Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
Front Zool. 2009 Dec 9;6:29. doi: 10.1186/1742-9994-6-29.
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.
古北区支持的鸟类物种相对较少，但最近的分子研究表明，可能还有隐藏的谱系尚未被识别。广泛调查细胞色素 c 氧化酶 I（COI）序列或 DNA 条码可以通过为物种分配提供分子诊断来提供帮助。条码已经在近北极地区得到了广泛的调查，这为该地区提供了一个有趣的比较；这些地区之间的动物群交流非常活跃。我们探索了古北区鸟类种内和种间的 COI 序列差异，包括来自俄罗斯、哈萨克斯坦和蒙古的样本。到目前为止，对于分析条码数据的最佳方法还没有共识。我们利用这个机会比较和对比了条码研究中常用的三种不同方法：基于聚类的、基于距离的和基于特征的方法。
我们从 1674 个代表 398 种古北区鸟类的标本中生成了 COI 序列。这些序列与北美同源种的已发表 COI 序列合并，创建了一个包含 599 种 2523 个序列的最终数据集。分析的 96%的物种可以使用所使用的方法之一或组合准确识别。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。对于一些选择的物种组，基于特征的方法提供了额外的分辨率。在五个无法区分的物种组中，大多数是对，除了一个由鲱鸥复合体组成的更大的组。多达 44 个物种表现出深刻的种内分化，其中许多与先前描述的系统地理格局和特有热点相对应。
古北区东部鸟类的 COI 序列差异与其他温带地区鸟类的观察结果基本一致。序列变化主要与分类学边界一致；这种趋势的偏差揭示了被忽视的生物模式，在某些情况下，还揭示了被忽视的物种。需要进一步研究来进一步完善一些古北区鸟类的分类地位，但像这样的大规模遗传调查可能有助于这项工作。DNA 条码是快速物种鉴定的实用手段，尽管有效的分析方法可能需要采用两级方法来区分密切相关的物种对。
