The Y chromosome was identified as a sex-determining chromosome byNettie Stevens atBryn Mawr College in 1905 during a study of themealwormTenebrio molitor.Edmund Beecher Wilson independently discovered the same mechanisms the same year, working withHemiptera. Stevens proposed that chromosomes always existed in pairs and that the smaller chromosome (now labelled "Y") was the pair of the X chromosome discovered in 1890 byHermann Henking. She realized that the previous idea ofClarence Erwin McClung, that the X chromosome determines sex, was wrong and thatsex determination is, in fact, due to the presence or absence of the Y chromosome. In the early 1920s,Theophilus Painter determined that X and Y chromosomes determined sex in humans (and other mammals).[4]
The chromosome was given the name "Y" simply to follow on from Henking's "X" alphabetically.[5][6] The idea that the Y chromosome was named after its similarity in appearance to the letter "Y" is mistaken. All chromosomes normally appear as an amorphous blob under the microscope and only take on a well-defined shape duringmitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, duringmitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.[5]: 65–66
Most therian mammals have only one pair of sex chromosomes in each cell. Males have one Y chromosome and oneX chromosome, while females have two X chromosomes. In mammals, the Y chromosome contains a gene,SRY, which triggers embryonic development as a male. The Y chromosomes of humans and other mammals also contain other genes needed for normal sperm production.[citation needed]
Among humans, males with an extra X chromosome haveKlinefelter Syndrome, and males with an extra Y chromosome haveJacob's Syndrome, as the presence of the Y chromosome determines sex.[7] Other conditions include females with three X chromosomes (orTrisomy X), andMonosomy X (orTurner Syndrome), females that are missing the second X chromosome. Other conditions that affect the development of an XY fetus, such as Swyer Syndrome, which is caused by a mutation in genes such as theSRY gene orMAP3K1.[8]
Manyectothermicvertebrates have no sex chromosomes.[9] If these species have different sexes, sex is determined environmentally rather than genetically. For some species, especiallyreptiles, sex depends on the incubation temperature.[10] Some vertebrates arehermaphrodites, though hermaphroditic species are most commonlysequential, meaning the organism switches sex, producing male or femalegametes at different points in its life, but never producing both at the same time. This is opposed tosimultaneous hermaphroditism, where the same organism produces male and female gametes at the same time. Most simultaneous hermaphrodite species are invertebrates, and among vertebrates, simultaneous hermaphroditism has only been discovered in a feworders of fish.[11]
The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes,[12][13] termedautosomes, when an ancestral animal developed an allelic variation (a so-called "sex locus") and simply possessing thisallele caused the organism to be male.[14] The chromosome with this allele became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes that were beneficial for males and harmful to (or had no effect on) females either developed on the Y chromosome or were acquired by the Y chromosome through the process oftranslocation.[15]
Until recently, the X and Y chromosomes in mammals were thought to have diverged around 300 million years ago.[16] However, research published in 2008 analyzing theplatypus genome[17] suggested that the XY sex-determination system would not have been present more than 166 million years ago, whenmonotremes split from other mammals.[18] This re-estimation of the age of thetherian XY system is based on the finding that sequences that are on the X chromosomes ofmarsupials andeutherian mammals are not present on the autosomes of platypus and birds.[18] The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.[19][20]
Most chromosomesrecombine during meiosis. However, in males, the X and Y pair in a shared region known as thepseudoautosomal region (PAR).[21] The PAR undergoes frequent recombination between the X and Y chromosomes,[21] but recombination is suppressed in other regions of the Y chromosome.[14] These regions contain sex-determining and other male-specific genes.[22] Without this suppression, these genes could be lost from the Y chromosome from recombination and cause issues such as infertility.[23]
The lack of recombination across the majority of the Y chromosome makes it a useful tool in studyinghuman evolution, since recombination complicates the mathematical models used to trace ancestries.[24]
By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes over the course of its existence, andlinear extrapolation of this 1,393-gene loss over 300 million years gives a rate of genetic loss of 4.6 genes per million years.[25] Continued loss of genes at this rate would result in a Y chromosome with no functional genes – that is the Y chromosome would lose complete function – within the next 10 million years, or half that time with the current age estimate of 160 million years.[14][26]Comparative genomic analysis reveals that many mammalian species are experiencing a similar loss of function in their heterozygous sex chromosome. Degeneration may simply be the fate of all non-recombining sex chromosomes, due to three common evolutionary forces: highmutation rate, inefficientselection, andgenetic drift.[14]
With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of thehuman genome.[27] However, these changes have been limited to non-coding sequences and comparisons of the human andchimpanzee Y chromosomes (first published in 2005) show that the human Y chromosome has not lost any genes since the divergence of humans and chimpanzees between 6–7 million years ago.[28] Additionally, a scientific report in 2012 stated that only one gene had been lost since humans diverged from therhesus macaque 25 million years ago.[29] These facts provide direct evidence that thelinear extrapolation model is flawed and suggest that the current human Y chromosome is either no longer shrinking or is shrinking at a much slower rate than the 4.6 genes per million years estimated by the linear extrapolation model.[citation needed]
The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively throughsperm, which undergo multiplecell divisions duringgametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of thetestis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater opportunity of mutation than the rest of the genome.[14] The increased mutation opportunity for the Y chromosome is reported by Graves as a factor 4.8.[14] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.[30]
The observation that the Y chromosome experiences littlemeioticrecombination and has an accelerated rate ofmutation and degradative change compared to the rest of thegenome suggests an evolutionary explanation for the adaptive function ofmeiosis with respect to the main body of genetic information. Brandeis[31] proposed that the basic function of meiosis (particularly meiotic recombination) is the conservation of the integrity of the genome, a proposal consistent with the idea that meiosis is an adaptation forrepairing DNA damage.[32]
Without the ability to recombine duringmeiosis, the Y chromosome is unable to expose individualalleles to natural selection. Deleterious alleles are allowed to "hitchhike" with beneficial neighbors, thus propagating maladapted alleles into the next generation. Conversely, advantageous alleles may be selected against if they are surrounded by harmful alleles (background selection). Due to this inability to sort through its gene content, the Y chromosome is particularly prone to the accumulation of"junk" DNA. Massive accumulations of retrotransposable elements are scattered throughout the Y.[14] The random insertion of DNA segments often disrupts encoded gene sequences and renders them nonfunctional. However, the Y chromosome has no way of weeding out these "jumping genes". Without the ability to isolate alleles, selection cannot effectively act upon them.[citation needed]
A clear, quantitative indication of this inefficiency is theentropy rate of the Y chromosome. Whereas all other chromosomes in thehuman genome have entropy rates of 1.5–1.9 bits per nucleotide (compared to the theoretical maximum of exactly 2 for no redundancy), the Y chromosome's entropy rate is only 0.84.[33] From the definition ofentropy rate, the Y chromosome has a much lower information content relative to its overall length, and is more redundant.
Even if a well adapted Y chromosome manages to maintain genetic activity by avoiding mutation accumulation, there is no guarantee it will be passed down to the next generation. The population size of the Y chromosome is inherently limited to 1/4 that of autosomes: diploid organisms contain two copies of autosomal chromosomes while only half the population contains 1 Y chromosome. Thus, genetic drift is an exceptionally strong force acting upon the Y chromosome. Through sheer random assortment, an adult male may never pass on his Y chromosome if he only has female offspring. Thus, although a male may have a well adapted Y chromosome free of excessive mutation, it may never make it into the next gene pool.[14] The repeat random loss of well-adapted Y chromosomes, coupled with the tendency of the Y chromosome to evolve to have more deleterious mutations rather than less for reasons described above, contributes to the species-wide degeneration of Y chromosomes throughMuller's ratchet.[34]
As has been already mentioned, the Y chromosome is unable to recombine duringmeiosis like the other human chromosomes; however, in 2003, researchers fromMIT discovered a process which may slow down the process of degradation.They found that human Y chromosome is able to "recombine" with itself, usingpalindromebase pair sequences.[35] Such a "recombination" is calledgene conversion.
In the case of the Y chromosomes, thepalindromes are notnoncoding DNA; these strings of nucleotides contain functioning genes important for male fertility. Most of the sequence pairs are greater than 99.97% identical. The extensive use of gene conversion may play a role in the ability of the Y chromosome to edit out genetic mistakes and maintain the integrity of the relatively few genes it carries. In other words, since the Y chromosome is single, it has duplicates of its genes on itself instead of having a second, homologous, chromosome. When errors occur, it can use other parts of itself as a template to correct them.[35]
Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes ofchimpanzees,bonobos andgorillas. The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other.[35]
Gene conversion tracts formed duringmeiosis are long, about 2,068 base pairs, and significantly biased towards the fixation of G or C nucleotides (GC biased).[36] Therecombination intermediates preceding gene conversion were found to rarely take the alternate route of crossover recombination.[36] The Y-Y gene conversion rate in humans is about 1.52 x 10−5 conversions/base/year.[37] These gene conversion events may reflect a basic function of meiosis, that of conserving the integrity of the genome.
According to some theories, in the terminal stages of the degeneration of the Y chromosome, other chromosomes may increasingly take over genes and functions formerly associated with it and finally, within the framework of this theory, the Y chromosome disappears entirely, and a new sex-determining system arises.[14][neutrality isdisputed][improper synthesis?]
Several species ofrodent in the sister familiesMuridae andCricetidae have reached a stage where the XY system has been modified,[38][39] in the following ways:
TheTranscaucasian mole vole,Ellobius lutescens, theZaisan mole vole,Ellobius tancrei, and the Japanese spinous country ratsTokudaia osimensis andTokudaia tokunoshimensis, have lost the Y chromosome andSRY entirely.[14][40][41]Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome.[41] Both sexes ofTokudaia spp. andEllobius lutescens have an XO genotype (Turner syndrome),[41] whereas allEllobius tancrei possess an XX genotype.[14] The new sex-determining system(s) for these rodents remains unclear.
Thewood lemmingMyopus schisticolor, theArctic lemming,Dicrostonyx torquatus, and multiple species in the grass mouse genusAkodon have evolved fertile females who possess the genotype generally coding for males, XY, in addition to the ancestral XX female, through a variety of modifications to the X and Y chromosomes.[38][42][43]
In thecreeping vole,Microtus oregoni, the females, with just one X chromosome each, produce X gametes only, and the males, XY, produce Y gametes, or gametes devoid of any sex chromosome, throughnondisjunction.[44]
Outside of the rodents, theblack muntjac,Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes andautosomes.[45]
Modern data cast doubt on the hypothesis that the Y-chromosome will disappear.[16] This conclusion was reached by scientists who studied the Y chromosomes of rhesus monkeys. When genomically comparing the Y chromosome of rhesus monkeys and humans, scientists found very few differences, given that humans and rhesus monkeys diverged 30 million years ago.[46][clarification needed]
Outside of mammals, some organisms have lost the Y chromosome, such as most species of nematodes. However, in order for the complete elimination of Y to occur, it was necessary to develop an alternative way of determining sex (for example, by determining sex by the ratio of the X chromosome to autosomes), and any genes necessary for male function had to be moved to other chromosomes.[16] In the meantime, modern data demonstrate the complex mechanisms of Y chromosome evolution and the fact that the disappearance of the Y chromosome is not guaranteed.
Fisher's principle outlines why almost all species usingsexual reproduction have asex ratio of 1:1.W. D. Hamilton gave the following basic explanation in his 1967 paper on "Extraordinary sex ratios",[47] given the condition that males and females cost equal amounts to produce:
Suppose male births are less common than female.
A newborn male then has better mating prospects than a newborn female, and therefore can expect to have more offspring.
Therefore, parents genetically disposed to produce males tend to have more than average numbers of grandchildren born to them.
Therefore, the genes for male-producing tendencies spread, and male births become more common.
As the 1:1 sex ratio is approached, the advantage associated with producing males dies away.
The same reasoning holds if females are substituted for males throughout. Therefore, 1:1 is the equilibrium ratio.
Many groups of organisms in addition to therian mammals have Y chromosomes, but these Y chromosomes do not share common ancestry with therian Y chromosomes. Such groups include monotremes,Drosophila, some other insects, some fish, some reptiles, and some plants. InDrosophila melanogaster, the Y chromosome does not trigger male development. Instead, sex is determined by the number of X chromosomes. TheD. melanogaster Y chromosome does contain genes necessary for male fertility. So XXYD. melanogaster are female, andD. melanogaster with a single X (X0), are male but sterile. There are some species of Drosophila in which X0 males are both viable and fertile.[citation needed]
Other organisms have mirror image sex chromosomes: where the homogeneous sex is the male, with two Z chromosomes, and the female is the heterogeneous sex with a Z chromosome and a W chromosome.[48] For example, the ZW sex-determination system is found inbirds,snakes, andbutterflies; the females have ZW sex chromosomes, and males have ZZ sex chromosomes.[48][49][50]
There are some species, such as theJapanese rice fish, in which the XY system is still developing and cross over between the X and Y is still possible. Because the male specific region is very small and contains no essential genes, it is even possible to artificially induce XX males and YY females to no ill effect.[51]
Monotremes likeplatypuses possess four or five pairs of XY sex chromosomes, each pair consisting of sex chromosomes with homologous regions. The chromosomes of neighboring pairs are partially homologous, such that a chain is formed duringmitosis.[19] The first X chromosome in the chain is also partially homologous with the last Y chromosome, indicating that profound rearrangements, some adding new pieces from autosomes, have occurred in history.[52][53]: fig. 5
Platypus sex chromosomes have strong sequence similarity with the avianZ chromosome, indicating closehomology,[17] and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination.[18]
This section mayrequirecleanup to meet Wikipedia'squality standards. The specific problem is:Too many subsections. Article might benefit from moving h3 subsections into h2 sections, if we can somehow reconcile the gap between all therians and humans. "Origins and evolution" section has a human focus, but the discussion does include all therians. Relevant discussion may be found on thetalk page. Please helpimprove this section if you can.(October 2021) (Learn how and when to remove this message)
All single-copy Y-linked genes arehemizygous (present on only one chromosome) except in cases ofaneuploidy such asXYY syndrome orXXYY syndrome. Traits that are inherited via the Y chromosome are calledY-linked traits, or holandric traits (fromAncient Greek ὅλοςhólos, "whole" + ἀνδρόςandrós, "male").[58]
At the end of theHuman Genome Project (and after many updates) almost half of the Y chromosome remained un-sequenced even in 2021; a different Y chromosome from the HG002 (GM24385) genome was completely sequenced in January 2022 and is included in the new "complete genome" humanreference genome sequence, CHM13.[56] The completesequencing of a human Y chromosome was shown to contain 62,460,029 base pairs and 41 additionalgenes.[56] This added 30 million base pairs,[56] but it was discovered that the Y chromosome can vary a lot in size between individuals, from 45.2 million to 84.9 million base pairs.[59]
Since almost half of the human Y sequence was unknown before 2022, it could not be screened out as contamination in microbial sequencing projects. As a result, the NCBI RefSeq bacterial genome database mistakenly includes some Y chromosome data.[56]
This articleis missing information about NRY/MSY structure - How there's a huge chunk ofheterochromatin in q, nomenclature of the palindromes andamplicons, TTTY transcripts, etc. Best if we add a figure that mashes together the tops of Colaco 2018 Fig 1 and PMID 12815422 fig 3.. Please expand the article to include this information. Further details may exist on thetalk page.(October 2021)
G-banding ideogram of human Y chromosome in resolution 850 bphs. Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e.g.Ensembl,UCSC Genome Browser).
G-banding patterns of human Y chromosome in three different resolutions (400,[60]550[61] and 850[3]). Band length in this diagram is based on the ideograms from ISCN (2013).[62] This type of ideogram represents actual relative band length observed under a microscope at the different moments during themitotic process.[63]
G-bands of human Y chromosome in resolution 850 bphs[3]
The human Y chromosome is normally unable to recombine with the X chromosome, except for small pieces ofpseudoautosomal regions (PARs) at thetelomeres (which comprise about 5% of the chromosome's length). These regions are relics of ancienthomology between the X and Y chromosomes. The bulk of the Y chromosome, which does not recombine, is called the "NRY", or non-recombining region of the Y chromosome.[68]Single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.
More specifically, PAR1 is at 0.1–2.7 Mb. PAR2 is at 56.9–57.2 Mb. The non-recombining region (NRY) or male-specific region (MSY) sits between. Their sizes is now known perfectly from CHM13: 2.77 Mb and 329.5 kb. Until CHM13 the data in PAR1 and PAR2 was just copied over from X chromosome.[59]
Older gene count estimates of human Y chromosome used only partial sequences. Only the T2T sequence (2023) was able to produce a complete sequence of the human Y chromosome.[56]
In general, the human Y chromosome is extremely gene poor—it is one of the largestgene deserts in the human genome. Disregardingpseudoautosomal genes, genes encoded on the human Y chromosome include:
Genes on the non-recombining portion of the Y chromosome[75]
Second AZF region on arm q. Prone to NAHR [non-allelic homologous recombination] with AZFc. Overlaps with AZFc. Contains three single-copy gene regions and repeats.
Males can lose the Y chromosome in a subset of cells, known asmosaic loss. Mosaic loss is strongly associated with age,[78] and smoking is another important risk factor for mosaic loss.[79]
Mosaic loss may be related to health outcomes, indicating that the Y chromosome plays important roles outside of sex determination.[79][80] Males with a higher percentage ofhematopoieticstem cells lacking the Y chromosome have a higher risk of certaincancers and have a shorter life expectancy.[80] In many cases, a cause and effect relationship between the Y chromosome and health outcomes has not been determined, and some propose loss of the Y chromosome could be a "neutralkaryotype related to normalaging".[81] However, a 2022 study showed that mosaic loss of the Y chromosome causally contributes tofibrosis,heart risks, and mortality.[82]
Further studies are needed to understand how mosaic Y chromosome loss may contribute to other sex differences in health outcomes, such as how male smokers have between 1.5 and 2 times the risk of non-respiratory cancers as female smokers.[83][84] Potential countermeasures identified so far include not smoking orstopping smoking and at least one potential drug that "may help counteract the harmful effects of the chromosome loss" is under investigation.[85][86][better source needed]
Y chromosome microdeletion (YCM) is a family of genetic disorders caused by missing genes in the Y chromosome. Many affected men exhibit no symptoms and lead normal lives. However, YCM is also known to be present in a significant number of men with reduced fertility or reduced sperm count.[citation needed]
This results in the person presenting a femalephenotype (i.e., is born with female-like genitalia) even though that person possesses an XYkaryotype. The lack of the second X results in infertility. In other words, viewed from the opposite direction, the person goes throughdefeminization but fails to completemasculinization.[citation needed]
The cause can be seen as an incomplete Y chromosome: the usual karyotype in these cases is 45X, plus a fragment of Y. This usually results in defective testicular development, such that the infant may or may not have fully formed male genitalia internally or externally. The full range of ambiguity of structure may occur, especially ifmosaicism is present. When the Y fragment is minimal and nonfunctional, the child is usually a girl with the features ofTurner syndrome ormixed gonadal dysgenesis.
Klinefelter syndrome (47, XXY) is not ananeuploidy of the Y chromosome, but a condition of having an extra X chromosome, which usually results in defective postnatal testicular function. The mechanism is not fully understood; it does not seem to be due to direct interference by the extra X with expression of Y genes.[citation needed]
47, XYY syndrome (simply known as XYY syndrome) is caused by the presence of a single extra copy of the Y chromosome in each of a male's cells. 47, XYY males have one X chromosome and two Y chromosomes, for a total of 47 chromosomes per cell. Researchers have found that an extra copy of the Y chromosome is associated with increased stature and an increased incidence of learning problems in some boys and men, but the effects are variable, often minimal, and the vast majority do not know their karyotype.[87]
In 1965 and 1966Patricia Jacobs and colleagues published a chromosome survey of 315 male patients atScotland's only special security hospital for thedevelopmentally disabled,finding a higher than expected number of patients to have an extra Y chromosome.[88] The authors of this study wondered "whether an extra Y chromosome predisposes its carriers to unusually aggressive behaviour", and this conjecture "framed the next fifteen years of research on the human Y chromosome".[89]
Through studies over the next decade, this conjecture was shown to be incorrect: the elevated crime rate of XYY males is due to lower median intelligence and not increased aggression,[90] and increased height was the only characteristic that could be reliably associated with XYY males.[91] The "criminal karyotype" concept is therefore inaccurate.[87]
Greater degrees of Y chromosome polysomy (having more than one extra copy of the Y chromosome in every cell, e.g., XYYY) are considerably more rare. The extra genetic material in these cases can lead to skeletal abnormalities, dental abnormalities, decreased IQ, delayed development, and respiratory issues, but the severity features of these conditions are variable.[92]
XX male syndrome occurs due to agenetic recombination in the formation of the malegametes, causing theSRY portion of the Y chromosome to move to the X chromosome.[93] When such an X chromosome is present in a zygote, male gonads develop because of the SRY gene.[93]
In humangenetic genealogy (the application ofgenetics totraditional genealogy), use of the information contained in the Y chromosome is of particular interest because, unlike other chromosomes, the Y chromosome is passed exclusively from father to son, on the patrilineal line.Mitochondrial DNA, maternally inherited to both sons and daughters, is used in an analogous way to trace the matrilineal line.[citation needed]
Research is currently investigating whether male-pattern neural development is a direct consequence of Y-chromosome-related gene expression or an indirect result of Y-chromosome-relatedandrogenic hormone production.[94]
In 1974, male chromosomes were discovered in fetal cells in the blood circulation of women.[95]
In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal blood stream for as long as 27 years.[96]
A 2004 study at theFred Hutchinson Cancer Research Center, Seattle, investigated the origin of male chromosomes found in the peripheral blood of women who had not had male progeny. A total of 120 subjects (women who had never had sons) were investigated, and it was found that 21% of them had male DNA in their peripheral blood. The subjects were categorised into four groups based on their case histories:[97]
Group A (8%) had had only female progeny.
Patients in Group B (22%) had a history of one or more miscarriages.
Patients Group C (57%) had their pregnancies medically terminated.
Group D (10%) had never been pregnant before.
The study noted that 10% of the women had never been pregnant before, raising the question of where the Y chromosomes in their blood could have come from. The study suggests that possible reasons for occurrence of male chromosome microchimerism could be one of the following:[97]
miscarriages,
pregnancies,
vanished male twin,
possibly from sexual intercourse.
A 2012 study at the same institute has detected cells with the Y chromosome in multiple areas of the brains of deceased women.[98]
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^gpos: Region which is positively stained byG banding, generallyAT-rich and gene poor;gneg: Region which is negatively stained by G banding, generallyCG-rich and gene rich;acenCentromere.var: Variable region;stalk: Stalk.
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