IB-CAS  > 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, Miao1,2; Folk, Ryan A.; Gitzendanner, Matthew A.; Soltis, Pamela S.; Chen, Zhiduan1; Soltis, Douglas E.; Guralnick, Robert P.
2020
Source PublicationAMERICAN JOURNAL OF BOTANY
ISSN0002-9122
Volume107Issue:6Pages:895-909
AbstractPremise 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.
Keyworddiversification mega-phylogeny modeling rosids sampling bias
Subject AreaPlant Sciences
DOI10.1002/ajb2.1479
Indexed BySCI
Language英语
WOS KeywordEXTINCTION RATES ; MOLECULAR PHYLOGENIES ; R PACKAGE ; MODELS ; DIVERSITY ; TREE ; LIKELIHOOD ; SPECIATION ; EVOLUTION ; RADIATION
WOS Research AreaPlant Sciences
WOS IDWOS:000539128100001
PublisherWILEY
SubtypeArticle
Publication PlaceHOBOKEN
EISSN1537-2197
Funding OrganizationNational 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]
Corresponding Author Emaildsoltis@ufl.edu ; robgur@gmail.com
OAGreen Submitted, hybrid, Green Published
Citation statistics
Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/21725
Collection系统与进化植物学国家重点实验室
Affiliation1.[Sun, Miao; Soltis, Pamela S.; Soltis, Douglas E.; Guralnick, Robert P.] Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA
2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
3.Aarhus Univ, Dept Biosci, DK-8000 Aarhus, Denmark
4.Folk, Ryan A.] Mississippi State Univ, Dept Biol Sci, Mississippi State, MS 39762 USA
5.Gitzendanner, Matthew A.; Soltis, Douglas E.] Univ Florida, Dept Biol, Gainesville, FL 32611 USA
6.Gitzendanner, Matthew A.; Soltis, Pamela S.; Soltis, Douglas E.; Guralnick, Robert P.] Univ Florida, Biodivers Inst, Gainesville, FL 32611 USA
7.Soltis, Pamela S.; Soltis, Douglas E.] Univ Florida, Genet Inst, Gainesville, FL 32608 USA
Recommended Citation
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.
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