# Mechanism to limit the exponential growth of the number of ancestors that are n-generations away from an organism?

The context is organisms with sexual reproduction, with 2 parents per organism. Construct the family tree of one such organism, back into geologic time.

Take a(n) as being the number of ancestors that are n generations distant. The function a(n) has an exponential character (at least in the beginning, with n sufficiently small).

For 2^n, simple math gives:

• After 20 generations, you have about 10^6 ancestors.
• After 30 generations, you have about 10^9 ancestors.
• After 50 generations, you have about 10^15 ancestors.
• After 1000 generations, you have about 10^300 ancestors.

I've read one estimate that there are about 10^80 atoms in the Universe. What does this mean?

It's important to note the the members of generation n usually aren't all alive at the same time. As an example, for humans, the birth-dates of generation-20 are roughly between the years 1720-1520, for example.

It doesn't take very many generations for a(n) to exceed p(t), the population as a function of time. This is accounted for (at least for sufficiently low n) by the fact that a(n) represents organisms that aren't alive simultaneously, while p(t) does. I understand that. But, this effect, important as it is, seems to be linear with time. As such, it doesn't seem capable of limiting the exponential growth of a(n).

In this context, inbreeding is often raised. But, in my opinion, inbreeding is not germane. Here, all that matters is that each organism has 2 parents. Period. Whether or not inbreeding was involved doesn't change that basic fact. All inbreeding means is that one ancestor is a member of more than 1 generation. That's not relevant to my question.

Edit later: No, inbreeding is germane. It means that 2 members of a(n) can have the same two parents in a(n+1). That reduces the exponential growth of a(n).

It seems that a(n) must be limited by something, for sufficiently large n. What is that something?

Of course a(n) is limited, and much more tightly than by the number of atoms that exist. The analysis in the question goes off track with "inbreeding is not germane. Here, all that matters is that each organism has 2 parents. Period."

Consider a person whose parents are first cousins. Then:

• a(1) = 2
• a(2) = 4
• a(3) = 6, not 8

While each of the two parents has four grandparents, together the two parents have only six grandparents because they share one pair of grandparents. This is due to pedigree collapse.

This table shows the actual collapse for some people with ancestry known to nine generations and with significant inbreeding (from de.Wikipedia):

## Prokaryote and eukaryote evolvability

The concept of evolvability covers a broad spectrum of, often contradictory, ideas. At one end of the spectrum it is equivalent to the statement that evolution is possible, at the other end are untestable post hoc explanations, such as the suggestion that current evolutionary theory cannot explain the evolution of evolvability. We examine similarities and differences in eukaryote and prokaryote evolvability, and look for explanations that are compatible with a wide range of observations. Differences in genome organisation between eukaryotes and prokaryotes meets this criterion. The single origin of replication in prokaryote chromosomes (versus multiple origins in eukaryotes) accounts for many differences because the time to replicate a prokaryote genome limits its size (and the accumulation of junk DNA). Both prokaryotes and eukaryotes appear to switch from genetic stability to genetic change in response to stress. We examine a range of stress responses, and discuss how these impact on evolvability, particularly in unicellular organisms versus complex multicellular ones. Evolvability is also limited by environmental interactions (including competition) and we describe a model that places limits on potential evolvability. Examples are given of its application to predator competition and limits to lateral gene transfer. We suggest that unicellular organisms evolve largely through a process of metabolic change, resulting in biochemical diversity. Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry.

## Contents

### Hominidae Edit

The great apes (hominidae) show some cognitive and empathic abilities. Chimpanzees can make tools and use them to acquire foods and for social displays they have mildly complex hunting strategies requiring cooperation, influence and rank they are status conscious, manipulative and capable of deception they can learn to use symbols and understand aspects of human language including some relational syntax, concepts of number and numerical sequence. [2]

### Homininae Edit

Around 10 million years ago, the Earth's climate entered a cooler and drier phase, which led eventually to the Quaternary glaciation beginning some 2.6 million years ago. One consequence of this was that the north African tropical forest began to retreat, being replaced first by open grasslands and eventually by desert (the modern Sahara). As their environment changed from continuous forest to patches of forest separated by expanses of grassland, some primates adapted to a partly or fully ground-dwelling life. Here they were exposed to predators, such as the big cats, from whom they had previously been safe.

These environmental pressures caused selection to favor bipedalism: walking on hind legs. This gave the Homininae's eyes greater elevation, the ability to see approaching danger further off, and a more efficient means of locomotion. [ citation needed ] It also freed the arms from the task of walking and made the hands available for tasks such as gathering food. At some point the bipedal primates developed handedness, giving them the ability to pick up sticks, bones and stones and use them as weapons, or as tools for tasks such as killing smaller animals, cracking nuts, or cutting up carcasses. In other words, these primates developed the use of primitive technology. Bipedal tool-using primates from the subtribe Hominina date back to as far as about 5 to 7 million years ago, such as one of the earliest species, Sahelanthropus tchadensis.

From about 5 million years ago, the hominin brain began to develop rapidly in both size and differentiation of function. There has been a gradual increase in brain volume as humans progressed along the timeline of evolution (see Homininae), starting from about 600 cm 3 in Homo habilis up to 1500 cm 3 in Homo neanderthalensis. Thus, in general there's a correlation between brain volume and intelligence. [ citation needed ] However, modern Homo sapiens have a brain volume slightly smaller (1250 cm 3 ) than neanderthals, and the Flores hominids (Homo floresiensis), nicknamed hobbits, had a cranial capacity of about 380 cm 3 (considered small for a chimpanzee) about a third of that of H. erectus. It is proposed that they evolved from H. erectus as a case of insular dwarfism. With their three times smaller brain the Flores hominids apparently used fire and made tools as sophisticated as those of their ancestor H.erectus.

### Homo Edit

Roughly 2.4 million years ago Homo habilis had appeared in East Africa: the first known human species, and the first known to make stone tools, yet the disputed findings of signs of tool use from even earlier ages and from the same vicinity as multiple Australopithecus fossils may put to question how much more intelligent than its predecessors H. habilis was.

The use of tools conferred a crucial evolutionary advantage, and required a larger and more sophisticated brain to co-ordinate the fine hand movements required for this task. [3] Our knowledge of the complexity of behaviour of Homo habilis is not limited to stone culture, they also had habitual therapeutic use of toothpicks. [4] The evolution of a larger brain created a problem for early humans, however. A larger brain requires a larger skull, and thus requires the female to have a wider birth canal for the newborn's larger skull to pass through. But if the female's birth canal grew too wide, her pelvis would be so wide that she would lose the ability to run, which was a necessary skill 2 million years ago. [ citation needed ]

The solution to this was to give birth at an early stage of fetal development, before the skull grew too large to pass through the birth canal. This adaptation enabled the human brain to continue to grow, but it imposed a new discipline. The need to care for helpless infants for long periods of time forced humans to become less mobile. [ citation needed ] Human bands increasingly stayed in one place for long periods, so that females could care for infants, while males hunted food and fought with other bands that competed for food sources. [ citation needed ] . It is to be noted that traditional claims about men's and women's gender roles have been challenged in the past years. [5] Regardless, humans' increasingly sedentary lifestyle to protect their more vulnerable offspring led them to grow even more dependent on tool-making to compete with other animals and other humans, and rely less on body size and strength. [ citation needed ]

About 200,000 years ago Europe and the Middle East were colonized by Neanderthal man, extinct by 39,000 years ago following the appearance of modern humans in the region from 40,000 to 45,000 years ago.

### Homo sapiens Edit

#### Homo sapiens intelligence Edit

The eldest findings of Homo sapiens in Jebel Irhoud, Morocco date back ca. 300,000 years [6] [7] Ca. 200,000 year old fossils of Homo sapiens were found in East Africa. It is unclear to what extent these early modern humans had developed language, music, religion, etc.

According to proponents of the Toba catastrophe theory, the climate in non-tropical regions of the earth experienced a sudden freezing about 70,000 years ago, because of a huge explosion of the Toba volcano that filled the atmosphere with volcanic ash for several years. This reduced the human population to less than 10,000 breeding pairs in equatorial Africa, from which all modern humans are descended. Being unprepared for the sudden change in climate, the survivors were those intelligent enough to invent new tools and ways of keeping warm and finding new sources of food (for example, adapting to ocean fishing based on prior fishing skills used in lakes and streams that became frozen). [ citation needed ]

Around 80,000–100,000 years ago, three main lines of Homo sapiens diverged, bearers of mitochondrial haplogroup L1 (mtDNA) / A (Y-DNA) colonizing Southern Africa (the ancestors of the Khoisan/Capoid peoples), bearers of haplogroup L2 (mtDNA) / B (Y-DNA) settling Central and West Africa (the ancestors of Niger–Congo and Nilo-Saharan speaking peoples), while the bearers of haplogroup L3 remained in East Africa. [ citation needed ]

The "Great Leap Forward" leading to full behavioral modernity sets in only after this separation. Rapidly increasing sophistication in tool-making and behaviour is apparent from about 80,000 years ago, and the migration out of Africa follows towards the very end of the Middle Paleolithic, some 60,000 years ago. Fully modern behaviour, including figurative art, music, self-ornamentation, trade, burial rites etc. is evident by 30,000 years ago. The oldest unequivocal examples of prehistoric art date to this period, the Aurignacian and the Gravettian periods of prehistoric Europe, such as the Venus figurines and cave painting (Chauvet Cave) and the earliest musical instruments (the bone pipe of Geissenklösterle, Germany, dated to about 36,000 years ago). [8]

The human brain has evolved gradually over the passage of time a series of incremental changes occurred as a result of external stimuli and conditions. It is crucial to keep in mind that evolution operates within a limited framework at a given point in time. In other words, the adaptations that a species can develop are not infinite and are defined by what has already taken place in the evolutionary timeline of a species. Given the immense anatomical and structural complexity of the brain, its evolution (and the congruent evolution of human intelligence), can only be reorganized in a finite number of ways. The majority of said changes occur either in terms of size or in terms of developmental timeframes. [9]

There have been studies that strongly support the idea that the level of intelligence associated with humans is not unique to our species. Scholars suggest that this could have, in part, been caused by convergent evolution. One common characteristic that is present in species of "high degree intelligence" (i.e. dolphins, great apes, and humans - Homo sapiens) is a brain of enlarged size. Along with this, there is a more developed neocortex, a folding of the cerebral cortex, and von Economo neurons. Said neurons are linked to social intelligence and the ability to gauge what another is thinking or feeling and, interestingly, are also present in bottlenose dolphins. [10] The cerebral cortex is divided into four lobes (frontal, parietal, occipital, and temporal) each with specific functions. The cerebral cortex is significantly larger in humans than in any other animal and is responsible for higher thought processes such as: reasoning, abstract thinking, and decision making. [11]

Another characteristic that makes humans special and sets them apart from any other species is our ability to produce and understand complex, syntactic language. The cerebral cortex, particularly in the temporal, parietal, and frontal lobes, are populated with neural circuits dedicated to language. There are two main areas of the brain commonly associated with language, namely: Wernicke's area and Broca's area. The former is responsible for the understanding of speech and the latter for the production of speech. Homologous regions have been found in other species (i.e. Area 44 and 45 have been studied in chimpanzees) but they are not as strongly related to or involved in linguistic activities as in humans. [12]

A big portion of the scholarly literature focus on the evolution, and subsequent influence, of culture. This is in part because the leaps human intelligence has taken are far greater than those that would have resulted if our ancestors had simply responded to their environments, inhabiting them as hunter-gatherers. [13] (Richardson 273).

In short, the immense complexity and marvel of superior human intelligence only emerge inside of a specific culture and history. Selection for cooperation aided our ancestors in surviving harsh ecological conditions and did so by creating a specific type of intelligence. An intelligence that, today, is highly variant from individual to individual.

### Social brain hypothesis Edit

The social brain hypothesis was proposed by British anthropologist Robin Dunbar, who argues that human intelligence did not evolve primarily as a means to solve ecological problems, but rather as a means of surviving and reproducing in large and complex social groups. [14] [15] Some of the behaviors associated with living in large groups include reciprocal altruism, deception and coalition formation. These group dynamics relate to Theory of Mind or the ability to understand the thoughts and emotions of others, though Dunbar himself admits in the same book that it is not the flocking itself that causes intelligence to evolve (as shown by ruminants). [14]

Dunbar argues that when the size of a social group increases, the number of different relationships in the group may increase by orders of magnitude. Chimpanzees live in groups of about 50 individuals whereas humans typically have a social circle of about 150 people, which is also the typical size of social communities in small societies and personal social networks [16] this number is now referred to as Dunbar's number. In addition, there is evidence to suggest that the success of groups is dependent on their size at foundation, with groupings of around 150 being particularly successful, potentially reflecting the fact that communities of this size strike a balance between the minimum size of effective functionality and the maximum size for creating a sense of commitment to the community. [17] According to the social brain hypothesis, when hominids started living in large groups, selection favored greater intelligence. As evidence, Dunbar cites a relationship between neocortex size and group size of various mammals. [14]

#### Criticism Edit

Phylogenetic studies of brain sizes in primates show that while diet predicts primate brain size, sociality does not predict brain size when corrections are made for cases in which diet affects both brain size and sociality. The exceptions to the predictions of the social intelligence hypothesis, which that hypothesis has no predictive model for, are successfully predicted by diets that are either nutritious but scarce or abundant but poor in nutrients. [18] Researchers have found that frugivores tend to exhibit larger brain size than folivores. [19] One potential explanation for this finding is that frugivory requires 'extractive foraging,' or the process of locating and preparing hard-shelled foods, such as nuts, insects, and fruit. [20] Extractive foraging requires higher cognitive processing, which could help explain larger brain size. [20] However, other researchers argue that extractive foraging was not a catalyst in the evolution of primate brain size, demonstrating that some non primates exhibit advanced foraging techniques. [20] Other explanations for the positive correlation between brain size and frugivory highlight how the high-energy, frugivore diet facilitates fetal brain growth and requires spatial mapping to locate the embedded foods. [19]

Meerkats have far more social relationships than their small brain capacity would suggest. Another hypothesis is that it is actually intelligence that causes social relationships to become more complex, because intelligent individuals are more difficult to learn to know. [21]

There are also studies that show that Dunbar's number is not the upper limit of the number of social relationships in humans either. [22] [23]

The hypothesis that it is brain capacity that sets the upper limit for the number of social relationships is also contradicted by computer simulations that show simple unintelligent reactions to be sufficient to emulate "ape politics" [24] and by the fact that some social insects such as the paper wasp do have hierarchies in which each individual has its place (as opposed to herding without social structure) and maintains their hierarchies in groups of approximately 80 individuals with their brains smaller than that of any mammal. [25]

Insects provide an opportunity to explore this since they exhibit an unparalleled diversity of social forms to permanent colonies containing many individuals working together as a collective organism and have evolved an impressive range of cognitive skills despite their small nervous systems. [26] [27] [28] Social insects are shaped by ecology, including their social environment. Studies aimed to correlating brain volume to complexity have failed to identify clear correlations between sociality and cognition because of cases like social insects. In humans, societies are usually held together by the ability of individuals to recognize features indicating group membership. Social insects, likewise, often recognize members of their colony allowing them to defend against competitors. Ants do this by comparing odors which require fine discrimination of multicomponent variable cues. [29] Studies suggest this recognition is achieved through simple cognitive operations that do not involve long-term memory but through sensory adaptation or habituation. [30] In honeybees, their symbolic 'dance' is a form of communication that they use to convey information with the rest of their colony. In an even more impressive social use of their dance language, bees indicate suitable nest locations to a swarm in search of a new home. The swarm builds a consensus from multiple 'opinions' expressed by scouts with different information, to finally agree on a single destination to which the swarm relocates. [31]

### Reduction in aggression Edit

Another theory that tries to explain the growth of human intelligence is the reduced aggression theory (aka self-domestication theory). According to this strand of thought what led to the evolution of advanced intelligence in Homo sapiens was a drastic reduction of the aggressive drive. This change separated us from other species of monkeys and primates, where this aggressivity is still in plain sight, and eventually lead to the development of quintessential human traits such as empathy, social cognition and culture. [32] [33] This theory has received strong support from studies of animal domestication where selective breeding for tameness has, in only a few generations, led to the emergence of impressive "humanlike" abilities. Tamed foxes, for example, exhibit advanced forms of social communication (following pointing gestures), pedomorphic physical features (childlike faces, floppy ears) and even rudimentary forms of theory of mind (eye contact seeking, gaze following). [34] [35] Evidence also comes from the field of ethology (which is the study of animal behavior, focused on observing species in their natural habitat rather than in controlled laboratory settings) where it has been found that animals with a gentle and relaxed manner of interacting with each other – like for example stumptailed macaques, orangutans and bonobos – have more advanced socio-cognitive abilities than those found among the more aggressive chimpanzees and baboons. [36] It is hypothesized that these abilities derive from a selection against aggression. [33] [37] [38] [39]

On a mechanistic level these changes are believed to be the result of a systemic downregulation of the sympathetic nervous system (the fight-or-flight reflex). Hence, tamed foxes show a reduced adrenal gland size and have an up to fivefold reduction in both basal and stress-induced blood cortisol levels. [40] [41] Similarly, domesticated rats and guinea pigs have both reduced adrenal gland size and reduced blood corticosterone levels. [42] [43] It seems as though the neoteny of domesticated animals significantly prolongs the immaturity of their hypothalamic-pituitary-adrenal system (which is otherwise only immature for a short period when they are pups/kittens) and this opens up a larger "socialization window" during which they can learn to interact with their caretakers in a more relaxed way.

This downregulation of sympathetic nervous system reactivity is also believed to be accompanied by a compensatory increase in a number of opposing organs and systems. Although these are not as well specified various candidates for such "organs" have been proposed: the parasympathetic system as a whole, the septal area over the amygdala, [32] the oxytocin system, [44] the endogenous opioids [45] and various forms of quiescent immobilization which antagonize the fight-or-flight reflex. [46] [47]

## 9.1 How Microbes Grow

Jeni, a 24-year-old pregnant woman in her second trimester, visits a clinic with complaints of high fever, 38.9 °C (102 °F), fatigue, and muscle aches—typical flu-like signs and symptoms. Jeni exercises regularly and follows a nutritious diet with emphasis on organic foods, including raw milk that she purchases from a local farmer’s market. All of her immunizations are up to date. However, the health-care provider who sees Jeni is concerned and orders a blood sample to be sent for testing by the microbiology laboratory.

The bacterial cell cycle involves the formation of new cells through the replication of DNA and partitioning of cellular components into two daughter cells. In prokaryotes, reproduction is always asexual, although extensive genetic recombination in the form of horizontal gene transfer takes place, as will be explored in a different chapter. Most bacteria have a single circular chromosome however, some exceptions exist. For example, Borrelia burgdorferi , the causative agent of Lyme disease, has a linear chromosome.

### Binary Fission

The most common mechanism of cell replication in bacteria is a process called binary fission , which is depicted in Figure 9.2. Before dividing, the cell grows and increases its number of cellular components. Next, the replication of DNA starts at a location on the circular chromosome called the origin of replication, where the chromosome is attached to the inner cell membrane. Replication continues in opposite directions along the chromosome until the terminus is reached.

The center of the enlarged cell constricts until two daughter cells are formed, each offspring receiving a complete copy of the parental genome and a division of the cytoplasm (cytokinesis). This process of cytokinesis and cell division is directed by a protein called FtsZ . FtsZ assembles into a Z ring on the cytoplasmic membrane (Figure 9.3). The Z ring is anchored by FtsZ-binding proteins and defines the division plane between the two daughter cells. Additional proteins required for cell division are added to the Z ring to form a structure called the divisome . The divisome activates to produce a peptidoglycan cell wall and build a septum that divides the two daughter cells. The daughter cells are separated by the division septum, where all of the cells’ outer layers (the cell wall and outer membranes, if present) must be remodeled to complete division. For example, we know that specific enzymes break bonds between the monomers in peptidoglycans and allow addition of new subunits along the division septum.

• What is the name of the protein that assembles into a Z ring to initiate cytokinesis and cell division?

### Generation Time

In eukaryotic organisms, the generation time is the time between the same points of the life cycle in two successive generations. For example, the typical generation time for the human population is 25 years. This definition is not practical for bacteria, which may reproduce rapidly or remain dormant for thousands of years. In prokaryotes (Bacteria and Archaea), the generation time is also called the doubling time and is defined as the time it takes for the population to double through one round of binary fission. Bacterial doubling times vary enormously. Whereas Escherichia coli can double in as little as 20 minutes under optimal growth conditions in the laboratory, bacteria of the same species may need several days to double in especially harsh environments. Most pathogens grow rapidly, like E. coli, but there are exceptions. For example, Mycobacterium tuberculosis , the causative agent of tuberculosis, has a generation time of between 15 and 20 hours. On the other hand, M. leprae, which causes Hansen’s disease (leprosy), grows much more slowly, with a doubling time of 14 days.

### Micro Connections

#### Calculating Number of Cells

It is possible to predict the number of cells in a population when they divide by binary fission at a constant rate. As an example, consider what happens if a single cell divides every 30 minutes for 24 hours. The diagram in Figure 9.4 shows the increase in cell numbers for the first three generations.

The number of cells increases exponentially and can be expressed as 2 n , where n is the number of generations. If cells divide every 30 minutes, after 24 hours, 48 divisions would have taken place. If we apply the formula 2 n , where n is equal to 48, the single cell would give rise to 2 48 or 281,474,976,710,656 cells at 48 generations (24 hours). When dealing with such huge numbers, it is more practical to use scientific notation. Therefore, we express the number of cells as 2.8 × 10 14 cells.

In our example, we used one cell as the initial number of cells. For any number of starting cells, the formula is adapted as follows:

Nn is the number of cells at any generation n, N0 is the initial number of cells, and n is the number of generations.

• With a doubling time of 30 minutes and a starting population size of 1 × 10 5 cells, how many cells will be present after 2 hours, assuming no cell death?

### The Growth Curve

Microorganisms grown in closed culture (also known as a batch culture ), in which no nutrients are added and most waste is not removed, follow a reproducible growth pattern referred to as the growth curve . An example of a batch culture in nature is a pond in which a small number of cells grow in a closed environment. The culture density is defined as the number of cells per unit volume. In a closed environment, the culture density is also a measure of the number of cells in the population. Infections of the body do not always follow the growth curve, but correlations can exist depending upon the site and type of infection. When the number of live cells is plotted against time, distinct phases can be observed in the curve (Figure 9.5).

#### The Lag Phase

The beginning of the growth curve represents a small number of cells, referred to as an inoculum , that are added to a fresh culture medium , a nutritional broth that supports growth. The initial phase of the growth curve is called the lag phase , during which cells are gearing up for the next phase of growth. The number of cells does not change during the lag phase however, cells grow larger and are metabolically active, synthesizing proteins needed to grow within the medium. If any cells were damaged or shocked during the transfer to the new medium, repair takes place during the lag phase. The duration of the lag phase is determined by many factors, including the species and genetic make-up of the cells, the composition of the medium, and the size of the original inoculum.

#### The Log Phase

In the logarithmic (log) growth phase , sometimes called exponential growth phase , the cells are actively dividing by binary fission and their number increases exponentially. For any given bacterial species, the generation time under specific growth conditions (nutrients, temperature, pH, and so forth) is genetically determined, and this generation time is called the intrinsic growth rate . During the log phase, the relationship between time and number of cells is not linear but exponential however, the growth curve is often plotted on a semilogarithmic graph, as shown in Figure 9.6, which gives the appearance of a linear relationship.

Cells in the log phase show constant growth rate and uniform metabolic activity. For this reason, cells in the log phase are preferentially used for industrial applications and research work. The log phase is also the stage where bacteria are the most susceptible to the action of disinfectants and common antibiotics that affect protein, DNA, and cell-wall synthesis.

#### Stationary Phase

As the number of cells increases through the log phase, several factors contribute to a slowing of the growth rate. Waste products accumulate and nutrients are gradually used up. In addition, gradual depletion of oxygen begins to limit aerobic cell growth. This combination of unfavorable conditions slows and finally stalls population growth. The total number of live cells reaches a plateau referred to as the stationary phase (Figure 9.5). In this phase, the number of new cells created by cell division is now equivalent to the number of cells dying thus, the total population of living cells is relatively stagnant. The culture density in a stationary culture is constant. The culture’s carrying capacity, or maximum culture density, depends on the types of microorganisms in the culture and the specific conditions of the culture however, carrying capacity is constant for a given organism grown under the same conditions.

During the stationary phase, cells switch to a survival mode of metabolism. As growth slows, so too does the synthesis of peptidoglycans, proteins, and nucleic-acids thus, stationary cultures are less susceptible to antibiotics that disrupt these processes. In bacteria capable of producing endospores, many cells undergo sporulation during the stationary phase. Secondary metabolites, including antibiotics, are synthesized in the stationary phase. In certain pathogenic bacteria, the stationary phase is also associated with the expression of virulence factors, products that contribute to a microbe’s ability to survive, reproduce, and cause disease in a host organism. For example, quorum sensing in Staphylococcus aureus initiates the production of enzymes that can break down human tissue and cellular debris, clearing the way for bacteria to spread to new tissue where nutrients are more plentiful.

#### The Death Phase

As a culture medium accumulates toxic waste and nutrients are exhausted, cells die in greater and greater numbers. Soon, the number of dying cells exceeds the number of dividing cells, leading to an exponential decrease in the number of cells (Figure 9.5). This is the aptly named death phase , sometimes called the decline phase. Many cells lyse and release nutrients into the medium, allowing surviving cells to maintain viability and form endospores. A few cells, the so-called persisters , are characterized by a slow metabolic rate. Persister cells are medically important because they are associated with certain chronic infections, such as tuberculosis, that do not respond to antibiotic treatment.

#### Sustaining Microbial Growth

The growth pattern shown in Figure 9.5 takes place in a closed environment nutrients are not added and waste and dead cells are not removed. In many cases, though, it is advantageous to maintain cells in the logarithmic phase of growth. One example is in industries that harvest microbial products. A chemostat (Figure 9.7) is used to maintain a continuous culture in which nutrients are supplied at a steady rate. A controlled amount of air is mixed in for aerobic processes. Bacterial suspension is removed at the same rate as nutrients flow in to maintain an optimal growth environment.

• During which phase does growth occur at the fastest rate?
• Name two factors that limit microbial growth.

### Measurement of Bacterial Growth

Estimating the number of bacterial cells in a sample, known as a bacterial count, is a common task performed by microbiologists. The number of bacteria in a clinical sample serves as an indication of the extent of an infection. Quality control of drinking water, food, medication, and even cosmetics relies on estimates of bacterial counts to detect contamination and prevent the spread of disease. Two major approaches are used to measure cell number. The direct methods involve counting cells, whereas the indirect methods depend on the measurement of cell presence or activity without actually counting individual cells. Both direct and indirect methods have advantages and disadvantages for specific applications.

#### Direct Cell Count

Direct cell count refers to counting the cells in a liquid culture or colonies on a plate. It is a direct way of estimating how many organisms are present in a sample. Let’s look first at a simple and fast method that requires only a specialized slide and a compound microscope.

The simplest way to count bacteria is called the direct microscopic cell count , which involves transferring a known volume of a culture to a calibrated slide and counting the cells under a light microscope. The calibrated slide is called a Petroff-Hausser chamber (Figure 9.8) and is similar to a hemocytometer used to count red blood cells. The central area of the counting chamber is etched into squares of various sizes. A sample of the culture suspension is added to the chamber under a coverslip that is placed at a specific height from the surface of the grid. It is possible to estimate the concentration of cells in the original sample by counting individual cells in a number of squares and determining the volume of the sample observed. The area of the squares and the height at which the coverslip is positioned are specified for the chamber. The concentration must be corrected for dilution if the sample was diluted before enumeration.

Cells in several small squares must be counted and the average taken to obtain a reliable measurement. The advantages of the chamber are that the method is easy to use, relatively fast, and inexpensive. On the downside, the counting chamber does not work well with dilute cultures because there may not be enough cells to count.

Using a counting chamber does not necessarily yield an accurate count of the number of live cells because it is not always possible to distinguish between live cells, dead cells, and debris of the same size under the microscope. However, newly developed fluorescence staining techniques make it possible to distinguish viable and dead bacteria. These viability stains (or live stains) bind to nucleic acids, but the primary and secondary stains differ in their ability to cross the cytoplasmic membrane. The primary stain, which fluoresces green, can penetrate intact cytoplasmic membranes, staining both live and dead cells. The secondary stain, which fluoresces red, can stain a cell only if the cytoplasmic membrane is considerably damaged. Thus, live cells fluoresce green because they only absorb the green stain, whereas dead cells appear red because the red stain displaces the green stain on their nucleic acids (Figure 9.9).

Another technique uses an electronic cell counting device ( Coulter counter ) to detect and count the changes in electrical resistance in a saline solution. A glass tube with a small opening is immersed in an electrolyte solution. A first electrode is suspended in the glass tube. A second electrode is located outside of the tube. As cells are drawn through the small aperture in the glass tube, they briefly change the resistance measured between the two electrodes and the change is recorded by an electronic sensor (Figure 9.10) each resistance change represents a cell. The method is rapid and accurate within a range of concentrations however, if the culture is too concentrated, more than one cell may pass through the aperture at any given time and skew the results. This method also does not differentiate between live and dead cells.

Direct counts provide an estimate of the total number of cells in a sample. However, in many situations, it is important to know the number of live, or viable , cells. Counts of live cells are needed when assessing the extent of an infection, the effectiveness of antimicrobial compounds and medication, or contamination of food and water.

• Why would you count the number of cells in more than one square in the Petroff-Hausser chamber to estimate cell numbers?
• In the viability staining method, why do dead cells appear red?

### Plate Count

The viable plate count , or simply plate count , is a count of viable or live cells. It is based on the principle that viable cells replicate and give rise to visible colonies when incubated under suitable conditions for the specimen. The results are usually expressed as colony-forming unit s per milliliter (CFU/mL) rather than cells per milliliter because more than one cell may have landed on the same spot to give rise to a single colony. Furthermore, samples of bacteria that grow in clusters or chains are difficult to disperse and a single colony may represent several cells. Some cells are described as viable but nonculturable and will not form colonies on solid media. For all these reasons, the viable plate count is considered a low estimate of the actual number of live cells. These limitations do not detract from the usefulness of the method, which provides estimates of live bacterial numbers.

Microbiologists typically count plates with 30–300 colonies. Samples with too few colonies (<30) do not give statistically reliable numbers, and overcrowded plates (>300 colonies) make it difficult to accurately count individual colonies. Also, counts in this range minimize occurrences of more than one bacterial cell forming a single colony. Thus, the calculated CFU is closer to the true number of live bacteria in the population.

There are two common approaches to inoculating plates for viable counts: the pour plate and the spread plate methods. Although the final inoculation procedure differs between these two methods, they both start with a serial dilution of the culture.

#### Serial Dilution

The serial dilution of a culture is an important first step before proceeding to either the pour plate or spread plate method. The goal of the serial dilution process is to obtain plates with CFUs in the range of 30–300, and the process usually involves several dilutions in multiples of 10 to simplify calculation. The number of serial dilutions is chosen according to a preliminary estimate of the culture density. Figure 9.11 illustrates the serial dilution method.

A fixed volume of the original culture, 1.0 mL, is added to and thoroughly mixed with the first dilution tube solution, which contains 9.0 mL of sterile broth. This step represents a dilution factor of 10, or 1:10, compared with the original culture. From this first dilution, the same volume, 1.0 mL, is withdrawn and mixed with a fresh tube of 9.0 mL of dilution solution. The dilution factor is now 1:100 compared with the original culture. This process continues until a series of dilutions is produced that will bracket the desired cell concentration for accurate counting. From each tube, a sample is plated on solid medium using either the pour plate method (Figure 9.12) or the spread plate method (Figure 9.13). The plates are incubated until colonies appear. Two to three plates are usually prepared from each dilution and the numbers of colonies counted on each plate are averaged. In all cases, thorough mixing of samples with the dilution medium (to ensure the cell distribution in the tube is random) is paramount to obtaining reliable results.

The dilution factor is used to calculate the number of cells in the original cell culture. In our example, an average of 50 colonies was counted on the plates obtained from the 1:10,000 dilution. Because only 0.1 mL of suspension was pipetted on the plate, the multiplier required to reconstitute the original concentration is 10 × 10,000. The number of CFU per mL is equal to 50 × 10 × 10,000 = 5,000,000. The number of bacteria in the culture is estimated as 5 million cells/mL. The colony count obtained from the 1:1000 dilution was 389, well below the expected 500 for a 10-fold difference in dilutions. This highlights the issue of inaccuracy when colony counts are greater than 300 and more than one bacterial cell grows into a single colony.

A very dilute sample—drinking water, for example—may not contain enough organisms to use either of the plate count methods described. In such cases, the original sample must be concentrated rather than diluted before plating. This can be accomplished using a modification of the plate count technique called the membrane filtration technique . Known volumes are vacuum-filtered aseptically through a membrane with a pore size small enough to trap microorganisms. The membrane is transferred to a Petri plate containing an appropriate growth medium. Colonies are counted after incubation. Calculation of the cell density is made by dividing the cell count by the volume of filtered liquid.

Watch this video for demonstrations of serial dilutions and spread plate techniques.

#### The Most Probable Number

The number of microorganisms in dilute samples is usually too low to be detected by the plate count methods described thus far. For these specimens, microbiologists routinely use the most probable number (MPN) method , a statistical procedure for estimating of the number of viable microorganisms in a sample. Often used for water and food samples, the MPN method evaluates detectable growth by observing changes in turbidity or color due to metabolic activity.

A typical application of MPN method is the estimation of the number of coliforms in a sample of pond water. Coliforms are gram-negative rod bacteria that ferment lactose. The presence of coliforms in water is considered a sign of contamination by fecal matter. For the method illustrated in Figure 9.14, a series of three dilutions of the water sample is tested by inoculating five lactose broth tubes with 10 mL of sample, five lactose broth tubes with 1 mL of sample, and five lactose broth tubes with 0.1 mL of sample. The lactose broth tubes contain a pH indicator that changes color from red to yellow when the lactose is fermented. After inoculation and incubation, the tubes are examined for an indication of coliform growth by a color change in media from red to yellow. The first set of tubes (10-mL sample) showed growth in all the tubes the second set of tubes (1 mL) showed growth in two tubes out of five in the third set of tubes, no growth is observed in any of the tubes (0.1-mL dilution). The numbers 5, 2, and 0 are compared with Figure B1 in Appendix B, which has been constructed using a probability model of the sampling procedure. From our reading of the table, we conclude that 49 is the most probable number of bacteria per 100 mL of pond water.no lo

• What is a colony-forming unit?
• What two methods are frequently used to estimate bacterial numbers in water samples?

### Indirect Cell Counts

Besides direct methods of counting cells, other methods, based on an indirect detection of cell density, are commonly used to estimate and compare cell densities in a culture. The foremost approach is to measure the turbidity (cloudiness) of a sample of bacteria in a liquid suspension. The laboratory instrument used to measure turbidity is called a spectrophotometer (Figure 9.15). In a spectrophotometer, a light beam is transmitted through a bacterial suspension, the light passing through the suspension is measured by a detector, and the amount of light passing through the sample and reaching the detector is converted to either percent transmission or a logarithmic value called absorbance (optical density). As the numbers of bacteria in a suspension increase, the turbidity also increases and causes less light to reach the detector. The decrease in light passing through the sample and reaching the detector is associated with a decrease in percent transmission and increase in absorbance measured by the spectrophotometer.

Measuring turbidity is a fast method to estimate cell density as long as there are enough cells in a sample to produce turbidity. It is possible to correlate turbidity readings to the actual number of cells by performing a viable plate count of samples taken from cultures having a range of absorbance values. Using these values, a calibration curve is generated by plotting turbidity as a function of cell density. Once the calibration curve has been produced, it can be used to estimate cell counts for all samples obtained or cultured under similar conditions and with densities within the range of values used to construct the curve.

Measuring dry weight of a culture sample is another indirect method of evaluating culture density without directly measuring cell counts. The cell suspension used for weighing must be concentrated by filtration or centrifugation, washed, and then dried before the measurements are taken. The degree of drying must be standardized to account for residual water content. This method is especially useful for filamentous microorganisms, which are difficult to enumerate by direct or viable plate count.

As we have seen, methods to estimate viable cell numbers can be labor intensive and take time because cells must be grown. Recently, indirect ways of measuring live cells have been developed that are both fast and easy to implement. These methods measure cell activity by following the production of metabolic products or disappearance of reactants. Adenosine triphosphate (ATP) formation, biosynthesis of proteins and nucleic acids, and consumption of oxygen can all be monitored to estimate the number of cells.

• What is the purpose of a calibration curve when estimating cell count from turbidity measurements?
• What are the newer indirect methods of counting live cells?

### Alternative Patterns of Cell Division

Binary fission is the most common pattern of cell division in prokaryotes, but it is not the only one. Other mechanisms usually involve asymmetrical division (as in budding) or production of spores in aerial filaments.

In some cyanobacteria , many nucleoids may accumulate in an enlarged round cell or along a filament, leading to the generation of many new cells at once. The new cells often split from the parent filament and float away in a process called fragmentation (Figure 9.16). Fragmentation is commonly observed in the Actinomycetes , a group of gram-positive, anaerobic bacteria commonly found in soil. Another curious example of cell division in prokaryotes, reminiscent of live birth in animals, is exhibited by the giant bacterium Epulopiscium . Several daughter cells grow fully in the parent cell, which eventually disintegrates, releasing the new cells to the environment. Other species may form a long narrow extension at one pole in a process called budding . The tip of the extension swells and forms a smaller cell, the bud that eventually detaches from the parent cell. Budding is most common in yeast (Figure 9.16), but it is also observed in prosthecate bacteria and some cyanobacteria.

The soil bacteria Actinomyces grow in long filaments divided by septa, similar to the mycelia seen in fungi, resulting in long cells with multiple nucleoids. Environmental signals, probably related to low nutrient availability, lead to the formation of aerial filaments. Within these aerial filaments , elongated cells divide simultaneously. The new cells, which contain a single nucleoid, develop into spores that give rise to new colonies.

### Biofilms

In nature, microorganisms grow mainly in biofilms , complex and dynamic ecosystems that form on a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rocks in river beds. Biofilms are not restricted to solid surface substrates, however. Almost any surface in a liquid environment containing some minimal nutrients will eventually develop a biofilm. Microbial mats that float on water, for example, are biofilms that contain large populations of photosynthetic microorganisms. Biofilms found in the human mouth may contain hundreds of bacterial species. Regardless of the environment where they occur, biofilms are not random collections of microorganisms rather, they are highly structured communities that provide a selective advantage to their constituent microorganisms.

#### Biofilm Structure

Observations using confocal microscopy have shown that environmental conditions influence the overall structure of biofilms. Filamentous biofilms called streamers form in rapidly flowing water, such as freshwater streams, eddies, and specially designed laboratory flow cells that replicate growth conditions in fast-moving fluids. The streamers are anchored to the substrate by a “head” and the “tail” floats downstream in the current. In still or slow-moving water, biofilms mainly assume a mushroom-like shape. The structure of biofilms may also change with other environmental conditions such as nutrient availability.

Detailed observations of biofilms under confocal laser and scanning electron microscopes reveal clusters of microorganisms embedded in a matrix interspersed with open water channels. The extracellular matrix consists of extracellular polymeric substances (EPS) secreted by the organisms in the biofilm. The extracellular matrix represents a large fraction of the biofilm, accounting for 50%–90% of the total dry mass. The properties of the EPS vary according to the resident organisms and environmental conditions.

EPS is a hydrated gel composed primarily of polysaccharides and containing other macromolecules such as proteins, nucleic acids, and lipids. It plays a key role in maintaining the integrity and function of the biofilm. Channels in the EPS allow movement of nutrients, waste, and gases throughout the biofilm. This keeps the cells hydrated, preventing desiccation. EPS also shelters organisms in the biofilm from predation by other microbes or cells (e.g., protozoans, white blood cells in the human body).

#### Biofilm Formation

Free-floating microbial cells that live in an aquatic environment are called planktonic cells. The formation of a biofilm essentially involves the attachment of planktonic cells to a substrate, where they become sessile (attached to a surface). This occurs in stages, as depicted in Figure 9.17. The first stage involves the attachment of planktonic cells to a surface coated with a conditioning film of organic material. At this point, attachment to the substrate is reversible, but as cells express new phenotypes that facilitate the formation of EPS, they transition from a planktonic to a sessile lifestyle. The biofilm develops characteristic structures, including an extensive matrix and water channels. Appendages such as fimbriae , pili , and flagella interact with the EPS, and microscopy and genetic analysis suggest that such structures are required for the establishment of a mature biofilm. In the last stage of the biofilm life cycle, cells on the periphery of the biofilm revert to a planktonic lifestyle, sloughing off the mature biofilm to colonize new sites. This stage is referred to as dispersal .

Within a biofilm, different species of microorganisms establish metabolic collaborations in which the waste product of one organism becomes the nutrient for another. For example, aerobic microorganisms consume oxygen, creating anaerobic regions that promote the growth of anaerobes. This occurs in many polymicrobial infections that involve both aerobic and anaerobic pathogens.

The mechanism by which cells in a biofilm coordinate their activities in response to environmental stimuli is called quorum sensing . Quorum sensing—which can occur between cells of different species within a biofilm—enables microorganisms to detect their cell density through the release and binding of small, diffusible molecules called autoinducers . When the cell population reaches a critical threshold (a quorum), these autoinducers initiate a cascade of reactions that activate genes associated with cellular functions that are beneficial only when the population reaches a critical density. For example, in some pathogens, synthesis of virulence factors only begins when enough cells are present to overwhelm the immune defenses of the host. Although mostly studied in bacterial populations, quorum sensing takes place between bacteria and eukaryotes and between eukaryotic cells such as the fungus Candida albicans , a common member of the human microbiota that can cause infections in immunocompromised individuals.

The signaling molecules in quorum sensing belong to two major classes. Gram-negative bacteria communicate mainly using N-acylated homoserine lactones, whereas gram-positive bacteria mostly use small peptides (Figure 9.18). In all cases, the first step in quorum sensing consists of the binding of the autoinducer to its specific receptor only when a threshold concentration of signaling molecules is reached. Once binding to the receptor takes place, a cascade of signaling events leads to changes in gene expression. The result is the activation of biological responses linked to quorum sensing, notably an increase in the production of signaling molecules themselves, hence the term autoinducer.

#### Biofilms and Human Health

The human body harbors many types of biofilms, some beneficial and some harmful. For example, the layers of normal microbiota lining the intestinal and respiratory mucosa play a role in warding off infections by pathogens. However, other biofilms in the body can have a detrimental effect on health. For example, the plaque that forms on teeth is a biofilm that can contribute to dental and periodontal disease. Biofilms can also form in wounds, sometimes causing serious infections that can spread. The bacterium Pseudomonas aeruginosa often colonizes biofilms in the airways of patients with cystic fibrosis , causing chronic and sometimes fatal infections of the lungs. Biofilms can also form on medical devices used in or on the body, causing infections in patients with in-dwelling catheters , artificial joints, or contact lenses .

Pathogens embedded within biofilms exhibit a higher resistance to antibiotics than their free-floating counterparts. Several hypotheses have been proposed to explain why. Cells in the deep layers of a biofilm are metabolically inactive and may be less susceptible to the action of antibiotics that disrupt metabolic activities. The EPS may also slow the diffusion of antibiotics and antiseptics, preventing them from reaching cells in the deeper layers of the biofilm. Phenotypic changes may also contribute to the increased resistance exhibited by bacterial cells in biofilms. For example, the increased production of efflux pumps , membrane-embedded proteins that actively extrude antibiotics out of bacterial cells, have been shown to be an important mechanism of antibiotic resistance among biofilm-associated bacteria. Finally, biofilms provide an ideal environment for the exchange of extrachromosomal DNA , which often includes genes that confer antibiotic resistance.

## Factors that cause population changes

Each species has a different optimum temperature at which it’s best able to survive, the further the temperature from optimum the smaller the population is likely to be. Organisms that are plants or cold-blooded experience their metabolic rate slowing when the temperature is too low as their enzymes work more slowly, however if the temperature is too high these enzymes begin to denature. Some organisms are warm blooded, meaning they’re able to maintain a relatively constant core temperature. From this, some would assume that their population size will be unaffected by the temperature of the environment. However if the temperature is too extreme, the organisms will use a lot of their energy to maintain their core temperature, sometimes these organisms will die as they don’t have enough energy for all metabolic processes.

Light (AKA solar energy) is the primary source of all energy in ecosystems. Solar energy catalyses the reaction of photosynthesis, so the more light available, the more plants that are able to grow. Increasing the light in an ecosystem could mean that the ecosystem is able to support a larger population. Light availability will also influence the rate of growth of the whole population, as well as specific species. Similarly, pH is an important abiotic factor in ecosystems. pH will influence enzyme action, different species will have different optimum pH’s. When the pH is optimum for a species it’s population is able to increase within that specific ecosystem. If the pH is too far from optimum pH, eventually that species will die out in that area or move away from that area.

Water is a very important abiotic factor to consider, water is involved in most metabolic processes. Therefore in areas with scarce water the populations are very small and only a few species will be found in these areas (low species diversity)- this is because in order for organisms to survive in these extreme conditions they must be well adapted. Humidity is therefore also important to consider, humidity affects the transpiration rates in plants as well as the evaporation of water from animals and soils.

## 13.2 Archaea

The word archaea comes from the Ancient Greek ἀρχαῖα, meaning “ancient things”, as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth’s primitive atmosphere and the organisms’ antiquity, but as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.

Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and have been detected only by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding unlike bacteria, no known species of Archaea form endospores. The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.

Archaea are a major part of Earth’s life. They are part of the microbiota of all organisms. In the human microbiota, they are important in the gut, mouth, and on the skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation nitrogen cycling organic compound turnover and maintaining microbial symbiotic and syntrophic communities, for example.

No clear examples of archaeal pathogens or parasites are known. Instead they are often mutualists or commensals, such as the methanogens (methane-producing strains) that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.

### 13.2.1 Origin and evolution

The age of the Earth is about 4.54 billion years. Scientific evidence suggests that life began on Earth at least 3.5 billion years ago. The earliest evidence for life on Earth is graphite found to be biogenic in 3.7-billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48-billion-year-old sandstone discovered in Western Australia. In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia.

Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago though such data have since been questioned. These lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which includes Earth’s oldest known sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on Earth.

Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibility is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. It is possible that the last common ancestor of bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are “extreme environments” for archaea, and organisms that live in cooler environments appeared only later. Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term prokaryote may suggest a false similarity between them. However, structural and functional similarities between lineages often occur because of shared ancestral traits or evolutionary convergence. These similarities are known as a grade, and prokaryotes are best thought of a grade of life, characterized by such features as an absence of membrane-bound organelles.

The following table (13.2 compares some major characteristics of the three domains, to illustrate their similarities and differences.

Table 13.2: A comparison of major characterisitcs of the domains of Bacteria, Archaea and Eukaryia
Property Bacteria Archaea Eukarya
Cell wall Pseudopeptidoglycan, glycoprotein, or S-layer Peptidoglycan, S-layer, or no cell wall Various structures
Gene structure Circular chromosomes, similar translation and transcription to Eukarya Circular chromosomes, unique translation and transcription Multiple, linear chromosomes, but translation and transcription similar to Archaea
Internal cell structure No membrane-bound organelles (?[62]) or nucleus No membrane-bound organelles or nucleus Membrane-bound organelles and nucleus
Metabolism[63] Various, including diazotrophy, with methanogenesis unique to Archaea Various, including photosynthesis, aerobic and anaerobic respiration, fermentation, diazotrophy, and autotrophy Photosynthesis, cellular respiration, and fermentation no diazotrophy
Reproduction Asexual reproduction, horizontal gene transfer Asexual reproduction, horizontal gene transfer Sexual and asexual reproduction
Protein synthesis initiation Methionine Formylmethionine Methionine
RNA polymerase Many One Many
Toxin Sensitive to diphtheria toxin Resistant to diphtheria toxin Sensitive to diphtheria toxin

Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this nucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms. The more similar the patterns between species, the more closely they are related.

Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. The development of the nucleus occurred after the split between Bacteria and this common ancestor.

One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea. Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas.

### 13.2.2 Relationship to Bacteria

The relationships among the three domains are of central importance for understanding the origin of life. Most of the metabolic pathways, which are the object of the majority of an organism’s genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition. In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I but the phylogeny of these genes was interpreted to reveal interdomain gene transfer, and might not reflect the organismal relationship(s).

It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria, and that these antibiotics act primarily on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics’ target genes, and that these strains represented the common ancestors of present-day Archaea. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms Cavalier-Smith has made a similar suggestion. This proposal is also supported by other work investigating protein structural relationships and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.

### 13.2.3 Relation to Eukaryotes

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer. The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm this hypothesis explains various genetic similarities but runs into difficulties explaining cell structure. An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea.

A lineage of archaea discovered in 2015, Lokiarchaeum (of proposed new Phylum “Lokiarchaeota”), named for a hydrothermal vent called Loki’s Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes.

Several sister phyla of “Lokiarchaeota” have since been found (“Thorarchaeota”, “Odinarchaeota”, “Heimdallarchaeota”), all together comprising a newly proposed supergroup Asgard, which may appear as a sister taxon to Proteoarchaeota.

Details of the relation of Asgard members and eukaryotes are still under consideration, although, in January 2020, scientists reported that Candidatus Prometheoarchaeum syntrophicum, a type of Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago.

### 13.2.4 Morphology

Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum. Archaea in the genus Haloquadratum such as Haloquadratum walsbyi are flat, square specimens that live in hypersaline pools. These unusual shapes are probably maintained by both their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea, and filaments form within their cells, but in contrast with other organisms, these cellular structures are poorly understood. In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae.

Some species form aggregates or filaments of cells up to 200 μm long. These organisms can be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells. Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells’ surfaces and connect them into a dense bush-like agglomeration. The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. Multi-species colonies exist, such as the “string-of-pearls” community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long these filaments are made of a particular bacteria species.

### 13.2.5 Structure, Composition Development, And Operation

Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space the exception to this general rule is Ignicoccus, which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.

### 13.2.6 Cell Wall And Flagella

Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall. In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. Unlike bacteria, archaea lack peptidoglycan in their cell walls. Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure it lacks D-amino acids and N-acetylmuramic acid, substituting the latter with N-Acetyltalosaminuronic acid.

Archaeal flagella are known as archaella, that operate like bacterial flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by a proton gradient across the membrane, but archaella are notably different in composition and development. The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, while archaeal flagella appear to have evolved from bacterial type IV pili. In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.

### 13.2.7 Membranes

Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. In all organisms, cell membranes are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate “head”), and a “greasy” non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer.

The phospholipids of archaea are unusual in four ways:

• They have membranes composed of glycerol-ether lipids, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids. The difference is the type of bond that joins the lipids to the glycerol moiety the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond.
• The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called enantiomers. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by enzymes adapted for the other. The archaeal phospholipids are built on a backbone of sn-glycerol-1-phosphate, which is an enantiomer of sn-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life’s history, indicating an early split from the other two domains.
• Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprenoid chains with multiple side-branches, sometimes with cyclopropane or cyclohexane rings. By contrast, the fatty acids in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.
• In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile) this fusion may make their membranes more rigid and better able to resist harsh environments. For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism’s survival in its highly acidic habitat.

### 13.2.8 Metabolism

Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell’s activities. One compound acts as an electron donor and one as an electron acceptor. The energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, the same basic process that happens in the mitochondrion of eukaryotic cells.

Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways are shared among all forms of life for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.

Table 13.3: Nutritional types in archaeal metabolism
Nutritional Type Source of Energy Source of Carbon Examples
Phototrophs Sunlight Organic compounds Halobacterium
Lithotrophs Inorganic compounds Organic compounds or carbon fixation Ferroglobus, Methanobacteria or Pyrolobus
Organotrophs Organic compounds Organic compounds or carbon fixation Pyrococcus, Sulfolobus or Methanosarcinales

Some Euryarchaeota are methanogens (archaea that produce methane as a result of metabolism) living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.

Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or another metabolic pathway called the 3-hydroxypropionate/ 4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis. Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.

Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of and into the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.

### 13.2.9 Genetics

Archaea usually have a single circular chromosome, with as many as 5,751,492 base pairs in Methanosarcina acetivorans, the largest known archaeal genome. The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known it is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.

Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.

Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, while archaeal translation shows signs of both bacterial and eukaryotic equivalents. Although archaea have only one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter, but other archaeal transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.

### 13.2.10 Ecology

Archaea exist in a broad range of habitats, and are now recognized as a major part of global ecosystems, and may represent about 20% of microbial cells in the oceans. However, the first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils.

Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.

Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism.

Other archaea exist in very acidic or alkaline conditions. For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 molar sulfuric acid.

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. Some extremophile habitats are not dissimilar to those on Mars, leading to the suggestion that viable microbes could be transferred between planets in meteorites.

Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas. Even more significant are the large numbers of archaea found throughout the world’s oceans in non-extreme habitats among the plankton community (as part of the picoplankton). Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture. Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy.

Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom. It has been demonstrated that in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of

0.3 to 0.5 gigatons of carbon per year globally.

### 13.2.11 Significance in Technology And Industry

Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions. These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey. Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds. This stability makes them easier to use in structural biology. Consequently, the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.

In contrast with the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas. In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.

Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.

## Contents

### Research history Edit

In the 13th century the category of reptile was recognized in Europe as consisting of a miscellany of egg-laying creatures, including "snakes, various fantastic monsters, lizards, assorted amphibians, and worms", as recorded by Vincent of Beauvais in his Mirror of Nature. [8] In the 18th century, the reptiles were, from the outset of classification, grouped with the amphibians. Linnaeus, working from species-poor Sweden, where the common adder and grass snake are often found hunting in water, included all reptiles and amphibians in class "III – Amphibia" in his Systema Naturæ. [9] The terms reptile and amphibian were largely interchangeable, reptile (from Latin repere, 'to creep') being preferred by the French. [10] Josephus Nicolaus Laurenti was the first to formally use the term Reptilia for an expanded selection of reptiles and amphibians basically similar to that of Linnaeus. [11] Today, the two groups are still commonly treated under the single heading herpetology.

It was not until the beginning of the 19th century that it became clear that reptiles and amphibians are, in fact, quite different animals, and Pierre André Latreille erected the class Batracia (1825) for the latter, dividing the tetrapods into the four familiar classes of reptiles, amphibians, birds, and mammals. [12] The British anatomist Thomas Henry Huxley made Latreille's definition popular and, together with Richard Owen, expanded Reptilia to include the various fossil "antediluvian monsters", including dinosaurs and the mammal-like (synapsid) Dicynodon he helped describe. This was not the only possible classification scheme: In the Hunterian lectures delivered at the Royal College of Surgeons in 1863, Huxley grouped the vertebrates into mammals, sauroids, and ichthyoids (the latter containing the fishes and amphibians). He subsequently proposed the names of Sauropsida and Ichthyopsida for the latter two groups. [13] In 1866, Haeckel demonstrated that vertebrates could be divided based on their reproductive strategies, and that reptiles, birds, and mammals were united by the amniotic egg.

The terms Sauropsida ('lizard faces') and Theropsida ('beast faces') were used again in 1916 by E.S. Goodrich to distinguish between lizards, birds, and their relatives on the one hand (Sauropsida) and mammals and their extinct relatives (Theropsida) on the other. Goodrich supported this division by the nature of the hearts and blood vessels in each group, and other features, such as the structure of the forebrain. According to Goodrich, both lineages evolved from an earlier stem group, Protosauria ("first lizards") in which he included some animals today considered reptile-like amphibians, as well as early reptiles. [14]

In 1956, D.M.S. Watson observed that the first two groups diverged very early in reptilian history, so he divided Goodrich's Protosauria between them. He also reinterpreted Sauropsida and Theropsida to exclude birds and mammals, respectively. Thus his Sauropsida included Procolophonia, Eosuchia, Millerosauria, Chelonia (turtles), Squamata (lizards and snakes), Rhynchocephalia, Crocodilia, "thecodonts" (paraphyletic basal Archosauria), non-avian dinosaurs, pterosaurs, ichthyosaurs, and sauropterygians. [15]

In the late 19th century, a number of definitions of Reptilia were offered. The traits listed by Lydekker in 1896, for example, include a single occipital condyle, a jaw joint formed by the quadrate and articular bones, and certain characteristics of the vertebrae. [16] The animals singled out by these formulations, the amniotes other than the mammals and the birds, are still those considered reptiles today. [17]

The synapsid/sauropsid division supplemented another approach, one that split the reptiles into four subclasses based on the number and position of temporal fenestrae, openings in the sides of the skull behind the eyes. This classification was initiated by Henry Fairfield Osborn and elaborated and made popular by Romer's classic Vertebrate Paleontology. [18] [19] Those four subclasses were:

– no fenestrae – cotylosaurs and Chelonia (turtles and relatives) [note 1] – one low fenestra – pelycosaurs and therapsids (the 'mammal-like reptiles') – one high fenestra (above the postorbital and squamosal) – protorosaurs (small, early lizard-like reptiles) and the marine sauropterygians and ichthyosaurs, the latter called Parapsida in Osborn's work. – two fenestrae – most reptiles, including lizards, snakes, crocodilians, dinosaurs and pterosaurs

The composition of Euryapsida was uncertain. Ichthyosaurs were, at times, considered to have arisen independently of the other euryapsids, and given the older name Parapsida. Parapsida was later discarded as a group for the most part (ichthyosaurs being classified as incertae sedis or with Euryapsida). However, four (or three if Euryapsida is merged into Diapsida) subclasses remained more or less universal for non-specialist work throughout the 20th century. It has largely been abandoned by recent researchers: In particular, the anapsid condition has been found to occur so variably among unrelated groups that it is not now considered a useful distinction. [20]

### Phylogenetics and modern definition Edit

By the early 21st century, vertebrate paleontologists were beginning to adopt phylogenetic taxonomy, in which all groups are defined in such a way as to be monophyletic that is, groups which include all descendants of a particular ancestor. The reptiles as historically defined are paraphyletic, since they exclude both birds and mammals. These respectively evolved from dinosaurs and from early therapsids, which were both traditionally called reptiles. [21] Birds are more closely related to crocodilians than the latter are to the rest of extant reptiles. Colin Tudge wrote:

Despite the early proposals for replacing the paraphyletic Reptilia with a monophyletic Sauropsida, which includes birds, that term was never adopted widely or, when it was, was not applied consistently. [22]

When Sauropsida was used, it often had the same content or even the same definition as Reptilia. In 1988, Jacques Gauthier proposed a cladistic definition of Reptilia as a monophyletic node-based crown group containing turtles, lizards and snakes, crocodilians, and birds, their common ancestor and all its descendants. While Gauthier's definition was close to the modern consensus, nonetheless, it became considered inadequate because the actual relationship of turtles to other reptiles was not yet well understood at this time. [22] Major revisions since have included the reassignment of synapsids as non-reptiles, and classification of turtles as diapsids. [22]

A variety of other definitions were proposed by other scientists in the years following Gauthier's paper. The first such new definition, which attempted to adhere to the standards of the PhyloCode, was published by Modesto and Anderson in 2004. Modesto and Anderson reviewed the many previous definitions and proposed a modified definition, which they intended to retain most traditional content of the group while keeping it stable and monophyletic. They defined Reptilia as all amniotes closer to Lacerta agilis and Crocodylus niloticus than to Homo sapiens. This stem-based definition is equivalent to the more common definition of Sauropsida, which Modesto and Anderson synonymized with Reptilia, since the latter is better known and more frequently used. Unlike most previous definitions of Reptilia, however, Modesto and Anderson's definition includes birds, [22] as they are within the clade that includes both lizards and crocodiles. [22]

### Taxonomy Edit

General classification of extinct and living reptiles, focusing on major groups. [23] [24]

• Reptilia/Sauropsida
• Eureptilia
• Diapsida
• Neodiapsida
(placement uncertain) (paraphyletic) (placement uncertain) (placement uncertain)
• Sauria
• Lepidosauromorpha
(tuatara) (lizards & snakes)
• (paraphyletic)
• Archosauria
(crocodilians)
• ### Phylogeny Edit

The cladogram presented here illustrates the "family tree" of reptiles, and follows a simplified version of the relationships found by M.S. Lee, in 2013. [25] All genetic studies have supported the hypothesis that turtles are diapsids some have placed turtles within Archosauromorpha, [25] [26] [27] [28] [29] [30] though a few have recovered turtles as Lepidosauromorpha instead. [31] The cladogram below used a combination of genetic (molecular) and fossil (morphological) data to obtain its results. [25]

Synapsida (mammals and their extinct relatives)

### The position of turtles Edit

The placement of turtles has historically been highly variable. Classically, turtles were considered to be related to the primitive anapsid reptiles. [32] Molecular work has usually placed turtles within the diapsids. As of 2013, three turtle genomes have been sequenced. [33] The results place turtles as a sister clade to the archosaurs, the group that includes crocodiles, dinosaurs, and birds. [34] However, in their comparative analysis of the timing of organogenesis, Werneburg and Sánchez-Villagra (2009) found support for the hypothesis that turtles belong to a separate clade within Sauropsida, outside the saurian clade altogether. [35]

### Origin of the reptiles Edit

The origin of the reptiles lies about 310–320 million years ago, in the steaming swamps of the late Carboniferous period, when the first reptiles evolved from advanced reptiliomorphs. [36]

The oldest known animal that may have been an amniote is Casineria (though it may have been a temnospondyl). [37] [38] [39] A series of footprints from the fossil strata of Nova Scotia dated to 315 Ma show typical reptilian toes and imprints of scales. [40] These tracks are attributed to Hylonomus, the oldest unquestionable reptile known. [41] It was a small, lizard-like animal, about 20 to 30 centimetres (7.9 to 11.8 in) long, with numerous sharp teeth indicating an insectivorous diet. [42] Other examples include Westlothiana (for the moment considered a reptiliomorph rather than a true amniote) [43] and Paleothyris, both of similar build and presumably similar habit.

### Rise of the reptiles Edit

The earliest amniotes, including stem-reptiles (those amniotes closer to modern reptiles than to mammals), were largely overshadowed by larger stem-tetrapods, such as Cochleosaurus, and remained a small, inconspicuous part of the fauna until the Carboniferous Rainforest Collapse. [44] This sudden collapse affected several large groups. Primitive tetrapods were particularly devastated, while stem-reptiles fared better, being ecologically adapted to the drier conditions that followed. Primitive tetrapods, like modern amphibians, need to return to water to lay eggs in contrast, amniotes, like modern reptiles – whose eggs possess a shell that allows them to be laid on land – were better adapted to the new conditions. Amniotes acquired new niches at a faster rate than before the collapse and at a much faster rate than primitive tetrapods. They acquired new feeding strategies including herbivory and carnivory, previously only having been insectivores and piscivores. [44] From this point forward, reptiles dominated communities and had a greater diversity than primitive tetrapods, setting the stage for the Mesozoic (known as the Age of Reptiles). [45] One of the best known early stem-reptiles is Mesosaurus, a genus from the Early Permian that had returned to water, feeding on fish.

### Anapsids, synapsids, diapsids, and sauropsids Edit

It was traditionally assumed that the first reptiles retained an anapsid skull inherited from their ancestors. [46] This type of skull has a skull roof with only holes for the nostrils, eyes and a pineal eye. [32] The discoveries of synapsid-like openings (see below) in the skull roof of the skulls of several members of Parareptilia (the clade containing most of the amniotes traditionally referred to as "anapsids"), including lanthanosuchoids, millerettids, bolosaurids, some nycteroleterids, some procolophonoids and at least some mesosaurs [47] [48] [49] made it more ambiguous and it's currently uncertain whether the ancestral amniote had an anapsid-like or synapsid-like skull. [49] These animals are traditionally referred to as "anapsids", and form a paraphyletic basic stock from which other groups evolved. [22] Very shortly after the first amniotes appeared, a lineage called Synapsida split off this group was characterized by a temporal opening in the skull behind each eye to give room for the jaw muscle to move. These are the "mammal-like amniotes", or stem-mammals, that later gave rise to the true mammals. [50] Soon after, another group evolved a similar trait, this time with a double opening behind each eye, earning them the name Diapsida ("two arches"). [46] The function of the holes in these groups was to lighten the skull and give room for the jaw muscles to move, allowing for a more powerful bite. [32]

Turtles have been traditionally believed to be surviving parareptiles, on the basis of their anapsid skull structure, which was assumed to be primitive trait. [51] The rationale for this classification has been disputed, with some arguing that turtles are diapsids that evolved anapsid skulls in order to improve their armor. [36] Later morphological phylogenetic studies with this in mind placed turtles firmly within Diapsida. [52] All molecular studies have strongly upheld the placement of turtles within diapsids, most commonly as a sister group to extant archosaurs. [27] [28] [29] [30]

### Permian reptiles Edit

With the close of the Carboniferous, the amniotes became the dominant tetrapod fauna. While primitive, terrestrial reptiliomorphs still existed, the synapsid amniotes evolved the first truly terrestrial megafauna (giant animals) in the form of pelycosaurs, such as Edaphosaurus and the carnivorous Dimetrodon. In the mid-Permian period, the climate became drier, resulting in a change of fauna: The pelycosaurs were replaced by the therapsids. [53]

The parareptiles, whose massive skull roofs had no postorbital holes, continued and flourished throughout the Permian. The pareiasaurian parareptiles reached giant proportions in the late Permian, eventually disappearing at the close of the period (the turtles being possible survivors). [53]

Early in the period, the modern reptiles, or crown-group reptiles, evolved and split into two main lineages: the Archosauromorpha (forebears of turtles, crocodiles, and dinosaurs) and the Lepidosauromorpha (predecessors of modern lizards and tuataras). Both groups remained lizard-like and relatively small and inconspicuous during the Permian.

### Mesozoic reptiles Edit

The close of the Permian saw the greatest mass extinction known (see the Permian–Triassic extinction event), an event prolonged by the combination of two or more distinct extinction pulses. [54] Most of the earlier parareptile and synapsid megafauna disappeared, being replaced by the true reptiles, particularly archosauromorphs. These were characterized by elongated hind legs and an erect pose, the early forms looking somewhat like long-legged crocodiles. The archosaurs became the dominant group during the Triassic period, though it took 30 million years before their diversity was as great as the animals that lived in the Permian. [54] Archosaurs developed into the well-known dinosaurs and pterosaurs, as well as the ancestors of crocodiles. Since reptiles, first rauisuchians and then dinosaurs, dominated the Mesozoic era, the interval is popularly known as the "Age of Reptiles". The dinosaurs also developed smaller forms, including the feather-bearing smaller theropods. In the Cretaceous period, these gave rise to the first true birds. [55]

The sister group to Archosauromorpha is Lepidosauromorpha, containing lizards and tuataras, as well as their fossil relatives. Lepidosauromorpha contained at least one major group of the Mesozoic sea reptiles: the mosasaurs, which lived during the Cretaceous period. The phylogenetic placement of other main groups of fossil sea reptiles – the ichthyopterygians (including ichthyosaurs) and the sauropterygians, which evolved in the early Triassic – is more controversial. Different authors linked these groups either to lepidosauromorphs [1] or to archosauromorphs, [56] [57] [58] and ichthyopterygians were also argued to be diapsids that did not belong to the least inclusive clade containing lepidosauromorphs and archosauromorphs. [59]

### Cenozoic reptiles Edit

The close of the Cretaceous period saw the demise of the Mesozoic era reptilian megafauna (see the Cretaceous–Paleogene extinction event, also known as K-T extinction event). Of the large marine reptiles, only sea turtles were left and of the non-marine large reptiles, only the semi-aquatic crocodiles and broadly similar choristoderes survived the extinction, with the latter becoming extinct in the Miocene. [61] Of the great host of dinosaurs dominating the Mesozoic, only the small beaked birds survived. This dramatic extinction pattern at the end of the Mesozoic led into the Cenozoic. Mammals and birds filled the empty niches left behind by the reptilian megafauna and, while reptile diversification slowed, bird and mammal diversification took an exponential turn. [45] However, reptiles were still important components of the megafauna, particularly in the form of large and giant tortoises. [62] [63]

After the extinction of most archosaur and marine reptile lines by the end of the Cretaceous, reptile diversification continued throughout the Cenozoic. Squamates took a massive hit during the K–Pg event, only recovering ten million years after it, [64] but they underwent a great radiation event once they recovered, and today squamates make up the majority of living reptiles (> 95%). [65] [66] Approximately 10,000 extant species of traditional reptiles are known, with birds adding about 10,000 more, almost twice the number of mammals, represented by about 5,700 living species (excluding domesticated species). [67]

Species diversity of living reptiles (2013) [68]
Reptile group Described species Percent of reptile species
Squamates 9193 96.3%
- Lizards 5634 59%
- Snakes 3378 35%
- Amphisbaenians 181 2%
Turtles 327 3.4%
Crocodilians 25 0.3%
Rhynchocephalians 1 0.01%
Total 9546 100%

### Circulation Edit

All lepidosaurs and turtles have a three-chambered heart consisting of two atria, one variably partitioned ventricle, and two aortas that lead to the systemic circulation. The degree of mixing of oxygenated and deoxygenated blood in the three-chambered heart varies depending on the species and physiological state. Under different conditions, deoxygenated blood can be shunted back to the body or oxygenated blood can be shunted back to the lungs. This variation in blood flow has been hypothesized to allow more effective thermoregulation and longer diving times for aquatic species, but has not been shown to be a fitness advantage. [69]

For example, Iguana hearts, like the majority of the squamates hearts, are composed of three chambers with two aorta and one ventricle, cardiac involuntary muscles. [70] The main structures of the heart are the sinus venosus, the pacemaker, the left atrium, the right atruim, the atrioventricular valve, the cavum venosum, cavum arteriosum, the cavum pulmonale, the muscular ridge, the ventricular ridge, pulmonary veins, and paired aortic arches. [71]

Some squamate species (e.g., pythons and monitor lizards) have three-chambered hearts that become functionally four-chambered hearts during contraction. This is made possible by a muscular ridge that subdivides the ventricle during ventricular diastole and completely divides it during ventricular systole. Because of this ridge, some of these squamates are capable of producing ventricular pressure differentials that are equivalent to those seen in mammalian and avian hearts. [72]

Crocodilians have an anatomically four-chambered heart, similar to birds, but also have two systemic aortas and are therefore capable of bypassing their pulmonary circulation. [73]

### Metabolism Edit

Modern non-avian reptiles exhibit some form of cold-bloodedness (i.e. some mix of poikilothermy, ectothermy, and bradymetabolism) so that they have limited physiological means of keeping the body temperature constant and often rely on external sources of heat. Due to a less stable core temperature than birds and mammals, reptilian biochemistry requires enzymes capable of maintaining efficiency over a greater range of temperatures than in the case for warm-blooded animals. The optimum body temperature range varies with species, but is typically below that of warm-blooded animals for many lizards, it falls in the 24°–35 °C (75°–95 °F) range, [74] while extreme heat-adapted species, like the American desert iguana Dipsosaurus dorsalis, can have optimal physiological temperatures in the mammalian range, between 35° and 40 °C (95° and 104 °F). [75] While the optimum temperature is often encountered when the animal is active, the low basal metabolism makes body temperature drop rapidly when the animal is inactive.

As in all animals, reptilian muscle action produces heat. In large reptiles, like leatherback turtles, the low surface-to-volume ratio allows this metabolically produced heat to keep the animals warmer than their environment even though they do not have a warm-blooded metabolism. [76] This form of homeothermy is called gigantothermy it has been suggested as having been common in large dinosaurs and other extinct large-bodied reptiles. [77] [78]

The benefit of a low resting metabolism is that it requires far less fuel to sustain bodily functions. By using temperature variations in their surroundings, or by remaining cold when they do not need to move, reptiles can save considerable amounts of energy compared to endothermic animals of the same size. [79] A crocodile needs from a tenth to a fifth of the food necessary for a lion of the same weight and can live half a year without eating. [80] Lower food requirements and adaptive metabolisms allow reptiles to dominate the animal life in regions where net calorie availability is too low to sustain large-bodied mammals and birds.

It is generally assumed that reptiles are unable to produce the sustained high energy output necessary for long distance chases or flying. [81] Higher energetic capacity might have been responsible for the evolution of warm-bloodedness in birds and mammals. [82] However, investigation of correlations between active capacity and thermophysiology show a weak relationship. [83] Most extant reptiles are carnivores with a sit-and-wait feeding strategy whether reptiles are cold blooded due to their ecology is not clear. Energetic studies on some reptiles have shown active capacities equal to or greater than similar sized warm-blooded animals. [84]

### Respiratory system Edit

All reptiles breathe using lungs. Aquatic turtles have developed more permeable skin, and some species have modified their cloaca to increase the area for gas exchange. [85] Even with these adaptations, breathing is never fully accomplished without lungs. Lung ventilation is accomplished differently in each main reptile group. In squamates, the lungs are ventilated almost exclusively by the axial musculature. This is also the same musculature that is used during locomotion. Because of this constraint, most squamates are forced to hold their breath during intense runs. Some, however, have found a way around it. Varanids, and a few other lizard species, employ buccal pumping as a complement to their normal "axial breathing". This allows the animals to completely fill their lungs during intense locomotion, and thus remain aerobically active for a long time. Tegu lizards are known to possess a proto-diaphragm, which separates the pulmonary cavity from the visceral cavity. While not actually capable of movement, it does allow for greater lung inflation, by taking the weight of the viscera off the lungs. [86]

Crocodilians actually have a muscular diaphragm that is analogous to the mammalian diaphragm. The difference is that the muscles for the crocodilian diaphragm pull the pubis (part of the pelvis, which is movable in crocodilians) back, which brings the liver down, thus freeing space for the lungs to expand. This type of diaphragmatic setup has been referred to as the "hepatic piston". The airways form a number of double tubular chambers within each lung. On inhalation and exhalation air moves through the airways in the same direction, thus creating a unidirectional airflow through the lungs. A similar system is found in birds, [87] monitor lizards [88] and iguanas. [89]

Most reptiles lack a secondary palate, meaning that they must hold their breath while swallowing. Crocodilians have evolved a bony secondary palate that allows them to continue breathing while remaining submerged (and protect their brains against damage by struggling prey). Skinks (family Scincidae) also have evolved a bony secondary palate, to varying degrees. Snakes took a different approach and extended their trachea instead. Their tracheal extension sticks out like a fleshy straw, and allows these animals to swallow large prey without suffering from asphyxiation. [90]

#### Turtles and tortoises Edit

How turtles and tortoises breathe has been the subject of much study. To date, only a few species have been studied thoroughly enough to get an idea of how those turtles breathe. The varied results indicate that turtles and tortoises have found a variety of solutions to this problem.

The difficulty is that most turtle shells are rigid and do not allow for the type of expansion and contraction that other amniotes use to ventilate their lungs. Some turtles, such as the Indian flapshell (Lissemys punctata), have a sheet of muscle that envelops the lungs. When it contracts, the turtle can exhale. When at rest, the turtle can retract the limbs into the body cavity and force air out of the lungs. When the turtle protracts its limbs, the pressure inside the lungs is reduced, and the turtle can suck air in. Turtle lungs are attached to the inside of the top of the shell (carapace), with the bottom of the lungs attached (via connective tissue) to the rest of the viscera. By using a series of special muscles (roughly equivalent to a diaphragm), turtles are capable of pushing their viscera up and down, resulting in effective respiration, since many of these muscles have attachment points in conjunction with their forelimbs (indeed, many of the muscles expand into the limb pockets during contraction). [91]

Breathing during locomotion has been studied in three species, and they show different patterns. Adult female green sea turtles do not breathe as they crutch along their nesting beaches. They hold their breath during terrestrial locomotion and breathe in bouts as they rest. North American box turtles breathe continuously during locomotion, and the ventilation cycle is not coordinated with the limb movements. [92] This is because they use their abdominal muscles to breathe during locomotion. The last species to have been studied is the red-eared slider, which also breathes during locomotion, but takes smaller breaths during locomotion than during small pauses between locomotor bouts, indicating that there may be mechanical interference between the limb movements and the breathing apparatus. Box turtles have also been observed to breathe while completely sealed up inside their shells. [92]

### Skin Edit

Reptilian skin is covered in a horny epidermis, making it watertight and enabling reptiles to live on dry land, in contrast to amphibians. Compared to mammalian skin, that of reptiles is rather thin and lacks the thick dermal layer that produces leather in mammals. [93] Exposed parts of reptiles are protected by scales or scutes, sometimes with a bony base (osteoderms), forming armor. In lepidosaurians, such as lizards and snakes, the whole skin is covered in overlapping epidermal scales. Such scales were once thought to be typical of the class Reptilia as a whole, but are now known to occur only in lepidosaurians. [ citation needed ] The scales found in turtles and crocodiles are of dermal, rather than epidermal, origin and are properly termed scutes. [ citation needed ] In turtles, the body is hidden inside a hard shell composed of fused scutes.

Lacking a thick dermis, reptilian leather is not as strong as mammalian leather. It is used in leather-wares for decorative purposes for shoes, belts and handbags, particularly crocodile skin.

#### Shedding Edit

Reptiles shed their skin through a process called ecdysis which occurs continuously throughout their lifetime. In particular, younger reptiles tend to shed once every 5–6 weeks while adults shed 3–4 times a year. [94] Younger reptiles shed more because of their rapid growth rate. Once full size, the frequency of shedding drastically decreases. The process of ecdysis involves forming a new layer of skin under the old one. Proteolytic enzymes and lymphatic fluid is secreted between the old and new layers of skin. Consequently, this lifts the old skin from the new one allowing shedding to occur. [95] Snakes will shed from the head to the tail while lizards shed in a "patchy pattern". [95] Dysecdysis, a common skin disease in snakes and lizards, will occur when ecdysis, or shedding, fails. [96] There are numerous reasons why shedding fails and can be related to inadequate humidity and temperature, nutritional deficiencies, dehydration and traumatic injuries. [95] Nutritional deficiencies decrease proteolytic enzymes while dehydration reduces lymphatic fluids to separate the skin layers. Traumatic injuries on the other hand, form scars that will not allow new scales to form and disrupt the process of ecdysis. [96]

### Excretion Edit

Excretion is performed mainly by two small kidneys. In diapsids, uric acid is the main nitrogenous waste product turtles, like mammals, excrete mainly urea. Unlike the kidneys of mammals and birds, reptile kidneys are unable to produce liquid urine more concentrated than their body fluid. This is because they lack a specialized structure called a loop of Henle, which is present in the nephrons of birds and mammals. Because of this, many reptiles use the colon to aid in the reabsorption of water. Some are also able to take up water stored in the bladder. Excess salts are also excreted by nasal and lingual salt glands in some reptiles.

In all reptiles the urinogenital ducts and the anus both empty into an organ called a cloaca. In some reptiles, a midventral wall in the cloaca may open into a urinary bladder, but not all. It is present in all turtles and tortoises as well as most lizards, but is lacking in the monitor lizard, the legless lizards. It is absent in the snakes, alligators, and crocodiles. [97]

Many turtles, tortoises, and lizards have proportionally very large bladders. Charles Darwin noted that the Galapagos tortoise had a bladder which could store up to 20% of its body weight. [98] Such adaptations are the result of environments such as remote islands and deserts where water is very scarce. [99] : 143 Other desert-dwelling reptiles have large bladders that can store a long-term reservoir of water for up to several months and aid in osmoregulation. [100]

Turtles have two or more accessory urinary bladders, located lateral to the neck of the urinary bladder and dorsal to the pubis, occupying a significant portion of their body cavity. [101] Their bladder is also usually bilobed with a left and right section. The right section is located under the liver, which prevents large stones from remaining in that side while the left section is more likely to have calculi. [102]

### Digestion Edit

Most reptiles are insectivorous or carnivorous and have simple and comparatively short digestive tracts due to meat being fairly simple to break down and digest. Digestion is slower than in mammals, reflecting their lower resting metabolism and their inability to divide and masticate their food. [103] Their poikilotherm metabolism has very low energy requirements, allowing large reptiles like crocodiles and large constrictors to live from a single large meal for months, digesting it slowly. [80]

While modern reptiles are predominantly carnivorous, during the early history of reptiles several groups produced some herbivorous megafauna: in the Paleozoic, the pareiasaurs and in the Mesozoic several lines of dinosaurs. [45] Today, turtles are the only predominantly herbivorous reptile group, but several lines of agamas and iguanas have evolved to live wholly or partly on plants. [104]

Herbivorous reptiles face the same problems of mastication as herbivorous mammals but, lacking the complex teeth of mammals, many species swallow rocks and pebbles (so called gastroliths) to aid in digestion: The rocks are washed around in the stomach, helping to grind up plant matter. [104] Fossil gastroliths have been found associated with both ornithopods and sauropods, though whether they actually functioned as a gastric mill in the latter is disputed. [105] [106] Salt water crocodiles also use gastroliths as ballast, stabilizing them in the water or helping them to dive. [107] A dual function as both stabilizing ballast and digestion aid has been suggested for gastroliths found in plesiosaurs. [108]

### Nerves Edit

The reptilian nervous system contains the same basic part of the amphibian brain, but the reptile cerebrum and cerebellum are slightly larger. Most typical sense organs are well developed with certain exceptions, most notably the snake's lack of external ears (middle and inner ears are present). There are twelve pairs of cranial nerves. [109] Due to their short cochlea, reptiles use electrical tuning to expand their range of audible frequencies.

#### Intelligence Edit

Reptiles are generally considered less intelligent than mammals and birds. [32] The size of their brain relative to their body is much less than that of mammals, the encephalization quotient being about one tenth of that of mammals, [110] though larger reptiles can show more complex brain development. Larger lizards, like the monitors, are known to exhibit complex behavior, including cooperation [111] and cognitive abilities allowing them to optimize their foraging and territoriality over time. [112] Crocodiles have relatively larger brains and show a fairly complex social structure. The Komodo dragon is even known to engage in play, [113] as are turtles, which are also considered to be social creatures, [114] and sometimes switch between monogamy and promiscuity in their sexual behavior. [ citation needed ] One study found that wood turtles were better than white rats at learning to navigate mazes. [115] Another study found that giant tortoises are capable of learning through operant conditioning, visual discrimination and retained learned behaviors with long-term memory. [116] Sea turtles have been regarded as having simple brains, but their flippers are used for a variety of foraging tasks (holding, bracing, corralling) in common with marine mammals. [117]

### Vision Edit

Most reptiles are diurnal animals. The vision is typically adapted to daylight conditions, with color vision and more advanced visual depth perception than in amphibians and most mammals.

Reptiles usually have excellent vision, allowing them to detect shapes and motions at long distances. They often have only a few Rod cells and have poor vision in low-light conditions. At the same time they have cells called "double cones" which give them sharp color vision and enable them to see ultraviolet wavelengths. [118] In some species, such as blind snakes, vision is reduced.

Many lepidosaurs have a photosensory organ on the top of their heads called the parietal eye, which are also called third eye, pineal eye or pineal gland. This "eye" does not work the same way as a normal eye does as it has only a rudimentary retina and lens and thus, cannot form images. It is however sensitive to changes in light and dark and can detect movement. [118]

Some snakes have extra sets of visual organs (in the loosest sense of the word) in the form of pits sensitive to infrared radiation (heat). Such heat-sensitive pits are particularly well developed in the pit vipers, but are also found in boas and pythons. These pits allow the snakes to sense the body heat of birds and mammals, enabling pit vipers to hunt rodents in the dark. [119]

Most reptiles including birds possess a nictitating membrane, a translucent third eyelid which is drawn over the eye from the inner corner. Notably, it protects a crocodilian's eyeball surface while allowing a degree of vision underwater. [120] However, many squamates, geckos and snakes in particular, lack eyelids, which are replaced by a transparent scale. This is called the brille, spectacle, or eyecap. The brille is usually not visible, except for when the snake molts, and it protects the eyes from dust and dirt. [121]

### Reproduction Edit

Reptiles generally reproduce sexually, [122] though some are capable of asexual reproduction. All reproductive activity occurs through the cloaca, the single exit/entrance at the base of the tail where waste is also eliminated. Most reptiles have copulatory organs, which are usually retracted or inverted and stored inside the body. In turtles and crocodilians, the male has a single median penis, while squamates, including snakes and lizards, possess a pair of hemipenes, only one of which is typically used in each session. Tuatara, however, lack copulatory organs, and so the male and female simply press their cloacas together as the male discharges sperm. [123]

Most reptiles lay amniotic eggs covered with leathery or calcareous shells. An amnion, chorion, and allantois are present during embryonic life. The eggshell (1) protects the crocodile embryo (11) and keeps it from drying out, but it is flexible to allow gas exchange. The chorion (6) aids in gas exchange between the inside and outside of the egg. It allows carbon dioxide to exit the egg and oxygen gas to enter the egg. The albumin (9) further protects the embryo and serves as a reservoir for water and protein. The allantois (8) is a sac that collects the metabolic waste produced by the embryo. The amniotic sac (10) contains amniotic fluid (12) which protects and cushions the embryo. The amnion (5) aids in osmoregulation and serves as a saltwater reservoir. The yolk sac (2) surrounding the yolk (3) contains protein and fat rich nutrients that are absorbed by the embryo via vessels (4) that allow the embryo to grow and metabolize. The air space (7) provides the embryo with oxygen while it is hatching. This ensures that the embryo will not suffocate while it is hatching. There are no larval stages of development. Viviparity and ovoviviparity have evolved in many extinct clades of reptiles and in squamates. In the latter group, many species, including all boas and most vipers, utilize this mode of reproduction. The degree of viviparity varies some species simply retain the eggs until just before hatching, others provide maternal nourishment to supplement the yolk, and yet others lack any yolk and provide all nutrients via a structure similar to the mammalian placenta. The earliest documented case of viviparity in reptiles is the Early Permian mesosaurs, [124] although some individuals or taxa in that clade may also have been oviparous because a putative isolated egg has also been found. Several groups of Mesozoic marine reptiles also exhibited viviparity, such as mosasaurs, ichthyosaurs, and Sauropterygia, a group that include pachypleurosaurs and Plesiosauria. [7]

Asexual reproduction has been identified in squamates in six families of lizards and one snake. In some species of squamates, a population of females is able to produce a unisexual diploid clone of the mother. This form of asexual reproduction, called parthenogenesis, occurs in several species of gecko, and is particularly widespread in the teiids (especially Aspidocelis) and lacertids (Lacerta). In captivity, Komodo dragons (Varanidae) have reproduced by parthenogenesis.

Parthenogenetic species are suspected to occur among chameleons, agamids, xantusiids, and typhlopids.

Some reptiles exhibit temperature-dependent sex determination (TDSD), in which the incubation temperature determines whether a particular egg hatches as male or female. TDSD is most common in turtles and crocodiles, but also occurs in lizards and tuatara. [125] To date, there has been no confirmation of whether TDSD occurs in snakes. [126]

Many small reptiles, such as snakes and lizards that live on the ground or in the water, are vulnerable to being preyed on by all kinds of carnivorous animals. Thus avoidance is the most common form of defense in reptiles. [127] At the first sign of danger, most snakes and lizards crawl away into the undergrowth, and turtles and crocodiles will plunge into water and sink out of sight.

### Camouflage and warning Edit

Reptiles tend to avoid confrontation through camouflage. Two major groups of reptile predators are birds and other reptiles, both of which have well developed color vision. Thus the skins of many reptiles have cryptic coloration of plain or mottled gray, green, and brown to allow them to blend into the background of their natural environment. [128] Aided by the reptiles' capacity for remaining motionless for long periods, the camouflage of many snakes is so effective that people or domestic animals are most typically bitten because they accidentally step on them. [129]

When camouflage fails to protect them, blue-tongued skinks will try to ward off attackers by displaying their blue tongues, and the frill-necked lizard will display its brightly colored frill. These same displays are used in territorial disputes and during courtship. [130] If danger arises so suddenly that flight is useless, crocodiles, turtles, some lizards, and some snakes hiss loudly when confronted by an enemy. Rattlesnakes rapidly vibrate the tip of the tail, which is composed of a series of nested, hollow beads to ward off approaching danger.

In contrast to the normal drab coloration of most reptiles, the lizards of the genus Heloderma (the Gila monster and the beaded lizard) and many of the coral snakes have high-contrast warning coloration, warning potential predators they are venomous. [131] A number of non-venomous North American snake species have colorful markings similar to those of the coral snake, an oft cited example of Batesian mimicry. [132] [133]

### Alternative defense in snakes Edit

Camouflage does not always fool a predator. When caught out, snake species adopt different defensive tactics and use a complicated set of behaviors when attacked. Some first elevate their head and spread out the skin of their neck in an effort to look large and threatening. Failure of this strategy may lead to other measures practiced particularly by cobras, vipers, and closely related species, which use venom to attack. The venom is modified saliva, delivered through fangs from a venom gland. [134] [135] Some non-venomous snakes, such as American hognose snakes or European grass snake, play dead when in danger some, including the grass snake, exude a foul-smelling liquid to deter attackers. [136] [137]

### Defense in crocodilians Edit

When a crocodilian is concerned about its safety, it will gape to expose the teeth and yellow tongue. If this doesn't work, the crocodilian gets a little more agitated and typically begins to make hissing sounds. After this, the crocodilian will start to change its posture dramatically to make itself look more intimidating. The body is inflated to increase apparent size. If absolutely necessary it may decide to attack an enemy.

Some species try to bite immediately. Some will use their heads as sledgehammers and literally smash an opponent, some will rush or swim toward the threat from a distance, even chasing the opponent onto land or galloping after it. [138] The main weapon in all crocodiles is the bite, which can generate very high bite force. Many species also possess canine-like teeth. These are used primarily for seizing prey, but are also used in fighting and display. [139]

### Shedding and regenerating tails Edit

Geckos, skinks, and other lizards that are captured by the tail will shed part of the tail structure through a process called autotomy and thus be able to flee. The detached tail will continue to wiggle, creating a deceptive sense of continued struggle and distracting the predator's attention from the fleeing prey animal. The detached tails of leopard geckos can wiggle for up to 20 minutes. [140] In many species the tails are of a separate and dramatically more intense color than the rest of the body so as to encourage potential predators to strike for the tail first. In the shingleback skink and some species of geckos, the tail is short and broad and resembles the head, so that the predators may attack it rather than the more vulnerable front part. [141]

Reptiles that are capable of shedding their tails can partially regenerate them over a period of weeks. The new section will however contain cartilage rather than bone, and will never grow to the same length as the original tail. It is often also distinctly discolored compared to the rest of the body and may lack some of the external sculpting features seen in the original tail. [142]

### In cultures and religions Edit

Dinosaurs have been widely depicted in culture since the English palaeontologist Richard Owen coined the name dinosaur in 1842. As soon as 1854, the Crystal Palace Dinosaurs were on display to the public in south London. [143] [144] One dinosaur appeared in literature even earlier, as Charles Dickens placed a Megalosaurus in the first chapter of his novel Bleak House in 1852. [145] The dinosaurs featured in books, films, television programs, artwork, and other media have been used for both education and entertainment. The depictions range from the realistic, as in the television documentaries of the 1990s and first decade of the 21st century, or the fantastic, as in the monster movies of the 1950s and 1960s. [144] [146] [147]

The snake or serpent has played a powerful symbolic role in different cultures. In Egyptian history, the Nile cobra adorned the crown of the pharaoh. It was worshipped as one of the gods and was also used for sinister purposes: murder of an adversary and ritual suicide (Cleopatra). In Greek mythology snakes are associated with deadly antagonists, as a chthonic symbol, roughly translated as earthbound. The nine-headed Lernaean Hydra that Hercules defeated and the three Gorgon sisters are children of Gaia, the earth. Medusa was one of the three Gorgon sisters who Perseus defeated. Medusa is described as a hideous mortal, with snakes instead of hair and the power to turn men to stone with her gaze. After killing her, Perseus gave her head to Athena who fixed it to her shield called the Aegis. The Titans are depicted in art with their legs replaced by bodies of snakes for the same reason: They are children of Gaia, so they are bound to the earth. [148] In Hinduism, snakes are worshipped as gods, with many women pouring milk on snake pits. The cobra is seen on the neck of Shiva, while Vishnu is depicted often as sleeping on a seven-headed snake or within the coils of a serpent. There are temples in India solely for cobras sometimes called Nagraj (King of Snakes), and it is believed that snakes are symbols of fertility. In the annual Hindu festival of Nag Panchami, snakes are venerated and prayed to. [149] In religious terms, the snake and jaguar are arguably the most important animals in ancient Mesoamerica. "In states of ecstasy, lords dance a serpent dance great descending snakes adorn and support buildings from Chichen Itza to Tenochtitlan, and the Nahuatl word coatl meaning serpent or twin, forms part of primary deities such as Mixcoatl, Quetzalcoatl, and Coatlicue." [150] In Christianity and Judaism, a serpent appears in Genesis to tempt Adam and Eve with the forbidden fruit from the Tree of Knowledge of Good and Evil. [151]

The turtle has a prominent position as a symbol of steadfastness and tranquility in religion, mythology, and folklore from around the world. [152] A tortoise's longevity is suggested by its long lifespan and its shell, which was thought to protect it from any foe. [153] In the cosmological myths of several cultures a World Turtle carries the world upon its back or supports the heavens. [154]

### Medicine Edit

Deaths from snakebites are uncommon in many parts of the world, but are still counted in tens of thousands per year in India. [155] Snakebite can be treated with antivenom made from the venom of the snake. To produce antivenom, a mixture of the venoms of different species of snake is injected into the body of a horse in ever-increasing dosages until the horse is immunized. Blood is then extracted the serum is separated, purified and freeze-dried. [156] The cytotoxic effect of snake venom is being researched as a potential treatment for cancers. [157]

Lizards such as the Gila monster produce toxins with medical applications. Gila toxin reduces plasma glucose the substance is now synthesised for use in the anti-diabetes drug exenatide (Byetta). [158] Another toxin from Gila monster saliva has been studied for use as an anti-Alzheimer's drug. [159]

Geckos have also been used as medicine, especially in China. [160] Turtles have been used in Chinese traditional medicine for thousands of years, with every part of the turtle believed to have medical benefits. There is a lack of scientific evidence that would correlate claimed medical benefits to turtle consumption. Growing demand for turtle meat has placed pressure on vulnerable wild populations of turtles. [161]

### Commercial farming Edit

Crocodiles are protected in many parts of the world, and are farmed commercially. Their hides are tanned and used to make leather goods such as shoes and handbags crocodile meat is also considered a delicacy. [162] The most commonly farmed species are the saltwater and Nile crocodiles. Farming has resulted in an increase in the saltwater crocodile population in Australia, as eggs are usually harvested from the wild, so landowners have an incentive to conserve their habitat. Crocodile leather is made into wallets, briefcases, purses, handbags, belts, hats, and shoes. Crocodile oil has been used for various purposes. [163]

Snakes are also farmed, primarily in East and Southeast Asia, and their production has become more intensive in the last decade. Snake farming has been troubling for conservation in the past as it can lead to overexploitation of wild snakes and their natural prey to supply the farms. However, farming snakes can limit the hunting of wild snakes, while reducing the slaughter of higher-order vertebrates like cows. The energy efficiency of snakes is higher than expected for carnivores, due to their ectothermy and low metabolism. Waste protein from the poultry and pig industries is used as feed in snake farms. [164] Snake farms produce meat, snake skin, and antivenom.

Turtle farming is another known but controversial practice. Turtles have been farmed for a variety of reasons, ranging from food to traditional medicine, the pet trade, and scientific conservation. Demand for turtle meat and medicinal products is one of the main threats to turtle conservation in Asia. Though commercial breeding would seem to insulate wild populations, it can stoke the demand for them and increase wild captures. [165] [161] Even the potentially appealing concept of raising turtles at a farm to release into the wild is questioned by some veterinarians who have had some experience with farm operations. They caution that this may introduce into the wild populations infectious diseases that occur on the farm, but have not (yet) been occurring in the wild. [166] [167]

### Reptiles in captivity Edit

In the Western world, some snakes (especially docile species such as the ball python and corn snake) are kept as pets. [168] Numerous species of lizard are kept as pets, including bearded dragons, [169] iguanas, anoles, [170] and geckos (such as the popular leopard gecko and the crested gecko). [169]

Turtles and tortoises are an increasingly popular pet, but keeping them can be challenging due to particular requirements, such as temperature control and a varied diet, as well as the long lifespans of turtles, who can potentially outlive their owners. Good hygiene and significant maintenance is necessary when keeping reptiles, due to the risks of Salmonella and other pathogens. [171]

A herpetarium is a zoological exhibition space for reptiles or amphibians.

## Replication

Both criteria described above require that ‘sympatric’ deme–habitat combinations have higher fitness than the ‘allopatric’ ones. However, demes may be genetically differentiated for reasons other than divergent selection (e.g. drift, migration or history). Combined with genotype × environment interaction, any genetic differentiation among demes will produce some deme × habitat interaction, which may accidentally cause the expected ‘sympatric vs. allopatric’ difference. Therefore, independent of the issues discussed in the preceding section, it is desirable to show that the ‘sympatric vs. allopatric’ difference is unlikely to be explained by deme × test habitat interaction unrelated to local selection. This requires replication at the level of the deme if only two demes are studied, these two interaction terms are impossible to separate. The lack of replication prevents one from concluding that the differentiation is because of divergent selection, rather than chance events in the demes’ history. Of course, with only two demes under study convincing evidence for driving role of divergent selection can still come from a detailed study of natural selection, dispersal, and the pattern of genetic differentiation between the demes (see the following section). Nonetheless, replication at the level of the deme is needed to demonstrate local adaptation on the basis of the fitness pattern alone.

There are two basic ways in which local adaptation studies can be replicated at the level of the deme, depending on whether a priori knowledge or a hypothesis exists about environmental factors relevant for the divergent selection that drives local adaptation.

The first approach (which we refer to as ‘parallel local adaptation’) is to classify the habitats in several (usually two) clearly defined and reproducible types of habitat, based on differences in a factor or factors hypothesized to be relevant for differential selection underlying local adaptation. Examples include normal vs. contaminated soils ( McNeilly 1968 ), ruderal vs. agricultural habitats ( Leiss & Müller-Schärer 2001 ), or different host species ( Via 1991 ). Several replicate demes originating from each habitat type are sampled and tested in each habitat type. These demes could be sampled independently (e.g. Leiss & Müller-Schärer 2001 ), or paired between habitat types based on geographic proximity (e.g. Berglund et al. 2004 ). Most studies in this category involve a common-garden assay in a controlled environment, but some have been done with reciprocal transplant in the field (e.g. Via 1991 ). Because the focus in ‘parallel local adaptation’ is on the specific ecological factors which define habitat types, the main effect of the habitat is treated from the statistical viewpoint as fixed (type I) factors ( Sokal & Rohlf 1981 , section 8.6). In contrast, the demes included in the study will usually be treated as a sample of all demes evolved in the focal habitat types one would usually want to generalize the findings to other demes. This perspective implies that deme should be treated as random (type II) statistical factor ( Sokal & Rohlf 1981 , section 8.7).

The second approach, which we refer to as ‘unique local adaptation’, does not make an assumption about the ecological factor(s) behind divergent selection. Instead, the habitat of each deme is considered unique. Multiple demes can be sampled, and the fitness of each deme tested in its own and at least two other (away) habitats (e.g. Lively 1989 Roy 1998 Kaltz et al. 1999, 1999 ). From the statistical viewpoint, the habitats included in the study are thus a random sample of all habitats, suggesting that both deme and habitat should be treated as a random (type II) factors. Assaying each deme in more than one ‘away’ habitat allows one to split the deme × habitat interaction into a component because of the ‘sympatric vs. allopatric’ contrast, and the residual component not related to local adaptation. This residual deme × test habitat interaction forms the baseline for testing the significance of the ‘sympatric vs. allopatric’ contrast ( Kaltz et al. 1999 Thrall et al. 2002 ).

These two basic approaches –‘parallel’ and ‘unique’ local adaptation – can be modified in several ways. The geographic or spatial distance between the habitat of origin and the test habitat can be incorporated as an explanatory variable (for various designs and statistical approaches see e.g. Ebert 1994 Kaltz et al. 1999 Joshi et al. 2001 Thrall et al. 2002 Belotte et al. 2003 ). Similarly, one can measure an ‘ecological distance’ between habitats along an environmental axis defined by quantitative environmental parameters (e.g. Rice & Mack 1991 Lively & Jokela 1996 ). Finally, one could combine the ‘parallel’ and ‘unique’ approaches in a single design, simultaneously testing for ‘parallel’ local adaptation to a specific environmental factor defining broad habitat types (transplants across habitat types), and for ‘unique’ local adaptation to sites within each habitat type (transplants across sites within each habitat type).

Finally, we would like to reiterate that local adaptation as defined above is not a property of individual populations, but of a set of demes (i.e. a metapopulation). Nonetheless, it may be of interest to identify subsets of demes that do show a pattern of local adaptation vs. those that do not, especially if these subsets can be characterized by specific properties such as history, spatial arrangement, habitat size, spatial isolation, or deme size or age (see below).

## Discussion

We have presented a model to explain the observed universal scaling of phylogenetic trees. We incorporate niche construction as an explicit evolutionary process in the tree growth. By analyzing the Niche Inheritance Model, we make two significant conclusions. First, a large niche construction effect, together with the absorbing boundary, leads to an apparent power-law regime in the tree topology. This is in the same range of A as observed in actual phylogenetic trees (5). The existence of the power-law C ( A ) relation is a critical phenomenon, arising from the scale interference in time due to the singular dependence in the small speciation rate and small niche size limit. We demonstrate this by analyzing the cross-over of C ( A ) from A η at small A to A ⁡ ln ⁡ A at large A, with a r ϵ -dependent threshold, reflecting a singular behavior in the Niche Inheritance Model as r ϵ → 0 . The second conclusion is that the Niche Inheritance Model is also able to recapitulate the scaling of the EAD. The EAD is not quite as sensitive a test of scaling as the topological scaling law for C ( A ) , since the Kingman coalescent and Yule processes both exhibit power-law scale invariance in the EAD. However, quantitatively, the power-law exponents are different from what one sees in nature. In our model, the niche construction effect generates a power-law scaling, and the exponent depends on the construction strength, which reflects the long memory of niche construction through the growth of the phylogenetic tree.

Our model has simple rules for the evolution of the tree. The significance is that there is a local in-time interplay between the speciation rate and niche availability and that this can generate a critical behavior in C ( A ) because of the singularity induced by the cutoff of r ϵ = 0 at negative n. Our model shows that one must search for singular effects if a power-law C ( A ) is to be recovered, just as is the case in the modern theory of critical phenomena. It might come as a surprise that such a simple model is able to recapitulate the otherwise inexplicable finding of a topological scaling law in phylogenetic trees. However, in matters of scaling, it is well established that minimal models suffice to capture the phenomena precisely, because extra layers of realism do not introduce new singularities that can change the scaling predictions (40).

There are several issues that require further investigation. First, we have predicted a scaling form for the cross-over point A T as a function of r ϵ , separating the power law and the A ⁡ ln ⁡ A regions. Actual phylogenetic trees, however, have small sizes, and the cross-over is undetectable. Therefore, we cannot be sure whether or not actual phylogenetic trees follow the critical scaling. Second, the exponent of the power-law behavior in our model is close to, but not exactly equal to, the reported values. We do not yet know if the scaling laws and scaling functions are universal, and, if not, what are the relevant or marginal operators in the branching process that control the scaling laws. The fact that the exponent for the EAD is sensitive to σ n suggests that the absorbing boundary may actually be a marginal variable and not a relevant one. In order to understand this point, a technical renormalization group analysis is required and would be the next step. Third, our model does not capture the decreasing cladogenesis rate that has been reported in actual phylogenetic trees (24, 65, 66). It remains to be examined whether incorporating mechanisms to model the empirical cladogenesis rate reduction would change the scaling and how.

Our results show that niche construction is more than a feedback between evolutionary and ecological processes arising when their timescales are not widely separated. Niche construction not only leads to a perturbation in the evolutionary trajectories of all components of an ecosystem, but also creates an indelible footprint on the evolutionary process that cannot be eliminated, even for very long times. These memory effects manifest themselves through the anomalous scaling laws that characterize observed phylogenetic trees.