Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate
change is necessary for maintaining global biodiversity moving forward.
Studies to date have largely focused on sequence variation, yet there is
growing evidence that suggests that changes in genome structure may be an
even more significant source of adaptive potential. The American pika
(Ochotona princeps) is an alpine specialist that shows some evidence of
adaptation to climate along elevational gradients, but previous work has
been limited to single nucleotide polymorphism (SNP)-based analyses within
a fraction of the species range. Here, we investigated the role of copy
number variation underlying patterns of local adaptation in the American
pika using genome-wide data previously collected across the entire species
range. We identified 37-193 putative copy number variants (CNVs)
associated with environmental variation (temperature, precipitation, solar
radiation) within each of the six major American pika lineages, with
patterns of divergence largely following elevational and latitudinal
gradients. Genes associated (n=158) with independent annotations across
lineages, variables, and/or CNVs had functions related to mitochondrial
structure/function, immune response, hypoxia, olfaction, and DNA repair,
some of which have been previously linked to putative high elevation
and/or climate adaptation that may serve as important targets in future
studies.

深入理解气候变化适应的遗传基础，对于未来维持全球生物多样性至关重要。迄今为止的研究主要集中在序列变异上，但越来越多的证据表明，基因组结构的变化可能是适应性潜力更重要的来源。美洲鼠兔（Ochotona princeps）是一种高山特化物种，已有证据表明其沿海拔梯度对气候存在适应性，但此前的研究仅限于基于单核苷酸多态性（single nucleotide polymorphism, SNP）的分析，且仅覆盖该物种分布范围的一小部分。本研究利用此前在该物种全分布范围内收集的全基因组数据，探究了拷贝数变异（copy number variation, CNV）在美洲鼠兔局部适应模式中的作用。我们在美洲鼠兔的六个主要谱系中，各鉴定出37至193个与环境变异（温度、降水、太阳辐射）相关的潜在拷贝数变异体（CNVs），其分化模式在很大程度上遵循海拔和纬度梯度。在谱系、变量和/或CNVs间具有独立注释的相关基因（n=158），其功能涉及线粒体结构/功能、免疫应答、缺氧、嗅觉及DNA修复等；其中部分基因此前已被认为与潜在的高海拔和/或气候适应相关，或可作为未来研究的重要靶点。