Y chromosome

The Y chromosome is one of two sex chromosomes (allosomes) in mammals, including humans, and many other animals. The other is the X chromosome. Y is the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY, which triggers testis development. The DNA in the human Y chromosome is composed of about 59 million base pairs.[5] The Y chromosome is passed only from father to son. With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome.[6] To date, over 200 Y-linked genes have been identified.[7] All Y-linked genes are expressed and (apart from duplicated genes) hemizygous (present on only one chromosome) except in the cases of aneuploidy such as XYY syndrome or XXYY syndrome.

Human Y chromosome
Human male karyotpe high resolution - Y chromosome cropped.png
Human Y chromosome (after G-banding)
Human male karyotpe high resolution - Chromosome Y
Y chromosome in human male karyogram
Features
Length (bp)57,227,415 bp
(GRCh38)[1]
No. of genes63 (CCDS)[2]
TypeAllosome
Centromere positionAcrocentric[3]
(10.4 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome Y
EntrezChromosome Y
NCBIChromosome Y
UCSCChromosome Y
Full DNA sequences
RefSeqNC_000024 (FASTA)
GenBankCM000686 (FASTA)

Overview

Discovery

The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens at Bryn Mawr College in 1905 during a study of the mealworm Tenebrio molitor. Edmund Beecher Wilson independently discovered the same mechanisms the same year. Stevens proposed that chromosomes always existed in pairs and that the Y chromosome was the pair of the X chromosome discovered in 1890 by Hermann Henking. She realized that the previous idea of Clarence Erwin McClung, that the X chromosome determines sex, was wrong and that sex determination is, in fact, due to the presence or absence of the Y chromosome. Stevens named the chromosome "Y" simply to follow on from Henking's "X" alphabetically.[8][9]

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 during mitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.[10]

Variations

Most therian mammals have only one pair of sex chromosomes in each cell. Males have one Y chromosome and one X 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.

There are exceptions, however. For example, the platypus relies on an XY sex-determination system based on five pairs of chromosomes.[11] Platypus sex chromosomes have strong sequence similarity with the avian Z chromosome, (indicating close homology),[12] and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination.[13] Among humans, some men have two Xs and a Y ("XXY", see Klinefelter syndrome), or one X and two Ys (see XYY syndrome), and some women have three Xs or a single X instead of a double X ("X0", see Turner syndrome). There are other exceptions in which SRY is damaged (leading to an XY female), or copied to the X (leading to an XX male).

Origins and evolution

Before Y chromosome

Many ectothermic vertebrates have no sex chromosomes. If they have different sexes, sex is determined environmentally rather than genetically. For some of them, especially reptiles, sex depends on the incubation temperature; others are hermaphroditic (meaning they contain both male and female gametes in the same individual).

Origin

The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes,[14][15] termed autosomes, when an ancestral animal developed an allelic variation, a so-called "sex locus" – simply possessing this allele caused the organism to be male.[16] 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 through the process of translocation.[17]

Until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago.[18] However, research published in 2010,[19] and particularly research published in 2008 documenting the sequencing of the platypus genome,[12] has suggested that the XY sex-determination system would not have been present more than 166 million years ago, at the split of the monotremes from other mammals.[13] This re-estimation of the age of the therian XY system is based on the finding that sequences that are on the X chromosomes of marsupials and eutherian mammals are present on the autosomes of platypus and birds.[13] The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.[11][20]

Recombination inhibition

Recombination between the X and Y chromosomes proved harmful—it resulted in males without necessary genes formerly found on the Y chromosome, and females with unnecessary or even harmful genes previously only found on the Y chromosome. As a result, genes beneficial to males accumulated near the sex-determining genes, and recombination in this region was suppressed in order to preserve this male specific region.[16] Over time, the Y chromosome changed in such a way as to inhibit the areas around the sex determining genes from recombining at all with the X chromosome. As a result of this process, 95% of the human Y chromosome is unable to recombine. Only the tips of the Y and X chromosomes recombine. The tips of the Y chromosome that could recombine with the X chromosome are referred to as the pseudoautosomal region. The rest of the Y chromosome is passed on to the next generation intact, allowing for its use in tracking human evolution.

Degeneration

By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes over the course of its existence, and linear extrapolation of this 1,393-gene loss over 300 million years gives a rate of genetic loss of 4.6 genes per million years.[21] Continued loss of genes at the rate of 4.6 genes per million years 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.[16][22] 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: high mutation rate, inefficient selection, and genetic drift.[16]

However, comparisons of the human and chimpanzee 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,[23] and a scientific report in 2012 stated that only one gene had been lost since humans diverged from the rhesus macaque 25 million years ago.[24] These facts provide direct evidence that the linear 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.

High mutation rate

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 through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater risk of mutation than the rest of the genome.[16] The increased mutation risk for the Y chromosome is reported by Graves as a factor 4.8.[16] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.[25]

The observation that the Y chromosome experiences little meiotic recombination and has an accelerated rate of mutation and degradative change compared to the rest of the genome suggests an evolutionary explanation for the adaptive function of meiosis with respect to the main body of genetic information. Brandeis[26] 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 for repairing DNA damage.[27]

Inefficient selection

Without the ability to recombine during meiosis, the Y chromosome is unable to expose individual alleles to natural selection. Deleterious alleles are allowed to "hitchhike" with beneficial neighbors, thus propagating maladapted alleles in to 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.[16] 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.

A clear, quantitative indication of this inefficiency is the entropy rate of the Y chromosome. Whereas all other chromosomes in the human 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.[28] This means the Y chromosome has a much lower information content relative to its overall length; it is more redundant.

Genetic drift

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 in to the next gene pool.[16] 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 through Muller's ratchet.[29]

Gene conversion

As it has been already mentioned, the Y chromosome is unable to recombine during meiosis like the other human chromosomes; however, in 2003, researchers from MIT discovered a process which may slow down the process of degradation. They found that human Y chromosome is able to "recombine" with itself, using palindrome base pair sequences.[30] Such a "recombination" is called gene conversion.

In the case of the Y chromosomes, the palindromes are not noncoding DNA; these strings of bases 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.

Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes of chimpanzees, bonobos and gorillas. 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.

Future evolution

In the terminal stages of the degeneration of the Y chromosome, other chromosomes increasingly take over genes and functions formerly associated with it. Finally, the Y chromosome disappears entirely, and a new sex-determining system arises.[16] Several species of rodent in the sister families Muridae and Cricetidae have reached these stages,[31][32] in the following ways:

  • The Transcaucasian mole vole, Ellobius lutescens, the Zaisan mole vole, Ellobius tancrei, and the Japanese spinous country rats Tokudaia osimensis and Tokudaia tokunoshimensis, have lost the Y chromosome and SRY entirely.[16][33][34] Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome.[34] Both sexes of Tokudaia spp. and Ellobius lutescens have an XO genotype (Turner syndrome),[34] whereas all Ellobius tancrei possess an XX genotype.[16] The new sex-determining system(s) for these rodents remains unclear.
  • The wood lemming Myopus schisticolor, the Arctic lemming, Dicrostonyx torquatus, and multiple species in the grass mouse genus Akodon 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.[31][35][36]
  • In the creeping 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, through nondisjunction.[37]

Outside of the rodents, the black muntjac, Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and autosomes.[38]

1:1 sex ratio

Fisher's principle outlines why almost all species using sexual reproduction have a sex ratio of 1:1. W. D. Hamilton gave the following basic explanation in his 1967 paper on "Extraordinary sex ratios",[39] given the condition that males and females cost equal amounts to produce:

  1. Suppose male births are less common than female.
  2. A newborn male then has better mating prospects than a newborn female, and therefore can expect to have more offspring.
  3. Therefore, parents genetically disposed to produce males tend to have more than average numbers of grandchildren born to them.
  4. Therefore, the genes for male-producing tendencies spread, and male births become more common.
  5. As the 1:1 sex ratio is approached, the advantage associated with producing males dies away.
  6. The same reasoning holds if females are substituted for males throughout. Therefore, 1:1 is the equilibrium ratio.

Non-mammal Y chromosome

Many groups of organisms in addition to mammals have Y chromosomes, but these Y chromosomes do not share common ancestry with mammalian Y chromosomes. Such groups include Drosophila, some other insects, some fish, some reptiles, and some plants. In Drosophila melanogaster, the Y chromosome does not trigger male development. Instead, sex is determined by the number of X chromosomes. The D. melanogaster Y chromosome does contain genes necessary for male fertility. So XXY D. melanogaster are female, and D. 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.

ZW chromosomes

Other organisms have mirror image sex chromosomes: where the homogeneous sex is the male, said to have two Z chromosomes, and the female is the heterogeneous sex, and said to have a Z chromosome and a W chromosome. For example, female birds, snakes, and butterflies have ZW sex chromosomes, and males have ZZ sex chromosomes.

Non-inverted Y chromosome

There are some species, such as the Japanese rice fish, 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.[40]

Human Y chromosome

In humans, the Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents approximately 1% of the total DNA in a male cell.[41] The human Y chromosome contains over 200 genes, at least 72 of which code for proteins.[5] Traits that are inherited via the Y chromosome are called Y-linked, or holandric traits.

Some cells, especially in older men and smokers, lack a Y chromosome. It has been found that men with a higher percentage of hematopoietic stem cells in blood lacking the Y chromosome (and perhaps a higher percentage of other cells lacking it) have a higher risk of certain cancers and have a shorter life expectancy. Men with "loss of Y" (which was defined as no Y in at least 18% of their hematopoietic cells) have been found to die 5.5 years earlier on average than others. This has been interpreted as a sign that the Y chromosome plays a role going beyond sex determination and reproduction[42] (although the loss of Y may be an effect rather than a cause). Male smokers have between 1.5 and 2 times the risk of non-respiratory cancers as female smokers.[43][44]

Non-combining region of Y (NRY)

The human Y chromosome is normally unable to recombine with the X chromosome, except for small pieces of pseudoautosomal regions at the telomeres (which comprise about 5% of the chromosome's length). These regions are relics of ancient homology 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.[45] The single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.

Genes

Number of genes

The following are some of the gene count estimates of human Y chromosome. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.[46]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 63 [2] 2016-09-08
HGNC 45 55 381 [47] 2017-05-12
Ensembl 63 109 392 [48] 2017-03-29
UniProt 47 [49] 2018-02-28
NCBI 73 122 400 [50][51][52] 2017-05-19

Gene list

In general, the human Y chromosome is extremely gene poor—it is one of the largest gene deserts in the human genome. Disregarding pseudoautosomal genes, genes encoded on the human Y chromosome include:

Y-chromosome-linked diseases

Diseases linked to the Y chromosome typically involve an aneuploidy, an atypical number of chromosomes.

Y chromosome microdeletion

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.

Defective Y chromosome

This results in the person presenting a female phenotype (i.e., is born with female-like genitalia) even though that person possesses an XY karyotype. The lack of the second X results in infertility. In other words, viewed from the opposite direction, the person goes through defeminization but fails to complete masculinization.

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 if mosaicism is present. When the Y fragment is minimal and nonfunctional, the child is usually a girl with the features of Turner syndrome or mixed gonadal dysgenesis.

XXY

Klinefelter syndrome (47, XXY) is not an aneuploidy 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.

XYY

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.[57]

In 1965 and 1966 Patricia Jacobs and colleagues published a chromosome survey of 315 male patients at Scotland's only special security hospital for the developmentally disabled, finding a higher than expected number of patients to have an extra Y chromosome.[58] 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".[59]

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,[60] and increased height was the only characteristic that could be reliably associated with XYY males.[61] The "criminal karyotype" concept is therefore inaccurate.[57]

Rare

The following Y-chromosome-linked diseases are rare, but notable because of their elucidating of the nature of the Y chromosome.

Greater degrees of Y chromosome polysomy (having more than one extra copy of the Y chromosome in every cell, e.g., XYYY) are rare. The extra genetic material in these cases can lead to skeletal abnormalities, decreased IQ, and delayed development, but the severity features of these conditions are variable.

XX male syndrome occurs when there has been a recombination in the formation of the male gametes, causing the SRY portion of the Y chromosome to move to the X chromosome. When such an X chromosome contributes to the child, the development will lead to a male, because of the SRY gene.

Genetic genealogy

In human genetic genealogy (the application of genetics to traditional 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.

Brain function

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-related androgenic hormone production.[62]

Microchimerism

The presence of male chromosomes in fetal cells in the blood circulation of women was discovered in 1974.[63]

In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal blood stream for as long as 27 years.[64]

A 2004 study at the Fred 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. The subjects were categorised into four groups based on their case histories:[65]

  • 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:[65]

  • 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.[66]

Cytogenetic band

Human chromosome Y ideogram vertical
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).
Human chromosome Y - 400 550 850 bphs
G-banding patterns of human Y chromosome in three different resolutions (400,[67] 550[68] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[69] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[70]
G-bands of human Y chromosome in resolution 850 bphs[4]
Chr. Arm[71] Band[72] ISCN
start[73]
ISCN
stop[73]
Basepair
start
Basepair
stop
Stain[74] Density
Y p 11.32 0 149 1 300,000 gneg
Y p 11.31 149 298 300,001 600,000 gpos 50
Y p 11.2 298 1043 600,001 10,300,000 gneg
Y p 11.1 1043 1117 10,300,001 10,400,000 acen
Y q 11.1 1117 1266 10,400,001 10,600,000 acen
Y q 11.21 1266 1397 10,600,001 12,400,000 gneg
Y q 11.221 1397 1713 12,400,001 17,100,000 gpos 50
Y q 11.222 1713 1881 17,100,001 19,600,000 gneg
Y q 11.223 1881 2160 19,600,001 23,800,000 gpos 50
Y q 11.23 2160 2346 23,800,001 26,600,000 gneg
Y q 12 2346 3650 26,600,001 57,227,415 gvar

See also

References

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  71. ^ "p": Short arm; "q": Long arm.
  72. ^ For cytogenetic banding nomenclature, see article locus.
  73. ^ a b These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for Human Cytogenetic Nomenclature (2013). Arbitrary unit.
  74. ^ gpos: Region which is positively stained by G banding, generally AT-rich and gene poor; gneg: Region which is negatively stained by G banding, generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk.

External links

Autosome

An autosome is a chromosome that is not an allosome (a sex chromosome). The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome pairs which may have different structures. The DNA in autosomes is collectively known as atDNA or auDNA.For example, humans have a diploid genome that usually contains 22 pairs of autosomes and one allosome pair (46 chromosomes total). The autosome pairs are labeled with numbers (1–22 in humans) roughly in order of their sizes in base pairs, while allosomes are labelled with their letters. By contrast, the allosome pair consists of two X chromosomes in females or one X and one Y chromosome in males. Unusual combinations of XYY, XXY, XXX, XXXX, XXXXX or XXYY, among other allosome combinations, are known to occur and usually cause developmental abnormalities.

Autosomes still contain sexual determination genes even though they are not sex chromosomes. For example, the SRY gene on the Y chromosome encodes the transcription factor TDF and is vital for male sex determination during development. TDF functions by activating the SOX9 gene on chromosome 17, so mutations of the SOX9 gene can cause humans with an ordinary Y chromosome to develop as females.All human autosomes have been identified and mapped by extracting the chromosomes from a cell arrested in metaphase or prometaphase and then staining them with a type of dye (most commonly, Giemsa). These chromosomes are typically viewed as karyograms for easy comparison. Clinical geneticists can compare the karyogram of an individual to a reference karyogram to discover the cytogenetic basis of certain phenotypes. For example, the karyogram of someone with Patau Syndrome would show that they possess three copies of chromosome 13. Karyograms and staining techniques can only detect large-scale disruptions to chromosomes—chromosomal aberrations smaller than a few million base pairs generally cannot be seen on a karyogram.

Genetics and archaeogenetics of South Asia

The study of the genetics and archaeogenetics of the ethnic groups of South Asia aims at uncovering these groups' genetic history. The geographic position of South Asia makes its biodiversity important for the study of the early dispersal of anatomically modern humans across Asia.

Studies based on mtDNA variation have reported genetic unity across various South Asian sub–populations. Conclusions of studies based on Y Chromosome variation and Autosomal DNA variation have been varied, although many researchers argue that most of the ancestral nodes of the phylogenetic tree of all the mtDNA types originated in South Asia. Recent genome studies appear to show that most South Asians are descendants of two major ancestral components, one restricted to South Asia (Ancestral South Indian) and the other component (Ancestral North Indian) more closely related to those in Central Asia, West Asia and Europe.It has been found that the ancestral node of the phylogenetic tree of all the mtDNA types (mitochondrial DNA haplogroups) typically found in Central Asia, the West Asia and Europe are also to be found in South Asia at relatively high frequencies. The inferred divergence of this common ancestral node is estimated to have occurred slightly less than 50,000 years ago. In India, the major maternal lineages are various M subclades, followed by R and U sublineages. These mitochondrial haplogroups' coalescence times have been approximated to date to 50,000 BP.The major paternal lineages represented by Y chromosomes are haplogroups R1a1, R2, H, L and J2. Many researchers have argued that Y-DNA Haplogroup R1a1 (M17) is of autochthonous South Asian origin. However, proposals for a Central Asian origin for R1a1 are also quite common.

Haplogroup

A haplotype is a group of alleles in an organism that are inherited together from a single parent, and a haplogroup (haploid from the Greek: ἁπλούς, haploûs, "onefold, simple" and English: group) is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. More specifically, a haplogroup is a combination of alleles at different chromosomes regions that are closely linked and that tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.

Each haplogroup originates from, and remains part of, a preceding single haplogroup (or paragroup). As such, any related group of haplogroups may be precisely modelled as a nested hierarchy, in which each set (haplogroup) is also a subset of a single broader set (as opposed, that is, to biparental models, such as human family trees).

Haplogroups are normally identified by an initial letter of the alphabet, and refinements consist of additional number and letter combinations, such as (for example) A → A1 → A1a.

In human genetics, the haplogroups most commonly studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, each of which can be used to define genetic populations. Y-DNA is passed solely along the patrilineal line, from father to son, while mtDNA is passed down the matrilineal line, from mother to offspring of both sexes. Neither recombines, and thus Y-DNA and mtDNA change only by chance mutation at each generation with no intermixture between parents' genetic material.

Haplogroup E-M96

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It is one of the two main branches of the older haplogroup DE, the other main branch being haplogroup D. The E-M96 clade is divided into two main subclades: the more common E-P147, and the less common E-M75.

Haplogroup J-M172

In human genetics, Haplogroup J-M172 or J2 is a Y-chromosome haplogroup which is a subclade (branch) of haplogroup J-M304. Haplogroup J-M172 is common in modern populations in Western Asia, Central Asia, South Asia, Europe and North Africa. It is thought that J-M172 may have originated between the Caucasus Mountains, Mesopotamia and the Levant.It is further divided into two complementary clades, J-M410 and J-M12 (M12, M102, M221, M314).

Haplogroup J (Y-DNA)

Haplogroup J-M304, also known as J, is a human Y-chromosome DNA haplogroup. It is believed to have evolved in Western Asia. The clade spread from there during the Neolithic, primarily into North Africa, the Horn of Africa, Socotra, the Caucasus, Southern Europe, West Asia, Central Asia, South Asia, and Southeast Asia.

Haplogroup J-M304 is divided into two main subclades (branches), J-M267 and J-M172.

Haplogroup N-M231

Haplogroup N (M231) is a Y-chromosome DNA haplogroup defined by the presence of the single-nucleotide polymorphism (SNP) marker M231.It is most commonly found in males originating from northern Eurasia. It also has been observed at lower frequencies in populations native to other regions, including the Balkans, East Asia, Central Asia and the Pacific.

Haplogroup Q-M242

Haplogroup Q or Q-M242 is a Y-chromosome DNA haplogroup. It has one primary subclade, Haplogroup Q1 (L232/S432), which includes numerous subclades that have been sampled and identified in males among modern populations.

Q-M242 is the predominant Y-DNA haplogroup among Native Americans and several peoples of Central Asia and Northern Siberia. It is also the predominant Y-DNA of the Akha tribe in northern Thailand and the Dayak people of Indonesia.

Haplogroup R1a

Haplogroup R1a, or haplogroup R-M420, is a human Y-chromosome DNA haplogroup which is distributed in a large region in Eurasia, extending from Scandinavia and Central Europe to southern Siberia and South Asia.While R1a originated ca. 22,000 to 25,000 years ago, its subclade M417 (R1a1a1) diversified ca. 5,800 years ago. The distribution of M417-subclades R1a-Z282 (including R1a-Z280) in Central and Eastern Europe and R1a-Z93 in Asia suggests that R1a1a diversified within the Eurasian Steppes or the Middle East and Caucasus region. The place of origin of these subclades plays a role in the debate about the origins of Proto-Indo-Europeans.

The SNP mutation R-M420 was discovered after R-M17 (R1a1a), which resulted in a reorganization of the lineage in particular establishing a new paragroup (designated R-M420*) for the relatively rare lineages which are not in the R-SRY10831.2 (R1a1) branch leading to R-M17.

Haplogroup R1b

Haplogroup R1b (R-M343), also known as Hg1 and Eu18, is a human Y-chromosome haplogroup.

It is the most frequently occurring paternal lineage in Western Europe, as well as some parts of Russia (e.g. the Bashkir minority) and Central Africa (e.g. Chad and Cameroon). The clade is also present at lower frequencies throughout Eastern Europe, Western Asia, as well as parts of North Africa and Central Asia. R1b also reaches high frequencies in the Americas and Australasia, due largely to immigration from Western Europe. There is an ongoing debate regarding the origins of R1b subclades found at significant levels among some indigenous peoples of the Americas, such as speakers of Algic languages in central Canada.R1b has two primary branches: R1b1a-L754 and R1b1b-PH155. R1b1a1a2-M269, which predominates in Western Europe, and R1b1a2-V88, which is common in Central Africa, are both subclades of R1b-L754. R1b1b-PH155 is so rare and widely dispersed that it is difficult to draw any conclusions about its origins. It has been found in Bahrain, Bhutan, Ladakh, Tajikistan, Turkey, and Western China.

According to autosomal DNA studies the majority of modern R1b and R1a would have expanded from the Caspian Sea along with the Indo-European languages.

Human Y-chromosome DNA haplogroup

In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by mutations in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). Mutations that are shared by many people are called single-nucleotide polymorphisms (SNPs).The human Y-chromosome accumulates roughly two mutations per generation. Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree that share hundreds or even thousands of mutations unique to each haplogroup.

The Y-chromosomal most recent common ancestor (Y-MRCA, informally known as Y-chromosomal Adam) is the most recent common ancestor (MRCA) from whom all currently living men are descended patrilineally. Y-chromosomal Adam is estimated to have lived roughly 236,000 years ago in Africa. By examining other bottlenecks most Eurasian men are descended from a man who lived 69,000 years ago. Other major bottlenecks occurred about 5,000 years ago and subsequently most Eurasian men can trace their ancestry back to a dozen ancestors who lived 5,000 years ago.

List of Y-chromosome haplogroups in populations of the world

The following articles are lists of human Y-chromosome DNA haplogroups found in populations around the world.

Y-DNA haplogroups by ethnic group

Y-DNA haplogroups in populations of Europe

Y-DNA haplogroups in populations of the Near East

Y-DNA haplogroups in populations of North Africa

Y-DNA haplogroups in populations of Sub-Saharan Africa

Y-DNA haplogroups in populations of the Caucasus

Y-DNA haplogroups in populations of South Asia

Y-DNA haplogroups in populations of East and Southeast Asia

Y-DNA haplogroups in populations of Central and North Asia

Y-DNA haplogroups in populations of Oceania

Y-DNA haplogroups in indigenous peoples of the Americas

List of haplogroups of historic people

Male

A male (♂) organism is the physiological sex that produces sperm. Each spermatozoon can fuse with a larger female gamete, or ovum, in the process of fertilization. A male cannot reproduce sexually without access to at least one ovum from a female, but some organisms can reproduce both sexually and asexually. Most male mammals, including male humans, have a Y chromosome, which codes for the production of larger amounts of testosterone to develop male reproductive organs.

Not all species share a common sex-determination system. In most animals, including humans, sex is determined genetically, but in some species it can be determined due to social, environmental, or other factors. For example, Cymothoa exigua changes sex depending on the number of females present in the vicinity.

Sex chromosome

An allosome (also referred to as a sex chromosome, heterotypical chromosome, heterochromosome, or idiochromosome) is a chromosome that differs from an ordinary autosome in form, size, and behavior. The human sex chromosomes, a typical pair of mammal allosomes, determine the sex of an individual created in sexual reproduction. Autosomes differ from allosomes because autosomes appear in pairs whose members have the same form but differ from other pairs in a diploid cell, whereas members of an allosome pair may differ from one another and thereby determine sex.

Nettie Stevens and Edmund Beecher Wilson both independently discovered sex chromosomes in 1905. However, Stevens is credited for discovering them earlier than Wilson.

Tokudaia

Tokudaia is a genus of murine rodent native to Japan. Known as Ryūkyū spiny rats or spinous country-rats, population groups exist on several non-contiguous islands. Despite differences in name and appearance, they are the closest living relatives of the Eurasian field mouse (Apodemus). Of the three species, both T. osimensis and T. tokunoshimensis have lost their Y chromosome and SRY gene; the sex chromosomes of T. muenninki, on the other hand, are abnormally large.Named species are:

Muennink's spiny rat, Tokudaia muenninki

Ryukyu spiny rat, Tokudaia osimensis

Tokunoshima spiny rat, Tokudaia tokunoshimensisAt least Tokudaia osimensis may be a cryptic species complex.

XXYY syndrome

XXYY syndrome is a sex chromosome anomaly in which males have an extra X and Y chromosome. Human cells usually contain two sex chromosomes, one from the mother and one from the father. Usually, females have two X chromosomes (XX) and males have one X and one Y chromosome (XY). The appearance of at least one Y chromosome with a properly functioning SRY gene makes a male. Therefore, humans with XXYY are genotypically male. Males with XXYY syndrome have 48 chromosomes instead of the typical 46. This is why XXYY syndrome is sometimes written as 48,XXYY syndrome or 48,XXYY. It affects an estimated one in every 18,000–40,000 male births.

XY sex-determination system

The XY sex-determination system is the sex-determination system found in humans, most other mammals, some insects (Drosophila), some snakes, and some plants (Ginkgo). In this system, the sex of an individual is determined by a pair of sex chromosomes. Females typically have two of the same kind of sex chromosome (XX), and are called the homogametic sex. Males typically have two different kinds of sex chromosomes (XY), and are called the heterogametic sex.

In humans the presence of the Y chromosome determines if an offspring develops as a male and the absence of the Y chromosome results in a female offspring. More specifically it is the SRY gene located on the Y chromosome that is of importance to male differentiation. Variations to the sex gene karyotype could include rare disorders such as XX males (often due to translocation of the SRY gene to the X chromosome) or XY gonadal dygenesis (due to mutations in the SRY gene). In addition, other rare genetic variations such as Turners (XO) and Klinefelters (XXY) are seen as well.

The XY system contrasts in several ways with the ZW sex-determination system found in birds, some insects, many reptiles, and various other animals, in which the heterogametic sex is female. It had been thought for several decades that in all snakes sex was determined by the ZW system, but there had been observations of unexpected effects in the genetics of species in the families Boidae and Pythonidae; for example, parthenogenic reproduction produced only females rather than males, which is the opposite of what is to be expected in the ZW system. In the early years of the 21st century such observations prompted research that demonstrated that all pythons and boas so far investigated definitely have the XY system of sex determination.A temperature-dependent sex determination system is found in some reptiles.

Y-chromosomal Aaron

Y-chromosomal Aaron is the name given to the hypothesized most recent common ancestor of the majority of the patrilineal Jewish priestly caste known as Kohanim (singular "Kohen", also spelled "Cohen"). According to the Hebrew Bible, this ancestor was Aaron, the brother of Moses.

The original scientific research was based on the hypothesis that a majority of present-day Jewish Kohanim share a pattern of values for six Y-STR markers, which researchers named the Cohen Modal Haplotype (CMH).Subsequent research using twelve Y-STR markers indicated that about half of contemporary Jewish Kohanim shared Y-chromosomal J1 M267, (specifically haplogroup J-P58, also called J1c3), while other Kohanim share a different ancestry, including haplogroup J2a (J-M410).

Molecular phylogenetics research published in 2013 and 2016 for haplogroup J1 (J-M267) places the Y-chromosomal Aaron within subhaplogroup Z18271, age estimate 2638–3280 years Before Present (yBP).

Y-chromosomal Adam

In human genetics, the Y-chromosomal most recent common ancestor (Y-MRCA, informally known as Y-chromosomal Adam) is the most recent common ancestor (MRCA) from whom all currently living men are descended patrilineally. The term Y-MRCA reflects the fact that the Y chromosomes of all currently living males are directly derived from the Y chromosome of this remote ancestor. The analogous concept of the matrilineal most recent common ancestor is known as "Mitochondrial Eve" (mt-MRCA, named for the matrilineal transmission of mtDNA), the most recent woman from whom all living humans are descended matrilineally. As with "Mitochondrial Eve", the title of "Y-chromosomal Adam" is not permanently fixed to a single individual, but can advance over the course of human history as paternal lineages become extinct.

Estimates of the time when Y-MRCA lived have also shifted as modern knowledge of human ancestry changes. In 2013, the discovery of a previously unknown Y-chromosomal haplogroup was announced,

which resulted in a slight adjustment of the estimated age of the human Y-MRCA.By definition, it is not necessary that the Y-MRCA and the mt-MRCA should have lived at the same time.

While estimates as of 2014 suggested the possibility that the two individuals may well have been roughly contemporaneous (albeit with uncertainties ranging in the tens of thousands of years), the discovery of archaic Y-haplogroup has pushed back the estimated age of the Y-MRCA beyond the most likely age of the mt-MRCA. As of 2015, estimates of the age of the Y-MRCA range around 200,000 to 300,000 years ago, roughly consistent with the emergence of anatomically modern humans.Y-chromosomal data taken from a Neanderthal from El Sidrón, Spain produced a Y-T-MRCA of 588,000 years ago for neanderthal and Homo sapiens patrilineages, dubbed ante Adam and 275,000 years ago for Y-MRCA.

Nuclear genome
Mitochondrial genome
Basic
concepts
Types
Processes
and evolution
Structures
See also
Biological terms
Sexual reproduction
Sexuality

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