Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

doi:10.1002/ajb2.1479

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids
	Sun, Miao 2,3; Folk, Ryan A.; Gitzendanner, Matthew A.; Soltis, Pamela S.; Chen, Zhiduan 3; Soltis, Douglas E.; Guralnick, Robert P.
刊名	AMERICAN JOURNAL OF BOTANY
	2020
卷号	107 期号:6 页码:895-909
关键词	diversification mega-phylogeny modeling rosids sampling bias
ISSN号	0002-9122
DOI	10.1002/ajb2.1479
文献子类	Article
英文摘要	Premise Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
学科主题	Plant Sciences
电子版国际标准刊号	1537-2197
出版地	HOBOKEN
WOS关键词	EXTINCTION RATES ; MOLECULAR PHYLOGENIES ; R PACKAGE ; MODELS ; DIVERSITY ; TREE ; LIKELIHOOD ; SPECIATION ; EVOLUTION ; RADIATION
WOS研究方向	Plant Sciences
语种	英语
出版者	WILEY
WOS记录号	WOS:000539128100001
资助机构	National Science FoundationNational Science Foundation (NSF) [DEB-1208809, DEB-1442280, DBI-1523667, DEB-1916632] ; U.S. Department of EnergyUnited States Department of Energy (DOE) [DE-SC0018247] ; Strategic Priority Research Program of the Chinese Academy of SciencesChinese Academy of Sciences [XDA19050103, XDB31000000] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31590822]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21725]
专题	系统与进化植物学国家重点实验室
作者单位	1.Folk, Ryan A.] Mississippi State Univ, Dept Biol Sci, Mississippi State, MS 39762 USA 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.[Sun, Miao; Soltis, Pamela S.; Soltis, Douglas E.; Guralnick, Robert P.] Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA 4.Soltis, Pamela S.; Soltis, Douglas E.] Univ Florida, Genet Inst, Gainesville, FL 32608 USA 5.Gitzendanner, Matthew A.; Soltis, Pamela S.; Soltis, Douglas E.; Guralnick, Robert P.] Univ Florida, Biodivers Inst, Gainesville, FL 32611 USA 6.Gitzendanner, Matthew A.; Soltis, Douglas E.] Univ Florida, Dept Biol, Gainesville, FL 32611 USA 7.Aarhus Univ, Dept Biosci, DK-8000 Aarhus, Denmark
推荐引用方式 GB/T 7714	Sun, Miao,Folk, Ryan A.,Gitzendanner, Matthew A.,et al. Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids[J]. AMERICAN JOURNAL OF BOTANY,2020,107(6):895-909.
APA	Sun, Miao.,Folk, Ryan A..,Gitzendanner, Matthew A..,Soltis, Pamela S..,Chen, Zhiduan.,...&Guralnick, Robert P..(2020).Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids.AMERICAN JOURNAL OF BOTANY,107(6),895-909.
MLA	Sun, Miao,et al."Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids".AMERICAN JOURNAL OF BOTANY 107.6(2020):895-909.