Y chromosome
The Y chromosome is one of two sex chromosomes in therian mammals and [|other organisms]. Along with the X chromosome, it is part of the XY sex-determination system, in which the Y is used for sex-determining as the presence of the Y chromosome typically causes offspring produced in sexual reproduction to develop phenotypically male. In mammals, the Y chromosome contains the SRY gene, which usually triggers the differentiation of male gonads. The Y chromosome is typically only passed from male parents to male offspring.
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, working with Hemiptera. Stevens proposed that chromosomes always existed in pairs and that the smaller 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. In the early 1920s, Theophilus Painter determined that X and Y chromosomes determined sex in humans.The chromosome was given the name "Y" simply to follow on from Henking's "X" alphabetically. 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.
Different variations
Most therian mammals have only one pair of sex chromosomes in each cell. Males usually have one Y chromosome and one X chromosome, while females usually have two X chromosomes. In mammals, the Y chromosome contains the SRY gene which triggers phenotypic male development. Differences in the Y chromosome are associated with both atypical sexual development and fertility conditions.In humans, people with an extra X chromosome often develop Klinefelter syndrome, and people with an extra Y chromosome develop Jacob's Syndrome, as genes on the Y chromosome generally trigger the development of a male phenotype. Other chromosomal variations include three X chromosomes, and Monosomy X, where individuals only have one X chromosome and no Y chromosome. Some individuals with an XY karyotype, develop phenotypically female due to mutation in genes such as the SRY gene or MAP3K1.
Origins and evolution
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 and simply possessing this allele caused the organism to develop phenotypically male. Over time, the two chromosomes diverged into separate X and Y configurations, with the Y chromosome losing many of its original genes, and gaining only a few others specifically involved in sex differentiationUntil 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 suggested that the XY sex-determination system would not have been present more than 166 million years ago, when monotremes split from other mammals. 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 not present on the autosomes of platypus and birds. The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.
Recombination inhibition
Most chromosomes recombine during meiosis. However, the X and Y pair in a shared region known as the pseudoautosomal region. The PAR undergoes frequent recombination between the X and Y chromosomes, but recombination is suppressed in other regions of the Y chromosome. These regions contain genes specifically involved in male sexual differentiation. 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 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 increased mutation opportunity for the Y chromosome is reported by Graves as a factor 4.8. However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.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 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. 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. 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, the Y chromosome's entropy rate is only 0.84. From the definition of entropy rate, the Y chromosome has a much lower information content relative to its overall length, and is more redundant.