Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
Mol Phylogenet Evol. 2012 Jan;62(1):397-406. doi: 10.1016/j.ympev.2011.10.012. Epub 2011 Oct 31.
Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography. This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at low cost. We explore cases of recent divergence in four phylogenetically diverse avian systems using a method for quick and cost-effective generation of primary DNA sequence data using pyrosequencing. NGS data were processed using an analytical pipeline that reduces many reads into two called alleles per locus per individual. Using single nucleotide polymorphisms (SNPs) mined from the loci, we detected population differentiation in each of the four bird systems, including: a case of ecological speciation in rails (Rallus); a rapid postglacial radiation in the genus Junco; recent in situ speciation among hummingbirds (Trochilus) in Jamaica; and subspecies of white-crowned sparrows (Zonotrichia leucophrys) along the Pacific coast. The number of recovered loci aligning closely to chromosomal locations on the zebra finch (Taeniopygia guttata) genome was highly correlated to the size of the chromosome, suggesting that loci are randomly distributed throughout the genome. Using eight loci found in Zonotrichia and Junco lineages, we were also able to generate a species tree of these sparrow sister genera, demonstrating the potential of this method for generating data amenable to coalescent-based analysis. We discuss improvements that should enhance the method's utility for primary data generation.
下一代测序 (NGS) 技术正在彻底改变许多生物学领域，但在系统发生地理学中却迟迟未能扎根。这部分是由于使用 NGS 以低成本对许多个体的同源 DNA 片段进行测序的难度。我们使用一种快速且具有成本效益的焦磷酸测序方法来探索四个在系统发生上多样化的鸟类系统中的近期分歧案例，以生成原始 DNA 序列数据。使用一种分析管道对 NGS 数据进行处理，该管道将每个个体每个基因座的许多读取减少为两个称为等位基因。从基因座中挖掘出的单核苷酸多态性 (SNP)，我们在四个鸟类系统中的每一个系统中都检测到了种群分化，包括：一种在 Rallus 属中的生态物种形成案例；Junco 属中快速的后冰川辐射；牙买加的蜂鸟（Trochilus）中最近的原地物种形成；以及太平洋沿岸的白冠麻雀亚种（Zonotrichia leucophrys）。与斑胸草雀（Taeniopygia guttata）基因组上的染色体位置紧密匹配的回收基因座数量与染色体的大小高度相关，这表明基因座随机分布在整个基因组中。使用在 Zonotrichia 和 Junco 谱系中发现的八个基因座，我们还能够生成这些麻雀姐妹属的种系发生树，证明了该方法在生成适合合并分析的数据方面的潜力。我们讨论了应提高该方法在原始数据生成方面的实用性的改进。
