Copyright Ó 2010 by the Genetics Society of America DOI: 10.1534/genetics.110.116756 Gene Duplication, Gene Conversion and the Evolution of the Y Chromosome Tim Connallon1 and Andrew G. Clark Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 Manuscript received March 17, 2010 Accepted for publication May 31, 2010 ABSTRACT Nonrecombining chromosomes, such as the Y, are expected to degenerate over time due to reduced efficacy of natural selection compared to chromosomes that recombine. However, gene duplication, coupled with gene conversion between duplicate pairs, can potentially counteract forces of evolutionary decay that accompany asexual reproduction. Using a combination of analytical and computer simulation methods, we explicitly show that, although gene conversion has little impact on the probability that duplicates become fixed within a population, conversion can be effective at maintaining the functionality of Y-linked duplicates that have already become fixed. The coupling of Y-linked gene duplication and gene conversion between paralogs can also prove costly by increasing the rate of nonhomologous crossovers between duplicate pairs. Such crossovers can generate an abnormal Y chromosome, as was recently shown to reduce male fertility in humans. The results represent a step toward explaining some of the more peculiar attributes of the human Y as well as preliminary Y-linked sequence data from other mammals and Drosophila. The results may also be applicable to the recently observed pattern of tetraploidy and gene conversion in asexual, bdelloid rotifers. ONRECOMBINING chromosomes are often asso- pseudogenes (Charlesworth and Charlesworth N ciated with genetic degradation and a loss of 2000; Bachtrog 2006; Engelstadter 2008). functional genes, and nowhere is this pattern more The issue is more complex when one considers data exaggerated than on the Y chromosome (Charlesworth from the well-characterized human Y chromosome. A and Charlesworth 2000; Bachtrog 2006). However, majority of functional Y-linked genes are members of in addition to the more widely recognized pattern of duplicate gene pairs residing within large palindromes gene loss, genome sequences of mammals and Drosoph- and are almost exclusively testis expressed (Skaletsky ila are also yielding evidence for Y-linked functional et al. 2003). In contrast to many of the single-copy genes gene gain followed by amplification of duplicate genes with X-linked homologs, members of Y-linked gene (Skaletsky et al. 2003; Koerich et al. 2008; Carvalho families are apparently not degenerating, but rather et al. 2009; Krsticevic et al. 2009; Hughes et al. 2010). have become fixed and maintained over many millions Duplication and retention of functional Y-linked gene of years (Skaletsky et al. 2003; Yu et al. 2008). Although copies is somewhat surprising because evolutionary the- Y chromosomes are not well characterized in other taxa, ory predicts an opposing pattern. First, to the extent currently available data suggest that duplication is a that gene duplicates are fixed via positive selection, common feature of Y chromosomes in other mammal they are less likely to become fixed on nonrecombining species as well as Drosophila (Rozen et al. 2003; Verkaar relative to recombining chromosomes (Otto and et al. 2004; Murphy et al. 2006; Alfo¨ldi2008; Wilkerson Goldstein 1992; Clark 1994; Yong 1998; Otto and et al. 2008; Krsticevic et al. 2009; Geraldes et al. 2010). Yong 2002; Tanaka and Takahasi 2009). Second, Thus, patterns of gene duplication and retention, for at regardless of whether Y-linked duplicates become fixed least a subset of Y-linked genes, may be a general rule of via genetic drift or by natural selection, the actions of Y chromosome evolution. Muller’s ratchet, genetic hitchhiking, and background Another attribute of the mammalian Y appears to be selection are expected to greatly increase the probabil- relevant for duplicate gene evolution. Comparative ity that Y-linked genes degenerate into nonfunctional analysis between humans and chimpanzees suggests ongoing recombination between the gene duplicate pairs that reside on the same Y chromosome. Such Supporting information is available online at http://www.genetics.org/ ‘‘intrachromosomal’’recombination includes both non- cgi/content/full/genetics.110.116756/DC1. reciprocal (gene conversion) and reciprocal exchange 1Corresponding author: Department of Molecular Biology and Genetics, ozen Cornell University, Biotechnology Bldg. (Room 227), Ithaca, NY 14853- (crossing over) between gene duplicate pairs (R 2703. E-mail: [email protected] et al. 2003; Lange et al. 2009). Gene conversion between Genetics 186: 277–286 (September 2010) 278 T. Connallon and A. G. Clark the duplicates potentially maintains gene function by develop and analyze a diffusion approximation and counteracting stochastic forces of Y chromosome de- perform stochastic simulations to examine the proba- generation (Rozen et al. 2003; Charlesworth 2003; bility that a rare gene duplicate eventually becomes Noordam and Repping 2006). The rationale behind fixed within a population of small size. this hypothesis is subtle. As with other clonally inherited Invasion of a new gene duplicate: Consider a single chromosomes, each evolutionary lineage of the Y is phys- Y-linked locus with a functional allele, A, and a non- ically coupled to, and its evolutionary fate is influenced functional allele, a.MutationfromA to a occurs at rate u by, the presence of deleterious mutations. Mutation- per generation and there is no back mutation. By bearing lineages represent evolutionary dead ends unless introducing a duplication of the locus, the population is they can somehow remove or compensate for deleterious expanded to include five genotypic classes: the original mutations. Recombination between duplicates can ‘‘res- single-copy classes (A and a), those with two functional cue’’ functionality via gene conversion between func- gene copies (AA), those with one functional and one tional and nonfunctional copies. nonfunctional copy (Aa), and those with two nonfunc- On the other hand, double-strand DNA breaks, which tional copies (aa). As in the single-locus case, transitions precede gene conversion events (Marais 2003), also between states (AA / Aa or aA; Aa or aA / aa) can occur precede crossing over. Crossovers between Y-linked by mutation, at rate of u per locus; because there are now genes can generate acentric and dicentric Y chromo- two loci, the mutation rate per chromosome is 2u. somes, resulting in infertility and disruption of the For Y chromosomes carrying duplicates, recombina- sex determination pathway (e.g., Repping et al. 2002; tion (crossing over and gene conversion) can poten- Heinritz et al. 2005; Lange et al. 2009). Considering tially occur between loci. Throughout our analysis, we both gene conversion and crossing over on the Y, re- examine cases where recombination occurs at a rate of d combination can be viewed as a factor that either con- per paralog pair, per generation. The probability that a strains (via gene conversion) or promotes (via crossing single recombination event is a crossover, which gen- over) Y chromosome degeneration. erates an abnormal (sterile) Y chromosome (e.g., These observations concerning Y chromosome gene Repping et al. 2002; Heinritz et al. 2005; Lange et al. content and recombination raise interesting questions 2009), is equal to the constant c . The remainder of that have not been formally addressed by evolutionary recombination events (1 À c) represent gene conversion theory (but see the recent study by Marais et al. 2010). events between duplicate pairs. Gene conversion in- First, what conditions favor the evolutionary invasion of volving Aa or aA individuals yields AA or aa sperm at rate Y-linked gene duplicates, and does recombination in- b and 1 À b, respectively. Thus, b can be viewed as a fluence the probability that duplicates eventually become biased gene conversion parameter, where the functional fixed within a population? Second, what affect does copy A preferentially replaces the nonfunctional a recombination have on Y-linked fitness and the mainte- whenever b . 0.5 (there is no bias when b ¼ 0.5). nance of functional duplicate genes? To address these Compared to individuals with two functional gene questions, we develop and analyze a series of population- copies, individuals with zero functional copies suffer a genetic models of Y chromosome evolution. We show fitness reduction of s, while those with one functional that, when direct selection on gene duplicates is weak, copy suffer a reduction of sh, where h is equivalent to a biased gene conversion can increase, whereas crossing dominance coefficient. Complete masking of a non- over will decrease, their probability of fixation. For dupli- functional allele occurs when h ¼ 0, and there is no cates with larger fitness effects, the probability of fixation direct fitness benefit of carrying two vs. one functional is largely independent of Y-linked recombination. Finally, gene. Partial masking occurs when 1 . h . 0; in such gene conversion has a major impact on the retention of cases, there is a fitness benefit of having two functional functional Y-linked genes that are already fixed within the copies. Genotypes, genotypic fitness, and zygotic fre- population and maintains multiple gene copies with or quencies are described in Table 1. without selection favoring these duplicates. MODEL AND RESULTS TABLE 1 Gene conversion and the invasion