Evaluation of a bayesian coalescent method of species delimitation

Systematic Biology

Volumn 60, Issue 6, 2011, Pages 747-761

  Zhang, Chi ^a,b   Zhang, De Xing ^a   Zhu, Tianqi ^c   Yang, Ziheng ^a,d  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c PEKING UNIVERSITY   (China)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian inference; coalescent; Lindley's paradox; simulation; Species delimitation; stepping stone model

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BUTTERFLY; CLASSIFICATION; COMPUTER SIMULATION; GENE FLOW; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MUTATION RATE; POPULATION GENETICS; POPULATION MIGRATION;

ALGORITHMS; ANIMAL MIGRATION; ANIMALS; BUTTERFLIES; CLASSIFICATION; COMPUTER SIMULATION; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; MUTATION RATE;

EID: 80054890844     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr071     Document Type: Article

References (56)

1. Ane C., Larget B., Baum D.A., Smith S.D., Rokas A. 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24:412-426. (Pubitemid 46204374)
2. Bauer A.M., Parham J.F., Brown R.M., Stuart B.L., Grismer L., Papen-fuss T.J., Bohme W., Savage J.M., Carranza S., Grismer J.L., Wag-nerm P., Schmitz A., Ananjeva N.B., Inger R.F. 2011. Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. Proc. R. Soc. Lond. B. Biol. Sci. 278:490-492.
3. Baum D.A., Shaw K.L. 1995. Genealogical perspectives on the species problem. In: Hoch P.C., Stephenson A.G., editors. Molecular and experimental approaches to plant biosystematics. St Louis (MO): Missouri Botanical Garden. p. 289-303.
4. Beerli P. 2004. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecol. 13:827-836. (Pubitemid 38390589)
5. Burgess R., Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25:1979-1994.
6. Carstens B.C., Richards C.L. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution. 61:1439-1454. (Pubitemid 46848830)
7. Coyne J.A., Orr H.A. 2004. Speciation. Sunderland (MA): Sinauer Associates.
8. Dasmahapatra K.K., Iamas G., Simpson F., Mallet J. 2010. The anatomy of a 'suture zone' in Amazonian butterfies: a coalescent-based test for vicariant geographic divergence and speciation. Mol. Ecol. 19:4283-4301.
9. Dobzhansky T.G. 1937. Genetics and the origin of species. New York: Columbia University Press.
10. Feller W. 1968. An introduction to probability theory and its applications. 3rd ed. New York: Wiley.
11. Felsenstein J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 59:139-147.
12. Felsenstein J. 2005. Phylip: phylogenetic inference program. Version 3.6. Seattle (WA): University of Washington.
13. Fujita M.K., Leache A.D. 2011. A coalescent perspective on delimiting and naming species: a reply to Bauer et al. Proc. R. Soc. Lond. B. Biol. Sci. 278:493-495.
14. Funk D.J., Omland K.E. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mi-tochondrial DNA. Annu. Rev. Ecol. Syst. 34:397-423. (Pubitemid 38171425)
15. Hajibabaei M., Singer G.A., Hebert P.D., Hickey D.A. 2007. DNA bar-coding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23:167-172. (Pubitemid 46497507)
16. Hebert P.D., Stoeckle M.Y., Zemlak T.S., Francis C.M. 2004. Identifica-tion of birds through DNA barcodes. PLoS Biol. 2:1657-1663.
17. Heled J., Drummond A.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
18. Hey J. 2010. Isolation with migration models for more than two populations. Mol. Biol. Evol. 27:905-920.
19. Hickerson M.J., Meyer C.P., Moritz C. 2006. DNA barcoding will often fail to discover new animal species over broad parameter space. Syst. Biol. 55:729-739.
20. Hudson R.R. 1983. Testing the constant-rate neutral alele model with protein sequence data. Evolution. 37:203-217.
21. Hudson R.R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338. (Pubitemid 34183119)
22. Hudson R.R., Coyne J.A. 2002. Mathematical consequences of the genealogical species concept. Evolution. 56:1557-1565.
23. Issac N.J.B., Mallet J., Mace G.M. 2004. Taxonomic infation: its infu-ence on macroecology and conservation. Trends Ecol. Evol. 19:464-469. (Pubitemid 39151665)
24. Jeffreys H. 1939. Theory of probability. Oxford: Clarendon Press.
25. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor. Mammalian protein metabolism. New York: Academic Press. p. 21-123.
26. Kingman J.F.C. 1982a. The coalescent. Stoch. Proc. Appl. 13:235-248.
27. Kingman J.F.C. 1982b. On the genealogy of large populations. J. Appl. Probab. 19A:27-43.
28. Knowles L.L., Carstens B.C. 2007. Delimiting species without mono-phyletic gene trees. Syst. Biol. 56:887-895. (Pubitemid 350129639)
29. Kubatko L.S., Carstens B.C., Knowles L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
30. Leache A.D., Fujita M.K. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc. R. Soc. Lond. B. Biol. Sci. 277:3071-3077.
31. Lindley D.V. 1957. A statistical paradox. Biometrika. 44:187-192.
32. Liu L. 2008. BEST: Bayesian estimation of species trees under the coa-lescent model. Bioinformatics. 24:2542-2543.
33. Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. 2009. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 53:320-328.
34. Mayr E. 1963. Animal species and evolution. Cambridge (MA): Belk-nap Press.
35. Neigel J.E., Avise J.C. 1986. Phylogenetic relationships of mitochon-drial DNA under various demographic models of speciation. In: Karlin S., Nevo E., editors. Evolutionary processes and theory. New York: Academic Press. p. 515-534.
36. Nielsen R., Matz M. 2006. Statistical approaches for DNA barcoding. Syst. Biol. 55:162-169.
37. O'Meara B.C. 2010. New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59:59-73.
38. Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656. (Pubitemid 37102224)
39. Schwarz G. 1978. Estimating the dimension of a model. Ann. Stat. 6:461-464.
40. Slatkin M. 1991. Inbreeding coefficients and coalescence times. Genet. Res. 58:167-175.
41. Spooner L.J. 2009. DNA barcoding will frequently fail in complicated groups: a example in wild potatoes. Am. J. Bot. 96:1177-1189.
42. Strobeck K. 1987. Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics. 117:149-153.
43. Tajima F. 1983. Evolutionary relationship of DNA sequences in fnite populations. Genetics. 105:437-460. (Pubitemid 14247444)
44. Takahata N. 1983. Gene identity and genetic differentiation of populations in the fnite island model. Genetics. 104:497-512. (Pubitemid 13011684)
45. Takahata N., Satta Y., Klein J. 1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48:198-221. (Pubitemid 26460272)
46. Wakeley J., Aliacar N. 2001. Gene genealogies in a metapopulation. Genetics. 159:893-905. (Pubitemid 33035128)
47. Wilkinson-Herbots H.M. 2008. The distribution of the coalescence time and the number of pairwise nucleotide differences in the "isolation with migration" model. Theor. Popul. Biol. 73:277-288.
48. Wu C.I., Ting C.T. 2004. Genes and speciation. Nat. Rev. Genet. 5:114-122.
49. Yang Z. 1996. Among-site rate variation and its impact on phyloge-netic analyses. Trends Ecol. Evol. 11:367-372. (Pubitemid 126381530)
50. Yang Z. 1997. On the estimation of ancestral population sizes. Genet. Res. 69:111-116.
51. Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics. 162:1811-1823. (Pubitemid 36114665)
52. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
53. Yang Z. 2010. A likelihood ratio test of speciation with gene fow using genomic sequence data. Genom. Biol. Evol. 2:200-211.
54. Yang Z., Rannala B. 2010. Bayesian species delimitation using multilo-cus sequence data. Proc. Natl. Acad. Sci. U.S.A. 107:9264-9269.
55. Zhang D.X., Hewitt G.M. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12:563-584. (Pubitemid 36380417)
56. Zhou R., Zeng K., Wu W., Chen X., Yang Z., Shi S., Wu C.-I. 2007. Population genetics of speciation in nonmodel organisms: I. ancestral polymorphism in mangroves. Mol. Biol. Evol. 24:2746-2754.