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| 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.
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| 2020 | |
| Source Publication | AMERICAN JOURNAL OF BOTANY
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| ISSN | 0002-9122 |
| Volume | 107Issue:6Pages:895-909 |
| Abstract | 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. |
| Keyword | diversification mega-phylogeny modeling rosids sampling bias |
| Subject Area | Plant Sciences |
| DOI | 10.1002/ajb2.1479 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | EXTINCTION RATES ; MOLECULAR PHYLOGENIES ; R PACKAGE ; MODELS ; DIVERSITY ; TREE ; LIKELIHOOD ; SPECIATION ; EVOLUTION ; RADIATION |
| WOS Research Area | Plant Sciences |
| WOS ID | WOS:000539128100001 |
| Publisher | WILEY |
| Subtype | Article |
| Publication Place | HOBOKEN |
| EISSN | 1537-2197 |
| Funding Organization | 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] |
| Corresponding Author Email | dsoltis@ufl.edu ; robgur@gmail.com |
| OA | Green Submitted, hybrid, Green Published |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/21725 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.[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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| Sun-2020-Estimating （1069KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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