Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown .
作者信息
Puttick Mark N, O'Reilly Joseph E, Oakley Derek, Tanner Alistair R, Fleming James F, Clark James, Holloway Lucy, Lozano-Fernandez Jesus, Parry Luke A, Tarver James E, Pisani Davide, Donoghue Philip C J
机构信息
School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
Department of Life Sciences, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK.
出版信息
Proc Biol Sci. 2017 Oct 11;284(1864). doi: 10.1098/rspb.2017.1636.
Abstract
摘要
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本文引用的文献
1
Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick .当考虑不确定性时，形态特征的贝叶斯和似然系统发育重建并不不一致：对普蒂克的评论 。
Proc Biol Sci. 2017 Oct 11;284(1864). doi: 10.1098/rspb.2017.0986.
2
Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.不确定树：区分表型数据系统发育分析的竞争方法。
Proc Biol Sci. 2017 Jan 11;284(1846). doi: 10.1098/rspb.2016.2290.
3
Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.贝叶斯方法比简约法表现更优，但代价是从离散形态数据估计系统发育时精度有所损失。
Biol Lett. 2016 Apr;12(4). doi: 10.1098/rsbl.2016.0081.
4
Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data.使用简单似然模型的贝叶斯分析在从离散形态数据估计系统发育方面比简约法表现更优。
PLoS One. 2014 Oct 3;9(10):e109210. doi: 10.1371/journal.pone.0109210. eCollection 2014.
5
Branch-length prior influences Bayesian posterior probability of phylogeny.分支长度先验影响系统发育的贝叶斯后验概率。
Syst Biol. 2005 Jun;54(3):455-70. doi: 10.1080/10635150590945313.
6
A likelihood approach to estimating phylogeny from discrete morphological character data.一种从离散形态特征数据估计系统发育的似然方法。
Syst Biol. 2001 Nov-Dec;50(6):913-25. doi: 10.1080/106351501753462876.
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