Before Y chromosome Many
ectothermic
vertebrates have no sex chromosomes. If these species have different sexes, sex is determined environmentally rather than genetically. For some species, especially
reptiles, sex depends on the incubation temperature. Some vertebrates are
hermaphrodites, though hermaphroditic species are most commonly
sequential, meaning the organism switches sex, producing male or female
gametes at different points in its life, but never producing both at the same time. This is opposed to
simultaneous 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 few
orders of fish.
Origin The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes, termed
autosomes, when an ancestral animal developed an allelic variation (a so-called "sex locus") and simply possessing this
allele caused the organism to develop phenotypically male. Until recently, the X and Y chromosomes in mammals were thought to have diverged around 300 million years ago. However, research published in 2008 analyzing the
platypus genome
Recombination inhibition Most chromosomes
recombine during
meiosis. However, the X and Y pair in a shared region known as the
pseudoautosomal region (PAR). The PAR undergoes frequent recombination between the X and Y chromosomes, Without regional suppression, the genes could be lost from the Y chromosome in recombination, causing developmental issues such as
infertility. The lack of recombination across the majority of the Y chromosome makes it a useful tool in studying
human evolution, since recombination complicates the mathematical models used to trace ancestries.
Degeneration By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes throughout 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. 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.
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. With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the
human genome. However, these changes have been limited to non-coding sequences and 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. Additionally, a scientific report in 2012 stated that only one gene had been lost since humans diverged from the
rhesus macaque 25 million years ago. 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. 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 concerning the main body of genetic information. Brandeis 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.
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 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
non-coding DNA. Massive accumulations of retrotransposable elements are scattered throughout the Y. From the definition of
entropy rate, the Y chromosome has a much lower information content relative to its overall length, and 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 into the next gene pool.
Gene conversion As has already been 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 can "recombine" with itself, using
palindrome base pair sequences. Such a "recombination" is called
gene conversion. In the case of the Y chromosomes, the
palindromes are not
noncoding 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. The
recombination intermediates preceding gene conversion were found to rarely take the alternate route of crossover recombination. These gene conversion events may reflect a basic function of meiosis, that of conserving the integrity of the genome.
Future evolution 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. 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.
Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome. • 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. Outside of the rodents, the
black muntjac,
Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and
autosomes. Modern data casts doubt on the hypothesis that the Y-chromosome will disappear. Outside of mammals, some organisms have lost the Y chromosome, such as most species of nematodes. However, 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. 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. ==Non-therian Y chromosome==