Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in the Yucatan jay (Cyanocorax yucatanicus), a tropical bird endemic to the Yucatán Peninsula. This peninsula is characterized by a precipitation and vegetation gradient—from dry to evergreen tropical forests—that is associated with morphological variation in this species. We found a moderate level of nucleotide diversity (π = .008) and little evidence for genetic differentiation among vegetation types. Analyses of neutral and putatively adaptive SNPs (identified by complementary genome-scan approaches) indicate that IBD is the most reliable explanation to account for frequency distribution of the former, while IBE has to be invoked to explain those of the later. These results suggest that selective factors acting along a vegetation gradient can promote local adaptation in the presence of gene flow in a vagile, nonmigratory and geographically restricted species. The putative candidate SNPs identified here are located within or linked to a variety of genes that represent ideal targets for future genomic surveys.

解析表型变异的遗传基础及其与环境的关联，是理解局部适应演化机制的核心所在。这类演化模式在沿生境梯度分布的种群中尤为值得关注——这类种群的遗传结构可由距离隔离（isolation by distance, IBD）和/或环境隔离（isolation by environment, IBE）驱动。本研究利用从双酶切限制性位点相关DNA测序（double-digest restriction site-associated DNA sequencing, ddRAD-Seq）的双端测序数据中获取的约1600个高质量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点变异，对尤卡坦半岛特有热带鸟类——尤卡坦松鸦（Cyanocorax yucatanicus）中与IBD和IBE相关的假说进行了检验。尤卡坦半岛存在降水与植被梯度变化：从干旱林到常绿热带林，这一梯度与该物种的形态变异存在关联。本研究发现该物种的核苷酸多样性（π = 0.008）处于中等水平，且未检测到不同植被类型间存在显著的遗传分化。通过互补基因组扫描法鉴定的中性与推定适应性SNP的分析结果显示：距离隔离是解释前者（中性SNP）频率分布的最可靠因素，而环境隔离则可用于解释后者（推定适应性SNP）的频率分布。上述结果表明，在活动能力较强但不迁徙且地理分布受限的物种中，沿植被梯度发挥作用的选择因子可在存在基因流的情况下促进局部适应。本研究鉴定出的推定候选SNP位点位于多种基因内部或与其连锁，这些基因可作为未来基因组研究的理想靶标。