Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.
复制标题
在高度濒临灭绝的伊比利亚山脉中，经常性人口瓶颈后的极端基因组侵蚀。
DOI：
10.1186/s13059-016-1090-1
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发表时间：
2016-12-14
期刊：
影响因子：
12.3
通讯作者：
Godoy JA
中科院分区：
文献类型：
--
作者：
Abascal F;Corvelo A;Cruz F;Villanueva-Cañas JL;Vlasova A;Marcet-Houben M;Martínez-Cruz B;Cheng JY;Prieto P;Quesada V;Quilez J;Li G;García F;Rubio-Camarillo M;Frias L;Ribeca P;Capella-Gutiérrez S;Rodríguez JM;Câmara F;Lowy E;Cozzuto L;Erb I;Tress ML;Rodriguez-Ales JL;Ruiz-Orera J;Reverter F;Casas-Marce M;Soriano L;Arango JR;Derdak S;Galán B;Blanc J;Gut M;Lorente-Galdos B;Andrés-Nieto M;López-Otín C;Valencia A;Gut I;García JL;Guigó R;Murphy WJ;Ruiz-Herrera A;Marques-Bonet T;Roma G;Notredame C;Mailund T;Albà MM;Gabaldón T;Alioto T;Godoy JA
对濒危物种的基因组研究提供了对它们进化和人口历史的洞察，揭示了可能限制它们生存能力的基因组侵蚀模式，并为有效保护它们提供了工具。伊比利亚山猫(Lynx Pardinus)是最濒危的猫科动物，也是濒临灭绝的物种的独特例子。我们生成了伊比利亚山猫基因组的第一个注释草稿，并对山猫的人口统计学、进化和种群遗传学进行了基于基因组的分析。我们在伊比利亚山猫的历史上发现了一系列严重的种群瓶颈，这些瓶颈早在20世纪已知的人口下降之前就出现了，并极大地影响了它的基因组进化。我们观察到与GC偏向基因转换相关的弱到强替换的比率显著降低，而转座元件的固定率增加。我们还在两个剩余的伊比利亚山猫种群中发现了多个遗传侵蚀的特征，包括高频率的潜在有害变异和替换，以及迄今为止报告的任何物种中最低的全基因组遗传多样性。在伊比利亚山猫基因组中观察到的基因组特征可能会降低适应性和适应潜力，从而阻碍短期和长期生存能力。本研究开发的知识和资源将促进猫科动物进化和保护基因组学的研究，并将有助于这一标志性物种的持续保护和管理。本文的在线版本(doi：10.1186/s1305910161090-1)包含补充材料，授权用户可以使用。
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species. The online version of this article (doi:10.1186/s13059-016-1090-1) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Al-Shahrour F;Minguez P;Tárraga J;Medina I;Alloza E;Montaner D;Dopazo J
通讯作者：
Dopazo J
影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
5.8
作者：
Al-Shahrour, F;Díaz-Uriarte, R;Dopazo, J
通讯作者：
Dopazo, J
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM