Environmental adaptation in an alpine ground beetle

We test for evidence of adaptive evolution in the alpine ground beetle Nebria vandykei. First, we explore the genetic pathways induced during environmental stress responses through RNA sequencing, showing that cold, heat and desiccation stress activate a largely non-overlapping set of molecular pathways. Using additional transcriptome sequencing, we estimate the evolutionary relationship of N. vandykei to related species in the subgenus Catonebria and several outgroups. Phylogenetic analyses suggest a history of admixture or very rapid diversification underlies the evolution of N. vandykei. Finally, using tests for positive selection polarized by high and low elevation relatives, we demonstrate selection acting on stress response pathways, as well as pathways known to function in tolerance to cold and hypoxic environments. , We sampled four closely related Nebria (Catonebria) taxa from western North America: N. meanyi, N. piperi, N. riversi, and N. vandykei. The species N. meanyi and N. piperi are found in small mid-elevation streams and large low-elevation rivers, respectively, while the other two taxa are alpine specialists that are found inhabiting talus, riparian, and seep habitats on or near high-elevation snowfields. We sampled 20 N. vandykei (grouped by physiological assay: control, cold stress, heat stress, and desiccation stress) and a single adult specimen from each of the other species, while three N. riversi were available from a previous project (NCBI accessions: SRR12967585, SRR12967587 and SRR12967588). We additionally sampled N. (Nivalonebria) paradisi and N. (Neaptenonebria) spatulata sierrae, the closest two outgroup lineages to Nebria (Catonebria), as well as outgroups that span the tribe Nebriini by including Leistus (Leistus) frater, Nippononebria (Vancouveria) altisierrae, and Nebria (..., Use text editor to open all files. Excel can be used to open the annotation files (.xlsx). R scripts (.R) can be opened in R.Â

我们测试了高山步甲虫Nebria vandykei的适应性进化（adaptive evolution）证据。首先，通过RNA测序（RNA sequencing）探索环境压力反应过程中诱导的遗传通路，结果显示冷、热及干燥应激激活的分子通路大多不重叠。利用额外的转录组测序（transcriptome sequencing），我们估计了N. vandykei与Catonebria亚属相关物种及若干外类群（outgroups）的进化关系。系统发育分析（phylogenetic analyses）表明，遗传混合（admixture）历史或极快速多样化是N. vandykei进化的基础。最后，基于高海拔与低海拔近缘种极化的正选择（positive selection）测试，我们证明选择作用于压力反应通路，以及已知在耐寒和低氧环境耐受中发挥功能的通路。

我们从北美西部采集了四个近缘的Nebria（Catonebria）类群（taxa）：N. meanyi、N. piperi、N. riversi和N. vandykei。其中N. meanyi和N. piperi分别见于小型中海拔溪流和大型低海拔河流，而另外两个类群为高山特化种（alpine specialists），栖息于高海拔雪原或其附近的碎石堆、河岸及渗流生境。我们采集了20个N. vandykei样本（按生理实验（physiological assay）分组：对照、冷应激、热应激、干燥应激），以及其他物种各1个成体标本；此外，3个N. riversi样本来自先前的项目（NCBI登录号：SRR12967585、SRR12967587和SRR12967588）。我们还采集了与Nebria（Catonebria）亲缘关系最近的两个外类群支系——N. (Nivalonebria) paradisi和N. (Neaptenonebria) spatulata sierrae，以及覆盖Nebriini族的外类群，包括Leistus (Leistus) frater、Nippononebria (Vancouveria) altisierrae和Nebria（...

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