Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters

doi:10.1017/pab.2025.10076

IVPP-IR

	Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters
	Liu, Xueer 1,2; Zhang, Chi 1,2
	2025-10-10
发表期刊	PALEOBIOLOGY
ISSN	0094-8373
页码	9
通讯作者	Zhang, Chi(zhangchi@ivpp.ac.cn)
摘要	Morphological characters are central to phylogenetic inference, especially for fossil taxa for which genomic data are unavailable. While Bayesian methods have gained popularity in recent years, they typically assume characters evolve independently, despite known correlations among characters. Here, we assess the impact of character correlation and evolutionary rate heterogeneity on Bayesian phylogenetic inference using extensive simulations of binary characters evolving under independent and correlated models. We find that Bayesian inference assuming character independence accurately recovers tree topologies even when characters are strongly correlated or evolve under heterogeneous rates. However, branch lengths or clock rates tend to be underestimated, particularly under extreme rate heterogeneity. These biases are partially corrected using models that integrate over character-state heterogeneity. Our results demonstrate that Bayesian methods are robust to violations of character independence in topological inference, supporting their continued use in morphological phylogenetics.
DOI	10.1017/pab.2025.10076
关键词[WOS]	MAXIMUM-LIKELIHOOD ; EVOLUTIONARY TREES ; DNA-SEQUENCES ; MODEL ; PARSIMONY ; FOSSILS ; TIME
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[2023YFF0804502] ; National Key Research and Development Program of China[42172006] ; National Natural Science Foundation of China
项目资助者	National Natural Science Foundation of China ; National Key Research and Development Program of China ; National Natural Science Foundation of China
WOS研究方向	Biodiversity & Conservation ; Environmental Sciences & Ecology ; Evolutionary Biology ; Paleontology
WOS类目	Biodiversity Conservation ; Ecology ; Evolutionary Biology ; Paleontology
WOS记录号	WOS:001590209700001
出版者	CAMBRIDGE UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.205/handle/311034/24908
专题	中国科学院古脊椎动物与古人类研究所
通讯作者	Zhang, Chi
作者单位	1.Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing 100044, Peoples R China 2.Univ Chinese Acad Sci, Beijing 101408, Peoples R China
推荐引用方式 GB/T 7714	Liu, Xueer,Zhang, Chi. Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters[J]. PALEOBIOLOGY,2025:9.
APA	Liu, Xueer,&Zhang, Chi.(2025).Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters.PALEOBIOLOGY,9.
MLA	Liu, Xueer,et al."Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters".PALEOBIOLOGY (2025):9.