Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.
Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.
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DOI：
10.1371/journal.pone.0032544
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Zhang AB
中科院分区：
文献类型：
--
作者：
Dai QY;Gao Q;Wu CS;Chesters D;Zhu CD;Zhang AB
近缘种与亲缘关系较近的物种不同，由于其遗传变异的重叠性，给系统发育重建和物种鉴定带来了很大的挑战。利用一个标准的细胞色素c氧化酶亚基I（COI）基因和两个可选择的内转录间隔区（ITS）基因（ITS 1和ITS 2），对我国松毛虫近缘种群进行了检测。5种不同的系统发育/DNA条形码分析方法（最大似然（ML）/邻接（NJ）、“最佳接近匹配”（BCM）、最小距离（MD）和基于BP的方法（BP）），代表了该领域常用的方法学（基于树和非基于树），被应用于单基因和多基因分析。结果表明：3个亲缘关系较远的种（Dendrolimus superans、D. houi，胡氏D. kikuchii的单基因和多基因系统发育关系，以及3个亲缘关系较近的种D. punctatus、油松毛虫D.油松D. spectabilis，这是传统的树构建方法所不能解决的问题。此外，我们发现标准COI条形码优于两个核ITS基因，无论使用何种方法。COI条形码的平均成功率为94.10%~ 97.40%，而ITS 1和ITS 2的成功率为64.70%~ 81.60%，表明ITS基因在这种情况下不太适合用于物种鉴定。我们建议使用一个综合考虑测序成功率和归属成功率的物种鉴定总成功率，因为多基因条形码系统的物种鉴定成功率通常被高估，特别是通过基于树的方法，其中只有成功测序的DNA序列才被用于构建系统发育树。非树型方法，如MD、BCM和BP方法，通过报告具有统计学意义的总体成功率，显示了优于树型方法的优势。此外，我们的研究结果还表明，最接近的种D. punctatus、油松毛虫D. tabulaeformis和D. spectabilis可能仍处于不完全的谱系分类过程中，其间偶尔会发生杂交。
Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), “best close match” (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10–97.40%, while ITS1 and ITS2 obtained a success rate of 64.70–81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our results indicate that the most closely related species D. punctatus, D. tabulaeformis, and D. spectabilis, may be still in the process of incomplete lineage sorting, with occasional hybridizations occurring among them.
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影响因子：
4.1
作者：
Lou, Melanie;Golding, G. Brian
通讯作者：
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
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