Multilocus inference of species trees and DNA barcoding.
Multilocus inference of species trees and DNA barcoding.
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DOI：
10.1098/rstb.2015.0335
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发表时间：
2016-09-05
期刊：
影响因子：
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通讯作者：
Posada D
中科院分区：
文献类型：
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作者：
Mallo D;Posada D
尽管从理论上讲，大型数据集应增加系统发育分辨率，但大量的多焦点数据集发现了不同基因组区域之间的系统发育不一致，这是由于随机误差和由于不同的进化过程的作用，例如不完整的谱系分类，基因重复，基因重复分类，以及损失和水平基因转移。这种不一致违反了DNA条形码方法的基本假设之一，该方法假设基因史和物种历史在这篇综述中是相同的。多焦点数据的系统发育分析的不同策略的优势和缺点。不和谐，比较物种重建的最受欢迎的方法，突出了我们在使用它们时需要面对的挑战，并讨论了当前条形码的潜在效用。多焦点条形码不仅会改善当前条形码方法，而且还可以促进事件过渡到基于物种树的条形码策略，这可以更好地适应条形码间隙太小或不存在的方案。
本文是“从DNA条形码到生物群落”的主题问题的一部分。
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’.