Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome

Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO > 95% using “insecta_ob9” reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.

摘要 解析环境变异如何影响种群遗传结构，有助于预测环境变化对种群连通性、遗传多样性及进化潜力的影响。本研究采用河流景观基因组学（riverscape genomics）建模方法，针对美国蒙大拿州西北部40个采样点的两种石蝇物种，探究气候与生境变量如何与遗传变异模式相关联：其中一种物种栖息于干流河道（Sweltsa coloradensis），另一种则栖息于支流（Sweltsa fidelis）。我们为Sweltsa coloradensis构建了基因组草图组装（N50=0.251 Mbp，采用"insecta_ob9"参考基因集时，BUSCO评估完整性超过95%）。我们对372个Sweltsa coloradensis个体进行了1930个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点的基因分型，对153个Sweltsa fidelis个体进行了520个SNP位点的基因分型。研究发现，Sweltsa coloradensis的遗传多样性高于Sweltsa fidelis，但两种物种在各自采样点间的遗传分化水平几乎一致（二者的全局位点中位数FST（Fixation Index，固定指数）均为0.000），尽管它们所处的河流网络位置存在差异。为开展景观基因组学研究及选择压力检测，我们构建了一套筛选标准更为宽松的数据集（其中Sweltsa coloradensis和Sweltsa fidelis分别包含3454和1070个SNP位点）。环境变量（夏季平均降水量、坡度、坡向、6月河流平均水温、土地覆盖类型）与Sweltsa coloradensis的19个推定适应性位点存在关联；而Sweltsa fidelis仅存在1个推定适应性位点（与坡向相关）。值得注意的是，本研究还检测到多种Sweltsa属物种间存在潜在杂交现象，这在此前从未被报道过。此类针对多个近缘物种的适应性变异开展检测的研究，有助于评估景观连通性，以及种群和群落对环境变化的脆弱性，而这类研究正是当前所亟需的。