The Spectre of Too Many Species

doi:10.1093/sysbio/syy051

CSpace > 应用数学研究所

	The Spectre of Too Many Species
	Leache, Adam D.1,2; Zhu, Tianqi3,4 ; Rannala, Bruce 5; Yang, Ziheng 3,6,7
	2019
发表期刊	SYSTEMATIC BIOLOGY
ISSN	1063-5157
卷号	68 期号:1 页码:168-181
摘要	Recent 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.
关键词	bpp multispecies coalescent Species delimitation taxonomy
DOI	10.1093/sysbio/syy051
语种	英语
资助项目	National 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研究方向	Evolutionary Biology
WOS类目	Evolutionary Biology
WOS记录号	WOS:000462179500012
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/34363
专题	应用数学研究所
通讯作者	Yang, Ziheng
作者单位	1.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
推荐引用方式 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.