Unlocking the vault: next-generation museum population genomics.
Unlocking the vault: next-generation museum population genomics.
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DOI：
10.1111/mec.12516
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发表时间：
2013-12
影响因子：
4.9
通讯作者：
Moritz C
中科院分区：
文献类型：
--
作者：
Bi K;Linderoth T;Vanderpool D;Good JM;Nielsen R;Moritz C
自然历史博物馆的藏品为了解物种如何应对环境变化提供了独特的资源，包括上世纪突然的人为气候变化。理想情况下，研究人员将对博物馆标本进行基因组规模的筛选，以探索环境变化的进化后果，但迄今为止，这种分析受到了历史样本中典型的高度降解DNA的众多挑战的严重限制。在这里，我们通过使用定制的、多路复用的外显子捕获来富集和测序来自20世纪早期世纪博物馆皮肤的~ 11，000个外显子（~ 4 Mb）来规避这些挑战。我们用这种方法来测试的基因组多样性的变化，伴随着气候相关的范围收缩的高山花栗鼠（塔米厄斯alpinus）在高的Sierra内华达州地区的加州，美国。我们开发了强大的生物信息学管道，可以严格检测和过滤来自皮肤的DNA中的碱基错误，其中大部分可能是由死后损伤引起的。此外，为了适应与中低覆盖率数据相关的基因分型不确定性，我们应用了最近开发的概率方法来调用SNP并估计等位基因频率和联合位点频谱。我们的研究结果表明，增加的遗传细分范围收缩，但没有改变整体的遗传多样性在非同义或同义的网站。本案例研究展示了将新兴的基因组学和统计学工具整合到基于博物馆收藏的人群基因组学应用中的优势。这些技术进步大大提高了博物馆藏品的价值，即使在缺乏预先存在的参考资料的情况下，也指出了进化和保护生物学的广泛潜在应用。
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 likely resulted from post-mortem damage. Furthermore, to accommodate genotyping uncertainties associated with low-medium coverage data, we applied a recently developed probabilistic method to call SNPs and estimate allele frequencies and the joint site frequency spectrum. Our results show increased genetic subdivision following range retraction, but no change in overall genetic diversity at either non-synonymous or synonymous sites. This case study showcases the advantages of integrating emerging genomic and statistical tools in museum collection-based population genomic applications. Such technical advances greatly enhance the value of museum collections, even where a pre-existing reference is lacking, and points to a broad range of potential applications in evolutionary and conservation biology.
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影响因子：
64.8
作者：
Bos, Kirsten I.;Schuenemann, Verena J.;Golding, G. Brian;Burbano, Hernan A.;Waglechner, Nicholas;Coombes, Brian K.;McPhee, Joseph B.;DeWitte, Sharon N.;Meyer, Matthias;Schmedes, Sarah;Wood, James;Earn, David J. D.;Herring, D. Ann;Bauer, Peter;Poinar, Hendrik N.;Krause, Johannes
通讯作者：
Krause, Johannes
影响因子：
6.5
作者：
Guschanski K;Krause J;Sawyer S;Valente LM;Bailey S;Finstermeier K;Sabin R;Gilissen E;Sonet G;Nagy ZT;Lenglet G;Mayer F;Savolainen V
通讯作者：
Savolainen V
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
4.9
作者：
Good, Jeffrey M.;Hird, Sarah;Sullivan, Jack
通讯作者：
Sullivan, Jack
影响因子：
6.3
作者：
Glenn, TC;Stephan, W;Braun, MJ
通讯作者：
Braun, MJ