DNA barcoding birds: from field collection to data analysis.
DNA barcoding birds: from field collection to data analysis.
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DOI：
10.1007/978-1-61779-591-6_7
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发表时间：
2012-01-01
期刊：
影响因子：
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通讯作者：
Tubaro, Pablo L
中科院分区：
文献类型：
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作者：
Lijtmaer, Dario A;Kerr, Kevin C R;Tubaro, Pablo L
截至2011年2月，COI DNA条形码序列（线粒体基因细胞色素c氧化酶I 5'端的648 bp片段，动物的标准DNA条形码）已从3，800个物种的23，000多个鸟类标本中收集，占世界鸟类的三分之一以上。在这里，我们详细介绍了从鸟类中获取DNA条形码的方法，涵盖了从野外收集到数据分析的整个过程。我们强调的过程中的关键方面，并更详细地描述那些特别是在鸟类的情况下有关。我们提供有关标本收集的基本信息，DNA提取和PCR的详细协议，以及测序方法的基本方面。特别是，我们强调了引物对和热循环配置文件与成功的扩增和测序范围广泛的鸟类。最后，我们简要地回顾了数据分析的方法，包括错误的检测（如污染，错误识别，或假基因的扩增），物种分辨率的评估，不同种内谱系的检测，和未知标本的鉴定。
As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5' end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens.