Data from: Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada (“Bi-State”) is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other Greater Sage-Grouse. The level of differentiation is much less than the divergence between Greater and Gunnison sage-grouse, supporting the idea that the Bi-State represents a unique population within the Greater Sage-Grouse. New genomic methods like the restriction-site-associated DNA (RAD-tag) method used here illustrate how increasing the number of markers and coverage of the genome can better characterize patterns of genetic variation, particularly among recently diverged taxa, providing vital information for conservation and management.

艾草松鸡（Sage-grouse）是北美西部艾草灌丛栖息地的标志性物种，其种群数量正持续下降，保护管理工作有赖于对整个分布景观内遗传变异的深入认知。目前学界已依据形态学特征、行为模式以及中性遗传标记的变异情况，确认艾草松鸡包含两个独立物种：大艾草松鸡（Greater Sage-Grouse, Centrocercus urophasianus）与甘尼森艾草松鸡（Gunnison Sage-Grouse, C. minimus）。沿加利福尼亚州与内华达州边境分布的邻域大艾草松鸡群体（被称为“双州种群（Bi-State）”），在相同的中性遗传标记上同样呈现出遗传分化，但其行为与形态特征并无显著差异。由于在近期分化的类群中划定分类学边界、确定保护单元往往颇具难度，且高度偏斜的交配系统会进一步加剧这一复杂性，因此我们借助新型基因组学方法，大幅提升了以更高分辨率表征遗传变异的能力。我们在甘尼森艾草松鸡、大艾草松鸡与双州种群艾草松鸡中鉴定出数千个单核苷酸多态性位点（single-nucleotide polymorphisms, SNPs），并利用这些位点全面分析了这三类群体的遗传多样性水平与遗传分化程度。甘尼森艾草松鸡与大艾草松鸡之间的成对多位点固定指数（FST）高达0.49，主坐标分析与基于模型的聚类均能将样本按物种明确区分。甘尼森艾草松鸡群体内的现存遗传变异水平较低。双州种群同样与大艾草松鸡存在显著遗传分化，尽管分化程度较弱（FST=0.09），遗传聚类结果也印证了其与大艾草松鸡之间的基因交流有所减少。在覆盖分布范围南部半区的大艾草松鸡样本中，未发现类似的遗传分化结构。据此，我们提供了更为确凿的遗传学证据，支持将甘尼森艾草松鸡认定为遗传多样性较低的独立物种。此外，本研究证实双州种群与其他大艾草松鸡群体存在遗传分化；其分化程度远低于大艾草松鸡与甘尼森艾草松鸡之间的分化程度，这契合“双州种群是大艾草松鸡内一个独特种群”的学术观点。本研究使用的限制性酶切位点关联DNA（restriction-site-associated DNA, RAD-tag）测序法这类新型基因组学方法表明，增加标记数量与基因组覆盖度，能够更好地表征近期分化类群的遗传变异格局，从而为保护与管理工作提供关键科学依据。