Secondary contact between closely related taxa represents a “moment of truth” for speciation — an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family — Myzomela cardinalis and Myzomela tristrami — carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.

Genomic structural mutations especially deletion are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species, including some crops, has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum (Sorghum bicolor (L.) Moench) is one of the most widely grown cereal crops in the world, and over the course of its history it has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity within the existing germplasm. In this study, we identified genome-wide deletions in the Biomass Association Panel (BAP), a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole genome resequencing data from every genotype, we found a total of 22,359 deletions after filtering. The size of deletions ranged from 51 to 89,716 bp with a median size of 956 bp. The global site frequency spectrum of the deletions fit a model of neutral evolution, suggesting that the majority of deletions were not under any types of selection. Clustering results based on SNPs separated the deletions of the genotypes into eight clusters which largely corresponded with geographic origins. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic (plant defense and bacterial resistance) and abiotic stress (drought and temperature) responses, supporting the possibility that at least some deletions contribute to local adaptation in sorghum.