How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Myr ago formed “neo-sex chromosomes” consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and while the added-Z has remained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for non-random maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex-linkage.

Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.

We report the discovery of a novel neo‐sex chromosome in an African warbler, Sylvietta brachyura (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome–sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single species‐representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In S. brachyura, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo‐sex chromosome in this lineage. Furthermore, the non‐recombining part of 4A in S. brachyura is smaller than in other Sylvioidea species, which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.

The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming “evolutionary strata” that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (tRC) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X‐Y or Z‐W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring tRC. Here, we assess two alternative phylogenetic approaches to estimate tRC; (i) the expected likelihood weight (ELW) approach that finds the most likely topology among a set of hypothetical topologies and (ii) the BEAST approach that estimates tRC with specified calibration priors on a reference species topology. By using Z and W gametologs of an old and a young evolutionary stratum on the neo‐sex chromosome of Sylvioidea songbirds, we show that the ELW and BEAST approaches yield similar tRC estimates, and that both outperform two frequently applied approaches utilizing synonymous substitution rates (dS) and maximum likelihood (ML) trees, respectively. Moreover, we demonstrate that both ELW and BEAST provide more precise tRC estimates when sequences of multiple species are included in the analyses.

Recombination generates new haplotypes and disconnects linked genes thereby increasing the efficiency of selection and the adaptive potential. Quantifying the recombination landscape, i.e., the recombination rate variation along chromosomes, is important for understanding how evolutionary processes such as selection and drift are acting on genes and chromosomes. Here, we present RecView, an interactive R application, designed to view and locate recombination positions along chromosomes using whole-genome genotype data of a three-generation pedigree. RecView visualises the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree. It also infers putative recombination positions with two algorithms, one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin, along the chromosome. Putative recombination positions are given in base pairs together with an estimated error based on the local density of informative alleles. We demonstrate the applicability of RecView using sequencing data of one 120 Mb-large chromosome of one offspring (and its four grandparents and two parents) of a passerine bird, the great reed warbler (Acrocephalus arundinaceus). On this chromosome, we detected five recombination events, three on the paternal chromosome and two on the maternal chromosome with both algorithms. To evaluate how sensitive the analysis is for SNP density, we downsampled our data to 10% of the original dataset. In conclusion, we provide an easy-to-use and highly effective application for viewing and locating recombination positions along chromosomes in small pedigrees. RecView and test data are available on GitHub (https://github.com/HKyleZhang/RecView.git).