retrieved November 10, 2019 . "With all respect to the scientists involved in this study, there may be other explanations for these suggestive tracks." – Daeschler as quoted in
- Dan Vergano (January 6, 2010). "Four-legged finding muddies paleontological waters". USA Today. Archived from the original on December 24, 2014.
- ^ [Neil Shubin] says that a model of Tiktaalik's skeleton would produce a print much like the one in the paper if it's mushed into sand, and different consistencies or angles would produce an even closer match. He adds, "There is nothing in Tiktaalik's described anatomy that suggests it didn't have a stride." in
- Ed Yong (January 6, 2010). "Fossil tracks push back the invasion of land by 18 million years". Discover. Archived from the original on May 16, 2010.
- King, Heather M. Shubin, Neil H. Coates, Michael I. Hale, Melina E. (December 27, 2011). "Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes". PNAS. 108 (52): 21146–21151. Bibcode:2011PNAS..10821146K. doi:10.1073/pnas.1118669109. PMC3248479 . PMID22160688. It follows that the attribution of some of the nondigited Devonian fossil trackways to limbed tetrapods may need to be revisited.
- ^ "You can see anatomical details consistent with a footprint, including sediments displaced by a foot coming down", "There is no way these could be formed by a natural process." - Ahlberg as quoted in
- Rex Dalton (January 6, 2010). "Discovery pushes back date of first four-legged animal". Nature: news.2010.1. doi:10.1038/news.2010.1. Archived from the original on March 8, 2014.
- Lucas, Spencer G. (2015). "Thinopus and a Critical Review of Devonian Tetrapod Footprints" (PDF) . Ichnos. 22 (3–4): 136–154. doi:10.1080/10420940.2015.1063491. S2CID130053031.
- Pierce, Stephanie E. Clack, Jennifer A. Hutchinson, John R. (28 June 2012). "Three-dimensional limb joint mobility in the early tetrapod Ichthyostega" (PDF) . Nature. 486 (7404): 523–526. Bibcode:2012Natur.486..523P. doi:10.1038/nature11124. PMID22722854. S2CID3127857.
- ^ ab
- Niedźwiedzki, Grzegorz Szrek, Piotr (2010). "Way to Go!" (PDF) . Academia. 2 (26): 28–31. ISSN1731-7401. OCLC786293607. Archived from the original (PDF) on January 19, 2015.
- ^ The 2007 artistic restoration of Tulerpeton by Dmitry Bogdanov available at Wikimedia is virtually identical to the 2008 rendering of a Zachelmie trackmaker by Grzegorz Niedźwiedzki.
- W.Ż. (February 4, 2010). "A Creature That Time Forgot". The Warsaw Voice. Warsaw. Archived from the original on December 22, 2014.
- "W Polsce odkryto ślady najstarszych kopalnych czworonogów" [Oldest tetrapod fossil footprints discovered in Poland]. Science & Scholarship in Poland (Polish Press Agency) (in Polish). Warsaw. January 7, 2010. Archived from the original on December 22, 2014.
- ^ "We now have to invent a common ancestor to the tetrapods and elpistostegids." – Janvier as quoted in
- Karen McVeigh (January 6, 2010). "Footprints show tetrapods walked on land 18m years earlier than thought". The Guardian. London. Archived from the original on March 2, 2014.
- Editor's summary (7 January 2010). "Four feet in the past: trackways pre-date earliest body fossils". Nature. 463 (7277): 40–1. Bibcode:2010Natur.463. 40J. doi:10.1038/463040a. PMID20054387. S2CID447958. Archived from the original on November 3, 2012. CS1 maint: uses authors parameter (link)
- "Ancient Four-Legged Beasts Leave Their Mark". Science. 6 January 2010. Archived from the original on September 30, 2013.
- Janvier, Philippe Clément, Gaël (7 January 2010). "Muddy tetrapod origins". Nature. 463 (7277): 40–41. Bibcode:2010Natur.463. 40J. doi:10.1038/463040a. PMID20054387. S2CID447958.
- ^ ab
- Friedman, Matt Brazeau, Martin D. (7 February 2011). "Sequences, stratigraphy and scenarios: what can we say about the fossil record of the earliest tetrapods?". Proceedings of the Royal Society B. 278 (1704): 432–439. doi:10.1098/rspb.2010.1321. PMC3013411 . PMID20739322.
- Gee, Henry (January 6, 2010). "First Footing". SciLogs. Archived from the original on December 22, 2014. It is possible that the close similarity between elpistostegids and tetrapods might have been the result of evolutionary convergence. The common ancestor of elpistostegids and tetrapods wouldn't have to have looked like Tiktaalik – it could have been a more undifferentiated, tetrapodomorph fish. Elpistostegids and tetrapodomorphs, each following their own paths, grew to look more and more like one other.
- Daeschler, Edward B. Shubin, Neil (8 January 1998). "Fish with fingers?". Nature. 391 (6663): 133. Bibcode:1998Natur.391..133D. doi:10.1038/34317. S2CID4386457.
- Davis, Marcus C. Shubin, Neil Daeschler, Edward B. (2004). "A new specimen of Sauripterus taylori (Sarcopterygii, Osteichthyes) from the Famennian Catskill Formation of North America". Journal of Vertebrate Paleontology. 24 (1): 26–40. doi:10.1671/1920-3. S2CID128815066.
- Sallan, Lauren Cole (22 August 2012). "Tetrapod-like axial regionalization in an early ray-finned fish". Proceedings of the Royal Society B. 279 (1741): 3264–3271. doi:10.1098/rspb.2012.0784. PMC3385743 . PMID22628471.
- Gorner, Peter (2006-04-05). "Fossil could be fish-to-land link". Chicago Tribune.
- Easton, John (2008-10-23). "Tiktaalik's internal anatomy explains evolutionary shift from water to land". University of Chicago Chronicle. University of Chicago. 28 (3). Archived from the original on 2012-04-07 . Retrieved 2009-07-19 .
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- Spotts, Peter (April 6, 2006). "Fossil fills gap in move from sea to land". The Christian Science Monitor. Archived from the original on April 6, 2006 . Retrieved 2006-04-05 .
- Holmes, Bob (5 April 2006). "First fossil of fish that crawled onto land discovered". New Scientist News. Archived from the original on 6 April 2006 . Retrieved 2006-04-07 .
- Coyne, Jerry (2009). Why Evolution is True. Viking. ISBN978-0-670-02053-9 . Archived from the original on 2019-10-07 . Retrieved 2019-09-03 .
- Jason P. Downs, Edward B. Daeschler, Farish A. Jenkins & Neil H. Shubin (16 October 2008). "The cranial endoskeleton of Tiktaalik roseae". Nature. 455 (7215): 925–929. Bibcode:2008Natur.455..925D. doi:10.1038/nature07189. PMID18923515. S2CID4411801. CS1 maint: multiple names: authors list (link)
- ^"Fishapod" Reveals Origins of Head and Neck Structures of First Land AnimalsArchived 2008-10-19 at the Wayback Machine Newswise, Retrieved on October 15, 2008.
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Characteristics of Vertebrates
The main distinguishing feature of vertebrates is their vertebral column, or backbone (see Figure below). The backbone runs from the head to the tail along the dorsal (top) side of the body. The vertebral column is the core of the endoskeleton. It allows a vertebrate to hold its shape. It also houses and protects the spinal (nerve) cord that passes through it. The vertebral column is made up of repeating units called vertebrae (singular, vertebra). In many species, there are shock-absorbing discs between the vertebrae to cushion them during movement.
Human Vertebral Column and Vertebrae. The human vertebral column consists of 33 vertebrae. Two vertebrae are shown here enlarged.
Another distinguishing feature of vertebrates is an endoskeleton made of bone or cartilage.Cartilage is a tough tissue that contains a protein called collagen. Bone is a hard tissue that consists of a collagen matrix, or framework, filled in with minerals such as calcium. Bone is less flexible than cartilage but stronger. An endoskeleton made of bone rather than cartilage allows animals to grow larger and heavier. Bone also provides more protection for soft tissues and internal organs.
As shown in Figure below, the vertebrate endoskeleton includes a cranium, or skull, to enclose and protect the brain. It also generally includes two pairs of limbs. Limb girdles (such as the human hips and shoulders) connect the limbs to the rest of the endoskeleton.
Vertebrate Endoskeletons. The vertebrate endoskeleton includes a vertebral column, cranium, limbs, and limb girdles. Can you find these parts in each endoskeleton shown here?
Other Vertebrate Traits
There are several additional traits found in virtually all vertebrates.
- Vertebrates have a system of muscles attached to the endoskeleton to enable movement. Muscles control movement by alternately contracting (shortening) and relaxing (lengthening). Generally, muscles work together in opposing pairs.
- Vertebrates have a closed circulatory system with a heart. Blood is completely contained within blood vessels that carry the blood throughout the body. The heart is divided into chambers that work together to pump blood. There are between two and four chambers in the vertebrate heart. With more chambers, there is more oxygen in the blood and more vigorous pumping action.
- Most vertebrates have skin covered with scales, feathers, fur, or hair. These features serve a variety of functions, such as waterproofing and insulating the body.
- Vertebrates have an excretory system that includes a pair of kidneys. Kidneys are organs that filter wastes from blood so they can be excreted from the body.
- Vertebrates have an endocrine system of glands that secrete hormones. Hormones are chemical messengers that control many body functions.
- Vertebrates have an adaptive immune system. The immune system is the organ system that defends the body from pathogens and other causes of disease. Being adaptive means that the immune system can "learn" to recognize specific pathogens. Then it can produce tailor-made proteins called antibodies to "attack" them. This allows the immune system to launch a rapid attack whenever the pathogens invade the body again.
- Vertebrates have a centralized nervous system. As shown in Figurebelow, the nervous system consists of a brain in the head region. It also includes a long spinal cord that runs from the brain to the tail end of the backbone. Long nerve fibers extend from the spinal cord to muscles and organs throughout the body.
Nervous System (Human). The vertebrate nervous system includes a brain and spinal cord. It also includes a body-wide network of nerves, called peripheral nerves. They connect the spinal cord with the rest of the body.
2 Answers 2
Hexapod mobility is something that's currently being studied in robotics. Ding et al. published a paper on the topic in 2010, where they discussed a variety of advantages that they saw in hexapod locomotion, such as:
- Increased static stability
- Increased efficiency while walking
- Ability to remain stable while using some legs as manipulators
- Ability to remain mobile after losing a leg by changing their walking pattern
A hexapod vertebrate would have similar advantages over a tetrapod vertebrate. For slow moving creatures, hexapod gaits would likely require less neural mass, since they're very statically stable. Faster moving creatures with more developed brains would likely rely on quadrupedal locomotion for speed, using the remaining two limbs as manipulators.
Beyond the question of feasibility in a terrestrial creature, the other pertinent question is whether six-limbed fish (or fish-like ancestors) would evolve. The most similar creatures to an ancestral fish, in terms of size, body plan, and ecological role, are likely the eurypterids, or sea scorpions. Like early vertebrates, eurypterids were mostly bilaterally symmetric free swimming creatures that used their limbs as paddles. Free swimming eurypterids generally had a single pair of primary swimming paddles, plus several pairs of crawling legs for moving along the bottom. Some eurypterids had an additional pair of grasping claws for manipulating their environments.
Interestingly, a similar gait has evolved in a modern fish: trigloporus lastoviza, though they've evolved a set of rays for locomoting across the ocean floor, rather than using their primary limbs. Ancestral hexapods would likely evolve on similar lines, but using primary limbs for sea floor locomotion instead of rays: four limbs for locomotion across the bottom of the ocean, an additional pair for swimming, and possibly an extra pair of limbs for manipulating their environments. Such an arrangement might even make it easier for them to transition to living on land, needing to transition only from crawling on the sea floor to crawling across the surface, rather than from swimming to crawling. The swimming limbs would likely either evolve to be used for locomotion or manipulation, or else be lost, leaving their descendants with four locomotion legs and two manipulators.
Vertebrates are among the most recognizable organisms of the animal kingdom (Figure 15.36). More than 62,000 vertebrate species have been identified. The vertebrate species now living represent only a small portion of the vertebrates that have existed. The best-known extinct vertebrates are the dinosaurs, a unique group of reptiles, reaching sizes not seen before or since in terrestrial animals. They were the dominant terrestrial animals for 150 million years, until they died out near the end of the Cretaceous period in a mass extinction. A great deal is known about the anatomy of the dinosaurs, given the preservation of their skeletal elements in the fossil record.
Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, and jawless fishes were the earliest of these. Jawless fishes—the present day hagfishes and lampreys—have a distinct cranium and complex sense organs including eyes, distinguishing them from the invertebrate chordates. The jawed fishes evolved later and are extraordinarily diverse today. Fishes are active feeders, rather than sessile, suspension feeders.
Jawless fishes are craniates (which includes all the chordate groups except the tunicates and lancelets) that represent an ancient vertebrate lineage that arose over one half-billion years ago. Some of the earliest jawless fishes were the ostracoderms (which translates as “shell-skin”). Ostracoderms, now extinct, were vertebrate fishes encased in bony armor, unlike present-day jawless fishes, which lack bone in their scales.
The clade Myxini includes 67 species of hagfishes. Hagfishes are eel-like scavengers that live on the ocean floor and feed on dead invertebrates, other fishes, and marine mammals (Figure 15.37a). Hagfishes are entirely marine and are found in oceans around the world except for the polar regions. A unique feature of these animals is the slime glands beneath the skin that are able to release an extraordinary amount of mucus through surface pores. This mucus may allow the hagfish to escape from the grip of predators. Hagfish are known to enter the bodies of dead or dying organisms to devour them from the inside.
The skeleton of a hagfish is composed of cartilage, which includes a cartilaginous notochord, which runs the length of the body, and a skull. This notochord provides support to the fish’s body. Although they are craniates, hagfishes are not vertebrates, since they do not replace the notochord with a vertebral column during development, as do the vertebrates.
The clade Petromyzontidae includes approximately 40 species of lampreys. Lampreys are similar to hagfishes in size and shape however, lampreys have a brain case and incomplete vertebrae. Lampreys lack paired appendages and bone, as do the hagfishes. As adults, lampreys are characterized by a toothed, funnel-like sucking mouth. Some species are parasitic as adults, attaching to and feeding on the body fluids of fish (Figure 15.37b). Most species are free-living.
Lampreys live primarily in coastal and fresh waters and have a worldwide temperate region distribution. All species spawn in fresh waters. Eggs are fertilized externally, and the larvae are distinctly different from the adult form, spending 3 to 15 years as suspension feeders. Once they attain sexual maturity, the adults reproduce and die within days. Lampreys have a notochord as adults.
Gnathostomes or “jaw-mouths” are vertebrates that have jaws and include both cartilaginous and bony fishes. One of the most significant developments in early vertebrate evolution was the origin of the jaw, which is a hinged structure attached to the cranium that allows an animal to grasp and tear its food. The evolution of jaws allowed early gnathostomes to exploit food resources that were unavailable to jawless fishes.
The clade Chondrichthyes , the cartilaginous fishes, is diverse, consisting of sharks (Figure 15.38a), rays, and skates, together with sawfishes and a few dozen species of fishes called chimaeras, or ghost sharks. Chondrichthyes have paired fins and a skeleton made of cartilage. This clade arose approximately 370 million years ago in the middle Devonian. They are thought to have descended from an extinct group that had a skeleton made of bone thus, the cartilaginous skeleton of Chondrichthyes is a later development. Parts of the shark skeleton are strengthened by granules of calcium carbonate, but this is not the same as bone.
Most cartilaginous fishes live in marine habitats, with a few species living in fresh water for some or all of their lives. Most sharks are carnivores that feed on live prey, either swallowing it whole or using their jaws and teeth to tear it into smaller pieces. Shark teeth likely evolved from the jagged scales that cover their skin. Some species of sharks and rays are suspension feeders that feed on plankton.
Sharks have well-developed sense organs that aid them in locating prey, including a keen sense of smell and electroreception, the latter being perhaps the most sensitive of any animal. Organs called ampullae of Lorenzini allow sharks to detect the electromagnetic fields that are produced by all living things, including their prey. Electroreception has only been observed in aquatic or amphibious animals. Sharks, together with most fishes, also have a sense organ called the lateral line , which is used to detect movement and vibration in the surrounding water, and a sense that is often considered homologous to “hearing” in terrestrial vertebrates. The lateral line is visible as a darker stripe that runs along the length of the fish’s body.
Sharks reproduce sexually and eggs are fertilized internally. Most species are ovoviviparous, that is, the fertilized egg is retained in the oviduct of the mother’s body, and the embryo is nourished by the egg yolk. The eggs hatch in the uterus and young are born alive and fully functional. Some species of sharks are oviparous: They lay eggs that hatch outside of the mother’s body. Embryos are protected by a shark egg case or “mermaid’s purse” that has the consistency of leather. The shark egg case has tentacles that snag in seaweed and give the newborn shark cover. A few species of sharks are viviparous, that is, the young develop within the mother’s body, and she gives live birth.
Rays and skates include more than 500 species and are closely related to sharks. They can be distinguished from sharks by their flattened bodies, pectoral fins that are enlarged and fused to the head, and gill slits on their ventral surface (Figure 15.38b). Like sharks, rays and skates have a cartilaginous skeleton. Most species are marine and live on the sea floor, with nearly a worldwide distribution.
Members of the clade Osteichthyes , or bony fishes, are characterized by a bony skeleton. The vast majority of present-day fishes belong to this group, which consists of approximately 30,000 species, making it the largest class of vertebrates in existence today.
Nearly all bony fishes have an ossified skeleton with specialized bone cells (osteocytes) that produce and maintain a calcium phosphate matrix. This characteristic has only reverted in a few groups of Osteichthyes, such as sturgeons and paddlefish, which have primarily cartilaginous skeletons. The skin of bony fishes is often covered in overlapping scales, and glands in the skin secrete mucus that reduces drag when swimming and aids the fish in osmoregulation. Like sharks, bony fishes have a lateral line system that detects vibrations in water. Unlike sharks, some bony fish depend on their eyesight to locate prey. Bony fish are also unusual in possessing taste cells in the head and trunk region of the body that allow them to detect extremely small concentrations of molecules in the water.
All bony fishes, like the cartilaginous fishes, use gills to breathe. Water is drawn over gills that are located in chambers covered and ventilated by a protective, muscular flap called the operculum. Unlike sharks, bony fishes have a swim bladder , a gas-filled organ that helps to control the buoyancy of the fish. Bony fishes are further divided into two clades with living members: Actinopterygii (ray-finned fishes) and Sarcopterygii (lobe-finned fishes).
The ray-finned fishes include many familiar fishes—tuna, bass, trout, and salmon (Figure 15.39a), among others. Ray-finned fishes are named for the form of their fins—webs of skin supported by bony spines called rays. In contrast, the fins of lobe-finned fishes are fleshy and supported by bone (Figure 15.39b). Living members of lobe-finned fishes include the less familiar lungfishes and coelacanth.
Amphibians are vertebrate tetrapods. Amphibia includes frogs, salamanders, and caecilians. The term amphibian means “dual life,” which is a reference to the metamorphosis that many frogs undergo from a tadpole to an adult and the mixture of aquatic and terrestrial environments in their life cycle. Amphibians evolved in the Devonian period and were the earliest terrestrial tetrapods.
As tetrapods, most amphibians are characterized by four well-developed limbs, although some species of salamanders and all caecilians possess only vestigial limbs. An important characteristic of extant amphibians is a moist, permeable skin, achieved by mucus glands. The moist skin allows oxygen and carbon dioxide exchange with the environment, a process called cutaneous respiration . All living adult amphibian species are carnivorous, and some terrestrial amphibians have a sticky tongue that is used to capture prey.
Amphibia comprise an estimated 6,500 extant species that inhabit tropical and temperate regions around the world. Amphibians can be divided into three clades: Urodela (“tailed-ones”), the salamanders and newts Anura (“tail-less ones”), the frogs and toads and Apoda (“legless ones”), the caecilians.
Living salamanders (Figure 15.40a) include approximately 500 species, some of which are aquatic, others terrestrial, and some that live on land only as adults. Adult salamanders usually have a generalized tetrapod body plan with four limbs and a tail. Some salamanders are lungless, and respiration occurs through the skin or external gills. Some terrestrial salamanders have primitive lungs a few species have both gills and lungs.
Concepts in Action
Watch this video about an unusually large salamander species.
Frogs (Figure 15.40b) are the most diverse group of amphibians, with approximately 5,000 species that live on all continents except Antarctica. Frogs have a body plan that is more specialized than the salamander body plan for movement on land. Adult frogs use their hind limbs to jump many times their body length on land. Frogs have a number of modifications that allow them to avoid predators, including skin that acts as camouflage and defensive chemicals that are poisonous to predators secreted from glands in the skin.
Frog eggs are fertilized externally, as they are laid in moist environments. Frogs demonstrate a range of parental behaviors, with some species exhibiting little care, to species that carry eggs and tadpoles on their hind legs or backs. The life cycle consists of two stages: the larval stage followed by metamorphosis to an adult stage. The larval stage of a frog, the tadpole , is often a filter-feeding herbivore. Tadpoles usually have gills, a lateral line system, long-finned tails, but no limbs. At the end of the tadpole stage, frogs undergo a gradual metamorphosis into the adult form. During this stage, the gills and lateral line system disappear, and four limbs develop. The jaws become larger and are suited for carnivorous feeding, and the digestive system transforms into the typical short gut of a predator. An eardrum and air-breathing lungs also develop. These changes during metamorphosis allow the larvae to move onto land in the adult stage (Figure 15.41).
Caecilians comprise an estimated 185 species. They lack external limbs and resemble giant earthworms. They inhabit soil and are found primarily in the tropics of South America, Africa, and southern Asia where they are adapted for a soil-burrowing lifestyle and are nearly blind. Unlike most of the other amphibians that breed in or near water, reproduction in a drier soil habitat means that caecilians must utilize internal fertilization, and most species give birth to live young (Figure 15.42).
Reptiles and Birds
The amniotes —reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted (shelled) egg and an embryo protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes could develop within an aquatic environment inside the egg. This led to less dependence on a water environment for development and allowed the amniotes to invade drier areas. This was a significant evolutionary change that distinguished them from amphibians, which were restricted to moist environments due to their shell-less eggs. Although the shells of various amniotic species vary significantly, they all allow retention of water. The membranes of the amniotic egg also allowed gas exchange and sequestering of wastes within the enclosure of an eggshell. The shells of bird eggs are composed of calcium carbonate and are hard and brittle, but possess pores for gas and water exchange. The shells of reptile eggs are more leathery and pliable. Most mammals do not lay eggs however, even with internal gestation, amniotic membranes are still present.
In the past, the most common division of amniotes has been into classes Mammalia, Reptilia, and Aves. Birds are descended, however, from dinosaurs, so this classical scheme results in groups that are not true clades. We will discuss birds as a group distinct from reptiles with the understanding that this does not reflect evolutionary history.
Reptiles are tetrapods. Limbless reptiles—snakes—may have vestigial limbs and, like caecilians, are classified as tetrapods because they are descended from four-limbed ancestors. Reptiles lay shelled eggs on land. Even aquatic reptiles, like sea turtles, return to the land to lay eggs. They usually reproduce sexually with internal fertilization. Some species display ovoviviparity, with the eggs remaining in the mother’s body until they are ready to hatch. Other species are viviparous, with the offspring born alive.
One of the key adaptations that permitted reptiles to live on land was the development of their scaly skin, containing the protein keratin and waxy lipids, which prevented water loss from the skin. This occlusive skin means that reptiles cannot use their skin for respiration, like amphibians, and thus all must breathe with lungs. In addition, reptiles conserve valuable body water by excreting nitrogen in the form of uric acid paste. These characteristics, along with the shelled, amniotic egg, were the major reasons why reptiles became so successful in colonizing a variety of terrestrial habitats far from water.
Reptiles are ectotherms, that is, animals whose main source of body heat comes from the environment. Behavioral maneuvers, like basking to heat themselves, or seeking shade or burrows to cool off, help them regulate their body temperature,
Class Reptilia includes diverse species classified into four living clades. These are the Crocodilia, Sphenodontia, Squamata, and Testudines.
The Crocodilia (“small lizard”) arose approximately 84 million years ago, and living species include alligators, crocodiles, and caimans. Crocodilians (Figure 15.43a) live throughout the tropics of Africa, South America, the southeastern United States, Asia, and Australia. They are found in freshwater habitats, such as rivers and lakes, and spend most of their time in water. Some species are able to move on land due to their semi-erect posture.
The Sphenodontia (“wedge tooth”) arose in the Mesozoic Era and includes only one living genus, Tuatara, with two species that are found in New Zealand. There are many fossil species extending back to the Triassic period (250–200 million years ago). Although the tuataras resemble lizards, they are anatomically distinct and share characteristics that are found in birds and turtles.
Squamata (“scaly”) arose in the late Permian living species include lizards and snakes, which are the largest extant clade of reptiles (Figure 15.43b). Lizards differ from snakes by having four limbs, eyelids, and external ears, which are lacking in snakes. Lizard species range in size from chameleons and geckos that are a few centimeters in length to the Komodo dragon, which is about 3 meters in length.
Snakes are thought to have descended from either burrowing lizards or aquatic lizards over 100 million years ago (Figure 15.43c). Snakes comprise about 3,000 species and are found on every continent except Antarctica. They range in size from 10 centimeter-long thread snakes to 7.5 meter-long pythons and anacondas. All snakes are carnivorous and eat small animals, birds, eggs, fish, and insects.
Turtles are members of the clade Testudines (“having a shell”) (Figure 15.43d). Turtles are characterized by a bony or cartilaginous shell, made up of the carapace on the back and the plastron on the ventral surface, which develops from the ribs. Turtles arose approximately 200 million years ago, predating crocodiles, lizards, and snakes. Turtles lay eggs on land, although many species live in or near water. Turtles range in size from the speckled padloper tortoise at 8 centimeters (3.1 inches) to the leatherback sea turtle at 200 centimeters (over 6 feet). The term “turtle” is sometimes used to describe only those species of Testudines that live in the sea, with the terms “tortoise” and “terrapin” used to refer to species that live on land and in fresh water, respectively.
Data now suggest that birds belong within the reptile clade, but they display a number of unique adaptations that set them apart. Unlike the reptiles, birds are endothermic, meaning they generate their own body heat through metabolic processes. The most distinctive characteristic of birds is their feathers, which are modified reptilian scales. Birds have several different types of feathers that are specialized for specific functions, like contour feathers that streamline the bird’s exterior and loosely structured down feathers that insulate (Figure 15.44a).
Feathers not only permitted the earliest birds to glide, and ultimately engage in flapping flight, but they insulated the bird’s body, assisting the maintenance of endothermy, even in cooler temperatures. Powering a flying animal requires economizing on the amount of weight carried. As body weight increases, the muscle output and energetic cost required for flying increase. Birds have made several modifications to reduce body weight, including hollow or pneumatic bones (Figure 15.44b) with air spaces that may be connected to air sacs and cross-linked struts within their bones to provide structural reinforcement. Parts of the vertebral skeleton and braincase are fused to increase its strength while lightening its weight. Most species of bird only possess one ovary rather than two, and no living birds have teeth in their jaw, further reducing body mass.
Birds possess a system of air sacs branching from their primary airway that divert the path of air so that it passes unidirectionally through the lung, during both inspiration and expiration. Unlike mammalian lungs in which air flows in two directions as it is breathed in and out, air flows continuously through the bird’s lung to provide a more efficient system of gas exchange.
Mammals are vertebrates that have hair and mammary glands used to provide nutrition for their young. Certain features of the jaw, skeleton, skin, and internal anatomy are also unique to mammals. The presence of hair is one of the key characteristics of a mammal. Although it is not very extensive in some groups, such as whales, hair has many important functions for mammals. Mammals are endothermic, and hair provides insulation by trapping a layer of air close to the body to retain metabolic heat. Hair also serves as a sensory mechanism through specialized hairs called vibrissae, better known as whiskers. These attach to nerves that transmit touch information, which is particularly useful to nocturnal or burrowing mammals. Hair can also provide protective coloration.
Mammalian skin includes secretory glands with various functions. Sebaceous glands produce a lipid mixture called sebum that is secreted onto the hair and skin for water resistance and lubrication. Sebaceous glands are located over most of the body. Sudoriferous glands produce sweat and scent, which function in thermoregulation and communication, respectively. Mammary glands produce milk that is used to feed newborns. While male monotremes and eutherians possess mammary glands, male marsupials do not.
The skeletal system of mammals possesses unique features that differentiate them from other vertebrates. Most mammals have heterodont teeth , meaning they have different types and shapes of teeth that allow them to feed on different kinds of foods. These different types of teeth include the incisors, the canines, premolars, and molars. The first two types are for cutting and tearing, whereas the latter two types are for crushing and grinding. Different groups have different proportions of each type, depending on their diet. Most mammals are also diphyodonts , meaning they have two sets of teeth in their lifetime: deciduous or “baby” teeth, and permanent teeth. In other vertebrates, the teeth can be replaced throughout life.
Modern mammals are divided into three broad groups: monotremes, marsupials, and eutherians (or placental mammals). The eutherians, or placental mammals, and the marsupials collectively are called therian mammals, whereas monotremes are called metatherians.
There are three living species of monotremes : the platypus and two species of echidnas, or spiny anteaters (Figure 15.45). The platypus and one species of echidna are found in Australia, whereas the other species of echidna is found in New Guinea. Monotremes are unique among mammals, as they lay leathery eggs, similar to those of reptiles, rather than giving birth to live young. However, the eggs are retained within the mother’s reproductive tract until they are almost ready to hatch. Once the young hatch, the female begins to secrete milk from pores in a ridge of mammary tissue along the ventral side of her body. Like other mammals, monotremes are endothermic but regulate body temperatures somewhat lower (90 °F, 32 °C) than placental mammals do (98 °F, 37 °C). Like reptiles, monotremes have one posterior opening for urinary, fecal, and reproductive products, rather than three separate openings like placental mammals do. Adult monotremes lack teeth.
Marsupials are found primarily in Australia and nearby islands, although about 100 species of opossums and a few species of two other families are found in the Americas. Australian marsupials number over 230 species and include the kangaroo, koala, bandicoot, and Tasmanian devil (Figure 15.46). Most species of marsupials possess a pouch in which the young reside after birth, receiving milk and continuing to develop. Before birth, marsupials have a less complex placental connection, and the young are born much less developed than in placental mammals.
Eutherians are the most widespread of the mammals, occurring throughout the world. There are several groups of eutherians, including Insectivora, the insect eaters Edentata, the toothless anteaters Rodentia, the rodents Chiroptera, the bats Cetacea, the aquatic mammals including whales Carnivora, carnivorous mammals including dogs, cats, and bears and Primates, which includes humans. Eutherian mammals are sometimes called placental mammals, because all species have a complex placenta that connects a fetus to the mother, allowing for gas, fluid, waste, and nutrient exchange. While other mammals may possess a less complex placenta or briefly have a placenta, all eutherians have a complex placenta during gestation.
Order Primates of class Mammalia includes lemurs, tarsiers, monkeys, and the apes, which include humans. Non-human primates live primarily in tropical or subtropical regions of South America, Africa, and Asia. They range in size from the mouse lemur at 30 grams (1 ounce) to the mountain gorilla at 200 kilograms (441 pounds). The characteristics and evolution of primates are of particular interest to us as they allow us to understand the evolution of our own species.
All primate species have adaptations for climbing trees, as they all descended from tree-dwellers, although not all species are arboreal. This arboreal heritage of primates resulted in hands and feet that are adapted for brachiation , or climbing and swinging through trees. These adaptations include, but are not limited to 1) a rotating shoulder joint, 2) a big toe that is widely separated from the other toes and thumbs that are widely separated from fingers (except humans), which allow for gripping branches, and 3) stereoscopic vision , two overlapping visual fields, which allows for the depth perception necessary to gauge distance. Other characteristics of primates are brains that are larger than those of many other mammals, claws that have been modified into flattened nails, typically only one offspring per pregnancy, and a trend toward holding the body upright.
Order Primates is divided into two groups: prosimians and anthropoids. Prosimians include the bush babies of Africa, the lemurs of Madagascar, and the lorises, pottos, and tarsiers of Southeast Asia. Anthropoids include monkeys, lesser apes, and great apes (Figure 15.47). In general, prosimians tend to be nocturnal, smaller in size than anthropoids, and have relatively smaller brains compared to anthropoids.
Why do most species have five digits on their hands and feet?
The condition of having no more than five fingers or toes--in this context, 'most species' means a subgroup of jawed vertebrates--probably evolved before the evolutionary divergence of amphibians (frogs, toads, salamanders and caecilians) and amniotes (birds, mammals, and reptiles in the loosest sense of the term). This event dates to approximately 340 million years ago in the Lower Carboniferous Period. Prior to this split, there is evidence of tetrapods from about 360 million years ago having limbs bearing arrays of six, seven and eight digits. Reduction from these polydactylous patterns to the more familiar arrangements of five or fewer digits accompanied the evolution of sophisticated wrist and ankle joints--both in terms of the number of bones present and the complex articulations among the constituent parts.
Early evolutionary experiments in hexa- or octodactyly (that is, creatures having six or eight digits) were associated with rather simple limb skeletons, much like those present in the flippers of modern whales and dolphins. This might provide a functional clue about one of the reasons for digit number reduction, which is related to the functional demands of simple "walking" limbs. Unlike paddles, such limbs have to provide purchase on a range of substrates, provide the platform for an efficient push-off and allow some rotation relative to the lower and upper limb bones as the rest of the body travels onward. In the very few instances of secondarily evolved polydactylous limbs from the fossil record, the phenomenon is associated with aquatic taxa. The classic instance of this is in the paddles of ichthyosaurs, extinct fishlike marine reptiles that lived more than 65 million years ago.
Is there really any good evidence that five, rather than, say, four or six, digits was biomechanically preferable for the common ancestor of modern tetrapods? The answer has to be "No," in part because a whole range of tetrapods have reduced their numbers of digits further still. In addition, we lack any six-digit examples to investigate. This leads to the second part of the answer, which is to note that although digit numbers can be reduced, they very rarely increase. In a general sense this trait reflects the developmental-evolutionary rule that it is easier to lose something than it is to regain it. Even so, given the immensity of evolutionary time and the extraordinary variety of vertebrate bodies, the striking absence of truly six-digit limbs in today's fauna highlights some sort of constraint. Moles' paws and pandas' thumbs are classic instances in which strangely re-modeled wrist bones serve as sixth digits and represent rather baroque solutions to the apparently straightforward task of growing an extra finger. Patterns of six (or more) digits can be achieved by laboratory-based developmental manipulations, some of which concern changes in gene activity that probably reflect transformations involved in the fin-to-limb evolutionary transition. Here might lie another part of the reason for the prevalence of five: pleiotropy, or the multiple effects of genes upon more than one physical characteristic. For instance, Hand-Foot-Genital syndrome is a rare condition in which, as the name implies, the genito-urinary tract and the limbs are malformed. Crucially, the genes responsible are within the set of those involved in digit number and patterning. Therefore, although this tells us nothing directly about the significance of digit number, it indicates something important about developmental stability: the mechanisms involved in patterning the tips of our limbs include those involved in our reproductive success. Thus, tweak at your peril.
Reptiles and Birds
The amniotes —reptiles, birds, and mammals—are distinguished from amphibians by their terrestrially adapted (shelled) egg and an embryo protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes could develop within an aquatic environment inside the egg. This led to less dependence on a water environment for development and allowed the amniotes to invade drier areas. This was a significant evolutionary change that distinguished them from amphibians, which were restricted to moist environments due to their shell-less eggs. Although the shells of various amniotic species vary significantly, they all allow retention of water. The membranes of the amniotic egg also allowed gas exchange and sequestering of wastes within the enclosure of an eggshell. The shells of bird eggs are composed of calcium carbonate and are hard and brittle, but possess pores for gas and water exchange. The shells of reptile eggs are more leathery and pliable. Most mammals do not lay eggs however, even with internal gestation, amniotic membranes are still present.
In the past, the most common division of amniotes has been into classes Mammalia, Reptilia, and Aves. Birds are descended, however, from dinosaurs, so this classical scheme results in groups that are not true clades. We will discuss birds as a group distinct from reptiles with the understanding that this does not reflect evolutionary history.
What If the First Animals to Crawl Out of the Ocean Had Six Limbs Instead of Four?
During the new DC Comics Universe series "Flashpoint," in which a time-traveling supervillain alters the past to warp the present, Life's Little Mysteries presents a 10-part series that examines what would happen if a major event in the history of the universe had gone just slightly different.
Part 5: What if . the first animals to crawl out of the ocean had six limbs instead of four?
All land vertebrates mammals, birds, reptiles and amphibians are or were tetrapods, which have two sets of paired limbs. (Snakes evolved from four-limbed lizards.) This shared body plan dates back to the late Devonian period, about 400 million years ago, when lobe-finned fish began exploiting new ecological niches in wetlands and eventually made the transition to terra firma.
Life would be: Quite likely in need of more pant legs and sleeves, at least if the descendent creatures were of the clothes-wearing variety.
Although paired upper and lower fins developed in bony fish, the precursors to tetrapods, there is not a lot of evidence that this anatomy was selected over, say, three pairs or four pairs for any evolutionarily reason. "You could consider it somewhat arbitrary," said Edward Daeschler, associate curator at the Academy of Natural Sciences in Philadelphia. Land vertebrates all share the same basic design, but could it be different? Absolutely."
Creatures with more than four limbs have not evolved in land species. In fact the trend is to simplify, as with snakes, which lost their limbs, and horses , which instead of having five digits have one (a hoof). Six, eight and even leggier arthropods (insects, arachnids and crustaceans) have, of course, been extraordinarily successful six-limbed beetles alone comprise a quarter of the 1.7 million described species. But the fact that these creatures have exoskeletons rather than bones inside their bodies limits their size, Daeschler told Life's Little Mysteries.
Large exoskeletons needed to support internal body tissue would be prohibitively cumbersome and heavy, plus would demand lots of energy to move and grow. Because intelligence is strongly linked to how big, intricate and energy-consuming an animal's brain is, that sentience is unlikely to evolve in bugs.
Previously: What would life be like if there were more than two dominant sexes ?
Next: What would the world be like if the moon had never formed ?
One of the strongest evidences for common descent comes from gene sequences. Comparative sequence analysis examines the relationship between the DNA sequences of different species,  producing several lines of evidence that confirm Darwin's original hypothesis of common descent. If the hypothesis of common descent is true, then species that share a common ancestor inherited that ancestor's DNA sequence, as well as mutations unique to that ancestor. More closely related species have a greater fraction of identical sequence and shared substitutions compared to more distantly related species.
The simplest and most powerful evidence is provided by phylogenetic reconstruction. Such reconstructions, especially when done using slowly evolving protein sequences, are often quite robust and can be used to reconstruct a great deal of the evolutionary history of modern organisms (and even in some instances of the evolutionary history of extinct organisms, such as the recovered gene sequences of mammoths or Neanderthals). These reconstructed phylogenies recapitulate the relationships established through morphological and biochemical studies.  The most detailed reconstructions have been performed on the basis of the mitochondrial genomes shared by all eukaryotic organisms,  which are short and easy to sequence the broadest reconstructions have been performed either using the sequences of a few very ancient proteins or by using ribosomal RNA sequence. [ citation needed ]
Phylogenetic relationships extend to a wide variety of nonfunctional sequence elements, including repeats, transposons, pseudogenes, and mutations in protein-coding sequences that do not change the amino-acid sequence. While a minority of these elements might later be found to harbor function, in aggregate they demonstrate that identity must be the product of common descent rather than common function. 
Universal biochemical organisation and molecular variance patterns Edit
All known extant (surviving) organisms are based on the same biochemical processes: genetic information encoded as nucleic acid (DNA, or RNA for many viruses), transcribed into RNA, then translated into proteins (that is, polymers of amino acids) by highly conserved ribosomes. Perhaps most tellingly, the Genetic Code (the "translation table" between DNA and amino acids) is the same for almost every organism, meaning that a piece of DNA in a bacterium codes for the same amino acid as in a human cell. ATP is used as energy currency by all extant life. A deeper understanding of developmental biology shows that common morphology is, in fact, the product of shared genetic elements.  For example, although camera-like eyes are believed to have evolved independently on many separate occasions,  they share a common set of light-sensing proteins (opsins), suggesting a common point of origin for all sighted creatures.   Another example is the familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes. 
DNA sequencing Edit
Comparison of DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications. Sequence comparison is considered a measure robust enough to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas, and 6.6% from baboons.   Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes.   The sequence of the 16S ribosomal RNA gene, a vital gene encoding a part of the ribosome, was used to find the broad phylogenetic relationships between all extant life. The analysis by Carl Woese resulted in the three-domain system, arguing for two major splits in the early evolution of life. The first split led to modern Bacteria and the subsequent split led to modern Archaea and Eukaryotes.  
Some DNA sequences are shared by very different organisms. It has been predicted by the theory of evolution that the differences in such DNA sequences between two organisms should roughly resemble both the biological difference between them according to their anatomy and the time that had passed since these two organisms have separated in the course of evolution, as seen in fossil evidence. The rate of accumulating such changes should be low for some sequences, namely those that code for critical RNA or proteins, and high for others that code for less critical RNA or proteins but for every specific sequence, the rate of change should be roughly constant over time. These results have been experimentally confirmed. Two examples are DNA sequences coding for rRNA, which is highly conserved, and DNA sequences coding for fibrinopeptides, amino acid chains discarded during the formation of fibrin, which are highly non-conserved. 
Proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions. Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent. Phylogenetic analyses of protein sequences from various organisms produce similar trees of relationship between all organisms.  The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right- or left-handed molecular chirality, the simplest hypothesis is that the choice was made randomly by early organisms and passed on to all extant life through common descent. Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, "dead" genes that steadily accumulate mutations. 
Pseudogenes, also known as noncoding DNA, are extra DNA in a genome that do not get transcribed into RNA to synthesize proteins. Some of this noncoding DNA has known functions, but much of it has no known function and is called "Junk DNA".     This is an example of a vestige since replicating these genes uses energy, making it a waste in many cases. A pseudogene can be produced when a coding gene accumulates mutations that prevent it from being transcribed, making it non-functional.  But since it is not transcribed, it may disappear without affecting fitness, unless it has provided some beneficial function as non-coding DNA. Non-functional pseudogenes may be passed on to later species, thereby labeling the later species as descended from the earlier species. [ citation needed ]
Other mechanisms Edit
A large body of molecular evidence supports a variety of mechanisms for large evolutionary changes, including: genome and gene duplication, which facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints horizontal gene transfer, the process of transferring genetic material to another cell that is not an organism's offspring, allowing for species to acquire beneficial genes from each other and recombination, capable of reassorting large numbers of different alleles and of establishing reproductive isolation. The endosymbiotic theory explains the origin of mitochondria and plastids (including chloroplasts), which are organelles of eukaryotic cells, as the incorporation of an ancient prokaryotic cell into ancient eukaryotic cell. Rather than evolving eukaryotic organelles slowly, this theory offers a mechanism for a sudden evolutionary leap by incorporating the genetic material and biochemical composition of a separate species. Evidence supporting this mechanism has been found in the protist Hatena: as a predator it engulfs a green algal cell, which subsequently behaves as an endosymbiont, nourishing Hatena, which in turn loses its feeding apparatus and behaves as an autotroph.  
Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor or by detecting their physical manifestations. As an example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis. [ original research? ] [ citation needed ]
Specific examples from comparative physiology and biochemistry Edit
Chromosome 2 in humans Edit
Evidence for the evolution of Homo sapiens from a common ancestor with chimpanzees is found in the number of chromosomes in humans as compared to all other members of Hominidae. All hominidae have 24 pairs of chromosomes, except humans, who have only 23 pairs. Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.  
The evidence for this includes:
- The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has near-identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan. 
- The presence of a vestigialcentromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere. 
- The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the middle. 
Chromosome 2 thus presents strong evidence in favour of the common descent of humans and other apes. According to J. W. Ijdo, "We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2." 
Cytochrome c and b Edit
A classic example of biochemical evidence for evolution is the variance of the ubiquitous (i.e. all living organisms have it, because it performs very basic life functions) protein Cytochrome c in living cells. The variance of cytochrome c of different organisms is measured in the number of differing amino acids, each differing amino acid being a result of a base pair substitution, a mutation. If each differing amino acid is assumed the result of one base pair substitution, it can be calculated how long ago the two species diverged by multiplying the number of base pair substitutions by the estimated time it takes for a substituted base pair of the cytochrome c gene to be successfully passed on. For example, if the average time it takes for a base pair of the cytochrome c gene to mutate is N years, the number of amino acids making up the cytochrome c protein in monkeys differ by one from that of humans, this leads to the conclusion that the two species diverged N years ago.
The primary structure of cytochrome c consists of a chain of about 100 amino acids. Many higher order organisms possess a chain of 104 amino acids. 
The cytochrome c molecule has been extensively studied for the glimpse it gives into evolutionary biology. Both chicken and turkeys have identical sequence homology (amino acid for amino acid), as do pigs, cows and sheep. Both humans and chimpanzees share the identical molecule, while rhesus monkeys share all but one of the amino acids:  the 66th amino acid is isoleucine in the former and threonine in the latter. 
What makes these homologous similarities particularly suggestive of common ancestry in the case of cytochrome c, in addition to the fact that the phylogenies derived from them match other phylogenies very well, is the high degree of functional redundancy of the cytochrome c molecule. The different existing configurations of amino acids do not significantly affect the functionality of the protein, which indicates that the base pair substitutions are not part of a directed design, but the result of random mutations that aren't subject to selection. 
In addition, Cytochrome b is commonly used as a region of mitochondrial DNA to determine phylogenetic relationships between organisms due to its sequence variability. It is considered most useful in determining relationships within families and genera. Comparative studies involving cytochrome b have resulted in new classification schemes and have been used to assign newly described species to a genus, as well as deepen the understanding of evolutionary relationships. 
Endogenous retroviruses Edit
Endogenous retroviruses (or ERVs) are remnant sequences in the genome left from ancient viral infections in an organism. The retroviruses (or virogenes) are always passed on to the next generation of that organism that received the infection. This leaves the virogene left in the genome. Because this event is rare and random, finding identical chromosomal positions of a virogene in two different species suggests common ancestry.  Cats (Felidae) present a notable instance of virogene sequences demonstrating common descent. The standard phylogenetic tree for Felidae have smaller cats (Felis chaus, Felis silvestris, Felis nigripes, and Felis catus) diverging from larger cats such as the subfamily Pantherinae and other carnivores. The fact that small cats have an ERV where the larger cats do not suggests that the gene was inserted into the ancestor of the small cats after the larger cats had diverged.  Another example of this is with humans and chimps. Humans contain numerous ERVs that comprise a considerable percentage of the genome. Sources vary, but 1%  to 8%  has been proposed. Humans and chimps share seven different occurrences of virogenes, while all primates share similar retroviruses congruent with phylogeny.  
Recent African origin of modern humans Edit
Mathematical models of evolution, pioneered by the likes of Sewall Wright, Ronald Fisher and J. B. S. Haldane and extended via diffusion theory by Motoo Kimura, allow predictions about the genetic structure of evolving populations. Direct examination of the genetic structure of modern populations via DNA sequencing has allowed verification of many of these predictions. For example, the Out of Africa theory of human origins, which states that modern humans developed in Africa and a small sub-population migrated out (undergoing a population bottleneck), implies that modern populations should show the signatures of this migration pattern. Specifically, post-bottleneck populations (Europeans and Asians) should show lower overall genetic diversity and a more uniform distribution of allele frequencies compared to the African population. Both of these predictions are borne out by actual data from a number of studies. 
Comparative study of the anatomy of groups of animals or plants reveals that certain structural features are basically similar. For example, the basic structure of all flowers consists of sepals, petals, stigma, style and ovary yet the size, colour, number of parts and specific structure are different for each individual species. The neural anatomy of fossilized remains may also be compared using advanced imaging techniques. 
Once thought of as a refutation to evolutionary theory, atavisms are "now seen as potent evidence of how much genetic potential is retained. after a particular structure has disappeared from a species".  "Atavisms are the reappearance of a lost character typical of remote ancestors and not seen in the parents or recent ancestors. "  and are an "[indication] of the developmental plasticity that exists within embryos. "  Atavisms occur because genes for previously existing phenotypical features are often preserved in DNA, even though the genes are not expressed in some or most of the organisms possessing them.  Numerous examples have documented the occurrence of atavisms alongside experimental research triggering their formation. Due to the complexity and interrelatedness of the factors involved in the development of atavisms, both biologists and medical professionals find it "difficult, if not impossible, to distinguish [them] from malformations." 
Some examples of atavisms found in the scientific literature include:
- Hind limbs in whales.  (see figure 2a)
- Reappearance of limbs in limbless vertebrates. 
- Back pair of flippers on a bottlenose dolphin. 
- Extra toes of the modern horse.  (not pseudo-tails)  and extra nipples in humans. 
- Re-evolution of sexuality from parthenogenesis in orbitid mites. 
- Teeth in chickens.  in dogs. 
- Reappearance of wings on wingless stick insects  and earwigs. 
- Atavistic muscles in several birds  and mammals such as the beagle and the jerboa. 
- Extra toes in guinea pigs. 
Evolutionary developmental biology and embryonic development Edit
Evolutionary developmental biology is the biological field that compares the developmental process of different organisms to determine ancestral relationships between species. A large variety of organism's genomes contain a small fraction of genes that control the organisms development. Hox genes are an example of these types of nearly universal genes in organisms pointing to an origin of common ancestry. Embryological evidence comes from the development of organisms at the embryological level with the comparison of different organisms embryos similarity. Remains of ancestral traits often appear and disappear in different stages of the embryological development process.
- Hair growth and loss (lanugo) during human development. 
- Development and degeneration of a yolk sac.
- Terrestrial frogs and salamanders passing through the larval stage within the egg—with features of typically aquatic larvae—but hatch ready for life on land 
- The appearance of gill-like structures (pharyngeal arch) in vertebrate embryo development. Note that in fish, the arches continue to develop as branchial arches while in humans, for example, they give rise to a variety of structures within the head and neck.
Homologous structures and divergent (adaptive) evolution Edit
If widely separated groups of organisms are originated from a common ancestry, they are expected to have certain basic features in common. The degree of resemblance between two organisms should indicate how closely related they are in evolution:
- Groups with little in common are assumed to have diverged from a common ancestor much earlier in geological history than groups with a lot in common
- In deciding how closely related two animals are, a comparative anatomist looks for structures that are fundamentally similar, even though they may serve different functions in the adult. Such structures are described as homologous and suggest a common origin.
- In cases where the similar structures serve different functions in adults, it may be necessary to trace their origin and embryonic development. A similar developmental origin suggests they are the same structure, and thus likely derived from a common ancestor.
When a group of organisms share a homologous structure that is specialized to perform a variety of functions to adapt different environmental conditions and modes of life, it is called adaptive radiation. The gradual spreading of organisms with adaptive radiation is known as divergent evolution.
Nested hierarchies and classification Edit
Taxonomy is based on the fact that all organisms are related to each other in nested hierarchies based on shared characteristics. Most existing species can be organized rather easily in a nested hierarchical classification. This is evident from the Linnaean classification scheme. Based on shared derived characters, closely related organisms can be placed in one group (such as a genus), several genera can be grouped together into one family, several families can be grouped together into an order, etc.  The existence of these nested hierarchies was recognized by many biologists before Darwin, but he showed that his theory of evolution with its branching pattern of common descent could explain them.   Darwin described how common descent could provide a logical basis for classification: 
All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical that community of descent is the hidden bond which naturalists have been unconsciously seeking, .
Evolutionary trees Edit
An evolutionary tree (of Amniota, for example, the last common ancestor of mammals and reptiles, and all its descendants) illustrates the initial conditions causing evolutionary patterns of similarity (e.g., all Amniotes produce an egg that possesses the amnios) and the patterns of divergence amongst lineages (e.g., mammals and reptiles branching from the common ancestry in Amniota). Evolutionary trees provide conceptual models of evolving systems once thought limited in the domain of making predictions out of the theory.  However, the method of phylogenetic bracketing is used to infer predictions with far greater probability than raw speculation. For example, paleontologists use this technique to make predictions about nonpreservable traits in fossil organisms, such as feathered dinosaurs, and molecular biologists use the technique to posit predictions about RNA metabolism and protein functions.   Thus evolutionary trees are evolutionary hypotheses that refer to specific facts, such as the characteristics of organisms (e.g., scales, feathers, fur), providing evidence for the patterns of descent, and a causal explanation for modification (i.e., natural selection or neutral drift) in any given lineage (e.g., Amniota). Evolutionary biologists test evolutionary theory using phylogenetic systematic methods that measure how much the hypothesis (a particular branching pattern in an evolutionary tree) increases the likelihood of the evidence (the distribution of characters among lineages).    The severity of tests for a theory increases if the predictions "are the least probable of being observed if the causal event did not occur."  "Testability is a measure of how much the hypothesis increases the likelihood of the evidence." 
Vestigial structures Edit
Evidence for common descent comes from the existence of vestigial structures.  These rudimentary structures are often homologous to structures that correspond in related or ancestral species. A wide range of structures exist such as mutated and non-functioning genes, parts of a flower, muscles, organs, and even behaviors. This variety can be found across many different groups of species. In many cases they are degenerated or underdeveloped. The existence of vestigial organs can be explained in terms of changes in the environment or modes of life of the species. Those organs are typically functional in the ancestral species but are now either semi-functional, nonfunctional, or re-purposed.
Scientific literature concerning vestigial structures abounds. One study compiled 64 examples of vestigial structures found in the literature across a wide range of disciplines within the 21st century.  The following non-exhaustive list summarizes Senter et al. alongside various other examples:
- The presence of remnant mitochondria (mitosomes) that have lost the ability to synthesize ATP in Entamoeba histolytica, Trachipleistophora hominis, Cryptosporidium parvum, Blastocystis hominis, and Giardia intestinalis. 
- Remnant chloroplast organelles (leucoplasts) in non-photosynthetic algae species (Plasmodium falciparum, Toxoplasma gondii, Aspasia longa, Anthophysa vegetans, Ciliophrys infusionum, Pteridomonas danica, Paraphysomonas, Spumella and Epifagus americana. 
- Missing stamens (unvascularized staminodes) on Gilliesia and Gethyum flowers. 
- Non-functioning androecium in female flowers and non-functioning gynoecium in male flowers of the cactus species Consolea spinosissima. 
- Remnant stamens on female flowers of Fragaria virginiana  all species in the genus Schiedea  and on Penstemon centranthifolius, P. rostriflorus, P. ellipticus, and P. palmeri. 
- Vestigial anthers on Nemophila menziesii. 
- Reduced hindlimbs and pelvic girdle embedded in the muscles of extant whales (see figure 2b).  Occasionally, the genes that code for longer extremities cause a modern whale to develop legs. On 28 October 2006, a four-finned bottlenose dolphin was caught and studied due to its extra set of hind limbs.  These legged Cetacea display an example of an atavism predicted from their common ancestry.
- Nonfunctional hind wings in Carabus solieri and other beetles. 
- Remnant eyes (and eye structures) in animals that have lost sight such as blind cavefish (e.g. Astyanax mexicanus),  mole rats, snakes, spiders, salamanders, shrimp, crayfish, and beetles. 
- Vestigial eye in the extant Rhineura floridana and remnant jugal in the extinct Rhineura hatchery (reclassified as Protorhineura hatcherii). 
- Functionless wings in flightless birds such as ostriches, kiwis, cassowaries, and emus. 
- The presence of the plica semilunaris in the human eye—a vestigial remnant of the nictitating membrane.  in primates. 
- Reduced hind limbs and pelvic girdle structures in legless lizards, skinks, amphisbaenians, and some snakes. 
- Reduced and missing olfactory apparatus in whales that still possess vestigial olfactory receptor subgenomes. 
- Vestigial teeth in narwhal. 
- Rudimentary digits of Ateles geoffroyi, Colobus guereza, and Perodicticus potto. 
- Vestigial dental primordia in the embryonic tooth pattern in mice. 
- Reduced or absent vomeronasal organ in humans and Old World monkeys. 
- Presence of non-functional sinus hair muscles in humans used in whisker movement. 
- Degenerating palmaris longus muscle in humans.  , anthropoid primates (Simians), guinea pigs, some bat species, and some Passeriformes have lost the ability to synthesize vitamin C (ascorbic acid), yet still possess the genes involved. This inability is due to mutations of the L-gulono-γ-lactone oxidase (GLO) gene— and in primates, teleost fish, and guinea pigs it is irreversible. 
- Remnant abdominal segments in cirripedes (barnacles). 
- Non-mammalian vertebrate embryos depend on nutrients from the yolk sac. Humans and other mammal genomes contain broken, non-functioning genes that code for the production of yolk. alongside the presence of an empty yolk sac with the embryo. 
- Dolphin embryonic limb buds. 
- Leaf formation in some cacti species. 
- Presence of a vestigial endosymbiont Lepidodinium viride within the dinoflagellate Gymnodinium chlorophorum. 
- The species Dolabrifera dolabrifera has an ink gland but is "incapable of producing ink or its associated anti-predator proteins". 
Specific examples from comparative anatomy Edit
Insect mouthparts and appendages Edit
Many different species of insects have mouthparts derived from the same embryonic structures, indicating that the mouthparts are modifications of a common ancestor's original features. These include a labrum (upper lip), a pair of mandibles, a hypopharynx (floor of mouth), a pair of maxillae, and a labium. (Fig. 2c) Evolution has caused enlargement and modification of these structures in some species, while it has caused the reduction and loss of them in other species. The modifications enable the insects to exploit a variety of food materials.
Insect mouthparts and antennae are considered homologues of insect legs. Parallel developments are seen in some arachnids: The anterior pair of legs may be modified as analogues of antennae, particularly in whip scorpions, which walk on six legs. These developments provide support for the theory that complex modifications often arise by duplication of components, with the duplicates modified in different directions.
Pelvic structure of dinosaurs Edit
Similar to the pentadactyl limb in mammals, the earliest dinosaurs split into two distinct orders—the saurischia and ornithischia. They are classified as one or the other in accordance with what the fossils demonstrate. Figure 2d, shows that early saurischians resembled early ornithischians. The pattern of the pelvis in all species of dinosaurs is an example of homologous structures. Each order of dinosaur has slightly differing pelvis bones providing evidence of common descent. Additionally, modern birds show a similarity to ancient saurischian pelvic structures indicating the evolution of birds from dinosaurs. This can also be seen in Figure 5c as the Aves branch off the Theropoda suborder.
Pentadactyl limb Edit
The pattern of limb bones called pentadactyl limb is an example of homologous structures (Fig. 2e). It is found in all classes of tetrapods (i.e. from amphibians to mammals). It can even be traced back to the fins of certain fossil fishes from which the first amphibians evolved such as tiktaalik. The limb has a single proximal bone (humerus), two distal bones (radius and ulna), a series of carpals (wrist bones), followed by five series of metacarpals (palm bones) and phalanges (digits). Throughout the tetrapods, the fundamental structures of pentadactyl limbs are the same, indicating that they originated from a common ancestor. But in the course of evolution, these fundamental structures have been modified. They have become superficially different and unrelated structures to serve different functions in adaptation to different environments and modes of life. This phenomenon is shown in the forelimbs of mammals. For example:
- In monkeys, the forelimbs are much elongated, forming a grasping hand used for climbing and swinging among trees. have lost their first digit, while the second and fifth digits are reduced. The remaining two digits are longer and stouter than the rest and bear a hoof for supporting the body.
- In horses, the forelimbs are highly adapted for strength and support. Fast and long-distance running is possible due to the extensive elongation of the third digit that bears a hoof.
- The mole has a pair of short, spade-like forelimbs for burrowing. use their enlarged third digit for tearing into ant and termite nests.
- In cetaceans, the forelimbs become flippers for steering and maintaining equilibrium during swimming.
- In bats, the forelimbs have become highly modified and evolved into functioning wings. Four digits have become elongated, while the hook-like first digit remains free and is used to grip.
Recurrent laryngeal nerve in giraffes Edit
The recurrent laryngeal nerve is a fourth branch of the vagus nerve, which is a cranial nerve. In mammals, its path is unusually long. As a part of the vagus nerve, it comes from the brain, passes through the neck down to heart, rounds the dorsal aorta and returns up to the larynx, again through the neck. (Fig. 2f)
This path is suboptimal even for humans, but for giraffes it becomes even more suboptimal. Due to the lengths of their necks, the recurrent laryngeal nerve may be up to 4 m (13 ft) long, despite its optimal route being a distance of just several inches.
The indirect route of this nerve is the result of evolution of mammals from fish, which had no neck and had a relatively short nerve that innervated one gill slit and passed near the gill arch. Since then, the gill it innervated has become the larynx and the gill arch has become the dorsal aorta in mammals.  
Route of the vas deferens Edit
Similar to the laryngeal nerve in giraffes, the vas deferens is part of the male anatomy of many vertebrates it transports sperm from the epididymis in anticipation of ejaculation. In humans, the vas deferens routes up from the testicle, looping over the ureter, and back down to the urethra and penis. It has been suggested that this is due to the descent of the testicles during the course of human evolution—likely associated with temperature. As the testicles descended, the vas deferens lengthened to accommodate the accidental "hook" over the ureter.  
When organisms die, they often decompose rapidly or are consumed by scavengers, leaving no permanent evidences of their existence. However, occasionally, some organisms are preserved. The remains or traces of organisms from a past geologic age embedded in rocks by natural processes are called fossils. They are extremely important for understanding the evolutionary history of life on Earth, as they provide direct evidence of evolution and detailed information on the ancestry of organisms. Paleontology is the study of past life based on fossil records and their relations to different geologic time periods.
For fossilization to take place, the traces and remains of organisms must be quickly buried so that weathering and decomposition do not occur. Skeletal structures or other hard parts of the organisms are the most commonly occurring form of fossilized remains. There are also some trace "fossils" showing moulds, cast or imprints of some previous organisms.
As an animal dies, the organic materials gradually decay, such that the bones become porous. If the animal is subsequently buried in mud, mineral salts infiltrate into the bones and gradually fill up the pores. The bones harden into stones and are preserved as fossils. This process is known as petrification. If dead animals are covered by wind-blown sand, and if the sand is subsequently turned into mud by heavy rain or floods, the same process of mineral infiltration may occur. Apart from petrification, the dead bodies of organisms may be well preserved in ice, in hardened resin of coniferous trees (figure 3a), in tar, or in anaerobic, acidic peat. Fossilization can sometimes be a trace, an impression of a form. Examples include leaves and footprints, the fossils of which are made in layers that then harden.
Fossil record Edit
It is possible to decipher how a particular group of organisms evolved by arranging its fossil record in a chronological sequence. Such a sequence can be determined because fossils are mainly found in sedimentary rock. Sedimentary rock is formed by layers of silt or mud on top of each other thus, the resulting rock contains a series of horizontal layers, or strata. Each layer contains fossils typical for a specific time period when they formed. The lowest strata contain the oldest rock and the earliest fossils, while the highest strata contain the youngest rock and more recent fossils.
A succession of animals and plants can also be seen from fossil discoveries. By studying the number and complexity of different fossils at different stratigraphic levels, it has been shown that older fossil-bearing rocks contain fewer types of fossilized organisms, and they all have a simpler structure, whereas younger rocks contain a greater variety of fossils, often with increasingly complex structures. 
For many years, geologists could only roughly estimate the ages of various strata and the fossils found. They did so, for instance, by estimating the time for the formation of sedimentary rock layer by layer. Today, by measuring the proportions of radioactive and stable elements in a given rock, the ages of fossils can be more precisely dated by scientists. This technique is known as radiometric dating.
Throughout the fossil record, many species that appear at an early stratigraphic level disappear at a later level. This is interpreted in evolutionary terms as indicating the times when species originated and became extinct. Geographical regions and climatic conditions have varied throughout Earth's history. Since organisms are adapted to particular environments, the constantly changing conditions favoured species that adapted to new environments through the mechanism of natural selection.
Extent of the fossil record Edit
Despite the relative rarity of suitable conditions for fossilization, an estimated 250,000 fossil species have been named.  The number of individual fossils this represents varies greatly from species to species, but many millions of fossils have been recovered: for instance, more than three million fossils from the last ice age have been recovered from the La Brea Tar Pits in Los Angeles.  Many more fossils are still in the ground, in various geological formations known to contain a high fossil density, allowing estimates of the total fossil content of the formation to be made. An example of this occurs in South Africa's Beaufort Formation (part of the Karoo Supergroup, which covers most of South Africa), which is rich in vertebrate fossils, including therapsids (reptile-mammal transitional forms).  It has been estimated that this formation contains 800 billion vertebrate fossils.  Palentologists have documented numerous transitional forms and have constructed "an astonishingly comprehensive record of the key transitions in animal evolution".  Conducting a survey of the paleontological literature, one would find that there is "abundant evidence for how all the major groups of animals are related, much of it in the form of excellent transitional fossils". 
The fossil record is an important source for scientists when tracing the evolutionary history of organisms. However, because of limitations inherent in the record, there are not fine scales of intermediate forms between related groups of species. This lack of continuous fossils in the record is a major limitation in tracing the descent of biological groups. When transitional fossils are found that show intermediate forms in what had previously been a gap in knowledge, they are often popularly referred to as "missing links".
There is a gap of about 100 million years between the beginning of the Cambrian period and the end of the Ordovician period. The early Cambrian period was the period from which numerous fossils of sponges, cnidarians (e.g., jellyfish), echinoderms (e.g., eocrinoids), molluscs (e.g., snails) and arthropods (e.g., trilobites) are found. The first animal that possessed the typical features of vertebrates, the Arandaspis, was dated to have existed in the later Ordovician period. Thus few, if any, fossils of an intermediate type between invertebrates and vertebrates have been found, although likely candidates include the Burgess Shale animal, Pikaia gracilens,  and its Maotianshan shales relatives, Myllokunmingia, Yunnanozoon, Haikouella lanceolata,  and Haikouichthys. 
Some of the reasons for the incompleteness of fossil records are:
- In general, the probability that an organism becomes fossilized is very low
- Some species or groups are less likely to become fossils because they are soft-bodied
- Some species or groups are less likely to become fossils because they live (and die) in conditions that are not favourable for fossilization
- Many fossils have been destroyed through erosion and tectonic movements
- Most fossils are fragmentary
- Some evolutionary change occurs in populations at the limits of a species' ecological range, and as these populations are likely small, the probability of fossilization is lower (see punctuated equilibrium)
- Similarly, when environmental conditions change, the population of a species is likely to be greatly reduced, such that any evolutionary change induced by these new conditions is less likely to be fossilized
- Most fossils convey information about external form, but little about how the organism functioned
- Using present-day biodiversity as a guide, this suggests that the fossils unearthed represent only a small fraction of the large number of species of organisms that lived in the past.
Specific examples from paleontology Edit
Evolution of the horse Edit
Due to an almost-complete fossil record found in North American sedimentary deposits from the early Eocene to the present, the horse provides one of the best examples of evolutionary history (phylogeny).
This evolutionary sequence starts with a small animal called Hyracotherium (commonly referred to as Eohippus), which lived in North America about 54 million years ago then spread across to Europe and Asia. Fossil remains of Hyracotherium show it to have differed from the modern horse in three important respects: it was a small animal (the size of a fox), lightly built and adapted for running the limbs were short and slender, and the feet elongated so that the digits were almost vertical, with four digits in the forelimbs and three digits in the hindlimbs and the incisors were small, the molars having low crowns with rounded cusps covered in enamel. 
The probable course of development of horses from Hyracotherium to Equus (the modern horse) involved at least 12 genera and several hundred species. The major trends seen in the development of the horse to changing environmental conditions may be summarized as follows:
- Increase in size (from 0.4 m to 1.5 m — from 15 in to 60 in)
- Lengthening of limbs and feet
- Reduction of lateral digits
- Increase in length and thickness of the third digit
- Increase in width of incisors
- Replacement of premolars by molars and
- Increases in tooth length, crown height of molars.
Fossilized plants found in different strata show that the marshy, wooded country in which Hyracotherium lived became gradually drier. Survival now depended on the head being in an elevated position for gaining a good view of the surrounding countryside, and on a high turn of speed for escape from predators, hence the increase in size and the replacement of the splayed-out foot by the hoofed foot. The drier, harder ground would make the original splayed-out foot unnecessary for support. The changes in the teeth can be explained by assuming that the diet changed from soft vegetation to grass. A dominant genus from each geological period has been selected (see figure 3e) to show the slow alteration of the horse lineage from its ancestral to its modern form. 
Transition from fish to amphibians Edit
Prior to 2004, paleontologists had found fossils of amphibians with necks, ears, and four legs, in rock no older than 365 million years old. In rocks more than 385 million years old they could only find fish, without these amphibian characteristics. Evolutionary theory predicted that since amphibians evolved from fish, an intermediate form should be found in rock dated between 365 and 385 million years ago. Such an intermediate form should have many fish-like characteristics, conserved from 385 million years ago or more, but also have many amphibian characteristics as well. In 2004, an expedition to islands in the Canadian arctic searching specifically for this fossil form in rocks that were 375 million years old discovered fossils of Tiktaalik.  Some years later, however, scientists in Poland found evidence of fossilised tetrapod tracks predating Tiktaalik. 
Data about the presence or absence of species on various continents and islands (biogeography) can provide evidence of common descent and shed light on patterns of speciation.
Continental distribution Edit
All organisms are adapted to their environment to a greater or lesser extent. If the abiotic and biotic factors within a habitat are capable of supporting a particular species in one geographic area, then one might assume that the same species would be found in a similar habitat in a similar geographic area, e.g. in Africa and South America. This is not the case. Plant and animal species are discontinuously distributed throughout the world:
- Africa has Old World monkeys, apes, elephants, leopards, giraffes, and hornbills.
- South America has New World monkeys, cougars, jaguars, sloths, llamas, and toucans.
- Deserts in North and South America have native cacti, but deserts in Africa, Asia, and Australia have succulent (apart from Rhipsalis baccifera) which are native euphorbs that resemble cacti but are very different. 
Even greater differences can be found if Australia is taken into consideration, though it occupies the same latitude as much of South America and Africa. Marsupials like kangaroos, bandicoots, and quolls make up about half of Australia's indigenous mammal species.  By contrast, marsupials are today totally absent from Africa and form a smaller portion of the mammalian fauna of South America, where opossums, shrew opossums, and the monito del monte occur. The only living representatives of primitive egg-laying mammals (monotremes) are the echidnas and the platypus. The short-beaked echidna (Tachyglossus aculeatus) and its subspecies populate Australia, Tasmania, New Guinea, and Kangaroo Island while the long-beaked echidna (Zaglossus bruijni) lives only in New Guinea. The platypus lives in the waters of eastern Australia. They have been introduced to Tasmania, King Island, and Kangaroo Island. These Monotremes are totally absent in the rest of the world.  On the other hand, Australia is missing many groups of placental mammals that are common on other continents (carnivorans, artiodactyls, shrews, squirrels, lagomorphs), although it does have indigenous bats and murine rodents many other placentals, such as rabbits and foxes, have been introduced there by humans. [ citation needed ]
Other animal distribution examples include bears, located on all continents excluding Africa, Australia and Antarctica, and the polar bear solely in the Arctic Circle and adjacent land masses.  Penguins are found only around the South Pole despite similar weather conditions at the North Pole. Families of sirenians are distributed around the earth's waters, where manatees are located in western Africa waters, northern South American waters, and West Indian waters only while the related family, the dugongs, are located only in Oceanic waters north of Australia, and the coasts surrounding the Indian Ocean. The now extinct Steller's sea cow resided in the Bering Sea. 
The same kinds of fossils are found from areas known to be adjacent to one another in the past but that, through the process of continental drift, are now in widely divergent geographic locations. For example, fossils of the same types of ancient amphibians, arthropods and ferns are found in South America, Africa, India, Australia and Antarctica, which can be dated to the Paleozoic Era, when these regions were united as a single landmass called Gondwana. 
Island biogeography Edit
Types of species found on islands Edit
Evidence from island biogeography has played an important and historic role in the development of evolutionary biology. For purposes of biogeography, islands are divided into two classes. Continental islands are islands like Great Britain, and Japan that have at one time or another been part of a continent. Oceanic islands, like the Hawaiian islands, the Galápagos Islands and St. Helena, on the other hand are islands that have formed in the ocean and never been part of any continent. Oceanic islands have distributions of native plants and animals that are unbalanced in ways that make them distinct from the biotas found on continents or continental islands. Oceanic islands do not have native terrestrial mammals (they do sometimes have bats and seals), amphibians, or fresh water fish. In some cases they have terrestrial reptiles (such as the iguanas and giant tortoises of the Galápagos Islands) but often (such as in Hawaii) they do not. This is despite the fact that when species such as rats, goats, pigs, cats, mice, and cane toads, are introduced to such islands by humans they often thrive. Starting with Charles Darwin, many scientists have conducted experiments and made observations that have shown that the types of animals and plants found, and not found, on such islands are consistent with the theory that these islands were colonized accidentally by plants and animals that were able to reach them. Such accidental colonization could occur by air, such as plant seeds carried by migratory birds, or bats and insects being blown out over the sea by the wind, or by floating from a continent or other island by sea (for example, by some kinds of plant seeds like coconuts that can survive immersion in salt water), and reptiles that can survive for extended periods on rafts of vegetation carried to sea by storms. 
Many of the species found on remote islands are endemic to a particular island or group of islands, meaning they are found nowhere else on earth. Examples of species endemic to islands include many flightless birds of New Zealand, lemurs of Madagascar, the Komodo dragon of Komodo,  the dragon's blood tree of Socotra,  Tuatara of New Zealand,   and others. However, many such endemic species are related to species found on other nearby islands or continents the relationship of the animals found on the Galápagos Islands to those found in South America is a well-known example.  All of these facts, the types of plants and animals found on oceanic islands, the large number of endemic species found on oceanic islands, and the relationship of such species to those living on the nearest continents, are most easily explained if the islands were colonized by species from nearby continents that evolved into the endemic species now found there. 
Other types of endemism do not have to include, in the strict sense, islands. Islands can mean isolated lakes or remote and isolated areas. Examples of these would include the highlands of Ethiopia, Lake Baikal, fynbos of South Africa, forests of New Caledonia, and others. Examples of endemic organisms living in isolated areas include the kagu of New Caledonia,  cloud rats of the Luzon tropical pine forests of the Philippines,   the boojum tree (Fouquieria columnaris) of the Baja California peninsula,  and the Baikal seal. 
Adaptive radiations Edit
Oceanic islands are frequently inhabited by clusters of closely related species that fill a variety of ecological niches, often niches that are filled by very different species on continents. Such clusters, like the finches of the Galápagos, Hawaiian honeycreepers, members of the sunflower family on the Juan Fernandez Archipelago and wood weevils on St. Helena are called adaptive radiations because they are best explained by a single species colonizing an island (or group of islands) and then diversifying to fill available ecological niches. Such radiations can be spectacular 800 species of the fruit fly family Drosophila, nearly half the world's total, are endemic to the Hawaiian islands. Another illustrative example from Hawaii is the silversword alliance, which is a group of thirty species found only on those islands. Members range from the silverswords that flower spectacularly on high volcanic slopes to trees, shrubs, vines and mats that occur at various elevations from mountain top to sea level, and in Hawaiian habitats that vary from deserts to rainforests. Their closest relatives outside Hawaii, based on molecular studies, are tarweeds found on the west coast of North America. These tarweeds have sticky seeds that facilitate distribution by migrant birds.  Additionally, nearly all of the species on the island can be crossed and the hybrids are often fertile,  and they have been hybridized experimentally with two of the west coast tarweed species as well.  Continental islands have less distinct biota, but those that have been long separated from any continent also have endemic species and adaptive radiations, such as the 75 lemur species of Madagascar, and the eleven extinct moa species of New Zealand.  
Ring species Edit
A ring species is a connected series of populations, each of which can interbreed with its neighbors, with at least two "end" populations which are too distantly related to interbreed, though with the potential for gene flow between all the populations.  Ring species represent speciation and have been cited as evidence of evolution. They illustrate what happens over time as populations genetically diverge, specifically because they represent, in living populations, what normally happens over time between long deceased ancestor populations and living populations, in which the intermediates have become extinct. Richard Dawkins says that ring species "are only showing us in the spatial dimension something that must always happen in the time dimension". 
Specific examples from biogeography Edit
Distribution of Glossopteris Edit
The combination of continental drift and evolution can sometimes be used to predict what will be found in the fossil record. Glossopteris is an extinct species of seed fern plants from the Permian. Glossopteris appears in the fossil record around the beginning of the Permian on the ancient continent of Gondwana.  Continental drift explains the current biogeography of the tree. Present day Glossopteris fossils are found in Permian strata in southeast South America, southeast Africa, all of Madagascar, northern India, all of Australia, all of New Zealand, and scattered on the southern and northern edges of Antarctica. During the Permian, these continents were connected as Gondwana (see figure 4c) in agreement with magnetic striping, other fossil distributions, and glacial scratches pointing away from the temperate climate of the South Pole during the Permian.  
Metatherian distribution Edit
The history of metatherians (the clade containing marsupials and their extinct, primitive ancestors) provides an example of how evolutionary theory and the movement of continents can be combined to make predictions concerning fossil stratigraphy and distribution. The oldest metatherian fossils are found in present-day China.  Metatherians spread westward into modern North America (still attached to Eurasia) and then to South America, which was connected to North America until around 65 mya. Marsupials reached Australia via Antarctica about 50 mya, shortly after Australia had split off suggesting a single dispersion event of just one species.  Evolutionary theory suggests that the Australian marsupials descended from the older ones found in the Americas. Geologic evidence suggests that between 30 and 40 million years ago South America and Australia were still part of the Southern Hemisphere super continent of Gondwana and that they were connected by land that is now part of Antarctica. Therefore, when combining the models, scientists could predict that marsupials migrated from what is now South America, through Antarctica, and then to present-day Australia between 40 and 30 million years ago. A first marsupial fossil of the extinct family Polydolopidae was found on Seymour Island on the Antarctic Peninsula in 1982.  Further fossils have subsequently been found, including members of the marsupial orders Didelphimorphia (opossum) and Microbiotheria,  as well as ungulates and a member of the enigmatic extinct order Gondwanatheria, possibly Sudamerica ameghinoi.   
Migration, isolation, and distribution of the camel Edit
The history of the camel provides an example of how fossil evidence can be used to reconstruct migration and subsequent evolution. The fossil record indicates that the evolution of camelids started in North America (see figure 4e), from which, six million years ago, they migrated across the Bering Strait into Asia and then to Africa, and 3.5 million years ago through the Isthmus of Panama into South America. Once isolated, they evolved along their own lines, giving rise to the Bactrian camel and dromedary in Asia and Africa and the llama and its relatives in South America. Camelids then became extinct in North America at the end of the last ice age. 
Scientists have observed and documented a multitude of events where natural selection is in action. The most well known examples are antibiotic resistance in the medical field along with better-known laboratory experiments documenting evolution's occurrence. Natural selection is tantamount to common descent in that long-term occurrence and selection pressures can lead to the diversity of life on earth as found today. All adaptations—documented and undocumented changes concerned—are caused by natural selection (and a few other minor processes). It is well established that, ". natural selection is a ubiquitous part of speciation. ",  and is the primary driver of speciation. 
Artificial selection and experimental evolution Edit
Artificial selection demonstrates the diversity that can exist among organisms that share a relatively recent common ancestor. In artificial selection, one species is bred selectively at each generation, allowing only those organisms that exhibit desired characteristics to reproduce. These characteristics become increasingly well developed in successive generations. Artificial selection was successful long before science discovered the genetic basis. Examples of artificial selection include dog breeding, genetically modified food, flower breeding, and the cultivation of foods such as wild cabbage,  and others. [ citation needed ]
Experimental evolution uses controlled experiments to test hypotheses and theories of evolution. In one early example, William Dallinger set up an experiment shortly before 1880, subjecting microbes to heat with the aim of forcing adaptive changes. His experiment ran for around seven years, and his published results were acclaimed, but he did not resume the experiment after the apparatus failed. 
A large-scale example of experimental evolution is Richard Lenski's multi-generation experiment with Escherichia coli. Lenski observed that some strains of E. coli evolved a complex new ability, the ability to metabolize citrate, after tens of thousands of generations.   The evolutionary biologist Jerry Coyne commented as a critique of creationism, saying, "the thing I like most is it says you can get these complex traits evolving by a combination of unlikely events. That's just what creationists say can't happen."  In addition to the metabolic changes, the different bacterial populations were found to have diverged in respect to both morphology (the overall size of the cell) and fitness (of which was measured in competition with the ancestors). 
Historical lead tolerance in Daphnia Edit
A study of species of Daphnia and lead pollution in the 20th century predicted that an increase in lead pollution would lead to strong selection of lead tolerance. Researchers were able to use "resurrection ecology", hatching decades-old Daphnia eggs from the time when lakes were heavily polluted with lead. The hatchlings in the study were compared to current-day Daphnia, and demonstrated "dramatic fitness differences between old and modern phenotypes when confronted with a widespread historical environmental stressor". Essentially, the modern-day Daphnia were unable to resist or tolerate high levels of lead (this is due to the huge reduction of lead pollution in 21st century lakes). The old hatchlings, however, were able to tolerate high lead pollution. The authors concluded that "by employing the techniques of resurrection ecology, we were able to show clear phenotypic change over decades. ". 
Peppered moths Edit
A classic example was the phenotypic change, light-to-dark color adaptation, in the peppered moth, due to pollution from the Industrial Revolution in England.  
Antimicrobial resistance Edit
The development and spread of antibiotic-resistant bacteria is evidence for the process of evolution of species. Thus the appearance of vancomycin-resistant Staphylococcus aureus, and the danger it poses to hospital patients, is a direct result of evolution through natural selection. The rise of Shigella strains resistant to the synthetic antibiotic class of sulfonamides also demonstrates the generation of new information as an evolutionary process.  Similarly, the appearance of DDT resistance in various forms of Anopheles mosquitoes, and the appearance of myxomatosis resistance in breeding rabbit populations in Australia, are both evidence of the existence of evolution in situations of evolutionary selection pressure in species in which generations occur rapidly.
All classes of microbes develop resistance: including fungi (antifungal resistance), viruses (antiviral resistance), protozoa (antiprotozoal resistance), and bacteria (antibiotic resistance). This is to be expected when considering that all life exhibits universal genetic code and is therefore subject to the process of evolution through its various mechanisms.
Nylon-eating bacteria Edit
Another example of organisms adapting to human-caused conditions are Nylon-eating bacteria: a strain of Flavobacterium that are capable of digesting certain byproducts of nylon 6 manufacturing. There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. This is seen as a good example of evolution through mutation and natural selection that has been observed as it occurs and could not have come about until the production of nylon by humans.    
Plants and fungi Edit
Monkeyflower radiation Edit
Both subspecies Mimulus aurantiacus puniceus (red-flowered) and Mimulus aurantiacus australis (yellow-flowered) of monkeyflowers are isolated due to the preferences of their hummingbird and hawkmoth pollinators. The radiation of M. aurantiacus subspecies are mostly yellow colored however, both M. a. ssp. puniceus and M. a. ssp. flemingii are red. Phylogenetic analysis suggests two independent origins of red-colored flowers that arose due to cis-regulatory mutations in the gene MaMyb2 that is present in all M. aurantiacus subspecies. Further research suggested that two independent mutations did not take place, but one MaMyb2 allele was transferred via introgressive hybridization. 
Radiotrophic fungi Edit
Like the codfish, human-caused pollution can come in different forms. Radiotrophic fungi is a perfect example of natural selection taking place after a chemical accident. Radiotrophic fungi appears to use the pigment melanin to convert gamma radiation into chemical energy for growth and were first discovered in 2007 as black molds growing inside and around the Chernobyl Nuclear Power Plant. Research at the Albert Einstein College of Medicine showed that three melanin-containing fungi, Cladosporium sphaerospermum, Wangiella dermatitidis, and Cryptococcus neoformans, increased in biomass and accumulated acetate faster in an environment in which the radiation level was 500 times higher than in the normal environment.  
While studying guppies (Poecilia reticulata) in Trinidad, biologist John Endler detected selection at work on the fish populations. To rule out alternative possibilities, Endler set up a highly controlled experiment to mimic the natural habitat by constructing ten ponds within a laboratory greenhouse at Princeton University. Each pond contained gravel to exactly match that of the natural ponds. After capturing a random sample of guppies from ponds in Trinidad, he raised and mixed them to create similar genetically diverse populations and measured each fish (spot length, spot height, spot area, relative spot length, relative spot height, total patch area, and standard body lengths). For the experiment he added Crenicichla alta (P. reticulata's main predator) in four of the ponds, Rivulus hartii (a non-predator fish) in four of the ponds, and left the remaining two ponds empty with only the guppies. After 10 generations, comparisons were made between each pond's guppy populations and measurements were taken again. Endler found that the populations had evolved dramatically different color patterns in the control and non-predator pools and drab color patterns in the predator pool. Predation pressure had caused a selection against standing out from background gravel. 
In parallel, during this experiment, Endler conducted a field experiment in Trinidad where he caught guppies from ponds where they had predators and relocated them to ponds upstream where the predators did not live. After 15 generations, Endler found that the relocated guppies had evolved dramatic and colorful patterns. Essentially, both experiments showed convergence due to similar selection pressures (i.e. predator selection against contrasting color patterns and sexual selection for contrasting color patterns). 
In a later study by David Reznick, the field population was examined 11 years later after Endler relocated the guppies to high streams. The study found that the populations has evolved in a number of different ways: bright color patterns, late maturation, larger sizes, smaller litter sizes, and larger offspring within litters.  Further studies of P. reticulata and their predators in the streams of Trinidad have indicated that varying modes of selection through predation have not only changed the guppies color patterns, sizes, and behaviors, but their life histories and life history patterns. 
Natural selection is observed in contemporary human populations, with recent findings demonstrating that the population at risk of the severe debilitating disease kuru has significant over-representation of an immune variant of the prion protein gene G127V versus non-immune alleles. Scientists postulate one of the reasons for the rapid selection of this genetic variant is the lethality of the disease in non-immune persons.   Other reported evolutionary trends in other populations include a lengthening of the reproductive period, reduction in cholesterol levels, blood glucose and blood pressure. 
A well known example of selection occurring in human populations is lactose tolerance. Lactose intolerance is the inability to metabolize lactose, because of a lack of the required enzyme lactase in the digestive system. The normal mammalian condition is for the young of a species to experience reduced lactase production at the end of the weaning period (a species-specific length of time). In humans, in non-dairy consuming societies, lactase production usually drops about 90% during the first four years of life, although the exact drop over time varies widely.  Lactase activity persistence in adults is associated with two polymorphisms: C/T 13910 and G/A 22018 located in the MCM6 gene.  This gene difference eliminates the shutdown in lactase production, making it possible for members of these populations to continue consumption of raw milk and other fresh and fermented dairy products throughout their lives without difficulty. This appears to be an evolutionarily recent (around 10,000 years ago [and 7,500 years ago in Europe]  ) adaptation to dairy consumption,  and has occurred independently in both northern Europe and east Africa in populations with a historically pastoral lifestyle.  
Italian wall lizards Edit
In 1971, ten adult specimens of Podarcis sicula (the Italian wall lizard) were transported from the Croatian island of Pod Kopište to the island Pod Mrčaru (about 3.5 km to the east). Both islands lie in the Adriatic Sea near Lastovo, where the lizards founded a new bottlenecked population.   The two islands have similar size, elevation, microclimate, and a general absence of terrestrial predators  and the P. sicula expanded for decades without human interference, even out-competing the (now locally extinct  ) Podarcis melisellensis population. 
In the 1990s, scientists returned to Pod Mrčaru and found that the lizards there differed greatly from those on Kopište. While mitochondrial DNA analyses have verified that P. sicula currently on Mrčaru are genetically very similar to the Kopište source population,  the new Mrčaru population of P. sicula had a larger average size, shorter hind limbs, lower maximal sprint speed and altered response to simulated predatory attacks compared to the original Kopište population.  These changes were attributed to "relaxed predation intensity" and greater protection from vegetation on Mrčaru. 
In 2008, further analysis revealed that the Mrčaru population of P. sicula have significantly different head morphology (longer, wider, and taller heads) and increased bite force compared to the original Kopište population.  This change in head shape corresponded with a shift in diet: Kopište P. sicula are primarily insectivorous, but those on Mrčaru eat substantially more plant matter.  The changes in foraging style may have contributed to a greater population density and decreased territorial behavior of the Mrčaru population. 
Another difference found between the two populations was the discovery, in the Mrčaru lizards, of cecal valves, which slow down food passage and provide fermenting chambers, allowing commensal microorganisms to convert cellulose to nutrients digestible by the lizards.  Additionally, the researchers discovered that nematodes were common in the guts of Mrčaru lizards, but absent from Kopište P. sicula, which do not have cecal valves.  The cecal valves, which occur in less than 1 percent of all known species of scaled reptiles,  have been described as an "adaptive novelty, a brand new feature not present in the ancestral population and newly evolved in these lizards". 
PAH resistance in killifish Edit
A similar study was also done regarding the polycyclic aromatic hydrocarbons (PAHs) that pollute the waters of the Elizabeth River in Portsmouth, Virginia. This chemical is a product of creosote, a type of tar. The Atlantic killifish (Fundulus heteroclitus) has evolved a resistance to PAHs involving the AHR gene (the same gene involved in the tomcods). This particular study focused on the resistance to "acute toxicity and cardiac teratogenesis" caused by PAHs. that mutated within the tomcods in the Hudson River. 
PCB resistance in codfish Edit
An example involving the direct observation of gene modification due to selection pressures is the resistance to PCBs in codfish. After General Electric dumped polychlorinated biphenyls (PCBs) in the Hudson River from 1947 through 1976, tomcods (Microgadus tomcod) living in the river were found to have evolved an increased resistance to the compound's toxic effects.  The tolerance to the toxins is due to a change in the coding section of specific gene. Genetic samples were taken from the cods from 8 different rivers in the New England region: the St. Lawrence River, Miramichi River, Margaree River, Squamscott River, Niantic River, the Shinnecock Basic, the Hudson River, and the Hackensack River. Genetic analysis found that in the population of tomcods in the four southernmost rivers, the gene AHR2 (aryl hydrocarbon receptor 2) was present as an allele with a difference of two amino acid deletions.  This deletion conferred a resistance to PCB in the fish species and was found in 99% of Hudson River tomcods, 92% in the Hackensack River, 6% in the Niantic River, and 5% in Shinnecock Bay.  This pattern along the sampled bodies of waters infers a direct correlation of selective pressures leading to the evolution of PCB resistance in Atlantic tomcod fish. 
Urban wildlife Edit
Urban wildlife is a broad and easily observable case of human-caused selection pressure on wildlife. With the growth in human habitats, different animals have adapted to survive within these urban environments. These types of environments can exert selection pressures on organisms, often leading to new adaptations. For example, the weed Crepis sancta, found in France, has two types of seed, heavy and fluffy. The heavy ones land nearby to the parent plant, whereas fluffy seeds float further away on the wind. In urban environments, seeds that float far often land on infertile concrete. Within about 5–12 generations, the weed evolves to produce significantly heavier seeds than its rural relatives.   Other examples of urban wildlife are rock pigeons and species of crows adapting to city environments around the world African penguins in Simon's Town baboons in South Africa and a variety of insects living in human habitations. Studies have been conducted and have found striking changes to animals' (more specifically mammals') behavior and physical brain size due to their interactions with human-created environments.  
White Sands lizards Edit
Animals that exhibit ecotonal variations allow for research concerning the mechanisms that maintain population differentiation. A wealth of information about natural selection, genotypic, and phenotypic variation   adaptation and ecomorphology  and social signaling  has been acquired from the studies of three species of lizards located in the White Sands desert of New Mexico. Holbrookia maculata, Aspidoscelis inornatus, and Sceloporus undulatus exhibit ecotonal populations that match both the dark soils and the white sands in the region. Research conducted on these species has found significant phenotypic and genotypic differences between the dark and light populations due to strong selection pressures. For example, H. maculata exhibits the strongest phenotypic difference (matches best with the substrate) of the light colored population coinciding with the least amount of gene flow between the populations and the highest genetic differences when compared to the other two lizard species. 
New Mexico's White Sands are a recent geologic formation (approximately 6000 years old  to possibly 2000 years old  ). This recent origin of these gypsum sand dunes suggests that species exhibiting lighter-colored variations have evolved in a relatively short time frame. The three lizard species previously mentioned have been found to display variable social signal coloration in coexistence with their ecotonal variants.  Not only have the three species convergently evolved their lighter variants due to the selection pressures from the environment, they've also evolved ecomorphological differences: morphology, behavior (in is case, escape behavior), and performance (in this case, sprint speed) collectively.  Roches' work found surprising results in the escape behavior of H. maculata and S. undulatus. When dark morphs were placed on white sands, their startle response was significantly diminished. This result could be due to varying factors relating to sand temperature or visual acuity however, regardless of the cause, "…failure of mismatched lizards to sprint could be maladaptive when faced with a predator". 
Speciation is the evolutionary process by which new biological species arise. Biologists research species using different theoretical frameworks for what constitutes a species (see species problem and species complex) and there exists debate with regard to delineation.  Nevertheless, much of the current research suggests that, ". speciation is a process of emerging genealogical distinctness, rather than a discontinuity affecting all genes simultaneously"  and, in allopatry (the most common form of speciation), "reproductive isolation is a byproduct of evolutionary change in isolated populations, and thus can be considered an evolutionary accident".  Speciation occurs as the result of the latter (allopatry) however, a variety of differing agents have been documented and are often defined and classified in various forms (e.g. peripatric, parapatric, sympatric, polyploidization, hybridization, etc.). Instances of speciation have been observed in both nature and the laboratory. A.-B Florin and A. Ödeen note that, "strong laboratory evidence for allopatric speciation is lacking. " however, contrary to laboratory studies (focused specifically on models of allopatric speciation), "speciation most definitely occurs [and] the vast amount of evidence from nature makes it unreasonable to argue otherwise".  Coyne and Orr compiled a list of 19 laboratory experiments on Drosophila presenting examples of allopatric speciation by divergent selection concluding that, "reproductive isolation in allopatry can evolve as a byproduct of divergent selection". 
Research documenting speciation is abundant. Biologists have documented numerous examples of speciation in nature—with evolution having produced far more species than any observer would consider necessary. For example, there are well over 350,000 described species of beetles.  Examples of speciation come from the observations of island biogeography and the process of adaptive radiation, both explained previously. Evidence of common descent can also be found through paleontological studies of speciation within geologic strata. The examples described below represent different modes of speciation and provide strong evidence for common descent. It is important to acknowledge that not all speciation research directly observes divergence from "start-to-finish". This is by virtue of research delimitation and definition ambiguity, and occasionally leads research towards historical reconstructions. In light of this, examples abound, and the following are by no means exhaustive—comprising only a small fraction of the instances observed. Once again, take note of the established fact that, ". natural selection is a ubiquitous part of speciation. ",  and is the primary driver of speciation,  so hereinafter, examples of speciation will often interdepend and correspond with selection.
Limitations exist within the fossil record when considering the concept of what constitutes a species. Paleontologists largely rely on a different framework: the morphological species concept.  Due to the absence of information such as reproductive behavior or genetic material in fossils, paleontologists distinguish species by their phenotypic differences.  Extensive investigation of the fossil record has led to numerous theories concerning speciation (in the context of paleontology) with many of the studies suggesting that stasis, punctuation, and lineage branching are common. In 1995, D. H. Erwin, et al. published a major work—New Approaches to Speciation in the Fossil Record—which compiled 58 studies of fossil speciation (between 1972 and 1995) finding most of the examples suggesting stasis (involving anagenesis or punctuation) and 16 studies suggesting speciation.  Despite stasis appearing to be the predominate conclusion at first glance, this particular meta-study investigated deeper, concluding that, ". no single pattern appears dominate. " with ". the preponderance of studies illustrating both stasis and gradualism in the history of a single lineage".  Many of the studies conducted utilize seafloor sediments that can provide a significant amount of data concerning planktonic microfossils.  The succession of fossils in stratigraphy can be used to determine evolutionary trends among fossil organisms. In addition, incidences of speciation can be interpreted from the data and numerous studies have been conducted documenting both morphological evolution and speciation.
Extensive research on the planktonic foraminifer Globorotalia truncatulinoides has provided insight into paleobiogeographical and paleoenvironmental studies alongside the relationship between the environment and evolution. In an extensive study of the paleobiogeography of G. truncatulinoides, researchers found evidence that suggested the formation of a new species (via the sympatric speciation framework). Cores taken of the sediment containing the three species G. crassaformis, G. tosaensis, and G. truncatulinoides found that before 2.7 Ma, only G. crassaformis and G. tosaensis existed. A speciation event occurred at that time, whereby intermediate forms existed for quite some time. Eventually G. tosaensis disappears from the record (suggesting extinction) but exists as an intermediate between the extant G. crassaformis and G. truncatulinoides. This record of the fossils also matched the already existing phylogeny constructed by morphological characters of the three species.  See figure 6a.
In a large study of five species of radiolarians (Calocycletta caepa, Pterocanium prismatium, Pseudoculous vema, Eucyrtidium calvertense, and Eucyrtidium matuyamai), the researchers documented considerable evolutionary change in each lineage. Alongside this, trends with the closely related species E. calvertense and E. matuyamai showed that about 1.9 Mya E. calvertense invaded a new region of the Pacific, becoming isolated from the main population. The stratigraphy of this species clearly shows that this isolated population evolved into E. Matuyamai. It then reinvaded the region of the still-existing and static E. calvertense population whereby a sudden decrease in body size occurred. Eventually the invader E. matuyamai disappeared from the stratum (presumably due to extinction) coinciding with a desistance of size reduction of the E. calvertense population. From that point on, the change in size leveled to a constant. The authors suggest competition-induced character displacement.  
Researchers conducted measurements on 5,000 Rhizosolenia (a planktonic diatom) specimens from eight sedimentary cores in the Pacific Ocean. The core samples spanned two million years and were chronologized using sedimentary magnetic field reversal measurements. All the core samples yielded a similar pattern of divergence: with a single lineage (R. bergonii) occurring before 3.1 Mya and two morphologically distinct lineages (daughter species: R. praebergonii) appearing after. The parameters used to measure the samples were consistent throughout each core.  An additional study of the daughter species R. praebergonii found that, after the divergence, it invaded the Indian Ocean.  
A recent study was conducted involving the planktonic foraminifer Turborotalia. The authors extracted "51 stratigraphically ordered samples from a site within the oceanographically stable tropical North Pacific gyre". Two hundred individual species were examined using ten specific morphological traits (size, compression index, chamber aspect ratio, chamber inflation, aperture aspect ratio, test height, test expansion, umbilical angle, coiling direction, and the number of chambers in the final whorl). Utilizing multivariate statistical clustering methods, the study found that the species continued to evolve non-directionally within the Eocene from 45 Ma to about 36 Ma. However, from 36 Ma to approximately 34 Ma, the stratigraphic layers showed two distinct clusters with significantly defining characteristics distinguishing one another from a single species. The authors concluded that speciation must have occurred and that the two new species were ancestral to the prior species. 
There exists evidence for vertebrate speciation despite limitations imposed by the fossil record. Studies have been conducted documenting similar patterns seen in marine invertebrates.  For example, extensive research documenting rates of morphological change, evolutionary trends, and speciation patterns in small mammals has significantly contributed to the scientific literature. 
A study of four mammalian genera: Hyopsodus, Pelycodus, Haplomylus (three from the Eocene), and Plesiadapis (from the Paleocene) found that—through a large number of stratigraphic layers and specimen sampling—each group exhibited, "gradual phyletic evolution, overall size increase, iterative evolution of small species, and character divergence following the origin of each new lineage".  The authors of this study concluded that speciation was discernible. In another study concerning morphological trends and rates of evolution found that the European arvicolid rodent radiated into 52 distinct lineages over a time frame of 5 million years while documenting examples of phyletic gradualism, punctuation, and stasis. 
Drosophila melanogaster Edit
William R. Rice and George W. Salt found experimental evidence of sympatric speciation in the common fruit fly. They collected a population of Drosophila melanogaster from Davis, California and placed the pupae into a habitat maze. Newborn flies had to investigate the maze to find food. The flies had three choices to take in finding food. Light and dark (phototaxis), up and down (geotaxis), and the scent of acetaldehyde and the scent of ethanol (chemotaxis) were the three options. This eventually divided the flies into 42 spatio-temporal habitats. They then cultured two strains that chose opposite habitats. One of the strains emerged early, immediately flying upward in the dark attracted to the acetaldehyde. The other strain emerged late and immediately flew downward, attracted to light and ethanol. Pupae from the two strains were then placed together in the maze and allowed to mate at the food site. They then were collected. A selective penalty was imposed on the female flies that switched habitats. This entailed that none of their gametes would pass on to the next generation. After 25 generations of this mating test, it showed reproductive isolation between the two strains. They repeated the experiment again without creating the penalty against habitat switching and the result was the same reproductive isolation was produced.   
Gall wasps Edit
A study of the gall-forming wasp species Belonocnema treatae found that populations inhabiting different host plants (Quercus geminata and Q. virginiana) exhibited different body size and gall morphology alongside a strong expression of sexual isolation. The study hypothesized that B. treatae populations inhabiting different host plants would show evidence of divergent selection promoting speciation. The researchers sampled gall wasp species and oak tree localities, measured body size (right hand tibia of each wasp), and counted gall chamber numbers. In addition to measurements, they conducted mating assays and statistical analyses. Genetic analysis was also conducted on two mtDNA sites (416 base pairs from cytochrome C and 593 base pairs from cytochrome oxidase ) to "control for the confounding effects of time since divergence among allopatric populations". 
In an additional study, the researchers studied two gall wasp species B. treatae and Disholcaspis quercusvirens and found strong morphological and behavioral variation among host-associated populations. This study further confounded prerequisites to speciation. 
Hawthorn fly Edit
One example of evolution at work is the case of the hawthorn fly, Rhagoletis pomonella, also known as the apple maggot fly, which appears to be undergoing sympatric speciation.  Different populations of hawthorn fly feed on different fruits. A distinct population emerged in North America in the 19th century some time after apples, a non-native species, were introduced. This apple-feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. The current hawthorn feeding population does not normally feed on apples. Some evidence, such as the fact that six out of thirteen allozyme loci are different, that hawthorn flies mature later in the season and take longer to mature than apple flies and that there is little evidence of interbreeding (researchers have documented a 4–6% hybridization rate) suggests that speciation is occurring.     
London Underground mosquito Edit
The London Underground mosquito is a species of mosquito in the genus Culex found in the London Underground. It evolved from the overground species Culex pipiens. This mosquito, although first discovered in the London Underground system, has been found in underground systems around the world. It is suggested that it may have adapted to human-made underground systems since the last century from local above-ground Culex pipiens,  although more recent evidence suggests that it is a southern mosquito variety related to Culex pipiens that has adapted to the warm underground spaces of northern cities. 
The two species have very different behaviours,  are extremely difficult to mate,  and with different allele frequency, consistent with genetic drift during a founder event.  More specifically, this mosquito, Culex pipiens molestus, breeds all-year round, is cold intolerant, and bites rats, mice, and humans, in contrast to the above ground species Culex pipiens that is cold tolerant, hibernates in the winter, and bites only birds. When the two varieties were cross-bred the eggs were infertile suggesting reproductive isolation.  
The genetic data indicates that the molestus form in the London Underground mosquito appears to have a common ancestry, rather than the population at each station being related to the nearest aboveground population (i.e. the pipiens form). Byrne and Nichols' working hypothesis was that adaptation to the underground environment had occurred locally in London only once. These widely separated populations are distinguished by very minor genetic differences, which suggest that the molestus form developed: a single mtDNA difference shared among the underground populations of ten Russian cities  a single fixed microsatellite difference in populations spanning Europe, Japan, Australia, the middle East and Atlantic islands. 
Snapping shrimp and the isthmus of Panama Edit
Debate exists determining when the isthmus of Panama closed. Much of the evidence supports a closure approximately 2.7 to 3.5 mya using ". multiple lines of evidence and independent surveys".  However, a recent study suggests an earlier, transient bridge existed 13 to 15 mya.  Regardless of the timing of the isthmus closer, biologists can study the species on the Pacific and Caribbean sides in, what has been called, "one of the greatest natural experiments in evolution."  Studies of snapping shrimp in the genus Alpheus have provided direct evidence of allopatric speciation events,  and contributed to the literature concerning rates of molecular evolution.  Phylogenetic reconstructions using "multilocus datasets and coalescent-based analytical methods" support the relationships of the species in the group  and molecular clock techniques support the separation of 15 pairs of Alpheus species between 3 and 15 million years ago. 
The botanist Verne Grant pioneered the field of plant speciation with his research and major publications on the topic.  As stated before, many biologists rely on the biological species concept, with some modern researchers utilizing the phylogenetic species concept. Debate exists in the field concerning which framework should be applied in the research.  Regardless, reproductive isolation is the primary role in the process of speciation and has been studied extensively by biologists in their respective disciplines.
Both hybridization and polyploidy have also been found to be major contributors to plant speciation.  With the advent of molecular markers, "hybridization [is] considerably more frequent than previously believed".  In addition to these two modes leading to speciation, pollinator preference and isolation, chromosomal rearrangements, and divergent natural selection have become critical to the speciation of plants. Furthermore, recent research suggests that sexual selection, epigenetic drivers, and the creation of incompatible allele combinations caused by balancing selection also contribute to the formation of new species.  Instances of these modes have been researched in both the laboratory and in nature. Studies have also suggested that, due to "the sessile nature of plants. [it increases] the relative importance of ecological speciation. " 
Hybridization between two different species sometimes leads to a distinct phenotype. This phenotype can also be fitter than the parental lineage and as such, natural selection may then favor these individuals. Eventually, if reproductive isolation is achieved, it may lead to a separate species. However, reproductive isolation between hybrids and their parents is particularly difficult to achieve and thus hybrid speciation is considered a rare event. However, hybridization resulting in reproductive isolation is considered an important means of speciation in plants,  since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals.  
Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis.  Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations.  Hybridization without change in chromosome number is called homoploid hybrid speciation. It is considered very rare but has been shown in Heliconius butterflies  and sunflowers. Polyploid speciation, which involves changes in chromosome number, is a more common phenomenon, especially in plant species.
Polyploidy is a mechanism that has caused many rapid speciation events in sympatry because offspring of, for example, tetraploid x diploid matings often result in triploid sterile progeny.  Not all polyploids are reproductively isolated from their parental plants, and gene flow may still occur for example through triploid hybrid x diploid matings that produce tetraploids, or matings between meiotically unreduced gametes from diploids and gametes from tetraploids. It has been suggested that many of the existing plant and most animal species have undergone an event of polyploidization in their evolutionary history.   Reproduction of successful polyploid species is sometimes asexual, by parthenogenesis or apomixis, as for unknown reasons many asexual organisms are polyploid. Rare instances of polyploid mammals are known, but most often result in prenatal death.
Researchers consider reproductive isolation as key to speciation.  A major aspect of speciation research is to determine the nature of the barriers that inhibit reproduction. Botanists often consider the zoological classifications of prezygotic and postzygotic barriers as inadequate.  The examples provided below give insight into the process of speciation.
Mimulus peregrinus Edit
The creation of a new allopolyploid species of monkeyflower (Mimulus peregrinus) was observed on the banks of the Shortcleuch Water—a river in Leadhills, South Lanarkshire, Scotland. Parented from the cross of the two species Mimulus guttatus (containing 14 pairs of chromosomes) and Mimulus luteus (containing 30-31 pairs from a chromosome duplication), M. peregrinus has six copies of its chromosomes (caused by the duplication of the sterile hybrid triploid). Due to the nature of these species, they have the ability to self-fertilize. Because of its number of chromosomes it is not able to pair with M. guttatus, M. luteus, or their sterile triploid offspring. M. peregrinus will either die, producing no offspring, or reproduce with itself effectively leading to a new species.  
Raphanobrassica includes all intergeneric hybrids between the genera Raphanus (radish) and Brassica (cabbages, etc.).   The Raphanobrassica is an allopolyploid cross between the radish (Raphanus sativus) and cabbage (Brassica oleracea). Plants of this parentage are now known as radicole. Two other fertile forms of Raphanobrassica are known. Raparadish, an allopolyploid hybrid between Raphanus sativus and Brassica rapa is grown as a fodder crop. "Raphanofortii" is the allopolyploid hybrid between Brassica tournefortii and Raphanus caudatus. The Raphanobrassica is a fascinating plant, because (in spite of its hybrid nature), it is not sterile. This has led some botanists to propose that the accidental hybridization of a flower by pollen of another species in nature could be a mechanism of speciation common in higher plants.
Senecio (groundsel) Edit
The Welsh groundsel is an allopolyploid, a plant that contains sets of chromosomes originating from two different species. Its ancestor was Senecio × baxteri, an infertile hybrid that can arise spontaneously when the closely related groundsel (Senecio vulgaris) and Oxford ragwort (Senecio squalidus) grow alongside each other. Sometime in the early 20th century, an accidental doubling of the number of chromosomes in an S. × baxteri plant led to the formation of a new fertile species.  
The York groundsel (Senecio eboracensis) is a hybrid species of the self-incompatible Senecio squalidus (also known as Oxford ragwort) and the self-compatible Senecio vulgaris (also known as common groundsel). Like S. vulgaris, S. eboracensis is self-compatible however, it shows little or no natural crossing with its parent species, and is therefore reproductively isolated, indicating that strong breed barriers exist between this new hybrid and its parents. It resulted from a backcrossing of the F1 hybrid of its parents to S. vulgaris. S. vulgaris is native to Britain, while S. squalidus was introduced from Sicily in the early 18th century therefore, S. eboracensis has speciated from those two species within the last 300 years.
Other hybrids descended from the same two parents are known. Some are infertile, such as S. x baxteri. Other fertile hybrids are also known, including S. vulgaris var. hibernicus, now common in Britain, and the allohexaploid S. cambrensis, which according to molecular evidence probably originated independently at least three times in different locations. Morphological and genetic evidence support the status of S. eboracensis as separate from other known hybrids. 
Thale cress Edit
Kirsten Bomblies et al. from the Max Planck Institute for Developmental Biology discovered two genes in the thale cress plant, Arabidopsis thaliana. When both genes are inherited by an individual, it ignites a reaction in the hybrid plant that turns its own immune system against it. In the parents, the genes were not detrimental, but they evolved separately to react defectively when combined.  To test this, Bomblies crossed 280 genetically different strains of Arabidopsis in 861 distinct ways and found that 2 percent of the resulting hybrids were necrotic. Along with allocating the same indicators, the 20 plants also shared a comparable collection of genetic activity in a group of 1,080 genes. In almost all of the cases, Bomblies discovered that only two genes were required to cause the autoimmune response. Bomblies looked at one hybrid in detail and found that one of the two genes belonged to the NB-LRR class, a common group of disease resistance genes involved in recognizing new infections. When Bomblies removed the problematic gene, the hybrids developed normally.  Over successive generations, these incompatibilities could create divisions between different plant strains, reducing their chances of successful mating and turning distinct strains into separate species. 
Tragopogon (salsify) Edit
Tragopogon is one example where hybrid speciation has been observed. In the early 20th century, humans introduced three species of salsify into North America. These species, the western salsify (Tragopogon dubius), the meadow salsify (Tragopogon pratensis), and the oyster plant (Tragopogon porrifolius), are now common weeds in urban wastelands. In the 1950s, botanists found two new species in the regions of Idaho and Washington, where the three already known species overlapped. One new species, Tragopogon miscellus, is a tetraploid hybrid of T. dubius and T. pratensis. The other new species, Tragopogon mirus, is also an allopolyploid, but its ancestors were T. dubius and T. porrifolius. These new species are usually referred to as "the Ownbey hybrids" after the botanist who first described them. The T. mirus population grows mainly by reproduction of its own members, but additional episodes of hybridization continue to add to the T. mirus population. 
T. dubius and T. pratensis mated in Europe but were never able to hybridize. A study published in March 2011 found that when these two plants were introduced to North America in the 1920s, they mated and doubled the number of chromosomes in there hybrid Tragopogon miscellus allowing for a "reset" of its genes, which in turn, allows for greater genetic variation. Professor Doug Soltis of the University of Florida said, "We caught evolution in the act…New and diverse patterns of gene expression may allow the new species to rapidly adapt in new environments".  
The bird species, Sylvia atricapilla, commonly referred to as blackcaps, lives in Germany and flies southwest to Spain while a smaller group flies northwest to Great Britain during the winter. Gregor Rolshausen from the University of Freiburg found that the genetic separation of the two populations is already in progress. The differences found have arisen in about 30 generations. With DNA sequencing, the individuals can be assigned to a correct group with an 85% accuracy. Stuart Bearhop from the University of Exeter reported that birds wintering in England tend to mate only among themselves, and not usually with those wintering in the Mediterranean.  It is still inference to say that the populations will become two different species, but researchers expect it due to the continued genetic and geographic separation. 
The shortfin molly (Poecilia mexicana) is a small fish that lives in the Sulfur Caves of Mexico. Years of study on the species have found that two distinct populations of mollies—the dark interior fish and the bright surface water fish—are becoming more genetically divergent.  The populations have no obvious barrier separating the two however, it was found that the mollies are hunted by a large water bug (Belostoma spp). Tobler collected the bug and both types of mollies, placed them in large plastic bottles, and put them back in the cave. After a day, it was found that, in the light, the cave-adapted fish endured the most damage, with four out of every five stab-wounds from the water bugs sharp mouthparts. In the dark, the situation was the opposite. The mollies' senses can detect a predator's threat in their own habitats, but not in the other ones. Moving from one habitat to the other significantly increases the risk of dying. Tobler plans on further experiments, but believes that it is a good example of the rise of a new species. 
Polar bear Edit
Natural selection, geographic isolation, and speciation in progress are illustrated by the relationship between the polar bear (Ursus maritimus) and the brown bear (Ursus arctos). Considered separate species throughout their ranges  however, it has been documented that they possess the capability to interbreed and produce fertile offspring. This introgressive hybridization has occurred both in the wild and in captivity and has been documented  and verified with DNA testing.  The oldest known fossil evidence of polar bears dates around 130,000 to 110,000 years ago  however, molecular data has revealed varying estimates of divergence time. Mitochondrial DNA analysis has given an estimate of 150,000 years ago  while nuclear genome analysis has shown an approximate divergence of 603,000 years ago.  Recent research using the complete genomes (rather than mtDNA or partial nuclear genomes) establishes the divergence of polar and brown bears between 479 and 343 thousand years ago.  Despite the differences in divergence rates, molecular research suggests the sister species have undergone a highly complex process of speciation and admixture between the two. 
The polar bear has acquired anatomical and physiological differences from the brown bear that allow it to comfortably survive in conditions that the brown bear likely could not. Notable examples include the ability to swim sixty miles or more at a time in freezing waters, fur that blends with the snow, and to stay warm in the arctic environment, an elongated neck that makes it easier to keep their heads above water while swimming, and oversized and heavy-matted webbed feet that act as paddles when swimming. It has also evolved small papillae and vacuole-like suction cups on the soles to make them less likely to slip on the ice, alongside smaller ears for a reduction of heat loss, eyelids that act like sunglasses, accommodations for their all-meat diet, a large stomach capacity to enable opportunistic feeding, and the ability to fast for up to nine months while recycling their urea.  
Animal coloration provided important early evidence for evolution by natural selection, at a time when little direct evidence was available. Three major functions of coloration were discovered in the second half of the 19th century, and subsequently used as evidence of selection: camouflage (protective coloration) mimicry, both Batesian and Müllerian and aposematism. After the circumstantial evidence provided by Darwin in On the Origin of Species, and given the absence of mechanisms for genetic variation or heredity at that time, naturalists including Darwin's contemporaries, Henry Walter Bates and Fritz Müller sought evidence from what they could observe in the field. 
Mimicry and aposematism Edit
Bates and Müller described forms of mimicry that now carry their names, based on their observations of tropical butterflies. These highly specific patterns of coloration are readily explained by natural selection, since predators such as birds which hunt by sight will more often catch and kill insects that are less good mimics of distasteful models than those that are better mimics but the patterns are otherwise hard to explain.  Darwinists such as Alfred Russel Wallace and Edward Bagnall Poulton, and in the 20th century Hugh Cott and Bernard Kettlewell, sought evidence that natural selection was taking place.   The efficacy of mimicry in butterflies was demonstrated in controlled experiments by Jane Van Zandt Brower in 1958.   
In 1889, Wallace noted that snow camouflage, especially plumage and pelage that changed with the seasons, suggested an obvious explanation as an adaptation for concealment.   Poulton's 1890 book, The Colours of Animals, written during Darwinism's lowest ebb, used all the forms of coloration to argue the case for natural selection.  Cott described many kinds of camouflage, mimicry and warning coloration in his 1940 book Adaptive Coloration in Animals, and in particular his drawings of coincident disruptive coloration in frogs convinced other biologists that these deceptive markings were products of natural selection.  Kettlewell experimented on peppered moth evolution, showing that the species had adapted as pollution changed the environment this provided compelling evidence of Darwinian evolution. 
Computer science allows the iteration of self-changing complex systems to be studied, allowing a mathematical understanding of the nature of the processes behind evolution providing evidence for the hidden causes of known evolutionary events. The evolution of specific cellular mechanisms like spliceosomes that can turn the cell's genome into a vast workshop of billions of interchangeable parts that can create tools that create us can be studied for the first time in an exact way.
"It has taken more than five decades, but the electronic computer is now powerful enough to simulate evolution",  assisting bioinformatics in its attempt to solve biological problems.
Computational evolutionary biology has enabled researchers to trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone. It has compared entire genomes permitting the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, and the prediction of factors important in speciation. It has also helped build complex computational models of populations to predict the outcome of the system over time and track and share information on an increasingly large number of species and organisms.
Future endeavors are to reconstruct a now more complex tree of life.
Christoph Adami, a professor at the Keck Graduate Institute made this point in Evolution of biological complexity:
To make a case for or against a trend in the evolution of complexity in biological evolution, complexity must be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon", within a fixed environment, genomic complexity is forced to increase. 
David J. Earl and Michael W. Deem—professors at Rice University made this point in Evolvability is a selectable trait:
Not only has life evolved, but life has evolved to evolve. That is, correlations within protein structure have evolved, and mechanisms to manipulate these correlations have evolved in tandem. The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution. Sensibly, rapid or extreme environmental change leads to selection for greater evolvability. This selection is not forbidden by causality and is strongest on the largest-scale moves within the mutational hierarchy. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. For example, the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low-fidelity polymerases during somatic hypermutation. A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of influenza A. 
"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins."  Evolutionary molecular engineering, also called directed evolution or in vitro molecular evolution involves the iterated cycle of mutation, multiplication with recombination, and selection of the fittest of individual molecules (proteins, DNA, and RNA). Natural evolution can be relived showing us possible paths from catalytic cycles based on proteins to based on RNA to based on DNA.    
The Avida computer simulation has been used to test evidence of common descent and natural selection.   In one example it has been used to demonstrate that natural selection can favor altruism, something that had been predicted but is difficult to test empirically. At the higher replication rates allowed by the simulation it becomes observable. 
Wolpert, L. Positional information and the spatial pattern of cellular differentiation. J. Theor. Biol. 25, 1–47 (1969).
Wolpert, L. Positional information revisited. Development 107, (Suppl.) 3–12 (1989).
Saunders, J. W. & Gasseling, M. T. in Epithelial–mesenchymal interactions (eds Fleischmeyer, R. & Billingham, R. E.) 78–97 (Williams & Wilkins, Baltimore, USA, 1968).
Tickle, C., Summerbell, D. & Wolpert, L. Positional signalling and specification of digits in chick limb morphogenesis. Nature 254, 199–202 (1975).
Saunders, J. W. in Limb and somite morphogenesis (eds Ede, D. A., Hinchliffe, J. R. & Balls, M.) 1–24 (Cambridge Univ. Press, Cambridge, UK, 1977).
Logan, M. Finger or toe: the molecular basis of limb identity. Development 130, 6401–6410 (2003).
Altabef, M., Clarke, J. D. & Tickle, C. Dorso–ventral ectodermal compartments and origin of apical ectodermal ridge in developing chick limb. Development 124, 4547–4556 (1997).
Martin, G. R. The roles of FGFs in early development of vertebrate limbs. Genes Dev. 12, 1571–1586 (1998).
Tickle, C., Shellswell, G., Crawley, A. & Wolpert, L. Positional signalling by mouse limb polarising region in the chick wing bud. Nature 259, 396–397 (1976).
Honig, L. S. & Summerbell, D. Maps of strength of positional signalling activity in the developing chick wing bud. J. Embryol. Exp. Morphol. 87, 163–174 (1985).
Bowen, J., Hinchliffe, J. R., Horder, T. J. & Reeve, A. M. The fate map of the chick forelimb-bud and its bearing on hypothesized developmental control mechanisms. Anat. Embryol. 179, 269–283 (1989).
Vargesson, N. et al. Cell fate in the chick limb bud and relationship to gene expression. Development 124, 1909–1918 (1997).
Zwilling, E. & Hansborough, L. Interaction between limb bud ectoderm and mesoderm in the chick embryo. III Experiments with polydactylous limbs. J. Exp. Zool. 132, 219–239 (1956).
Cooke, J. & Summerbell, D. Cell cycle and experimental pattern duplication in the chick wing during embryonic development. Nature 287, 697–701 (1980).
Tickle, C., Lee, J. & Eichele, G. A quantitative analysis of the effect of all-trans-retinoic acid on the pattern of chick wing development. Dev. Biol. 109, 82–95 (1985).
Riddle, R. D., Johnson, R. L., Laufer, E. & Tabin, C. Sonic hedgehog mediates the polarizing activity of the ZPA. Cell 75, 1401–1416 (1993).
Niederreither, K., Vermot, J., Schuhbar, B., Chambon, P. & Dolle, P. Embryonic retinoic acid synthesis is required for forelimb growth and antero–posterior patterning in the mouse. Development 129, 3563–3574 (2002).
Mercader, N. et al. Opposing RA and FGF signals control proximodistal vertebrate limb development through regulation of Meis genes. Development 127, 3961–3970 (2000).
Gritli-Linde, A., Lewis, P., McMahon, A. P. & Linde, A. The whereabouts of a morphogen: direct evidence for short- and graded long-range activity of hedgehog signaling peptides. Dev. Biol. 236, 364–386 (2001).
Zeng, X. et al. A freely diffusible form of Sonic hedgehog mediates long-range signalling. Nature 411, 716–720 (2001).
Yang, Y. et al. Relationship between dose, distance and time in Sonic Hedgehog-mediated regulation of anteroposterior polarity in the chick limb. Development 124, 4393–4404 (1997). The effects of SHH application to chick wing buds were characterized in terms of dose and time. The results directly showed the promotion of anterior to posterior positional values.
Chiang, C. et al. Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev. Biol. 236, 421–435 (2001).
Hooper, J. E. & Scott, M. P. Communicating with hedgehogs. Nature Rev. Mol. Cell Biol. 6, 306–317 (2005).
Litingtung, Y., Dahn, R. D., Li, Y. N., Fallon, J. F. & Chiang, C. Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity. Nature 418, 979–983 (2002).
Welscher, P. T. et al. Progression of vertebrate limb development through SHH-mediated counteraction of GLI3. Science 298, 827–830 (2002).
Wang, B., Fallon, J. F. & Beachy, P. A. Hedgehog-regulated processing of Gli3 produces an anterior/posterior repressor gradient in the developing vertebrate limb. Cell 100, 423–434 (2000).
Huangfu, D. et al. Hedgehog signalling in the mouse requires intraflagellar transport proteins. Nature 426, 83–87 (2003).
Liu, A., Wang, B. & Niswander, L. A. Mouse intraflagellar transport proteins regulate both the activator and repressor functions of Gli transcription factors. Development 132, 3103–3111 (2005).
Zuniga, A., Haramis, A. P., McMahon, A. P. & Zeller, R. Signal relay by BMP antagonism controls the SHH/FGF4 feedback loop in vertebrate limb buds. Nature 401, 598–602 (1999).
Duprez, D. M., Kostakopoulou, K., Francis-West, P. H., Tickle, C. & Brickell, P. M. Activation of Fgf-4 and HoxD gene expression by BMP-2 expressing cells in the developing chick limb. Development 122, 1821–1828 (1996).
Drossopoulou, G. et al. A model for anteroposterior patterning of the vertebrate limb based on sequential long- and short-range Shh signalling and Bmp signalling. Development 127, 1337–1348 (2000).
Tumpel, S. et al. Regulation of Tbx3 expression by anteroposterior signalling in vertebrate limb development. Dev. Biol. 250, 251–262 (2002).
Coelho, C. N. & Kosher, R. A. A gradient of gap junctional communication along the anterior–posterior axis of the developing chick limb bud. Dev. Biol. 148, 529–535 (1991).
Allen, F., Tickle, C. & Warner, A. The role of gap junctions in patterning of the chick limb bud. Development 108, 623–634 (1990).
Harfe, B. D. et al. Evidence for an expansion-based temporal Shh gradient in specifying vertebrate digit identities. Cell 118, 517–528 (2004). The fate of the cells that express SHH at different stages in mouse limb development was analysed. A model for the specification of mouse digits that integrates both the concentration and the length of exposure to SHH was proposed.
Ahn, S. & Joyner, A. L. Dynamic changes in the response of cells to positive hedgehog signaling during mouse limb patterning. Cell 118, 505–516 (2004). Detailed analysis of the fate of cells that express GLI1 at different stages during mouse limb development in response to SHH showed that cells that respond to SHH at late stages contribute to digits.
Haramis, A. G., Brown, J. M. & Zeller, R. The limb deformity mutation disrupts the SHH/FGF-4 feedback loop and regulation of 5′ HoxD genes during limb pattern formation. Development 121, 4237–4245 (1995).
Michos, O. et al. Gremlin-mediated BMP antagonism induces the epithelial–mesenchymal feedback signaling controlling metanephric kidney and limb organogenesis. Development 131, 3401–3410 (2004).
Shapiro, M. D., Hanken, J. & Rosenthal, N. Developmental basis of evolutionary digit loss in the australian lizard Hemiergis. J. Exp. Zoolog. B Mol. Dev. Evol. 297, 48–56 (2003).
Smith, J. C. Evidence for a positional memory in the development of the chick wing bud. J. Embryol. Exp. Morphol. 52, 105–113 (1979).
Amano, T. & Tamura, K. Region-specific expression of mario reveals pivotal function of the anterior nondigit region on digit formation in chick wing bud. Dev. Dyn. 233, 326–336 (2005).
Welten, M. C. M., Verbeek, F. J., Meijer, A. H. & Richardson, M. K. Gene expression and digit homology in the chicken embryo wing. Evol. Dev. 7, 18–28 (2005).
Summerbell, D., Lewis, J. H. & Wolpert, L. Positional information in chick limb morphogenesis. Nature 244, 492–496 (1973).
Dudley, A. T., Ros, M. A. & Tabin, C. J. A re-examination of proximodistal patterning during vertebrate limb development. Nature 418, 539–544 (2002).
Dolle, P., Izpisua-Belmonte, J.-C., Falkenstein, H., Renucci, A. & Duboule, D. Coordinate expression of the murine Hox-5 complex homeobox-containing genes during limb pattern formation. Nature 342, 767–772 (1989).
Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C. J. & Duboule, D. Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function. Nature 435, 1113–1116 (2005).
Izpisua-Belmonte, J. C., Tickle, C., Dolle, P., Wolpert, L. & Duboule, D. Expression of the homeobox Hox-4 genes and the specification of position in chick wing development. Nature 350, 585–589 (1991).
Morgan, B. A., Izpisua-Belmonte, J. C., Duboule, D. & Tabin, C. J. Targeted misexpression of Hox-4.6 in the avian limb bud causes apparent homeotic transformations. Nature 358, 236–239 (1992).
Knezevic, V. et al. Hoxd-12 differentially affects preaxial and postaxial chondrogenic branches in the limb and regulates Sonic hedgehog in a positive feedback loop. Development 124, 4523–4536 (1997).
Zakany, J., Kmita, M. & Duboule, D. A dual role for Hox genes in limb anterior–posterior asymmetry. Science 304, 1669–1672 (2004).
Wellik, D. M. & Capecchi, M. R. Hox10 and Hox11 genes are required to globally pattern the mammalian skeleton. Science 301, 363–367 (2003).
Ingham, P. W. & Fietz, M. J. Quantitative effects of hedgehog and decapentaplegic activity on the patterning of the Drosophila wing. Curr. Biol. 5, 432–440 (1995).
De Celis, J. F. Pattern formation in the Drosophila wing: the development of the veins. Bioessays 25, 443–451 (2003).
Lecuit, T. et al. Two distinct mechanisms for long-range patterning by Decapentaplegic in the Drosophila wing. Nature 381, 387–392 (1996).
Farrell, E. R., Tosh, G., Church, E. & Munsterberg, A. E. Cloning and expression of CSAL2, a new member of the spalt gene family in chick. Mech. Dev. 102, 227–230 (2001).
Zulch, A., Becker, M. B. & Gruss, P. Expression pattern of Irx1 and Irx2 during mouse digit development. Mech. Dev. 106, 159–162 (2001).
Suzuki, T., Takeuchi, J., Koshiba-Takeuchi, K. & Ogura, T. Tbx genes specify posterior digit identity through shh and BMP signaling. Dev. Cell 6, 43–53 (2004).
Rallis, C., Del Buono, J. & Logan, M. P. Tbx3 can alter limb position along the rostrocaudal axis of the developing embryo. Development 132, 1961–1970 (2005).
Bamshad, M. et al. Mutations in human TBX3 alter limb, apocrine, and genetical development in ulnar-mammary syndrome. Nature Genet. 16, 311–316 (1997).
Briscoe, J., Pierani, A., Jessell, T. M. & Ericson, J. A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube. Cell 101, 435–445 (2000).
Dahn, R. D. & Fallon, J. F. Interdigital regulation of digit identity and homeotic transformation by modulated BMP signaling. Science 289, 438–441 (2000). Series of grafting experiments and bead implants showing that morphogenesis of digit primordia is surprisingly plastic.
Sanz-Ezquerro, J. J. & Tickle, C. Fgf signaling controls the number of phalanges and tip formation in developing digits. Curr. Biol. 13, 1830–1836 (2003).
Spitz, F., Gonzalez, F. & Duboule, D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113, 405–417 (2003).
Smith, J. C. The time required for positional signalling in the chick wing bud. J. Embryol. Exp. Morphol. 60, 321–328 (1980).
Honig, L. S. Positional signal transmission in the developing chick limb. Nature 291, 72–73 (1981).
Tickle, C. The number of polarizing region cells required to specify additional digits in the developing chick wing. Nature 289, 295–298 (1981).
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