Population genomic evidence of selection on structural variants in a natural hybrid zone
Population genomic evidence of selection on structural variants in a natural hybrid zone
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DOI：
10.1111/mec.16469
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发表时间：
2022-05-07
影响因子：
4.9
通讯作者：
Gompert，Zachariah
中科院分区：
文献类型：
--
作者：
Zhang，Linyi;Chaturvedi，Samridhi;Gompert，Zachariah
结构变异（SV）可以通过直接引起生殖隔离或抑制大基因组区域的重组来促进物种形成。虽然每种机制的例子都有记录，但缺乏对 SV 在物种形成中的作用的系统测试。在这里，我们利用长读长（牛津纳米孔）全基因组测序和两个 Lycaeides 蝴蝶类群（L.melissa 和 Jackson HoleLycaeides）之间的杂交区来全面评估 SV 的全基因组基因渗入模式，并将这些模式与物种形成的假设联系起来。我们发现超过 100,000 个 SV 在两个杂交物种内部或之间分离。 SV 和 SNP 在物种间表现出相似的遗传分化水平，但倒位除外，倒位的差异更大。我们检测到混合区 SV 基因座间渗入模式的可信变异，1419 个具有祖先信息的 SV 中有 562 个表现出偏离基于基因组平均祖先的零期望的基因组克隆。总体而言，杂交体在 SV 基因座上表现出向 Jackson HoleLycaeides 祖先的方向性转变，这与这些基因座平均比 SNP 基因座经历更多选择的假设一致。令人惊讶的是，我们发现缺失，而不是倒位，显示出对 Jackson HoleLycaeides 过多血统的最大偏向。杂种中过量的 Jackson HoleLycaeides 血统对于 Z 连锁 SV 和包含许多基因的倒位也特别明显。总之，我们的结果表明 SV 无处不在，并表明 SV 通常（尤其是缺失）可能会不成比例地影响杂交适应性，从而导致生殖隔离。
Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long‐read (Oxford nanopore) whole‐genome sequencing and a hybrid zone between twoLycaeidesbutterfly taxa (L.melissaand Jackson HoleLycaeides) to comprehensively evaluate genome‐wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry‐informative SVs exhibiting genomic clines that deviated from null expectations based on genome‐average ancestry. Overall, hybrids exhibited a directional shift towards Jackson HoleLycaeidesancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson HoleLycaeides. Excess Jackson HoleLycaeidesancestry in hybrids was also especially pronounced for Z‐linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.