Data from: Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

Hybrid zones are geographic regions where isolating barriers between
divergent populations are challenged by admixture. Identifying factors
that facilitate or inhibit hybridization in sympatry can illuminate the
processes that maintain those reproductive barriers. We analyzed patterns
of hybridization and phenotypic variation across two newly-discovered
hybrid zones between three subspecies of barn swallow (Hirundo rustica).
These subspecies differ in ventral coloration and wing length, traits that
are targets of sexual and natural selection, respectively, and are
associated with genome-wide differentiation in allopatry. We tested the
hypothesis that the degree of divergence in these traits is associated
with the extent of hybridization in secondary contact. We applied measures
of population structure based on > 23,000 SNPs to confirm that
named subspecies correspond to distinct genomic clusters, and assessed
coincidence between geographic clines for ancestry and phenotype. Although
gene flow was ongoing across both hybrid zones and pairwise FST between
subspecies was extremely low, we found striking differences in the extent
of hybridization. In the more phenotypically differentiated subspecies
pair, clines for ancestry, wing length, and ventral coloration were steep
and coincident, suggestive of strong isolation and, potentially, selection
associated with phenotype. In the less phenotypically differentiated pair,
gene flow and phenotypic variation occured over a wide geographic span,
indicative of weaker isolation. Traits associated with genome-wide
differentiation in allopatry may thus also contribute to isolation in
sympatry. We discuss potentially important additional roles for
evolutionary history and ecology in shaping variation in the extent
hybridization between closely related pairs of subspecies.

杂交带（hybrid zone）是指分化种群间的生殖隔离屏障受到遗传渐渗挑战的地理区域。明确同域分布（sympatry）种群中促进或抑制杂交的关键因素，可为阐明维持此类生殖隔离的内在机制提供重要启示。我们以家燕（Hirundo rustica）3个亚种间新近发现的2个杂交带为研究对象，分析了其中的杂交模式与表型变异特征。这些亚种在腹部羽色与翼长性状上存在显著分化：其中腹部羽色是性选择（sexual selection）的作用靶标，翼长则受自然选择（natural selection）调控，且二者均与异域分布（allopatry）种群间的全基因组分化（genome-wide differentiation）显著相关。我们验证了如下假说：上述性状的分化程度，与亚种次生接触（secondary contact）区域内的杂交程度存在关联。我们基于超过23000个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点计算种群结构（population structure）指标，证实了已命名亚种对应独立基因组聚类（genomic clusters）的结论，并评估了祖源成分与表型的地理渐变群（geographic cline）之间的重合度。尽管两个杂交带内均存在持续的基因流（gene flow），且亚种间的成对固定指数（fixation index, FST）极低，但我们仍观测到不同杂交带的杂交程度存在显著差异。在表型分化程度更高的亚种对中，祖源成分、翼长与腹部羽色的地理渐变群均较为陡峭且重合度极高，这提示存在较强的生殖隔离，且可能存在与表型相关的选择作用。而在表型分化程度较低的亚种对中，基因流与表型变异的地理分布跨度更广，表明其生殖隔离强度较弱。由此可见，与异域种群全基因组分化相关的性状，同样可在同域分布种群间参与生殖隔离的维持。我们还进一步探讨了进化历史与生态因子在塑造近缘亚种对间杂交程度变异中的潜在重要作用。