Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

Many species are threatened with extinction and efforts are underway worldwide to restore imperiled species to their native ranges. Restoration requires knowledge of species’ historic diversity and distribution, which may not be available. For some species, many populations were extirpated and humans moved individuals beyond their native range before native diversity and distribution were documented. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution by assembling a large archive of historical records documenting human-mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) coupled with a phylogenetic analysis of 19th century (before intensive fish stocking) and contemporary DNA samples. Our study of the trout in the southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historic and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy, and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.众多物种正面临灭绝威胁，全球范围内正开展相关保护工作，以将受危物种种群恢复至其原生分布范围。物种恢复工作需要掌握物种的历史多样性与分布信息，但此类资料往往难以获取。对于部分物种而言，在其原生多样性与分布被正式记录之前，诸多种群就已遭到灭绝，且人类已将个体转移至其原生分布范围之外。此外，传统分类学评估往往无法准确反映系统发育多样性。我们通过整合一套涵盖人类活动介导的割喉鳟（cutthroat trout, Oncorhynchus clarkii）分布变化的大型历史记录档案，并结合19世纪（集约化鱼类放养前）与当代DNA样本的系统发育分析，展示了一种估算区域原生多样性与分布的通用研究方法。我们对落基山脉南部割喉鳟的研究发现了六个分化进化支系，其中两个可能已于20世纪早期灭绝。此前被正式宣告灭绝的第三个支系，竟在其原生分布范围外的一条溪流中被发现仍有存活种群。将历史与现代分布数据与鱼类放养记录进行对比后发现，当前割喉鳟的分布格局在很大程度上源于19世纪末至20世纪早期，从两个系统发育与地理特征均存在显著差异的来源地开展的高强度鱼类放养活动。我们对近期物种灭绝事件、未被描述的进化支系、分类学误差，以及鱼类人为迁移引发的分布范围剧变的研究记录，凸显了在制定并实施受危与濒危物种保护计划时，历史档案资料的重要价值。