Filling the gap - COI barcode resolution in eastern Palearctic birds.
Filling the gap - COI barcode resolution in eastern Palearctic birds.
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DOI：
10.1186/1742-9994-6-29
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发表时间：
2009-12-09
影响因子：
2.8
通讯作者：
Hebert PD
中科院分区：
文献类型：
--
作者：
Kerr KC;Birks SM;Kalyakin MV;Red'kin YA;Koblik EA;Hebert PD
古北界的鸟类物种相对较少，但最近的分子研究表明，神秘的谱系可能仍然存在未被识别。对细胞色素c氧化酶I（COI）序列或DNA条形码的广泛调查可以通过提供物种分配的分子诊断来帮助这方面的工作。条形码已经在新北区进行了广泛的调查，这提供了一个有趣的比较，这一地区之间的动物区系交换一直非常动态。我们探讨了COI序列内和古北鸟类物种之间的差异，包括来自俄罗斯，哈萨克斯坦和蒙古的样本。到目前为止，对于分析条形码数据的最佳方法还没有达成共识。我们利用这个机会，比较和对比三种不同的方法，常规采用条形码研究：基于聚类，基于距离，和基于字符的方法。我们从代表398个古北种的1,674个标本中产生了COI序列。将这些序列与已发表的北美同源物COI序列合并，创建了599个物种的2，523个序列的最终数据集。96%的物种分析可以准确地确定使用一种或多种方法的组合。大多数物种可以单独使用基于聚类或基于距离的方法快速分配。对于一些选定的物种组，基于特征的方法提供了额外的分辨率。在这五组难以区分的物种中，除了一个更大的组包括银鸥复合体之外，大多数都是成对的。多达44种物种表现出深刻的种内分歧，其中许多对应于先前描述的地理格局和特有热点。东部古北界鸟类的COI序列差异与其他温带地区的鸟类基本一致。序列变异主要与分类界限一致;偏离这一趋势揭示了被忽视的生物模式，在某些情况下，被忽视的物种。需要更多的研究来进一步完善一些古北鸟类的分类地位，但像这样的大型遗传调查可能会促进这一努力。DNA条形码是快速确定物种的一种实用手段，但有效的分析方法可能需要两个层次的方法来区分密切相关的物种对。
The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods. We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots. COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
9.8
作者：
Hebert PD;Stoeckle MY;Zemlak TS;Francis CM
通讯作者：
Francis CM
影响因子：
3.1
作者：
Areta, Juan I.;Pearman, Mark
通讯作者：
Pearman, Mark
影响因子：
7.7
作者：
Baker, Allan J.;Tavares, Erika Sendra;Elbourne, Rebecca F.
通讯作者：
Elbourne, Rebecca F.
综合分类学：传统方法和DNA条形码，用于鉴定丝虫类蠕虫和相关寄生虫（Nematoda）。
影响因子：
2.8
作者：
Ferri E;Barbuto M;Bain O;Galimberti A;Uni S;Guerrero R;Ferté H;Bandi C;Martin C;Casiraghi M
通讯作者：
Casiraghi M