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The Spectre of Too Many Species
Leache, Adam D.1,2; Zhu, Tianqi3,4; Rannala, Bruce5; Yang, Ziheng3,6,7
AbstractRecent simulation studies examining the performance of Bayesian species delimitation as implemented in the bpp program have suggested that bpp may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here, we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model (PSM) has no influence on the generation of gene trees and sequence data, which explains why no method can use such data to distinguish between population splits and speciation. We suggest that the PSM is unrealistic as its mechanism for assigning species status assumes instantaneous speciation, contradicting prevailing taxonomic practice. We confirm the suggestion, based on simulation, that in the case of speciation with gene flow, Bayesian model selection as implemented in bpp tends to detect population splits when the amount of data (the number of loci) increases. We discuss the use of a recently proposed empirical genealogical divergence index (gdi) for species delimitation and illustrate that parameter estimates produced by a full likelihood analysis as implemented in bpp provide much more reliable inference under the gdi than the approximate method phrapl. We distinguish between Bayesian model selection and parameter estimation and suggest that the model selection approach is useful for identifying sympatric cryptic species, while the parameter estimation approach may be used to implement empirical criteria for determining species status among allopatric populations.
Keywordbpp multispecies coalescent Species delimitation taxonomy
Funding ProjectNational Science Foundation[1456098] ; Natural Science Foundation of China[31671370] ; Natural Science Foundation of China[31301093] ; Natural Science Foundation of China[11201224] ; Natural Science Foundation of China[11301294] ; Youth Innovation Promotion Association of Chinese Academy of Sciences[2015080] ; Biotechnological and Biological Sciences Research Council[BB/P006493/1] ; Radcliffe Institute for Advanced Study at Harvard University
WOS Research AreaEvolutionary Biology
WOS SubjectEvolutionary Biology
WOS IDWOS:000462179500012
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Document Type期刊论文
Corresponding AuthorYang, Ziheng
Affiliation1.Univ Washington, Dept Biol, Seattle, WA 98195 USA
2.Univ Washington, Burke Museum Nat Hist & Culture, Seattle, WA 98195 USA
3.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China
4.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China
5.Univ Calif Davis, Dept Evolut & Ecol, One Shields Ave, Davis, CA 95645 USA
6.UCL, Dept Genet, London WC1E 6BT, England
7.Harvard Univ, Radcliffe Inst Adv Studies, Cambridge, MA 02138 USA
Recommended Citation
GB/T 7714
Leache, Adam D.,Zhu, Tianqi,Rannala, Bruce,et al. The Spectre of Too Many Species[J]. SYSTEMATIC BIOLOGY,2019,68(1):168-181.
APA Leache, Adam D.,Zhu, Tianqi,Rannala, Bruce,&Yang, Ziheng.(2019).The Spectre of Too Many Species.SYSTEMATIC BIOLOGY,68(1),168-181.
MLA Leache, Adam D.,et al."The Spectre of Too Many Species".SYSTEMATIC BIOLOGY 68.1(2019):168-181.
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