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Orr HA, Kim Y: An adaptive hypothesis for the evolution of the Y chromosome

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An adaptive hypothesis for the evolution of the Y chromosome

Sex chromosomes originate from autosomes,. They can arise in species with separate sexes where sex is determined by environmental cues (such as in turtles where temperature determines the sex of developing embryos) and can also arise in hermaphrodites (i.e. individuals with both male and female sex organs). illustrates a potential path leading to heteromorphic sex chromosomes, but others are possible. The first step in the evolution of Y chromosomes is likely to be the acquisition of a male-determining gene on one member of a pair of autosomes that ultimately will become the sex chromosomes (for example, a male-determining gene forming a proto-Y chromosome). Genetic sex determination with otherwise homomorphic sex chromosomes is observed in many taxa in amphibians, fish, reptiles and many invertebrates,. For heteromorphic sex chromosomes to originate after the acquisition of a male-determining gene, recombination needs to become suppressed between the homomorphic proto-sex chromosomes,. This allows the Y chromosome to evolve independently of its X homologue.

An adaptive hypothesis for the evolution of the Y chromosome.

Zhang, J. (1999) Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models. Mol Biol Evol 16: 868-875.

11/05/2004 · Recent Problems in Evolution

Duke Becker SE, Thomas R, Trifonov VA et al. (2011) Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. Chromosome Research 19: 685–708.

Banding similarities among the cat, raccoon and mongoose familieswere reported by Wurster-Hill and Gray (1975). More recently, attempts have been made topropose an ancestral karyotype for the order Carnivora (Dutrillaux and Couturier 1983,Couturier et al. 1986). This hypothetical karyotype is quite similar to that of the palmcivet (, family Viverridae). Seal karyotypes showbanding similarities with those of the carnivore families, but bears and dogs havekaryotypes that are quite different.
The hypothetical ancestral carnivore karyotype (see above paragraph)was compared with the hypothetical ancestral karyotype previously proposed for the NewWorld monkeys (Dutrillaux and Couturier 1981), prosimian primates (Rumpler et al. 1983b)and the squirrels (Petit et al. 1984, cited by Couturier et al. 1986). Although bandinghomeologies are claimed for significant portions of the karyotype, the method used hasbeen criticized (Ponsa et al. 1981). Dutrillaux and Couturier invoke gene mappingsimilarities to support their view of actual homology of the chromosomes.
Karyotypically, one of the most homogeneous families known is the catfamily (Wurster-Hill and Gray 1973). Mongooses show significant but varying degrees ofsimilarity with cats (Wurster-Hill and Gray 1975). Translocations involving a sexchromosome are known in at least two genera of mongooses (Pathak and Stock 1976, Fredga1972).

General Rebuttal to the Theory of Evolution

Weshow that a higher rate of protein sequence evolution of the neo-X-linked copy of Cyclin B relative to the neo-Y copy is driven bypositive selection, which is consistent with the adaptive hypothesisfor the evolution of the Y chromosome3.

The male-specific region of the mammalian Y chromosome (MSY) contains clusters of genes essential for male reproduction. The highly repetitive and degenerative nature of the Y chromosome impedes genomic and transcriptomic characterization. Although the Y chromosome sequence is available for the human, chimpanzee, and macaque, little is known about the annotation and transcriptome of nonprimate MSY. Here, we investigated the transcriptome of the MSY in cattle by direct testis cDNA selection and RNA-seq approaches. The bovine MSY differs radically from the primate Y chromosomes with respect to its structure, gene content, and density. Among the 28 protein-coding genes/families identified on the bovine MSY (12 single- and 16 multicopy genes), 16 are bovid specific. The 1,274 genes identified in this study made the bovine MSY gene density the highest in the genome; in comparison, primate MSYs have only 31-78 genes. Our results, along with the highly transcriptional activities observed from these Y-chromosome genes and 375 additional noncoding RNAs, challenge the widely accepted hypothesis that the MSY is gene poor and transcriptionally inert. The bovine MSY genes are predominantly expressed and are differentially regulated during the testicular development. Synonymous substitution rate analyses of the multicopy MSY genes indicated that two major periods of expansion occurred during the Miocene and Pliocene, contributing to the adaptive radiation of bovids. The massive amplification and vigorous transcription suggest that the MSY serves as a genomic niche regulating male reproduction during bovid expansion.

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N2 - The male-specific region of the mammalian Y chromosome (MSY) contains clusters of genes essential for male reproduction. The highly repetitive and degenerative nature of the Y chromosome impedes genomic and transcriptomic characterization. Although the Y chromosome sequence is available for the human, chimpanzee, and macaque, little is known about the annotation and transcriptome of nonprimate MSY. Here, we investigated the transcriptome of the MSY in cattle by direct testis cDNA selection and RNA-seq approaches. The bovine MSY differs radically from the primate Y chromosomes with respect to its structure, gene content, and density. Among the 28 protein-coding genes/families identified on the bovine MSY (12 single- and 16 multicopy genes), 16 are bovid specific. The 1,274 genes identified in this study made the bovine MSY gene density the highest in the genome; in comparison, primate MSYs have only 31-78 genes. Our results, along with the highly transcriptional activities observed from these Y-chromosome genes and 375 additional noncoding RNAs, challenge the widely accepted hypothesis that the MSY is gene poor and transcriptionally inert. The bovine MSY genes are predominantly expressed and are differentially regulated during the testicular development. Synonymous substitution rate analyses of the multicopy MSY genes indicated that two major periods of expansion occurred during the Miocene and Pliocene, contributing to the adaptive radiation of bovids. The massive amplification and vigorous transcription suggest that the MSY serves as a genomic niche regulating male reproduction during bovid expansion.

Accelerated Adaptive Evolution on a Newly Formed X Chromosome

AB - The male-specific region of the mammalian Y chromosome (MSY) contains clusters of genes essential for male reproduction. The highly repetitive and degenerative nature of the Y chromosome impedes genomic and transcriptomic characterization. Although the Y chromosome sequence is available for the human, chimpanzee, and macaque, little is known about the annotation and transcriptome of nonprimate MSY. Here, we investigated the transcriptome of the MSY in cattle by direct testis cDNA selection and RNA-seq approaches. The bovine MSY differs radically from the primate Y chromosomes with respect to its structure, gene content, and density. Among the 28 protein-coding genes/families identified on the bovine MSY (12 single- and 16 multicopy genes), 16 are bovid specific. The 1,274 genes identified in this study made the bovine MSY gene density the highest in the genome; in comparison, primate MSYs have only 31-78 genes. Our results, along with the highly transcriptional activities observed from these Y-chromosome genes and 375 additional noncoding RNAs, challenge the widely accepted hypothesis that the MSY is gene poor and transcriptionally inert. The bovine MSY genes are predominantly expressed and are differentially regulated during the testicular development. Synonymous substitution rate analyses of the multicopy MSY genes indicated that two major periods of expansion occurred during the Miocene and Pliocene, contributing to the adaptive radiation of bovids. The massive amplification and vigorous transcription suggest that the MSY serves as a genomic niche regulating male reproduction during bovid expansion.

How and Why Chromosome Inversions Evolve - PLOS

C. SOME POSSIBLE EXPLANATIONS (Building a Working Hypothesis):
1. They were designed that way.
2. Chromosome 2 split into two (fission) in the ancestral branch (or branches) that produced the apes.
3. Chromosome 2 formed from the joining (fusion) of two shorter chromosomes in an early human ancestor after the apes branched off.

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