Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?
Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?
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DOI：
10.1007/s10592-010-0096-6
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发表时间：
2010-10-01
影响因子：
2.2
通讯作者：
Jarman, Simon N.
中科院分区：
文献类型：
--
作者：
Deagle, Bruce E.;Chiaradia, Andre;Jarman, Simon N.
粪便或胃内容物的DNA条形码是一种新兴的饮食分析方法。我们pyrosequenced线粒体DNA 16S标记扩增的粪便圈养小企鹅（Eudyptula minor），以检查恢复的序列反映的比例的物种消费。我们还分析了从澳大利亚东南部的100个巢中收集的野生小企鹅粪便。在圈养研究中，皮尔彻德鱼是企鹅的主要食物，皮尔彻德鱼的DNA序列是最常见的序列。序列的其他三种鱼在恒定的质量比例（45：35：20）喂养都被检测到，但比例的序列（60：6：34）是相当大的不同，比饮食中的质量比例。基于鱼类mtDNA相对密度的校正因子并没有改善对饮食的估计。重复样品之间的一致性表明，所观察到的偏差导致猎物消化率的差异。从企鹅被圈养前食用的鱼类中检测到的DNA表明，粪便中的DNA信号在摄入后至少可以持续4天。在野生收集的粪便，24个不同的鱼类和1鱿鱼进行了鉴定，鱼，barracouta和皮尔彻德占这些序列的80%以上。我们的结果强调，在饮食条形码研究中回收的DNA序列可以提供有关饮食组成的半定量信息，但这些数据应具有较宽的置信区间。
DNA barcoding of faeces or stomach contents is an emerging approach for dietary analysis. We pyrosequenced mtDNA 16S markers amplified from faeces of captive little penguins (Eudyptula minor) to examine if recovered sequences reflect the proportions of species consumed. We also analysed wild little penguin faeces collected from 100 nests in southeast Australia. In the captive study, pilchards were the primary fish fed to the penguins and DNA sequences from pilchard were the most common sequences recovered. Sequences of three other fish fed in constant mass proportions (45:35:20) were all detected, but proportions of sequences (60:6:34) were considerably different than mass proportions in the diet. Correction factors based on relative mtDNA density in the fish did not improve diet estimates. Consistency between replicate samples suggests that the observed bias resulted from differences in prey digestibility. Detection of DNA from fish consumed before the penguins were brought into captivity indicates that a DNA signal in faeces can persist for at least 4 days after ingestion. In the wild-collected faeces, 24 distinct fish and 1 squid were identified; anchovy, barracouta and pilchard accounted for over 80% of these sequences. Our results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals.