Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification.
作者信息
Liu Liang, Zhang Jin, Rheindt Frank E, Lei Fumin, Qu Yanhua, Wang Yu, Zhang Yu, Sullivan Corwin, Nie Wenhui, Wang Jinhuan, Yang Fengtang, Chen Jinping, Edwards Scott V, Meng Jin, Wu Shaoyuan
机构信息
Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, Jiangsu, China.
Department of Statistics, University of Georgia, Athens, GA 30606.
出版信息
Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9433-E9434. doi: 10.1073/pnas.1715371114. Epub 2017 Oct 24.
Abstract
摘要
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本文引用的文献
1
Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals.系统发育基因组学警示信号：胎盘哺乳动物进化多样化中的同源性错误与僵尸谱系
Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9431-E9432. doi: 10.1073/pnas.1715318114. Epub 2017 Oct 24.
2
Phylotranscriptomic consolidation of the jawed vertebrate timetree.有颌脊椎动物时间树的系统转录组整合
Nat Ecol Evol. 2017 Sep;1(9):1370-1378. doi: 10.1038/s41559-017-0240-5. Epub 2017 Jul 24.
3
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.基因组证据显示，胎盘哺乳动物的辐射与 K-Pg 边界无关。
Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7282-E7290. doi: 10.1073/pnas.1616744114. Epub 2017 Aug 14.
4
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.基于快速合并算法从四重奏频率计算局部分支支持度
Mol Biol Evol. 2016 Jul;33(7):1654-68. doi: 10.1093/molbev/msw079. Epub 2016 Apr 15.
5
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.实施和测试多物种合并模型：系统发育基因组学的一个有价值的范例。
Mol Phylogenet Evol. 2016 Jan;94(Pt A):447-62. doi: 10.1016/j.ympev.2015.10.027. Epub 2015 Oct 27.
6
Resolving difficult phylogenetic questions: why more sequences are not enough.解决复杂的系统发育问题：为何更多序列并不足够。
PLoS Biol. 2011 Mar;9(3):e1000602. doi: 10.1371/journal.pbio.1000602. Epub 2011 Mar 15.
7
Why would phylogeneticists ignore computerized sequence alignment?为什么系统发育学家会忽略计算机化序列比对？
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8
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9
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