Unlocking the vault: next generation museum population genomics

Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here we circumvent these challenges by using custom, multiplexed, exon-capture to enrich and sequence ~11,000 exons (~4Mb) from early 20th century museum skins. We used this approach to test for changes in genomic diversity accompanying a climate-related range retraction in the alpine chipmunks (Tamias alpinus) in the high Sierra Nevada area of California, USA. We developed robust bioinformatic pipelines that rigorously detect and filter-out base misincorporations in DNA derived from skins, most of which li...

自然历史博物馆馆藏为解析物种如何响应环境变化（包括过去一个世纪以来突发的人为气候变化）提供了独特的研究资源。理想情况下，研究人员可对博物馆标本开展全基因组规模筛查，以探究环境变化引发的演化后果，但迄今为止，这类分析因处理历史标本典型的高度降解DNA所面临的多重挑战而受到严重限制。本研究通过定制化多重外显子捕获（exon-capture）技术，对20世纪早期博物馆馆藏皮肤标本中的约11000个外显子（约4Mb）进行富集与测序，从而克服了上述挑战。我们利用该方法，针对美国加利福尼亚州内华达山脉高海拔区域的高山花栗鼠（*Tamias alpinus*）展开研究，检测其伴随气候相关分布区收缩所发生的基因组多样性变化。我们开发了稳健的生物信息学分析流程（bioinformatic pipelines），可严格检测并滤除源自皮肤标本的DNA中的碱基错配掺入（base misincorporations），其中绝大多数……