Molecular evolution of a Y chromosome to autosome gene duplication in Drosophila

In contrast to the rest of the genome, the Y chromosome is restricted to males and lacks recombination. As a result, Y chromosomes are unable to respond efficiently to selection, and newly formed Y chromosomes degenerate until few genes remain. The rapid loss of genes from newly formed Y chromosomes has been well studied, but gene loss from highly degenerate Y chromosomes has only recently received attention. Here, we identify and characterize a Y to autosome duplication of the male fertility gene kl-5 that occurred during the evolution of the testacea group species of Drosophila. The duplication was likely DNA based, as other Y-linked genes remain on the Y chromosome, the locations of introns are conserved, and expression analyses suggest that regulatory elements remain linked. Genetic mapping reveals that the autosomal copy of kl-5 resides on the dot chromosome, a tiny autosome with strongly suppressed recombination. Molecular evolutionary analyses show that autosomal copies of kl-5 have reduced polymorphism and little recombination. Importantly, the rate of protein evolution of kl-5 has increased significantly in lineages where it is on the dot versus Y linked. Further analyses suggest this pattern is a consequence of relaxed purifying selection, rather than adaptive evolution. Thus, although the initial fixation of the kl-5 duplication may have been advantageous, slightly deleterious mutations have accumulated in the dot-linked copies of kl-5 faster than in the Y-linked copies. Because the dot chromosome contains seven times more genes than the Y and is exposed to selection in both males and females, these results suggest that the dot suffers the deleterious effects of genetic linkage to more selective targets compared with the Y chromosome. Thus, a highly degenerate Y chromosome may not be the worst environment in the genome, as is generally thought, but may in fact be protected from the accumulation of deleterious mutations relative to other nonrecombining regions that contain more genes.     

Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system

Classical genetic studies discovered loss of genes from the ancient sex chromosome systems of several animals (genetic degeneration), and complete genome sequencing confirms that the heterogametic sex is hemizygous for most sex-linked genes. Genetic degeneration is thought to result from the absence of recombination between the sex chromosome pair (reviewed by [1]) and is very rapid after sex chromosome-autosome fusions in Drosophila [2-4]. Plant sex chromosome systems allow study of the time course of degeneration, because they evolved from a state wholly without sex chromosomes (rather than after a large genome region fused to a preexisting sex chromosome), and, in several taxa, recombination stopped very recently. However, despite increasing genetic and physical mapping of plant nonrecombining sex-determining regions [5-8], it remains very difficult to discover sex-linked genes, and it is unclear whether Y-linked genes are losing full function. We therefore developed a high-throughput method using RNA-Seq to identify sex linkage in Silene latifolia. Recombination suppression between this plant's XY sex chromosome pair started only about 10 million years ago [9]. Our approach identifies several hundred new sex-linked genes, and we show that this young Y chromosome retains many genes, yet these already have slightly reduced gene expression and are accumulating changes likely to reduce protein functions.     

Indirect evidence from DNA sequence diversity for genetic degeneration of the Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs

The action of natural selection is expected to reduce the effective population size of a nonrecombining chromosome, and this is thought to be the chief factor leading to genetic degeneration of Y-chromosomes, which cease recombining during their evolution from ordinary chromosomes. Low effective population size of Y chromosomes can be tested by studying DNA sequence diversity of Y-linked genes. In the dioecious plant, Silene latifolia, which has sex chromosomes, one comparison (SlX1 vs. SlY1) indeed finds lower Y diversity compared with the homologous X-linked gene, and one Y-linked gene with no X-linked homologue has lower species-wide diversity than a homologous autosomal copy (SlAp3Y vs. SlAp3A). To test whether this is a general pattern for Y-linked genes, we studied two further recently described X and Y homologous gene pairs in samples from several populations of S. latifolia and S. dioica. Diversity is reduced for both Y-linked genes, compared with their X-linked homologues. Our new data are analysed to show that the low Y effective size cannot be explained by different levels of gene flow for the X vs. the Y chromosomes, either between populations or between these closely related species. Thus, all four Y-linked genes that have now been studied in these plants (the two studied here, and two previously studied genes, have low diversity). This supports other evidence for an ongoing degeneration process in these species.     

DOES LOCAL ADAPTATION CAUSE HIGH POPULATION DIFFERENTIATION OF SILENE LATIFOLIA Y CHROMOSOMES?

Natural selection can reduce the effective population size of the nonrecombining Y chromosome, whereas local adaptation of Y-linked genes can increase the population divergence and overall intra-species polymorphism of Y-linked sequences. The plant Silene latifolia evolved a Y chromosome relatively recently, and most known X-linked genes have functional Y homologues, making the species interesting for comparisons of X- and Y-linked diversity and subdivision. Y-linked genes show higher population differentiation, compared to X-linked genes, and this might be maintained by local adaptation in Y-linked genes (or low sequence diversity). Here we attempt to test between these causes by investigating DNA polymorphism and population differentiation using a larger set of Y-linked and X-linked S. latifolia genes (than used previously), and show that net sequence divergence for Y-linked sequences (measured by D(a) , also known as δ) is low, and not consistently higher than X-linked genes. This does not support local adaptation, instead, the higher values of differentiation measures for the Y-linked genes probably result largely from reduced total variation on the Y chromosome, which in turn reflect deterministic processes lowering effective population sizes of evolving Y-chromosomes.     

The Y chromosome as a target for acquired and amplified genetic material in evolution

The special properties of the Y chromosome stem form the fact that it is a non-recombining degenerate derivative of the X chromosome. The absence of homologous recombination between the X and the Y chromosome leads to gradual degeneration of various Y chromosome genes on an evolutionary timescale. The absence of recombination, however, also favors the accumulation of transposable elements on the Y chromosome during its evolution, as seen with both Drosophila and mammalian Y chromosomes. Alongside these processes, the acquisition and amplification of autosomal male benefit genes occur. This review will focus on recent studies that reveal the autosome-acquired genes on the Y chromosome of both Drosophila and humans. The evolution of the acquired and amplified genes on the Y chromosome is also discussed. Molecular and comparative analyses of Y-linked repeats in the Drosophila melanogaster genome demonstrate that there was a period of their degeneration followed by a period of their integration into RNAi silencing, which was beneficial for male fertility. Finally, the function of non-coding RNA produced by amplified Y chromosome genetic elements will be discussed.     

Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae

Evolution of the bear family Ursidae is well investigated in terms of morphological, paleontological, and genetic features. However, several phylogenetic ambiguities occur within the subfamily Ursinae (the family Ursidae excluding the giant panda and spectacled bear), which may correlate with behavioral traits of female philopatry and male-biased dispersal which form the basis of the observed matriarchal population structure in these species. In the process of bear evolution, we investigate the premise that such behavioral traits may be reflected in patterns of variation among genes with different modes of inheritance: matrilineal mitochondrial DNA (mtDNA), patrilineal Y chromosome, biparentally inherited autosomes, and the X chromosome. In the present study, we sequenced 3 Y-linked genes (3,453 bp) and 4 X-linked genes (4,960 bp) and reanalyzed previously published sequences from autosome genes (2,347 bp) in ursid species to investigate differences in evolutionary rates associated with patterns of inheritance. The results describe topological incongruence between sex-linked genes and autosome genes and between nuclear DNA and mtDNA. In more ancestral branches within the bear phylogeny, Y-linked genes evolved faster than autosome and X-linked genes, consistent with expectations based on male-driven evolution. However, this pattern changes among branches leading to each species within the lineage of Ursinae whereby the evolutionary rates of Y-linked genes have fewer than expected substitutions. This inconsistency between more recent nodes of the bear phylogeny with more ancestral nodes may reflect the influences of sex-biased dispersal as well as molecular evolutionary characteristics of the Y chromosome, and stochastic events in species natural history, and phylogeography unique to ursine bears.     

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.     

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes'' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.     

Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia

The human Y--probably because of its nonrecombining nature--has lost 97% of its genes since X and Y chromosomes started to diverge [1, 2]. There are clear signs of degeneration in the Drosophila miranda neoY chromosome (an autosome fused to the Y chromosome), with neoY genes showing faster protein evolution [3-6], accumulation of unpreferred codons [6], more insertions of transposable elements [5, 7], and lower levels of expression [8] than neoX genes. In the many other taxa with sex chromosomes, Y degeneration has hardly been studied. In plants, many genes are expressed in pollen [9], and strong pollen selection may oppose the degeneration of plant Y chromosomes [10]. Silene latifolia is a dioecious plant with young heteromorphic sex chromosomes [11, 12]. Here we test whether the S. latifolia Y chromosome is undergoing genetic degeneration by analyzing seven sex-linked genes. S. latifolia Y-linked genes tend to evolve faster at the protein level than their X-linked homologs, and they have lower expression levels. Several Y gene introns have increased in length, with evidence for transposable-element accumulation. We detect signs of degeneration in most of the Y-linked gene sequences analyzed, similar to those of animal Y-linked and neo-Y chromosome genes.     

Analysis and evolution of two functional Y-linked loci in a plant sex chromosome system.

White campion (Silene latifolia) is one of the few examples of plants with separate sexes and with X and Y sex chromosomes. The presence or absence of the Y chromosome determines which type of reproductive organs--male or female--will develop. Recently, we characterized the first active gene located on a plant Y chromosome, SlY1, and its X-linked homolog, SlX1. These genes encode WD-repeat proteins likely to be involved in cell proliferation. Here, we report the characterization of a novel Y-linked gene, SlY4, which also has a homolog on the X chromosome, SlX4. Both SlY4 and SlX4 potentially encode fructose-2,6-bisphosphatases. A comparative molecular analysis of the two sex-linked loci (SlY1/SlX1 and SlY4/SlX4) suggests selective constraint on both X- and Y-linked genes and thus that both X- and Y-linked copies are functional. Divergence between SlY4 and SlX4 is much greater than that between the SlY1 and SlX1 genes. These results suggest that, as for human XY-linked genes, the sex-linked plant loci ceased recombining at different times and reveal distinct events in the evolutionary history of the sex chromosomes.     

Autosomal genes involved in mammalian primary sex determination

Beginning with findings made during the late 1950s and early 1960s, evidence continues to accumulate in support of the hypothesis that the mammalian Y chromosome carries a gene that induces the undifferentiated foetal gonad in XY individuals to develop as a testis. Recently a DNA sequence has been isolated from the human Y chromosome that appears to be the hypothesized Y-linked testis-determining gene, and advances have also been made toward identifying genes that interact with the Y-linked testis-determining (Tdy) gene to initiate testis formation. These loci have been identified in specific stocks of mice carrying the mutant Thp or TOrl allele at the T locus located on chromosome 17, and in crosses involving the transfer of a Y chromosome from two populations of Mus domesticus into the genomes of specific inbred strains of mice. The data in both cases support the hypothesis that there are several loci involved in testis determination and that abnormal interaction of these loci disrupts initiation of testis determination, resulting in development of ovarian tissue in XY individuals.     

Extreme population structure and high interspecific divergence of the Silene Y chromosome

Previous studies have demonstrated that the diversity of Y-linked genes is substantially lower than that of their X-linked homologs in the plant Silene latifolia. This difference has been attributed to selective sweeps, Muller's ratchet, and background selection, processes that are predicted to severely affect the evolution of the nonrecombining Y chromosome. We studied the DNA diversity of a noncoding region of the homologous genes DD44Y and DD44X, sampling S. latifolia populations from a wide geographical area and also including the closely related species S. dioica, S. diclinis, and S. heuffelii. On the Y chromosome of S. latifolia, we found substantial DNA diversity. Geographical population structure was far higher than on the X chromosome and differentiation between the species was also higher for the Y than for the X chromosome. Our findings indicate that the loss of genetic diversity on the Y chromosome in Silene occurs within local populations rather than within entire species. These results are compatible with background selection, Muller's ratchet, and local selective sweeps, but not with species-wide selective sweeps. The higher interspecific divergence of DD44Y, compared to DD44X, supports the hypothesis that Y chromosome differentiation between incipient species precedes reproductive isolation of the entire genome, forming an early stage in the process of speciation.     

Substitution rates in a new Silene latifolia sex-linked gene, SlssX/Y

Dioecious white campion Silene latifolia has sex chromosomal sex determination, with homogametic (XX) females and heterogametic (XY) males. This species has become popular in studies of sex chromosome evolution. However, the lack of genes isolated from the X and Y chromosomes of this species is a major obstacle for such studies. Here, I report the isolation of a new sex-linked gene, Slss, with strong homology to spermidine synthase genes of other species. The new gene has homologous intact copies on the X and Y chromosomes (SlssX and SlssY, respectively). Synonymous divergence between the SlssX and SlssY genes is 4.7%, and nonsynonymous divergence is 1.4%. Isolation of a homologous gene from nondioecious S. vulgaris provided a root to the gene tree and allowed the estimation of the silent and replacement substitution rates along the SlssX and SlssY lineages. Interestingly, the Y-linked gene has higher synonymous and nonsynonymous substitution rates. The elevated synonymous rate in the SlssY gene, compared with SlssX, confirms our previous suggestion that the S. latifolia Y chromosome has a higher mutation rate, compared with the X chromosome. When differences in silent substitution rate are taken into account, the Y-linked gene still demonstrates significantly faster accumulation of nonsynonymous substitutions, which is consistent with the theoretical prediction of relaxed purifying selection in Y-linked genes, leading to the accumulation of nonsynonymous substitutions and genetic degeneration of the Y-linked genes.     

Origin and evolution of the Drosophila Y chromosome

Three recent findings are making a deep impact on our understanding of the Drosophila Y. First, the sequencing of the Drosophila genome and the development of proper computational methods increased the number of known single-copy Y-linked genes from 1 to 16, and revealed a chromosome packed with genes acquired from the autosomes. Second, this, coupled with the finding that B-chromosomes are able to show very regular segregation from the X chromosome, reinforce the hypothesis that the Drosophila Y is a specialized B-chromosome, instead of a degenerated homologue of the X. Third and finally, Y chromosomes seem to have a strong effect on male fitness.     

Defining regions and rearrangements of the Silene latifolia Y chromosome

We combine data from published marker genotyping of three sets of S. latifolia Y chromosome deletion mutants with changed sex phenotypes and add genotypes for several new genic markers to refine the deletion map of the Y chromosome and compare it with the X chromosome genetic map. We conclude that the Y chromosome of this species has been derived through multiple rearrangements of the ancestral gene arrangement and that none of the rearrangements so far detected was involved in stopping X-Y recombination. Different Y genotypes may also differ in their gene content and possibly arrangements, suggesting that mapping the Y-linked sex-determining genes will be difficult, even if many further genic markers are obtained. Even in determining the map of Y chromosome markers to discover all the rearrangements, physical mapping by FISH or other experiments will be essential. Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes.     

Actin-like sequences are present on human X and Y chromosomes.

The human genome contains greater than 20 actin-related sequences, six of which at least are expressed as protein. We have shown by blot hybridization the presence of actin-like sequences on both the X and the Y chromosomes. These sequences can be detected in HindIII digests of genomic DNA, using as probe cDNA clones corresponding to human alpha skeletal actin or to a hamster (beta or gamma) cytoskeletal actin; they show more homology to the latter probe. The actin probes also detect a polymorphic DNA fragment showing autosomal inheritance with a frequency for the major allele of 0.55 in the population studied. The X-linked actin sequence has been assigned to a centromeric region between Xp11 and Xq11 by hybridization to DNAs from a panel of human-mouse hybrid cell lines, and thus lies outside the postulated region of homology between the X and Y chromosomes. The Y-linked actin sequence can serve as a marker to analyse anomalies of sex determination or of gametogenesis in man. It was found in all XY males studied but was absent from the genomic DNA of four unrelated 'XX male' subjects and two XX hermaphrodites. This shows that the region of chromosome Y which contains the actin sequence is not translocated onto the X chromosome (or onto autosomes) in these patients.     

The process of a Y-loss event in an XO/XO mammal, the Ryukyu spiny rat

The Ryukyu spiny rat, Tokudaia osimensis, has an XO/XO sex chromosome constitution, lacking a Y chromosome and the mammalian sex-determining gene SRY. To investigate the Y-loss event, we traced three proto-Y-linked genes, RBMY1A1, EIF2S3Y, and KDM5D, in the genome. The original Y-linked RBMY1A1 was lost as well as SRY, and the remaining RBMY1A1 was a processed pseudogene on autosome. In contrast, EIF2S3Y and KDM5D were conserved in genomes of both sexes as a result of their translocation from the Y chromosome to the X chromosome and/or autosomes. Furthermore, these genes were expressed in gonads and brains of both sexes. Our study indicated a loss of Y-linked genes with important male functions to be necessary for the Y chromosome to disappear. These functions might have been retained through the acquisition of new genes, and therefore, the Y-loss has had no harmful effect on the maintenance of this species.