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Origin and Evolution of Y Chromosomes: Drosophila Tales

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Origin and Evolution of Y Chromosomes: Drosophila Tales Review Origin and evolution of Y chromosomes: Drosophila tales A. Bernardo Carvalho1, Leonardo B. Koerich1 and Andrew G. Clark2 1 Departamento de Gene´ tica, Universidade Federal do Rio de Janeiro, Caixa Postal 68011, CEP 21944-970, Rio de Janeiro, Brazil 2 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA Classically, Y chromosomes are thought to originate somes arise through this path (or by the related neo-Y from X chromosomes through a process of degeneration pathway; Box 1), invariably being homologous to X chromo- and gene loss. Now, the availability of 12 Drosophila somes. genomes provides an opportunity to study the origin Before 2000, an extensive identification of Y-linked and evolution of Y chromosomes in an informative phy- genes had been performed only for humans [7]. The genome logenetic context. Surprisingly, the majority of Droso- sequencing of Drosophila melanogaster in 2000, followed phila Y-linked genes are recent acquisitions from by Drosophila pseudoobscura (2003) and now by ten autosomes and Y chromosome gene gains are more additional Drosophila genomes (2007), uncovered several frequent than gene losses. Moreover, the Drosophila unexpected phenomena, including the lack of X–Y shared pseudoobscura Y chromosome lacks homology with genes, a wholesale replacement of the Y chromosome in the the Y of most Drosophila species. Thus, the Drosophila D. pseudoobscura lineage, and the preponderance of gene Y has a different evolutionary history from canonical Y gains (compared with gene losses) in the 12 sequenced chromosomes (such as the mammalian Y) and it also Drosophila species. Here, we review these data and explore might have a different origin. their consequences in the broader context of Diptera sex- chromosome evolution. We concentrate on single-copy Sex-chromosome origins genes on the Drosophila Y, with an emphasis on results Sex-chromosome evolution provides a particularly coher- [8,9] appearing since the last review on this subject [10]. ent and satisfying blend of empirical data and theory. Readers interested in the role of repetitive DNA in the According to canonical theory, X and Y chromosomes (for evolution of the Drosophila Y chromosome and on evol- the sake of simplicity we refer to the ‘W’ chromosome of utionary models of Y-degeneration should consult Refs birds and butterflies as ‘Y’ [1]) originate from an autosomal [4,11–13]. pair via a three-step process that begins with the acqui- sition of one or more strong sex-determining genes by one D. melanogaster Y chromosome: a lack of X–Y autosome, giving rise to nascent X and Y chromosomes. homology Natural selection then favors the suppression of recombi- The D. melanogaster Y chromosome comprises mainly nation between the two chromosomes. The lack of recom- repetitive DNA and is heterochromatic. It does not deter- bination, together with the joint effects of mutation, mine sex; instead, sex determination in Drosophila is natural selection and genetic drift, then leads to progress- basically accomplished by a count of the number of X ive degeneration and loss of Y chromosome genes until only chromosomes [14,15]. However, males devoid of Y chromo- the sex-determining gene(s) and a few relic genes survive somes (‘X0 males’) are sterile [16] and formal genetic [1–5]. As the X chromosome become progressively haploid studies identified six genes that are essential for male in males (hemizygous), natural selection favors increased fertility in the D. melanogaster Y [17–20]. Now, genome transcription of X-linked genes in males through several sequencing and the development of proper bioinformatics dosage-compensation mechanisms [1,2]. In the later methods enables a thorough molecular identification of the stages, the Y usually becomes heterochromatic, accumu- Y chromosome gene content [21–23]. Despite its large size lating large amounts of repetitive DNA. It also frequently (40 Mbp), it contains few single-copy protein-coding acquires male-specific genes from the autosomes [6,7] (or genes: 12 are currently known and indirect evidence female-specific genes in the case of the W chromosome, suggests an upper bound of 20 genes [21–24]. These genes where ZW is female and ZZ is male). Empirical data in a are unusually large, owing to Mbp-sized introns compris- variety of organisms including plants and birds support ing repetitive DNA [25]. D. melanogaster Y-linked genes this scenario, the evidence being particularly clear in have two additional important features; many (and prob- mammals. The most compelling evidence is provided by ably all) have male-related functions (e.g. encoding sperm the observation that, among the 27 different proteins flagella motor proteins) and all arose by duplication from encoded by the human Y, 18 have an ancestral, close autosomal genes [9,21–24]. The initial step of their origin counterpart on the X chromosome [6]. This generality, must have been a gene duplication that created a mutant Y coupled with the beautiful fit between theory and data, carrying a copy of an autosomal gene. Then, in some cases, has led to the widespread assumption that all Y chromo- the mutant Y became fixed in the population, either by Corresponding author: Bernardo Carvalho, A. ([email protected]). genetic drift or because it conferred a selective advantage 270 0168-9525/$ – see front matter ß 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.tig.2009.04.002 Available online 13 May 2009 Review Trends in Genetics Vol.25 No.6 Box 1. Neo-Y chromosomes cautiously wrote that ‘the genic content of the Y chromo- some would be fluid and may differ among (...) species [of X0/XX sex-chromosome systems are believed to have arisen from an XY/XX system via degeneration and loss of the Y [1].AY the Drosophilidae family]’ [22]. As described in the next chromosome can be ‘regenerated’ in these species when an section, when the 12 Drosophila genomes became avail- autosome fuses to the X chromosome and the new arrangement able, it was found that Y chromosome gene content differs is fixed within a population (Figure 1b). During male meiosis the free even among species of the same group [8,9]. homolog of the fused autosome continues to pair with the newly added portion of the X (termed ‘neo-X’) and moves to the opposite pole of the cell, behaving as a Y chromosome (hence its name, ‘neo- The 12 Drosophila Y chromosomes: a prominent role of Y’). Neo-Y chromosomes are male-restricted and the same evolu- gene gains tionary factors that cause the degeneration of Y chromosomes are Before examining the results of Koerich et al. [9], it is worth expected to act on them. Empirical data confirm that they mentioning a caveat. Ideally, the complete gene set of the Y accumulate repetitive DNA and that their genes degenerate. Indeed Drosophila neo-Y systems are popular models to study Y-chromo- chromosomes in the 12 species should be available before some degeneration [12,48]. There are important differences be- starting a comparative analysis, similar to the approach tween canonical Y and neo-Y evolution [38]; nonetheless, in both used (at least approximately) for analysing the euchro- cases the Y originated through degeneration (of the X or the neo-X). matic portion of the other chromosomes. However, given Fusions between the sex chromosomes (either the X or Y) and the notorious difficulties in sequencing and assembling autosomes also occur in XY/XX species. D. pseudoobscura and its close relatives exemplify the former case: their X chromosomes heterochromatic regions and the Y [27,28], Koerich et al. stem from a fusion between the ancestral X and an autosome [1]. [9] investigated Y-linkage in the Drosophila orthologs of After fixation of the X–autosome fusion the ancestral lineage must the D. melanogaster Y-linked genes. The ensuing ascer- have passed through a ‘X/Y/neo-Y’ stage, in which three chromo- tainment bias should be corrected when estimating gene somes pair during male meiosis (the female meiosis is normal). Not gain and loss rates [9]. The special case of two species (D. surprisingly, such an event causes meiotic problems, and a similar system in another Drosophila species generates 1–3% of sex- pseudoobscura and the closely related D. persimilis)is chromosome aneuploidy [49]. This intermediate stage is usually discussed in the next section, because the changes in their short lived and in a few million years only one Y chromosome Y-chromosome gene content were caused by a wholesale remains; it is believed that the neo-Y is lost or fused to the ancestral replacement of the Y, rather than by individual gains and Y [1]. However, the outcome was surprisingly different in the D. losses of genes [8]. pseudoobscura lineage: the ancestral Y was incorporated into an autosome and was replaced by a new Y chromosome, possibly Koerich et al. [9] found that, in many cases, the orthologs derived from the neo-Y [8]. of the D. melanogaster Y-linked genes were autosomal in other species. This change in chromosomal location can be explained either by an autosome-to-Y transposition in the to males that carried it. Given their redundancy, the D. melanogaster lineage (i.e. a gene gain in the Y) or by a Y- autosomal copy could have pseudogenized and disap- to-autosome transposition in the other lineage (i.e. a gene peared, the new Y-linked copy could have disappeared, loss in the Y). Additional data based on synteny, however, or the two copies could have retained functionality, have provided unambiguous answers (Figure 2). Among possibly by diverging to perform different functions [26]. the 12 known D. melanogaster Y-linked genes, seven were Different Y-linked genes illustrate each of these steps.
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