Countering criticisms of single mitochondrial DNA gene barcoding in birds
Countering criticisms of single mitochondrial DNA gene barcoding in birds
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DOI：
10.1111/j.1755-0998.2009.02650.x
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发表时间：
2009-05-01
影响因子：
7.7
通讯作者：
Elbourne, Rebecca F.
中科院分区：
文献类型：
--
作者：
Baker, Allan J.;Tavares, Erika Sendra;Elbourne, Rebecca F.
对单个mtDNA基因条形码的普遍批评包括无法识别新进化的物种，使用物种界限阈值，选择性扫描的影响和物种内互惠单系的偶然发生，无法处理杂交和不完整的谱系分类，以及多基因在物种识别中的优势。我们在鸟类中解决了这些批评，因为大多数物种都是已知的，因此提供了理想的测试数据集，我们通过选择的例子来论证，除了阈值之外，这些批评对鸟类分类学没有问题。即使是亲缘关系密切的姐妹种也有独特的COI条形码，但基于种内和种间变异比率的距离阈值不可能普遍适用。相反，更严格的物种划分方法应该采用基于聚结的技术，包括对偶然性互反单系的测试，以及谱系分离和序列分化的时间。不完整的谱系分类也很容易用DNA条形码检测到，而且通常是在较年轻的时间框架中，而不是在进化较慢的核基因中。当DNA条形码检测到不同的相互单系谱系时，COI序列可以与多个核基因结合，以区分由高雌性亲缘性或区域选择性扫描引起的物种形成或种群细分。尽管选择性扫描越来越多地被用来解释COI基因树中浅层种内聚聚的模式，但由于个体采样有限，并且检测单个基因的额外mtDNA单倍型的能力降低，因此在这种推测中需要谨慎。
General criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species-delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within-species and among-species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent-based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within-species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene.