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，全球范围内正推进相关工作，以将受危物种恢复至其原生分布范围。物种恢复工作有赖于其历史多样性与分布的相关资料，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，诸多种群已局部灭绝，且人类已将部分个体迁移至原生分布范围之外。此外，传统分类学评估往往无法精准反映系统发育多样性（phylogenetic diversity）。本研究以切喉鳟（Oncorhynchus clarkii）为研究对象，通过整合大量记录人类活动导致其分布变化的历史档案资料，并结合19世纪（集约化鱼类放流前）与当代DNA样本的系统发育分析，提出了一种估算区域原生多样性与分布的通用方法。我们对落基山脉南部切喉鳟的研究发现了6个分化支系，其中2个支系可能已于20世纪早期灭绝。此前被认定为灭绝的第三个支系，却在其原生分布范围之外的一条溪流中被发现仍有存活。将历史与现代分布数据同放流记录进行对比后发现，当前切喉鳟的分布格局主要源于19世纪末至20世纪初，从两个系统发育与地理均存在差异的来源地开展的集约化放流活动。本研究记录了近期发生的物种灭绝事件、未被描述的支系、分类学谬误，以及鱼类人为迁移引发的分布范围剧变，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。