School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
San Diego Zoo Global, San Diego, CA, USA.
Mol Ecol Resour. 2020 Nov;20(6):1526-1541. doi: 10.1111/1755-0998.13211. Epub 2020 Jul 24.
As species extinction rates increase, genomics provides a powerful tool to support intensive management of threatened species. We use the Tasmanian devil (Sarcophilus harrisii) to demonstrate how conservation genomics can be implemented in threatened species management. We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced-representation sequencing (RRS) of 98 founders of the same programme. A subset of the WGS samples was also sequenced by RRS, allowing us to directly compare genome-wide heterozygosity with estimates from RRS data. We found good congruence in interindividual variation and gene-ontology classifications between the two data sets, indicating that our RRS data reflect the genome well. We also attempted genome-wide association studies with both data sets (regarding breeding success), but the genomic data suffered from small sample size, while the RRS data suffered from lack of precision, highlighting a key trade-off in the design of conservation genomic research. Nevertheless, we identified a number of candidate genes that may be associated with variation in breeding success. Individual heterozygosity, as measured by WGS or RRS, was not associated with breeding success in captivity but was negatively associated with litter sizes of breeding females in the RRS data set. Our findings enable conservation managers to have confidence in RRS data while understanding its limitations, and provide avenues for further investigation into which processes underlie variation in breeding success in captive Tasmanian devils. We caution, however, that deep functional insights using RRS may be impaired by a lack of precision, especially when marker density is low.
随着物种灭绝率的增加，基因组学为支持受威胁物种的密集管理提供了强大的工具。我们使用袋獾（Sarcophilus harrisii）来演示保护基因组学如何在受威胁物种管理中实施。我们对来自圈养繁殖计划的 25 个个体进行了全基因组测序（WGS），并对同一计划的 98 个创始人进行了简化代表性测序（RRS）。WGS 样本的一部分也进行了 RRS 测序，使我们能够直接比较全基因组杂合度与 RRS 数据的估计值。我们发现两个数据集之间个体间变异和基因本体分类学之间存在良好的一致性，表明我们的 RRS 数据很好地反映了基因组。我们还尝试了这两个数据集的全基因组关联研究（关于繁殖成功率），但基因组数据受到样本量小的影响，而 RRS 数据受到缺乏精度的影响，突出了保护基因组学研究设计中的一个关键权衡。尽管如此，我们确定了一些可能与繁殖成功率变异相关的候选基因。通过 WGS 或 RRS 测量的个体杂合度与圈养繁殖成功率无关，但与 RRS 数据集的繁殖雌性产仔数呈负相关。我们的研究结果使保护管理者对 RRS 数据有信心，同时了解其局限性，并为进一步研究哪些过程导致圈养袋獾繁殖成功率的变化提供了途径。然而，我们警告说，由于缺乏精度，特别是在标记密度较低的情况下，使用 RRS 进行深入的功能洞察可能会受到影响。
