Estimation of a Killer Whale (Orcinus orca) Population's Diet Using Sequencing Analysis of DNA from Feces.
Estimation of a Killer Whale (Orcinus orca) Population's Diet Using Sequencing Analysis of DNA from Feces.
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DOI：
10.1371/journal.pone.0144956
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Park LK
中科院分区：
文献类型：
--
作者：
Ford MJ;Hempelmann J;Hanson MB;Ayres KL;Baird RW;Emmons CK;Lundin JI;Schorr GS;Wasser SK;Park LK
估计食物组成对于了解捕食者和猎物之间的相互作用，从而阐明生态系统功能是重要的。然而，许多物种的饮食很难直接观察。因此，对野外收集的粪便进行遗传分析是深入了解野生动物饮食的有用工具。在这项研究中，我们使用高通量DNA测序定量估计野生虎鲸（Orcinus orca）的濒危种群的饮食组成，在他们的夏季范围在萨利希海。我们将2006年至2011年5月至9月期间收集的175份粪便样本分为13个样本组。还创建了两个已知的DNA组成对照组。使用Illumina MiSeq测序系统在线粒体基因组中的16s基因的约330bp片段处对每组进行测序。经过几个质量控制步骤后，将4，987，107个单独的序列与包含19个潜在鱼类猎物物种的定制序列数据库进行比对，并确定每个粪便衍生序列的最可能物种。基于这些比对，鲑科动物占总序列的>98.6%，因此占推断的饮食。在六种鲑鱼中，奇努克鲑鱼占79.5%的序列，其次是银鲑（15%）。多年来，出现了一个明确的模式，奇努克鲑鱼在夏初占估计饮食的主导地位，而银鲑在夏末平均占饮食的40%以上。红鲑似乎偶尔重要，在一些样本组中>18%。很少观察到非鲑鱼。我们的研究结果是一致的，与早期的结果的基础上表面猎物仍然，并确认了奇努克鲑鱼在这个人口的夏季饮食的重要性。
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet.