Discovery and population genomics of structural variation in a songbird genus

Abstract

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra-and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly-and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.

Assortative mate choice and epistatic mating-trait architecture induce complex movement of the crow hybrid zone

“…Consistent with the proposition that the light allele of the second locus already segregated in the ancestral population of carrion crows (Weissensteiner et al, 2020) the maximum-likelihood parameter estimate of the initial allele frequency of the dark allele in carrion crows was below one (0.777). As maximum likelihood parameter values for the mate choice function we found (ζ, η) = (2.17, 0.617) and kilometer 302 on the transect as position of initial contact.…”

“…Examples for resulting mate-choice values for various parameter settings are shown in Fig. 2 B. 2.2.6 Fitting hybrid-zone model parameter to genotype data Weissensteiner et al (2020) inferred that the d allele of the NDP gene arose approximately 500,000 years ago and segregated in the ancestor of both carrion and hooded crows. Since the three genotypes DDll, DDld and DDdd all lead to the all-black phenotype, we therefore allow that the ancestral frequency of allele d in the west can initially be different from 1.…”

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

“…We also inspected consensus sequences with unusual classification for being avian repeats like many DNA transposon superfamilies [19]. We then concatenated the new de-novo libraries with the avian consensus sequences from Repbase [93], hooded crow [94], blue-capped cordon blue [95], flycatcher [96], and paradise crow [23], and used this final library to mask all six genomes with RepeatMasker [97]. The new repeat libraries are given in Supplementary File S7 .…”

A population genomics approach to uncover the CNVs, and their evolutionary significance, hidden in reduced‐representation sequencing data sets

“…Nelson & Cresko, 2018; Poelstra et al., 2014; Todesco et al., 2019). In some cases, SVs are the long‐sought “mutation” underpinning, or contributing to, the genetic basis of traits relevant to adaptation and speciation (Van’t Hof et al., 2016; Weissensteiner et al., 2020). The joint analysis of sequence and structural variation is therefore necessary to capture the different axes of diversity and differentiation within and among populations, to identify the genomic basis and architecture of traits relevant for adaptation and speciation, and to pinpoint the evolutionary and demographic factors generating these patterns.…”

“…However, SVs are rarely analysed in a population genetics framework (but seeWeissensteiner et al, 2020), often due to lack of appropriate genomic resources (e.g. a high-quality reference genome is recommended for SV analysis) and the potential high-sequencing cost associated with reliably genotyping SVs in a high number of individuals.…”