Conservation genomics helps avert multiple extinction factors in the critically endangered Siamese crocodile Crocodylus siamensis

Endangered populations require critical intervention to arrest as well as revert the effects of genetic impoverishment. While many studies do routinely access evolutionary dynamics of isolated populations and in many cases endangered populations, fewer studies bridge the gap between research and practical conservation management.In the past decade, sequencing of whole genomes and genome-wide markers have become a standard of molecular ecology as well as evolutionary studies, however much is yet to be done to utilize genome-wide data for field-based conservation of endangered populations.In our present investigation, we aimed to fill this void by using genome-wide markers to address conservation management of the critically endangered Siamese crocodiles. We obtained thousands of loci from reduced representation libraries and were able to identify host of genetic factors that afflict the species. Our results point towards contemporary as well as ancient introgression within Siamese crocodiles. We recovered genetic signatures of past population declines closely correlating with anthropogenic practice of poaching and harvest. In addition, we observed high extinction probability of local extinction in the wild in next few generations if drastic steps are not taken to replenish the genetic stock of the species. Our investigation into captive bred populations obtained evidence of inbreeding-related birth defects and identified genomic regions responsible for development associated with these regions.

濒危种群亟需采取关键干预手段，以遏制并逆转遗传耗竭（genetic impoverishment）所造成的负面影响。尽管诸多研究已常规开展孤立种群（以及多数场景下濒危种群）的演化动态探究，但能够弥合基础研究与实际保护管理之间鸿沟的研究仍相对匮乏。过去十余年间，全基因组测序与全基因组标记（genome-wide markers）已成为分子生态学与演化研究的常规手段，但如何将全基因组数据应用于濒危种群的野外保护，仍有大量工作有待开展。在本研究中，我们旨在借助全基因组标记填补这一研究空白，以探究极危物种暹罗鳄（Siamese crocodile）的保护管理策略。我们通过简化基因组文库（reduced representation libraries）获取了数千个基因座（loci），并成功识别出大量影响该物种的遗传因素。研究结果显示，暹罗鳄体内同时存在当代与古代的基因渐渗（introgression）现象。我们检出了指示过去种群衰退的遗传信号，该衰退与人类偷猎与捕获的人为活动密切相关。此外，若不采取有力措施补充该物种的遗传资源（genetic stock），我们预测该物种未来数代内的野生种群将面临极高的局域灭绝概率。我们针对人工繁育种群的研究发现了近交（inbreeding）相关出生缺陷的证据，并识别出与这类出生缺陷发育相关的基因组区域。