Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

Abstract

Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher F ST for Z-linked loci than for autosomes, as expected. The π Z /π A ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N eZ /N eA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

“…; reviewed by Oyler‐McCance et al . ). We note that our results are not consistent with one of the commonly proposed explanations – that there is a higher mutation rate (and therefore substitution rate) on the Z chromosome, due to the higher proportion of time that Z chromosomes occur in males (where mutation rates have been proposed to be higher).…”

“…; Oyler‐McCance et al . ) that the Z chromosome is particularly prone to recurrent selective episodes. In this respect, the entire Z chromosome displays similar characteristics of differentiation as the ‘islands of relative differentiation’ in the autosomal genome, suggesting the Z chromosome may also be subject to geographic sweeps followed by local reductions of variation.…”

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

“…Regardless of the geographic origin of divergence, both selection and neutral processes can produce the heterogeneity in differentiation we observe across these genomes. In the case of the Z chromosome, the nearly chromosome‐wide high level of differentiation is likely, in part, the result of the increased genetic drift resulting from the reduced recombination rate and lower effective population size of this chromosome (Oyler‐McCance, Cornman, Jones, & Fike, ). However, there are a few regions that appear to be largely undifferentiated on the Z chromosome.…”

Sex chromosomes and speciation in birds and other ZW systems

“…In the absence of selection, the substitution rate is predicted to be 2 3 l m þ 1 3 l f on the Z versus 1 2 l m þ 1 2 l f on the autosomes. Given this, the impact of a relatively large male bias in mutation rates is actually rather moderate: a male-female mutation rate ratio of 2 would produce a Z-to-autosome mutation rate ratio of roughly 1.11 (Axelsson et al, 2004;Oyler-McCance et al, 2015).…”