Do males of all sexual species have Y chromosomes?

Do males of all sexual species have Y chromosomes?

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I know for instance some cells are sexual, so, this got me wondering, do the males of all species that have distinct sexes have Y chromosomes?

Very short answer

No, not all males of all sexual species haveYchromosomes. You might want to have a look to the Wikipedia page on sex-determination systems.

Long answer

Diversity among the species that reproduce sexually

Not all species that have sexual reproduction have sexes. Yeasts, for example, have mating types but no sex.

Diversity among the species that have sexes

Sex is determined by both genetic and environmental factors. In some species, genetic factors are more important than environmental factors in other species it is the reverse. Species which sex is mostly determined by the genetics are said to have GSD (Genetic Sex Determination). For example, humans are GSD, as the female isXXand the male isXY. The species where sex is mostly determined by the environment are called ESD (Environmental Sex Determination). For examples, crocodiles are ESD as sex is determined by temperature. It is important to understand however that there is a whole continuum between these two extremes.

Diversity among the species that are GSD

Among the species that are GSD, some have sexual chromosomes some don't. Some have one locus (locus=position on a chromosome) that determines the sex, some have many loci (loci=plural of locus). Humans, for example, have sexual chromosomes (XandY) and have only one locus which determines the sex. This locus is called SRY and it codes for a protein called TDF.

Now you can split GSD with sexual chromosomes into two more categories (it is a bit more complex in reality):XYandZW.XYare those species where the male is heterogametic (XY), while the female is homogametic (XX). InZWsystems, the male is homogametic (ZZ) and the female is heterogametic (ZW). Birds and some plants have ZW systems for example, while mammals (except "basal" mammals) and Drosophila haveXYsystem.

See also the post What determines sex in birds?

Extra Information

Dosage Compensation

In species that have sex chromosomes, there is a difference in the number of copy of genes between the sexes. In eutherian mammals, for example, females have two copies of all the genes on the X chromosomes, while males only have one copy of most of these genes (plus a few Y chromosome genes). The set of methods to deal with this issue is called Dosage Compensation and there is also an impressive diversity dosage compensations.

Comments on this diversity of sexual systems

The diversity in a sex-determination system, dosage compensation and other things related to sex are impressive. It is even more impressive when we look at how many independent origins there are. Below are some other examples.

The Amazon molly (a fish) is a species that have sexual reproduction but there are no males. The females have to seek for sperm in a sister species in order to activate the development of the eggs but the genes of the father from the sister species are not used. (see this article)

There are also hermaphrodites including sequential hermaphrodites (first male, then females or the opposite) in plants and animals. There are also species where populations are made of hermaphrodites and females and others where there are hermaphrodites and males (very uncommon).

In some species, the sex is determined by social factors. In clownfish, the sex is determined by comparing its own size with the size of the other fishers living in the same anemone.

In an ant species (or two species actually), males and females can both reproduce by parthenogenesis (some kind of cloning but with meiosis and cross-over) but they the meet they reproduce together and their offsprings are sterile workers. So males and females are just like two sister species that reproduce sexually to create an army to protect and feed them. See more information in this paper

Here is a nice figure from Bachtrog et al. 2014 that offers an idea of the diversity of sex determination system (thank to @rg225 for pointing out this figure).

Book suggestion

The Evolution of Sex-Determination is a great book that may interest you.

No. There are many sex-determination systems. Mammals and fruitflies use the XX/XY sex-determination system - except for the platypus, which has 10 sex chromosomes.

ZW sex-determination system is used by birds and some reptiles. It's similar but with the male having two of the same chromosome (ZZ) and the female being the heterogametic sex (ZW). There's several other variations, such as X0 (XX for females, X for males, with no Y).

There are also animals with temperature-dependent sex determination and others use reverse their sex.

In the nucleus of each cell, the DNA molecule is packaged into thread-like structures called chromosomes.

Most human cells contain 23 pairs of chromosomes. One set of chromosomes comes from the mother, while the other comes from the father. The twenty third pair is called the sex chromosomes, while the rest of the 22 pairs are called autosomes.

Typically, biologically male individuals have one X and one Y chromosome (XY) while those who are biologically female have two X chromosomes. However, there are exceptions to this rule.

The sex chromosomes determine the sex of offspring. The father can contribute an X or a Y chromosome, while the mother always contributes an X.

The Y chromosome is one-third the size of the X chromosome and contains about 55 genes while the X chromosome has about 900 genes.

In genealogy, the male lineage is often traced using the Y chromosome because it is only passed down from the father.

All individuals carrying a Y chromosome are related through a single XY ancestor who (likely) lived around 300,000 years ago.

The Y chromosome contains a "male-determining gene," the SRY gene, that causes testes to form in the embryo and results in development of external and internal male genitalia. If there is a mutation in the SRY gene, the embryo will develop female genitalia despite having XY chromosomes.

Variation in the number of sex chromosomes in a cell is quite common. Some men have more than two sex chromosomes in all of their cells (the XXY variation is called the Klinefelter syndrome), and many men lose the Y chromosome from their cells as they age. Smoking may exacerbate this loss.

Some genes that were thought to be lost from the Y chromosome have actually relocated to other chromosomes.

Much of the Y chromosome is composed of repeating DNA segments. Specialized techniques are needed sequence and determine the arrangement of these highly similar segments.

Many health conditions are thought to be related to changes in genes expressed on the Y chromosome. This is currently an active area of research.

In the nucleus of each cell, the DNA molecule is packaged into thread-like structures called chromosomes.

Most human cells contain 23 pairs of chromosomes. One set of chromosomes comes from the mother, while the other comes from the father. The twenty third pair is called the sex chromosomes, while the rest of the 22 pairs are called autosomes.

Typically, biologically male individuals have one X and one Y chromosome (XY) while those who are biologically female have two X chromosomes. However, there are exceptions to this rule.

The sex chromosomes determine the sex of offspring. The father can contribute an X or a Y chromosome, while the mother always contributes an X.

The Y chromosome is one-third the size of the X chromosome and contains about 55 genes while the X chromosome has about 900 genes.

In genealogy, the male lineage is often traced using the Y chromosome because it is only passed down from the father.

All individuals carrying a Y chromosome are related through a single XY ancestor who (likely) lived around 300,000 years ago.

The Y chromosome contains a "male-determining gene," the SRY gene, that causes testes to form in the embryo and results in development of external and internal male genitalia. If there is a mutation in the SRY gene, the embryo will develop female genitalia despite having XY chromosomes.

Variation in the number of sex chromosomes in a cell is quite common. Some men have more than two sex chromosomes in all of their cells (the XXY variation is called the Klinefelter syndrome), and many men lose the Y chromosome from their cells as they age. Smoking may exacerbate this loss.

Some genes that were thought to be lost from the Y chromosome have actually relocated to other chromosomes.

Much of the Y chromosome is composed of repeating DNA segments. Specialized techniques are needed sequence and determine the arrangement of these highly similar segments.

Many health conditions are thought to be related to changes in genes expressed on the Y chromosome. This is currently an active area of research.


Monotreme mammals are receiving increasing attention in genomic research, with interests varying from karyotype evolution and gene mapping, to comparative sequencing. This should not come as a surprise, as monotremes (mammalian Subclass Prototheria) occupy a unique branch at the base of the mammalian phylogenetic tree, and serve as an evolutionary outgroup for marsupial and eutherian species (that together comprise Subclass Theria). The time of divergence of Prototheria and Theria is estimated to be in the Early Jurassic (166 million years ago (MYA)), while marsupials and eutherians diverged in the Late Jurassic (148 MYA) [1]. Five extant monotreme species are recognized platypus (Ornithorhynchus anatinus), short-beaked echidna (Tachyglossus aculeatus) and three long-beaked echidnas (Zaglossus bruneiji, Zaglossus attenboroughi, Zaglossus bartoni). Zaglossus bartoni is divided into three subspecies Z. b. smeenki, Z. b. diamondi, and Z. b. clunius [2].

A full karyotype characterization is essential for genomic research in any species. It is particularly important for monotremes because of their exceptional sex chromosome complement. The inclusion of a set of tiny chromosomes was recognized early and thought to be a reptilian feature [3], but this suggestion was later refuted [4]. A surprise was the discovery of several unpaired chromosomes [5]. A final identification and description of the platypus unpaired chromosomes was achieved only recently by our chromosome painting studies [6, 7]. The 21 autosome pairs were assigned by chromosome paints. Ten paints identified ten unpaired mitotic chromosomes as well as the ten members of the meiotic chain and the homologous regions between them. Five paints identified X chromosomes present in single copy in males but two copies in females, and five paints identified Y chromosomes that were present only in males. It was, therefore, concluded that the ten male unpaired chromosomes consisted of five X and five Y sex chromosomes. The ten sex chromosomes form a multivalent chain at meiosis held together by chiasmata within homologous pairing regions. Alternate segregation of these chromosomes into X1X2X3X4X5 and Y1Y2Y3Y4Y5 sperm was proposed and must be very efficient as shown by meiotic analysis of spermatids and sperm using the paint probes [6]. Remarkably, X5 shows some homology with the chicken Z, as demonstrated by its inclusion of the DMRT-1, DMRT-2 and DMRT-3 orthologues [6, 8]. Chicken Z is largely homologous to parts of human chromosomes 5 and 9, with some genes represented on 8 and 18 [9]. A region containing ATRX, RBMX and genes flanking XIST, present on Xq in human and other therians, maps to chromosome 6 in platypus [10], as does SOX3, the gene from which the sex-determining SRY gene evolved (M Wallis, personal communication), and this is consistent with the absence of a platypus homologue of the Y-linked SRY. Other genes involved in the eutherian sex determining pathway have recently been mapped to platypus autosomes, so do not qualify as candidate primary sex determining genes [11]. There is no platypus homologue of the human X-borne XIST in platypus [12] and marsupials [13]. In addition, platypus Ensembl release 44 and separate mapping work (F Veyrunes, personal communication) show an absence of human X-linked orthologues from platypus X- chromosomes, contradicting original localizations using radioactive fluorescent in situ hybridization (FISH) with heterologous cDNA probes [14–18]. It follows that SRY and the therian XY sex determining system have evolved between 166 and 148 MYA after the divergence of monotremes and before the divergence of marsupials, which is being explored further (F Veyrunes, personal communication).

To provide new clues to the organization, function and evolution of the platypus multiple sex chromosomes, we defined the sex chromosomes of the distantly related short-beaked echidna, T. aculeatus, and established the sex chromosome order in the echidna multivalent chain. Our genome-wide comparison using chromosome painting between echidna and platypus (called Tac (for T. aculeatus) and Oan (for O. anatinus) in this report) showed, surprisingly, that one member of the Oan chain is replaced by an autosome in Tac, and the X homologous to Oan X5 occupies a central position in the Tac chain rather than a position at the end as seen in Oan. To investigate the participation of the ancestral avian Z in the evolution of the monotreme sex chromosome system and to map genes to the members of the sex chromosomes, we also localized the platypus homologues of genes on chicken autosomes and Z. We conclude that the ancestral monotreme sex chromosome system bears considerable homology to the sex chromosomes of birds.

Sex, genes, the Y chromosome and the future of men

The human Y chromosome has retained only 3% of its ancestral genes. So why’s it a shadow of its former self? Credit: Rafael Anderson Gonzales Mendoza/Flickr, CC BY-NC-SA

The Y chromosome, that little chain of genes that determines the sex of humans, is not as tough as you might think. In fact, if we look at the Y chromosome over the course of our evolution we've seen it shrink at an alarming rate.

So will it one day completely disappear? And what happens to the human race if it does? It's a topic that's long been debated and we've covered before – but a paper published in Nature this year suggests the degradation of the chromosome has stabilised.

Humans, like other mammals, have what's called "chromosomal sex". Women have two copies of a medium-sized chromosome called X (which stands for "unknown" because it was originally a mystery). Males have a single X and a tiny Y.

The X bears about 1,600 genes with varied functions. But the Y has hardly any genes maybe 50, and only 27 of these are in the male-specific part of the Y. Many are present in multiple copies, most of them inactive, lying in giant loops of DNA. Most of the Y is made of repetitive "junk DNA". Thus the human Y shows all the signs of a degraded chromosome near the end of its life.

But the Y must contain a gene that determines maleness, because XXY people are male, and XO people with a single X but no Y are female.

We know that at 12 weeks an XY human embryo develops testes, which make male hormones and cause a baby to develop as a male. The identity of this male-determining gene on the Y – the SRY gene – was discovered in 1990 by a young Australian postdoc Andrew Sinclair (a PhD graduate from my lab). Babies with mutations in the SRY gene don't develop testes, and develop as females.

Sex in other vertebrates

Leave humans for a moment, and you see a huge variety of sex systems.

Some reptiles, fish and frogs are XX female: XY male like humans, but have different sex genes. Other vertebrates, such as birds and snakes, are just the opposite, with ZZ males and ZW females, and the sex gene is different again.

Many reptiles and some fish use environmental cues (usually temperature) rather than genetic triggers to determine sex.

So we are wrong if we think sex determination in human babies is typical of vertebrates.

Credit: Jenny Graves, Author provided

The degrading human Y

But back in the world of humans: what befell the Y to make it so much smaller than the X and lose most of its genes?

Our sex chromosomes were once just a pair of ordinary chromosomes, which they still are in birds and reptiles. We found they are still ordinary chromosomes even in monotreme mammals (platypuses and echidnas) which last shared a common ancestor with humans 166 million years ago.

This means that within the past 166 million years the human Y lost most of its 1,600-odd genes, a rate of nearly 10 per million years.

At this rate, the Y chromosome will disappear in about 4.5 million years. This back-of-the-envelope calculation, inserted as a throwaway line in a little paper in 2002, produced a hysterical reaction and loads of responses. When I talk about the disappearing Y, men in the audience shrink into their seats to protect their manhood.

But why the surprise? Degradation is typical of all sex chromosome systems. Acquisition of a gene that determines sex is the kiss of death for a chromosome, because other genes nearby on the Y evolve a male-specific function, and these genes are kept together by suppressing exchange with the X.

This means that the Y can't get rid of mutations or deletions or invading junk DNA by swapping good bits with the X.

The poor Y chromosome is also at a disadvantage because it is in the testis every generation. This is a dangerous place to be because cells must divide many times to make sperm, so mutations are much more frequent.

Has the human Y stabilised?

Of course, the loss of genes from the Y is unlikely to be linear. It could get faster as the Y becomes more unstable, or it could stabilize as the Y is stripped to essential genes.

Biologist David Page's group from Boston keenly defend the honour of the human Y, noting that although chimpanzees have lost a few genes since we shared a common ancestor 5 million years ago, humans haven't. In fact, humans have lost very few genes in the 25 million years since we diverged from monkeys.

So has the human Y finally stabilised? Maybe loss of any of the remaining 27 Y genes would compromise the viability, or fertility of the bearer. A 2014 paper from Page's group claiming that the Y is here to stay has unleashed another round of debate, recently aired on US National Public Radio (NPR).

Credit: _marmota/Flickr, CC BY-NC-SA

But looking more widely reveals that even genes on the human Y with important functions (such as making sperm) are missing from the mouse Y, and vice versa.

Most spectacularly, species in two rodent groups have lost their entire Y chromosome. Y genes have been either shunted to other chromosomes, or replaced – we don't know by what. So it must be possible to dispense with the Y and start over again.

If the human Y disappears, will men disappear? If they do, that'll be the end of the human race. We can't become a female-only species (as have some lizards, such as the New Mexico whiptail) because there are at least 30 "imprinted" genes that are active only if they come through the sperm. So we can't reproduce without men.

So does that mean humans will become extinct in 4.5 million years? Not necessarily. The Y-less rodents have evolved a new sex determining gene, so why not humans?

Three species of whiptail: little striped whiptail, ( Cnemidophorus inornatus), New Mexico whiptail (C. neomexicanus) and western whiptail (C. tigris). Credit: Alistair J. Cullum/Wikimedia Commons, CC BY

Perhaps this has already happened in some small isolated population, where genetic accidents are much more likely to take hold. We wouldn't know without screening chromosomes from every human population on the planet.

But a group of humans with new sex determining genes won't easily breed with humans who retain the present XY system. Children of, say, an XX woman and a man with a novel sex gene, are likely to be intersex or at least infertile. Such a reproductive barrier can drive incipient species apart, as happened with Y-less rodents. So if we return to Earth in 4.5 million years, we might find either no humans – or several different hominid species.

In any case, 4.5 million years is a long time. We have been human for less than 100,000 years. And I can think of several ways in which we are likely to become extinct long before we run out of Y chromosome.

This story is published courtesy of The Conversation (under Creative Commons-Attribution/No derivatives).

Genetic Degeneration

Although the extent of genetic degeneration increases with the time a region has been evolving under full sex linkage, theoretical modeling has identified other important factors (reviewed by Bachtrog 2008 ). Degeneration rates may therefore differ greatly between different organisms. Together with the scarcity of quantitative degeneration data and divergence time estimates, this contributes to the seemingly confusing picture mentioned above. Many studies describe depth of coverage ratios in the two sexes, which merely detects regions with degenerated sequences. Few indicate the proportion that are hemizygous in males, and the number of XY gene pairs whose Y copy is a pseudogene, and species with partially degenerated sex-linked regions or strata have been little studied.

Testable predictions are nevertheless available. First, most models predict that degeneration will be faster in sex-linked regions with many genes (although a recent model predicts degenerate of regions with few genes Lenormand et al. 2020 ). Estimates of numbers of “ancestral” genes should allow tests of these ideas. Single-gene systems, and small chromosomes that acquire a sex-determining gene, such as microchromosomes of lizards (Matsubara et al. 2014 ), might be expected to degenerate slowly, and data from such nonmodel species should become available.

Second, degeneration has a nonlinear time-course. Genes are predicted to initially lose functions rapidly by major effect mutations, followed by slower changes, and eventually deletion of sets of genes (Fig. 1). Data from sex-linked regions at all degeneration stages are therefore needed. Plants, which include many species with small or young sex-linked regions, may be less suitable than animals, because selection in the haploid phase, including the pollen of flowering plants, may oppose degeneration (Bergero and Charlesworth 2011 Chibalina and Filatov 2011 Hough et al. 2014 ). However, considerable degeneration has been documented in several plants (see above), so data from plants are still needed.

At all stages of degeneration of a nonrecombining region, the rates also depend on the specific properties of the genes present (e.g., Kramer et al. 2016 Rifkin et al. 2020 Bellott and Page 2021 ). A striking example is the neo-Y of D. busckii, which is more degenerated (with 58% nonfunctional genes) than the larger and older one in D. miranda (only 34% nonfunctional genes), probably because the latter evolved from a “dot” chromosome, whose genes show low selective constraints (Zhou and Bachtrog 2015 ).

The data currently available suggest that most animal strata with Y-X or W-Z Ks values above 20% show essentially complete degeneration of most ancestral genes. With Ks below this value, 50% or more of the ancestral genes present on the X are generally also present as likely functional copies on the Y, consistent with theoretical predictions (Bachtrog 2008 ). However, the Ks level and evolutionary time needed for strata to reach the stage of major gene loss, and for de novo evolution of dosage compensation, remain unclear. Deletions within fully sex-linked regions, contributing to heteromorphism, probably occur only in the late stages of degeneration, as large deletions are generally highly deleterious (Bull 1983 Manna et al. 2012 Bazrgar et al. 2013 ), unless the genes are all under weak selection, or the region has already degenerated and become a “gene desert” (Nóbrega et al. 2004 ).

Y and W Chromosome Assemblies: Approaches and Discoveries

Hundreds of vertebrate genomes have been sequenced and assembled to date. However, most sequencing projects have ignored the sex chromosomes unique to the heterogametic sex - Y and W - that are known as sex-limited chromosomes (SLCs). Indeed, haploid and repetitive Y chromosomes in species with male heterogamety (XY), and W chromosomes in species with female heterogamety (ZW), are difficult to sequence and assemble. Nevertheless, obtaining their sequences is important for understanding the intricacies of vertebrate genome function and evolution. Recent progress has been made towards the adaptation of next-generation sequencing (NGS) techniques to deciphering SLC sequences. We review here currently available methodology and results with regard to SLC sequencing and assembly. We focus on vertebrates, but bring in some examples from other taxa.

Keywords: W chromosome Y chromosome assembly heterogamety sex chromosomes sex determination.

A Long Time Ago, in a Gamete Far, Far Away.

Life on our planet began with single-cell organisms such as bacteria that reproduce asexually. There isn’t a mother and a father. A cell simply reproduces its genetic material and divides into two or more cells that are genetically identical to the parent cell.

About three or four billion years ago, these single-cell organisms without a distinct nucleus (prokaryotes, or bacteria) began exchanging genetic information in a limited fashion. Then about two billion years ago, organisms such as yeast, with distinct cellular nuclei and specialized structures called organelles (eukaryotes), put their genes in pairs so that they could be divided into two structurally identical gametes (one-cell reproductive units called spores in the case of yeast) and reassembled to create a new organism. This special kind of cell division is called meiosis.

Around 600 million years ago, animals began to evolve specialized gametes — structurally different single-cell units for females (eggs) and males (sperm). Sperm cells fertilize an egg, which then combines the genes of both parents. But such animals, including modern-day turtles, had no specialized sex chromosomes that determine the sex of the offspring. Males and females were genetically identical, and the sex was determined by the temperature at which the egg is incubated.

And finally, starting about 300 million years ago, our ancestors began to evolve sex chromosomes.

In humans, there are 23 pairs of chromosomes, which are structures found within the nucleus of every cell containing the tightly packed molecules known as deoxyribonucleic acid (DNA), the material that carries the genetic code.

One pair of the 23 chromosomes, known as sex chromosomes, determines at conception whether a fertilized egg will develop into a male or female. Today, human females have one pair of identical X chromosomes. Human males, instead of a matched pair, have one X and one smaller Y chromosome.

A human egg contains only an X chromosome. A human sperm contains either an X or a Y chromosome, thereby determining the sex of the offspring after fertilization. XX = female. XY = male.

Dr. Page and his colleagues have spent the better part of the last two decades reconstructing the evolutionary origins of the human X and Y chromosomes. They have traced the origins of these sex chromosomes to ordinary chromosomes called autosomes in evolutionary ancestors that humans share with birds.

“We have been distracted and deceived for the last 50 years by the existence of our sex chromosomes,” Page said. “Most genes that are actually involved in making the different anatomies of human males and females are not on the sex chromosomes. Most of them are on the autosomes. They are exactly the same in males and females. It’s just that the autosomes are read differently in males and females because of the sex chromosomes, just as the entirety of the genome is read differently in males and females.”


Charlesworth B. Sex determination: primitive Y chromosomes in fish. Curr Biol. 200414(18):R745–7.

Le Page Y, Diotel N, Vaillant C, Pellegrini E, Anglade I, Merot Y, Kah O. Aromatase, brain sexualization and plasticity: the fish paradigm. Eur J Neurosci. 201032(12):2105–15.

Sinclair AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, Smith MJ, Foster JW, Frischauf AM, Lovellbadge R, Goodfellow PN. A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature. 1990346(6281):240–4.

Smith CA, Roeszler KN, Ohnesorg T, Cummins DM, Farlie PG, Doran TJ, Sinclair AH. The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature. 2009461(7261):267–71.

Mank JE, Avise JC: Evolutionary diversity and turn-over of sex determination in teleost fishes. Sex Dev 2009, 3(2-3):60-67

Kottler VA, Schartl M. The colorful sex chromosomes of teleost fish. Genes (Basel). 20189(5):233.

Mank JE, Promislow DEL, Avise JC. Evolution of alternative sex-determining mechanisms in teleost fishes. Biol J Linn Soc. 200687(1):83–93.

Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, Kobayashi T, Morrey CE, Shibata N, Asakawa S, Shimizu N, et al. DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature. 2002417(6888):559–63.

Matsuda M, Nagahama Y, Kobayashi T, Matsuda C, Hamaguchi S, Sakaizumi M. The sex determining gene of medaka: a Y-specific DM domain gene (DMY) is required for male development. Fish Physiol Biochem. 200328(1–4):135–9.

Shibata Y, Paul-Prasanth B, Suzuki A, Usami T, Nakamoto M, Matsuda M, Nagahama Y. Expression of gonadal soma derived factor (GSDF) is spatially and temporally correlated with early testicular differentiation in medaka. Gene Expr Patterns. 201010(6):283–9.

Yano A, Guyomard R, Nicol B, Jouanno E, Quillet E, Klopp C, Cabau C, Bouchez O, Fostier A, Guiguen Y. An immune-related gene evolved into the master sex-determining gene in rainbow trout, Oncorhynchus mykiss. Curr Biol. 201222(15):1423–8.

Hattori RS, Murai Y, Oura M, Masuda S, Majhi SK, Sakamoto T, Fernandino JI, Somoza GM, Yokota M, Strussmann CA. A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination. Proc Natl Acad Sci U S A. 2012109(8):2955–9.

Kamiya T, Kai W, Tasumi S, Oka A, Matsunaga T, Mizuno N, Fujita M, Suetake H, Suzuki S, Hosoya S, et al. A trans-species missense SNP in Amhr2 is associated with sex determination in the tiger pufferfish, Takifugu rubripes (Fugu). PLoS Genet. 20128(7): e1002798.

Chen SL, Zhang GJ, Shao CW, Huang QF, Liu G, Zhang P, Song WT, An N, Chalopin D, Volff JN, et al. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet. 201446(3):253.

Cui Z, Liu Y, Wang W, Wang Q, Zhang N, Lin F, Wang N, Shao C, Dong Z, Li Y, et al. Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis). Sci Rep. 20177:42213.

Graves JA, Wakefield MJ, Toder R. The origin and evolution of the pseudoautosomal regions of human sex chromosomes. Hum Mol Genet. 19987(13):1991–6.

Bachtrog D. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet. 201314(2):113–24.

Zeng Q, Fu Q, Li Y, Waldbieser G, Bosworth B, Liu S, Yang Y, Bao L, Yuan Z, Li N, et al. Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Sci Rep. 20177:40347.

Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun. 20167:11757.

Li Y, Liu S, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann RG, Dunham R, Liu Z. Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish. DNA Res. 201522(1):39–52.

Simmons M, Mickett K, Kucuktas H, Li P, Dunham R, Liu ZJ. Comparison of domestic and wild channel catfish (Ictalurus punctatus) populations provides no evidence for genetic impact. Aquaculture. 2006252(2–4):133–46.

Liu S, Sun L, Li Y, Sun F, Jiang Y, Zhang Y, Zhang J, Feng J, Kaltenboeck L, Kucuktas H, et al. Development of the catfish 250K SNP array for genome-wide association studies. BMC Res Notes. 20147:135.

Tiersch TR, Simco BA, Davis KB, Chandler RW, Wachtel SS, Carmichael GJ. Stability of genome size among stocks of the channel catfish. Aquaculture. 199087(1):15–22.

Sun FY, Liu SK, Gao XY, Jiang YL, Perera D, Wang XL, Li C, Sun LY, Zhang JR, Kaltenboeck L, et al. Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome. PLoS One. 20138(7):e68452.

Patino R, Davis KB, Schoore JE, Uguz C, Strussmann CA, Parker NC, Simco BA, Goudie CA. Sex differentiation of channel catfish gonads: normal development and effects of temperature. J Exp Zool. 1996276(3):209–18.

Ninwichian P, Peatman E, Perera D, Liu S, Kucuktas H, Dunham R, Liu Z. Identification of a sex-linked marker for channel catfish. Anim Genet. 201243(4):476–7.

Graves JAM, Peichel CL. Are homologies in vertebrate sex determination due to shared ancestry or to limited options? Genome Biol. 201011(4):205.

Devlin RH, Nagahama Y. Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture. 2002208(3–4):191–364.

Diaz N, Piferrer F. Lasting effects of early exposure to temperature on the gonadal transcriptome at the time of sex differentiation in the European sea bass, a fish with mixed genetic and environmental sex determination. BMC Genomics. 201516:679.

Cabodi S, Moro L, Baj G, Smeriglio M, Di Stefano P, Gippone S, Surico N, Silengo L, Turco E, Tarone G, et al. p130Cas interacts with estrogen receptor alpha and modulates non-genomic estrogen signaling in breast cancer cells. J Cell Sci. 2004117(Pt 8):1603–11.

Martinez P, Bouza C, Hermida M, Fernandez J, Toro MA, Vera M, Pardo B, Millan A, Fernandez C, Vilas R, et al. Identification of the major sex-determining region of turbot (Scophthalmus maximus). Genetics. 2009183(4):1443–52.

Liao X, Xu G, Chen SL: Molecular method for sex identification of half-smooth tongue sole (Cynoglossus semilaevis) using a novel sex-linked microsatellite marker. Int J Mol Sci 2014, 15(7):12952-12958.

Foster JW, Brennan FE, Hampikian GK, Goodfellow PN, Sinclair AH, Lovell-Badge R, Selwood L, Renfree MB, Cooper DW, Graves JA. Evolution of sex determination and the Y chromosome: SRY-related sequences in marsupials. Nature. 1992359(6395):531–3.

Crews D, Bergeron JM, McLachlan JA. The role of estrogen in turtle sex determination and the effect of PCBs. Environ Health Perspect. 1995103 Suppl 7:73–7.

Morais da Silva S, Hacker A, Harley V, Goodfellow P, Swain A, Lovell-Badge R. Sox9 expression during gonadal development implies a conserved role for the gene in testis differentiation in mammals and birds. Nat Genet. 199614(1):62–8.

Kondo M, Hornung U, Nanda I, Imai S, Sasaki T, Shimizu A, Asakawa S, Hori H, Schmid M, Shimizu N, et al. Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka. Genome Res. 200616(7):815–26.

Kikuchi K, Hamaguchi S. Novel sex-determining genes in fish and sex chromosome evolution. Dev Dyn. 2013242(4):339–53.

Shao C, Li Q, Chen S, Zhang P, Lian J, Hu Q, Sun B, Jin L, Liu S, Wang Z, et al. Epigenetic modification and inheritance in sexual reversal of fish. Genome Res. 201424(4):604–15.

Karmin M, Saag L, Vicente M, Wilson Sayres MA, Jarve M, Talas UG, Rootsi S, Ilumae AM, Magi R, Mitt M, et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 201525(4):459–66.

Small CM, Bassham S, Catchen J, Amores A, Fuiten AM, Brown RS, Jones AG, Cresko WA. The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol. 201617(1):258.

Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 201011(9):403.

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003423(6942):825–37.

Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, et al. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature. 2010463(7280):536–9.

Hughes JF, Skaletsky H, Page DC. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (deleted in AZoospermia) genes. Bioessays. 201234(12):1035–44.

Soh YQ, Alfoldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, et al. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell. 2014159(4):800–13.

Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, et al. The pig X and Y chromosomes: structure, sequence, and evolution. Genome Res. 201626(1):130–9.

Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, et al. A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y. Genome Res. 201626(4):530–40.

Nanda I, Kondo M, Hornung U, Asakawa S, Winkler C, Shimizu A, Shan ZH, Haaf T, Shimizu N, Shima A, et al. A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc Natl Acad Sci U S A. 200299(18):11778–83.

Myosho T, Otake H, Masuyama H, Matsuda M, Kuroki Y, Fujiyama A, Naruse K, Hamaguchi S, Sakaizumi M. Tracing the emergence of a novel sex-determining gene in medaka, Oryzias luzonensis. Genetics. 2012191(1):163.

Takehana Y, Matsuda M, Myosho T, Suster ML, Kawakami K, Shin IT, Kohara Y, Kuroki Y, Toyoda A, Fujiyama A, et al. Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena. Nat Commun. 20145:4157.

Graves JA. How to evolve new vertebrate sex determining genes. Dev Dyn. 2013242(4):354–9.

Edwards TM, Moore BC, Guillette LJ Jr. Reproductive dysgenesis in wildlife: a comparative view. Int J Androl. 200629(1):109–21.

Matthiessen P, Sumpter JP. Effects of estrogenic substances in the aquatic environment. Exs. 199886:319–35.

Crews D, Bergeron JM. Role of reductase and aromatase in sex determination in the red-eared slider (Trachemys scripta), a turtle with temperature-dependent sex determination. J Endocrinol. 1994143(2):279–89.

Wibbels T, Crews D. Putative aromatase inhibitor induces male sex determination in a female unisexual lizard and in a turtle with temperature-dependent sex determination. J Endocrinol. 1994141(2):295–9.

Chardard D, Dournon C. Sex reversal by aromatase inhibitor treatment in the newt Pleurodeles waltl. J Exp Zool. 1999283(1):43–50.

Olmstead AW, Kosian PA, Korte JJ, Holcombe GW, Woodis KK, Degitz SJ. Sex reversal of the amphibian, Xenopus tropicalis, following larval exposure to an aromatase inhibitor. Aquat Toxicol. 200991(2):143–50.

Pieau C, Dorizzi M. Oestrogens and temperature-dependent sex determination in reptiles: all is in the gonads. J Endocrinol. 2004181(3):367–77.

Barske LA, Capel B. Estrogen represses SOX9 during sex determination in the red-eared slider turtle Trachemys scripta. Dev Biol. 2010341(1):305–14.

Shupnik MA. Crosstalk between steroid receptors and the c-Src-receptor tyrosine kinase pathways: implications for cell proliferation. Oncogene. 200423:7979.

Waldbieser GC, Wolters WR. SHORT COMMUNICATION: definition of the USDA103 strain of channel catfish (Ictalurus punctatus). Anim Genet. 200738(2):180–3.

Cheryl A, Goudie BDR, Simco BA, Davis KB. Feminization of channel catfish by oral administration of steroid sex hormones. Trans Am Fish Soc. 1983112(5):3.

Waldbieser GC, Bosworth BG. A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish, Ictalurus punctatus. Anim Genet. 201344(4):476–9.

Dunham RA, Lambert DM, Argue BJ, Ligeon C, Yant DR, Liu ZJ. Comparison of manual stripping and pen spawning for production of channel catfish × blue catfish hybrids and aquarium spawning of channel catfish. N Am J Aquac. 200062(4):260–5.

Su BF, Perera DA, Zohar Y, Abraham E, Stubblefield J, Fobes M, Beam R, Argue B, Ligeon C, Padi J, et al. Relative effectiveness of carp pituitary extract, luteininzing hormone releasing hormone analog (LHRHa) injections and LHRHa implants for producing hybrid catfish fry. Aquaculture. 2013372:133–6.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 201727(5):722–36.

Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 201632(14):2103–10.

Vaser R, Sovic I, Nagarajan N, Sikic M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 201727(5):737–46.

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 201310(6):563.

Tamazian G, Dobrynin P, Krasheninnikova K, Komissarov A, Koepfli KP, O'Brien SJ. Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences. GigaScience. 20165(1):38.

Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 201531(19):3210–2.

Broman KW, Wu H, Sen S, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 200319(7):889–90.

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 200919(9):1639–45.

Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 200432(Web Server issue):W309–12.

Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 200723(9):1061–7.

Wang Y, Li J, Paterson AH. MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics. 201329(11):1458–60.

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 20045(2):R12.

Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 200622(13):1658–9.

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 20129(4):357–9.

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 201112:323.

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 201026(1):139–40.

Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 201011(3):R25.

Xu Z, Chen J, Li X, Ge J, Pan J, Xu X. Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology. PLoS One. 20138(1):e54174.

Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell. 2006126(6):1203–17.

Y Chromosome Is More Than a Sex Switch

The small, stumpy Y chromosome—possessed by male mammals but not females, and often shrugged off as doing little more than determining the sex of a developing fetus—may impact human biology in a big way. Two independent studies have concluded that the sex chromosome, which shrank millions of years ago, retains the handful of genes that it does not by chance, but because they are key to our survival. The findings may also explain differences in disease susceptibility between men and women.

“The old textbook description says that once maleness is determined by a few Y chromosome genes and you have gonads, all other sex differences stem from there,” says geneticist Andrew Clark of Cornell University, who was not involved in either study. “These papers open up the door to a much richer and more complex way to think about the Y chromosome.”

The sex chromosomes of mammals have evolved over millions of years, originating from two identical chromosomes. Now, males possess one X and one Y chromosome and females have two Xs. The presence or absence of the Y chromosome is what determines sex—the Y chromosome contains several genes key to testes formation. But while the X chromosome has remained large throughout evolution, with about 2000 genes, the Y chromosome lost most of its genetic material early in its evolution it now retains less than 100 of those original genes. That’s led some scientists to hypothesize that the chromosome is largely indispensable and could shrink away entirely.

To determine which Y chromosome genes are shared across species, Daniel Winston Bellott, a biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, and colleagues compared the Y chromosomes of eight mammals, including humans, chimpanzees, monkeys, mice, rats, bulls, and opossums. The overlap, they found, wasn’t just in those genes known to determine the sex of an embryo. Eighteen diverse genes stood out as being highly similar between the species. The genes had broad functions including controlling the expression of genes in many other areas of the genome. The fact that all the species have retained these genes, despite massive changes to the overall Y chromosome, hints that they’re vital to mammalian survival.

“The thing that really came home to us was that these ancestral Y chromosome genes—these real survivors of millions of years of evolution—are regulators of lots of different processes,” Bellott says.

Bellott and his colleagues looked closer at the properties of the ancestral Y chromosome genes and found that the majority of them were dosage-dependent—that is, they required two copies of the gene to function. (For many genes on the sex chromosomes, only one copy is needed in females, the copy on the second X chromosome is turned off and in males, the gene is missing altogether.) But with these genes, the female has one on each X chromosome and the male has a copy on both the X and Y chromosomes. Thus, despite the disappearance of nearby genes, these genes have persisted on the Y chromosome, the team reports online today in Nature.

“The Y chromosome doesn’t just say you’re a male it doesn’t just say you’re a male and you’re fertile. It says that you’re a male, you’re fertile, and you’re going to survive,” Bellott explains. His group next plans to look in more detail at what the ancestral Y chromosome genes do, where they’re expressed in the body, and which are required for an organism’s survival.

In a second Nature paper, also published online today, another group of researchers used a different genetic sequencing approach, and a different set of mammals, to ask similar questions about the evolution of the Y chromosome. Like Bellott’s paper, the second study concluded that one reason that the Y chromosome has remained stable over recent history is the dosage dependence of the remaining genes.

“Knowing now that the Y chromosome can have effects all over the genome, I think it becomes even more important to look at its implications on diseases,” Clark says. “The chromosome is clearly much more than a single trigger that determines maleness.” Because genes on the Y chromosome often vary slightly in sequence—and even function—from the corresponding genes on the X, males could have slightly different patterns of gene expression throughout the body compared with females, due to not only their hormone levels, but also their entire Y chromosome. These gene expression variances could explain the differences in disease risks, or disease symptoms, between males and females, Clark says.

Snake Sex Determination Dogma Overturned

Abby Olena
Jul 6, 2017

Boa imperator and Python bivittatus TONY GAMBLE For more than 50 years, scientists have taken for granted that all snakes share a ZW sex determination system, in which males have two Z chromosomes and females have one Z and one W. But a study, published today (July 6) in Current Biology, reveals that the Central American boa (Boa imperator) and the Burmese python (Python bivittatus) use an XY sex determination system, which evolved independently in the two species.

&ldquoThis work is a culmination of a lot of questions that we&rsquove had about pythons and boas for a long time,&rdquo says Jenny Marshall Graves, a geneticist at La Trobe Univeristy in Melbourne, Australia, who did not participate in the study.

Some of these questions came up for Warren Booth, a geneticist and ecologist at the University of Tulsa, as he studied parthenogenesis&mdashthe growth and.

Booth contacted Tony Gamble, a geneticist at Marquette University in Milwaukee, Wisconsin, who studies sex chromosomes, to begin a collaboration to investigate whether boas and pythons might actually have X and Y chromosomes. Spurred by Booth’s questions, “I went back and reread some of the early papers” on snake sex chromosomes, says Gamble. “What became clear is that they didn’t show that boas and pythons had a ZW sex chromosome system. They just said it without any evidence.”

Historically, scientists used light microscopy to photograph and match up homologous chromosomes. “If you find an unmatched pair—two chromosomes that are morphologically different—in males, you have an XY sex chromosome system. If you find an unmatched pair in females, you have a ZW system,” says Gamble. “But the problem is that a large number of species don’t have sex chromosomes that are morphologically distinct from each other.”

In order to address this problem, Booth, Gamble, and colleagues digested the genomes of male and female boas, pythons, and Western diamondback rattlesnakes (Crotalus atrox), which are known to use a ZW sex determination system, with restriction enzymes to create fragments just hundreds of base pairs long. They sequenced the fragments, and then used a computer program to identify sex-specific genetic markers.

In a ZW system, where females have both a Z and a W, sex-specific markers will be found in larger numbers in females because they are likely found on the W chromosome, which males don’t have. In an XY system, where males have both an X and a Y, these sex-specific genetic markers will be found in males because they are likely Y-specific. As expected, the authors identified more markers in sequencing data from rattlesnake females than males. But they also found an excess of sex-specific genetic markers in male boa and python sequences, which suggested that these snakes have XY sex determination.

See “Lizard Swaps Mode of Deciding Its Sex”

The researchers validated the presence of some of the sex-specific markers using PCR, and then mapped them to boa and python genome data to confirm which chromosomes were the sex chromosomes. The team also used the boa and python genomes “to show that, while they both have XY systems, they have actually evolved those XYs independently on different chromosomes,” says Gamble.

The identification of the boa and python sex chromosomes “might be quite a big breakthrough to our understanding of sex determination in snakes,” says Graves. “Old fashioned genetic linkage studies will show us where the sex-linked gene is, and we know enough genomics now to be able to figure out what genes are in that patch of chromosome and ask, are any of them good candidates for sex determination?”

The authors “found that the python species has different sex chromosomes than boas, but there are many lineages between them,” says Lukáš Kratochvíl, an evolutionary biologist at Charles University in Prague, Czech Republic, who did not participate in the work. Investigating the sex chromosomes of these in-between snake lineages could provide insight into the evolution and stability of sex chromosomes in other animals, he adds.

Gamble agrees that the next step is exploring other species’ sex chromosome systems, but, for him, a bigger question also arises from this work. “There’s way more going on in snakes than anyone ever thought,” he says. “It was there for anyone to see, and so many scientists—including myself—failed to really look critically at this older literature. One has to wonder how frequently we do this. What other long-held assumptions do I take for granted as factual that could actually not have any empirical evidence behind them?”


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