New Methods to Calculate Concordance Factors for Phylogenomic Datasets

被引：373
作者：
Bui Quang Minh [1 ,2 ]
Hahn, Matthew W. [3 ,4 ]
Lanfear, Robert [2 ]
机构：
[1] Australian Natl Univ, Res Sch Comp Sci, Canberra, ACT, Australia
[2] Australian Natl Univ, Res Sch Biol, Dept Ecol & Evolut, Canberra, ACT, Australia
[3] Indiana Univ, Dept Biol, Bloomington, IN USA
[4] Indiana Univ, Dept Comp Sci, Bloomington, IN 47405 USA
来源：
MOLECULAR BIOLOGY AND EVOLUTION | 2020年 / 37卷 / 09期
基金：
澳大利亚研究理事会; 美国国家科学基金会;
关键词：
phylogenetic inference; concordance factor; phylogenomics; SPECTRAL-ANALYSIS; MISSING DATA; TREE; IMPACT; GENES;
D O I：
10.1093/molbev/msaa106
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
引用
收藏
页码：2727 / 2733
页数：7
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