Sex-linkage of sexually antagonistic genes is predicted by female, but not male, effects in birds

Variability in sex-determining mechanisms influences genome complexity in reptilia

In this review, we describe the history of amniote sex determination as a classic example of Darwinian evolution. We suggest that evolutionary changes in sex determination provide a foundation for understanding important aspects of chromosome and genome organization that otherwise appear haphazard in their origins and contents. Species with genotypic sex determination often possess heteromorphic sex chromosomes, whereas species with environmental sex determination lack them. Through a series of mutations followed by selection at key genes, sex-determining mechanisms have turned over many times throughout the amniote lineage. As a consequence, amniote genomes have undergone gains or losses of sex chromosomes. We review the genomic and ecological contexts in which either temperature-dependent or genotypic sex determination has evolved. Once genotypic sex determination emerges in a lineage, viviparity and heteromorphic sex chromosomes become more likely to evolve. For example, in extinct marine reptiles, genotypic sex determination apparently led to viviparity, which in turn facilitated their pelagic radiation. Sex chromosomes comprise genome regions that differ from autosomes in recombination rate, mutation rate, levels of polymorphism, and the presence of sex-determining and sexually antagonistic genes. In short, many aspects of amniote genome complexity, life history, and adaptive radiation appear contingent on evolutionary changes in sex-determining mechanisms.

Ontogenetic complexity of sexual dimorphism and sex-specific selection

Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific selection pressures shift over the life cycle. Here, we present a time-series global transcription profile for autosomal genes in male and female chicken, beginning with embryonic development and spanning to reproductive maturity, for the gonad. Overall, the amount and magnitude of sex-biased expression increased as a function of age, though sex-biased gene expression was surprisingly ephemeral, with very few genes exhibiting continuous sex bias in both embryonic and adult tissues. Despite a large predicted role of the sex chromosomes in sexual dimorphism, our study indicates that the autosomes house the majority of genes with sex-biased expression. Most interestingly, sex-specific evolutionary pressures shifted over the course of the life cycle, acting equally strongly on female-biased genes and male-biased genes but at different ages. Female-biased genes exhibited high rates of divergence late in embryonic development, shortly before arrested meiosis halts oogenesis. The level of divergence on female-biased late embryonic genes is similar to that seen in male-biased genes expressed in adult gonads, which correlates with the onset of spermatogenesis. These analyses reveal that sex-specific selection pressure varies over the life cycle as a function of male and female biology.

The chicken Z chromosome is enriched for genes with preferential expression in ovarian somatic cells

Theory predicts that sexually antagonistic mutations will be over- or under-represented on the X and Z chromosomes, depending on their average dominance coefficients. However, as little is known about the dominance coefficients for new mutations, the effect of sexually antagonistic selection is difficult to predict. To elucidate the role of sexually antagonistic selection in the evolution of Z chromosome gene content in chicken, we analyzed publicly available microarray data from several somatic tissues as well as somatic and germ cells of the ovary. We found that the Z chromosome is enriched for genes showing preferential expression in ovarian somatic cells, but not for genes with preferential expression in primary oocytes or non-sex-specific somatic tissues. Our results suggest that sexual antagonism leads to a higher abundance of female-benefit alleles on the Z chromosome. No bias toward Z-linkage for oocyte-enriched genes can be explained by lower intensity of sexually antagonistic selection in ovarian germ cells compared to ovarian somatic cells. An alternative explanation would be that meiotic Z chromosome inactivation hinders accumulation of oocyte-expressed genes on the Z chromosome. Our results are consistent with findings in mammals and indicate that recessive rather than dominant sexually antagonistic mutations shape the gene content of the X and Z chromosomes.

Avian sex chromosomes: dosage compensation matters

In 2001 it was established that, contrary to our previous understanding, a mechanism exists that equalises the expression levels of Z chromosome genes found in male (ZZ) and female (ZW) birds (McQueen et al. 2001). More recent large scale studies have revealed that avian dosage compensation is not a chromosome-wide phenomenon and that the degree of dosage compensation can vary between genes (Itoh et al. 2007; Ellegren et al. 2007). Although, surprisingly, dosage compensation has recently been described as absent in birds (Mank and Ellegren 2009b), this interpretation is not supported by the accumulated evidence, which indicates that a significant proportion of Z chromosome genes show robust dosage compensation and that a particular cluster of such dosage compensated genes can be found on the short arm of the Z chromosome. The implications of this new picture of avian dosage compensation for avian sex determination are discussed, along with a possible mechanism of avian dosage compensation.

The ontogeny of cross-sex genetic correlations: an analysis of patterns

The independent evolution of males and females is typically constrained by shared genetic variance. Despite substantial research, we still know little about the evolution of cross-sex genetic covariance and its standardized measure, the cross-sex genetic correlation (r(MF)). In particular, it is unclear if r(MF) tend to vary with age. We compiled 28 traits for which ontogenetic trends in r(MF) were documented. Decreases in r(MF) with age were observed significantly more often than increases and the mean effect size for the relationship between r(MF) and age was large and negative. This suggests that sexual dimorphism (SD) may typically evolve more readily for phenotypes expressed later in ontogeny and that evolutionary inferences related to the evolution of SD should be limited to the ontogenetic stage at which r(MF) was estimated. Knowledge about ontogenetic variation in r(MF) should help improving our understanding of evolutionary patterns related to SD and the resolution of intralocus sexual conflicts.

Slcyt, a newly identified sex-linked gene, has recently moved onto the X chromosome in Silene latifolia (Caryophyllaceae)

The sex chromosomes of the plant species Silene latifolia (white campion) are very young (only 5-10 My old), and all 11 X-linked genes so far described have Y-linked homologues. Theory predicts that X chromosomes should accumulate a nonrandom set of genes. However, little is known about the importance of gene movements between the X and the autosomes in plants, or in any very young sex chromosome system. Here, we isolate from cDNA a new gene, Slcyt, on the S. latifolia X, which encodes a cytochrome B protein. We genetically mapped SlCyt and found that it is located approximately 1 cM from the pseudoautosomal region. Genes in this region of the X chromosome have low divergence values from their homologous Y-linked genes, indicating that the X only recently stopped recombining with the Y. Genetic mapping in Silene vulgaris suggests that Slcyt originally belonged to a different linkage group from that of the other S. latifolia X-linked genes. Silene latifolia has no Y-linked homologue of Slcyt, and also no autosomal paralogues seem to exist. Slcyt moved from an autosome to the X very recently, as the Cyt gene is also X linked in Silene dioica, the sister species to S. latifolia, but is probably autosomal in Silene diclinis, implying that a translocation to the X probably occurred after the split between S. diclinis and S. latifolia/S. dioica. Diversity at Slcyt is extremely low (pi(syn) = 0.16%), and we find an excess of high frequency-derived variants and a negative Tajima's D, suggesting that the translocation was driven by selection.

Female meiotic sex chromosome inactivation in chicken

During meiotic prophase in male mammals, the heterologous X and Y chromosomes remain largely unsynapsed, and meiotic sex chromosome inactivation (MSCI) leads to formation of the transcriptionally silenced XY body. In birds, the heterogametic sex is female, carrying Z and W chromosomes (ZW), whereas males have the homogametic ZZ constitution. During chicken oogenesis, the heterologous ZW pair reaches a state of complete heterologous synapsis, and this might enable maintenance of transcription of Z- and W chromosomal genes during meiotic prophase. Herein, we show that the ZW pair is transiently silenced, from early pachytene to early diplotene using immunocytochemistry and gene expression analyses. We propose that ZW inactivation is most likely achieved via spreading of heterochromatin from the W on the Z chromosome. Also, persistent meiotic DNA double-strand breaks (DSBs) may contribute to silencing of Z. Surprisingly, gammaH2AX, a marker of DSBs, and also the earliest histone modification that is associated with XY body formation in mammalian and marsupial spermatocytes, does not cover the ZW during the synapsed stage. However, when the ZW pair starts to desynapse, a second wave of gammaH2AX accumulates on the unsynapsed regions of Z, which also show a reappearance of the DSB repair protein RAD51. This indicates that repair of meiotic DSBs on the heterologous part of Z is postponed until late pachytene/diplotene, possibly to avoid recombination with regions on the heterologously synapsed W chromosome. Two days after entering diplotene, the Z looses gammaH2AX and shows reactivation. This is the first report of meiotic sex chromosome inactivation in a species with female heterogamety, providing evidence that this mechanism is not specific to spermatogenesis. It also indicates the presence of an evolutionary force that drives meiotic sex chromosome inactivation independent of the final achievement of synapsis.