Patterns of Molecular Evolution of an Avian Neo-sex Chromosome Irene Pala,*,1 Dennis Hasselquist,1 Staffan Bensch,1 and Bengt Hansson*,1 1Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden *Corresponding author: E-mail: [email protected]; [email protected]. Associate editor: Yoko Satta Abstract Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome Downloaded from https://academic.oup.com/mbe/article/29/12/3741/1005710 by guest on 28 September 2021 system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral Research article sex chromosomes. In this study, we report the results of molecular analyses of neo-Z and neo-W gametologs and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae, and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe 1) lower genetic diversity of neo-Z genes compared with autosomal genes, 2) moderate synonymous and weak nonsynonymous sequence divergence between neo-Z and neo-W gametologs, and 3) lower GC content on neo-W than neo-Z gametologs. Phylogenetic reconstruction of eight neo-Z and neo-W gametologs suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e., after 42.2 Ma) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e., after 39.4 Ma). The Sylvioidea neo-sex chromosome shares classical evolutionary features with the ancestral sex chromosomes but, as expected from its more recent origin, shows weaker divergence between gametologs. Key words: neo-sex chromosome, ZW gametolog divergence, recombination cessation. Introduction The timing of recombination cessation may differ along the sex chromosome, from the initiation points to the regions Degeneration and Genetic Variation of Sex- where recombination still occurs, and this regional variation Linked Genes will be evident in the degree of sequence divergence of game- Sex chromosomes have evolved independently in many dif- tologous genes (i.e., homologous genes on the opposite sex ferent lineages and some common key features in the evolu- chromosomes; sensu Garcia-Moreno and Mindell 2000). By tion from an ancestral homologous pair have been analyzing divergence between gametologs, regions that have recognized. These include reduced recombination between ceased to recombine at different times, corresponding to the members of the sex chromosome and a progressive de- clusters of distinct divergence, evolutionary strata, were ini- generation of the sex-limited chromosome (i.e., Y in mam- tially identified in the human X chromosome (Lahn and Page mals and W in birds) (Bergero and Charlesworth 2009). 1999; Ross et al. 2005). More recently, such evolutionary According to the sexual antagonistic model, recombination strata, although not always in a linear fashion over the cessation is triggered by the presence of sexual antagonistic chromosome, have also been reported in other mammals alleles (beneficial to one sex and harmful to the other) asso- (Sandstedt and Tucker 2004;butseeMurtagh et al. 2012), ciated to a sex-determining factor at one of the sex chromo- plants (Nicolas et al. 2004; Bergero et al. 2007), and birds somes (Rice 1987). Once multiple loci are involved in the (Handley et al. 2004; Nam and Ellegren 2008), that is, in establishment and functionality of one of the sexes, reduced both male and female heterogametic systems. This suggests recombination between the two chromosomes will be that similar processes of chromosome evolution occur in selected for. As a consequence, the nonrecombining sex both types of sex chromosome systems (Charlesworth and chromosome is predicted to accumulate deleterious muta- Mank 2010). The presence of evolutionary strata has been tions, start degenerating, and progressively diverge relative to related to two main events in chromosome evolution: the the other member of the sex chromosome pair (Lahn and suppression of recombination as a means to resolve sexual Page 1999; Bachtrog 2005; Wilson and Makova 2009). The antagonism between clusters of genes located on sex degeneration of the nonrecombining sex chromosome is ex- chromosomes (van Doorn and Kirkpatrick 2007)andthe pected to be driven by multiple processes, including Muller’s occurrence of chromosomal rearrangements that can affect ratchet, background selection, and the Hill–Robertson effect the physical linearity of the blocks of reduced recombination with weak selection (Lahn and Page 1999; Charlesworth et al. (Lemaitre et al. 2009). 2005; Bergero and Charlesworth 2009; Wilson and Makova In birds, the evolution of gametologous genes and the oc- 2009). currence of evolutionary strata on sex chromosomes have ß The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: [email protected] Mol. Biol. Evol. 29(12):3741–3754 doi:10.1093/molbev/mss177 Advance Access publication July 23, 2012 3741 Pala et al. doi:10.1093/molbev/mss177 MBE been almost exclusively addressed in the chicken (Gallus stickleback (Gasterosteus aculeatus) where newly sex-linked gallus)(Ceplitis and Ellegren 2004; Handley et al. 2004; Nam genes on the neo-sex chromosome are involved in mate rec- and Ellegren 2008). In other bird groups, mainly in passerines ognition, reproductive isolation, and speciation (Kitano et al. (perching birds or song birds), studies have focused on the 2009, 2010). However, in birds, a very prominent group in the evolution of genes located on the Z chromosome (Borge et al. context of female heterogamety, the opportunity of using 2005), the putative role of this chromosome in reproductive neo-sex chromosomes as basis for the study of sex chromo- isolation (Storchova´ et al. 2010), and prominently in the com- some evolution has not yet been available. parative analysis of the organization of genes located on sex chromosomes between different species (Itoh et al. 2006; Neo-sex Chromosome in Sylvioidea Passerines Nanda et al. 2008; Vo¨lker et al. 2010). The general scarcity of information about gametologs in birds results mostly from We have recently detected a neo-sex chromosome in Sylvioi- a highly heterochromatic W chromosome, in which consid- dea passerine birds (Pala et al. 2011).Asignificantpart(ca. erable divergence in gene content and sequence variation 10 Mb) of chromosome 4a (in total 20.7 Mb), an autosome in Downloaded from https://academic.oup.com/mbe/article/29/12/3741/1005710 by guest on 28 September 2021 makes it difficult to isolate Z and W gene pairs within the zebra finch genome (Warren et al. 2010), has been trans- nonrecombining areas. To our knowledge, even in model located to the sex chromosomes in the Sylvioidea lineage speciessuchasthezebrafinch(Taeniopygia guttata), struc- (including, e.g., warblers and larks; fig. 1). The translocated ture and expression patterns of Z/W gametologs have only material is present in all Sylvioidea assayed so far but not in been investigated for the CHD1 gene pair (Fridolfsson and non-Sylvioidea species, which suggest that the translocation Ellegren 2000; Agate et al. 2004). In fact, the high divergence occurred at the base of the Sylvioidea branch of the avian between the sex chromosomes or more specifically the de- phylogeny, at approximately 42.2 Ma (Pala et al. 2011). Our generation of the sex-limited chromosome constitutes a previous results indicated the presence of both Z- and major drawback of using chromosomes with very deep diver- W-linked copies of the neo-sex chromosome in Sylvioidea gence times for assessing patterns of sex chromosome evolu- and show no indications of ongoing recombination (Pala tion. Very often in ancestral sex chromosome pairs, such as et al. 2011), which offers the possibility of isolating a the mammalian XY (approximately 150–170 Ma; Veyrunes number of these more recently formed gametologous genes. et al. 2008; Livernois et al. 2012) or the avian ZW (an at least The Sylvioidea neo-sex chromosome opens the unprece- 150-My-old sex chromosome pair; Nam and Ellegren 2008; dented possibility of studying the evolutionary trajectories of Livernois et al. 2012), direct comparisons of gametologous sex-linked genes and addressing the question of what initial genes are no longer possible. Even the 80–130-My-old X- factors affect sex chromosome evolution. In vertebrates, this and Y-added region in eutherian mammals has started to opportunity has seldom arisen (but see, e.g., Zhou et al. 2008; deteriorate (Waters et al. 2001; Livernois et al. 2012). Ross et al. 2009) and never before in a female heterogametic New sex chromosome elements, neo-sex chromosomes, system. Although with obvious differences, the two main sex can be formed either by translocations of autosomal parts chromosome systems (XY and ZW) have evolved from auto- to the sex chromosomes (Bachtrog 2003; Zhou et al. 2008; somes, with specific evolutionary processes modulating the Howell et al. 2009; Kitano et al. 2009)orthroughthetrans- progressive structural and functional divergence of each location of a master sex-determination locus (Tanaka et al. member of the pair (Fridolfsson et al. 1998; Graves 1998; 2007). Neo-sex chromosomes offer unique possibilities to Bergero and Charlesworth 2009). The Sylvioidea neo-sex studying the evolution of sex-linked genes because degener- chromosomes, with their autosomal origin and verified link- ation of the sex-limited chromosome is still limited. If, as age to ancestral Z, can be looked upon as an emergent sex hypothesized, reduced recombination and degeneration of chromosome pair, in which divergence might still be ongoing the sex-limited chromosome are key factors in the evolution (Pala et al.