Delimiting species using single-locus data and the generalized mixed yule coalescent approach: A revised method and evaluation on simulated data sets

Systematic Biology

Volumn 62, Issue 5, 2013, Pages 707-724

  Fujisawa, Tomochika ^a,b   Barraclough, Timothy G ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882749675     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt033     Document Type: Article

References (84)

1. Acinas S.G., Klepac-CerajV., Hunt D.E., Pharino C., Ceraj I., Distel D.L., Polz M.F. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554.
2. Agapow P.-M., Purvis A. 2002. Power of eight tree shape statistics to detect non-random diversification: a comparison by simulation of two models of cladogenesis. Syst. Biol. 51:866-872.
3. Avise J.C. 2009. Phylogeography: retrospect and prospect. J. Biogeog. 36:3-15.
4. Barraclough T.G., Birky C.W. Jr., Burt A. 2003. Diversification in sexual and asexual organisms. Evolution 57:2166-2172.
5. Barraclough T.G., Herniou E. 2003.Why do species exist? Insights from sexuals and asexuals. Zoology 106:275-282.
6. Barraclough T.G., Hughes M., Ashford-Hodges N., Fujisawa T. 2009. Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data. Biol. Lett. 5: 425-428.
7. Barraclough T.G., Nee S. 2001. Phylogenetics and speciation. Trends Ecol. Evol. 16:391-399.
8. BarracloughT.G.,VoglerA.P. 2002.Recent diversification rates inNorth American tiger beetles estimated froma datedmtDNAphylogenetic tree. Mol. Biol. Evol. 19:1706-1716.
9. Bergsten J., Bilton D.T., Fujisawa T., ElliotM., Monaghan M.T., BalkeM., Hendrich L., Geijer J., Herrmann J., Foster G.N., Ribera I., Nilsson A.N., Barraclough T.G., Vogler A.P. 2012. The effect of geographical scale of sampling on DNA barcoding. Syst. Biol. 61:851-869.
10. Birky C.W. Jr., Adams J., Gemmel M., Perry J. 2010. Using population genetic theory and dna sequences for species detection and identification in asexual organisms. Plos One 5:e10609.
11. Bortolussi N., Durand E., Blum M., Francois O. 2006. apTreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics 22:363-364.
12. Brito P., Edwards S.V. 2009. Multilocus phylogeography and phylogenetics using sequence-basedmarkers. Genetica 135:439-455.
13. Brower A.V.Z. 1994. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial-DNA evolution. Proc. Natl. Acad. Sci. USA 91:6491-6495.
14. Burnham K.P., Anderson D.R. 2002. Model selection and multimodel inference: a practical information-theoritic approach. New York: Springer Science+Business Media, Inc.
15. Camargo A., Avila L.J., Morando M., Sites J.W. Jr. 2012. Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae). Syst. Biol. 61: 272-288.
16. Carstens B.C., Dewey T.A. 2010. Species delimitation using a combined coalescent and information-theoretic approach: an example from north american Myotis bats. Syst. Biol. 59:400-414.
17. CBOL Plant Working Group. 2009. A DNA barcode for land plants Proc. Natl. Acad. Sci. USA 106:12794-12797.
18. Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10:195-205.
19. Charlesworth B., Charlesworth D., Barton N.H. 2003. The effects of genetic and geographic structure on neutral variation. Ann. Rev. Ecol. Evol. Syst. 34:99-125.
20. Cox D.R., Miller H.D. 1965. The theory of stochastic processes. London: Chapman & Hall.
21. Coyne J.A., OrrH.A. 1998. The evolutionary genetics of speciation. Phil. Trans. R. Soc. Lond. B 353:287-305.
22. Coyne J.A., Orr H.A. 2004. Speciation. Sunderland (MA): Sinauer Associates. Inc.
23. Davis J.I., Nixon K.C. 1992. Populations, genetic variation, and the delimitation of phylogenetic species. Syst. Biol. 41:421-435.
24. De Queiroz K. 2007. Species concepts and species delimitation. Syst. Biol. 56:879-886.
25. Dupuis J.R., Roe A.D., Sperling F.A.H. 2012. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol. Ecol. 21:4422-4436.
26. Esselstyn J.A., Evans B.J., Sedlock J.L., Anwarali Khan F.A., Heaney L.R. 2012. Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats. Proc. R. Soc. Lond. B. 279:3678-3686.
27. Etienne R.S., Haegeman B., Stadler T., Aze T., Pearson P.N., Purvis A., Phillimore A.B. 2012. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. Lond. B 279:1300-1309.
28. Ezard T., Fujisawa T., Barraclough T.G. 2009. SPLITS: SPecies' LImits by Threshold Statistics. R package version 1.0-18/r45. Available from: URL http://R-Forge.R-project.org/projects/splits/, last accessed June 2013.
29. Feulner P.G.D., Kirschbaum F., Mamonekene V., Ketmaier V., Tiedemann R. 2007. Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approach. J. Evol. Biol. 20:403-414.
30. Fontaneto D., Herniou E.A., Boschetti C., Caprioli M.,Melone G., Ricci C., BarracloughT.G. 2007. Independently evolving species in asexual bdelloid rotifers. PLoS Biol. 5:e87.
31. Funk D.J., Omland K.E. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Evol. Syst. 34:397-423.
32. Green J.L., Plotkin J.B. 2007. A statistical theory for sampling species abundances. Ecol. Lett. 10:1037-1045.
33. Hailer F., Kutschera V.E., Hallstrom B.M., Klassert D., Fain S.R., Leonard J.A., ArnasonU., JankeA. 2012.Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347.
34. Hebert P.D.N., Cywinska A., Ball S.L., DeWaard J.R. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270:313-321.
35. Hey J. 1991. The structure of genealogies and the distribution of fixed differences between DNA-sequence samples from naturalpopulations. Genetics 128:831-840.
36. Hey J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46:627-640.
37. Hey J. 2001. The mind of the species problem. Trends Ecol. Evol. 16: 326-329.
38. Hudson R.R. 1990. Gene genealogies and coalescent process. In: Futuyma D.J., Antonivics J., editors. OxfordSurveys in Evolutionary Biology. Oxford: Oxford University Press. p. 1-44.
39. Hudson R.R. 2002. Generating samples under aWright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
40. Hudson R.R., Coyne J.A. 2002. Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565.
41. Knowles L.L., Carstens B.C. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56:887-895.
42. Koufopanou V., Burt A., Taylor J.W. 1997. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. USA 94: 5478-5482.
43. Kubo T., Iwasa Y. 1995. Inferring the rates of branching and extinction from molecular phylogenies. Evolution 49:694-704.
44. Lahaye R., van Der Bank M., Bogarin D.,Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T.G., Savolainen V. 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA 105:2923-2928.
45. Leaché A.D., Koo M.S., Spencer C.L., Papenfuss T.J., Fisher R.N., McGuire J.A. 2009. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma). Proc. Natl. Acad. Sci. USA 106: 12418-12423.
46. Lim G.S., Balke M., Meier R. 2011. Determining species boundaries in a world full of rarity: sngletons, species delimitation methods. Syst. Biol. 61:165-169.
47. Lohse K. 2009. Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006). Syst. Biol. 58:439-442.
48. Luo A., Zhang A., Ho S.Y., XuW., Zhang Y, ShiW., Cameron S.L., Zhu C. 2011. Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals BMC Genomics 12:84.
49. Meyer C.P., Paulay G. 2005. DNA Barcoding: error rates based on comprehensive sampling. PLoS Biol. 3:e422.
50. Monaghan M.T., Wild R., Elliot M., Fujisawa T., Balke M., Inward D.J.G., Lees D.C., Ranaivosolo R., Eggleton P., Barraclough T.G., Vogler A.P. 2009. Accelerated species inventory on madagascar using coalescent-based models of species delineation. Syst. Biol. 58: 298-311.
51. Morlon H., Parsons T.L., Plotkin J.B. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 108:16327-16332.
52. Nee S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661-668.
53. Nee S., May R.M., Harvey P.H. 1994. The reconstructed evolutionary process. Phil. Trans. R. Soc. Lond. B 344:305-311.
54. O'Meara B.C. 2010. New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59:59-73.
55. Papadopoulou A., Bergsten J., Fujisawa T., Monaghan M.T., Barraclough T.G., Vogler A.P. 2008. Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters. Phil. Trans. R. Soc. Lond. B 363:2987-2996.
56. PapadopoulouA.,Monaghan M.T., Barraclough T.G., VoglerA.P. 2009. Sampling error does not invalidate the Yule-coalescent model for species delimitation. A response to Lohse (2009). Syst. Biol. 58: 442-444.
57. Paradis E., Claude J., StrimmerK. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20:289-290.
58. Phillimore A.B., Price T.D. 2008. Density-dependent cladogenesis in birds. PLoS Biol. 6:e71.
59. Pons J., Barraclough T.G., Gomez-Zurita J., Cardoso A., Duran D.P., Hazell S., Kamoun S., Sumlin W.D., Vogler A.P. 2006. Sequencebased species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55:595-609.
60. Pons J., Fujisawa T., Claridge E.M., Savill R.A., Barraclough T.G.,Vogler A.P. 2011. Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus Neocicindela). Mol. Phyl. Evol. 59:251-262.
61. Powell J.R. 2012. Accounting for uncertainty in species delineation during the analysis of environmentalDNAsequence data. Methods Ecol. Evol. 3:1-11.
62. Pybus O.G., Harvey P.H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267:2267-2272.
63. R Development Core Team. 2010. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
64. Rabosky D.L., Lovette I.J. 2008. Density-dependent diversification in North American wood warblers. Proc. R. Soc. Lond. B 275: 2363-2371.
65. Rambaut A. 2002. Phylo-O-Gen: Phylogenetic tree simulator package v1.1. Available from: URL http://tree.bio.ed.ac.uk/software/phylogen/, last accessed June 2013.
66. Rambaut A., Grassly N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS 13:235-238.
67. Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes usingDNA sequences from multiple loci. Genetics 164:1645-1656.
68. Reid N.M., Carstens B.C. 2012. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the General Mixed Yule Coalescent model. BMC Evol. Biol. 12:196.
69. Ricklefs R.E. 2007. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 22:601-610.
70. Rosenberg N.A., Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-390.
71. Sanderson M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of amolecular clock. Bioinformatics 19:301-302.
72. Schloss P.D., Handelsman J. 2006. Toward a census of bacteria in soil. PLoS Comp. Biol. 2:786-793.
73. Shaffer H.B., Thomson R.C. 2007. Delimiting species in recent radiations. Syst. Biol. 56:896-906.
74. Sites J.W., Marshall J.C. 2003. Delimiting species: a renaissance issue in systematic biology. Trends Ecol. Evol. 18:462-470.
75. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
76. Tang C.Q., Leasi F., Obertegger U., Kieneke A., Barraclough T.G., Fontaneto D. 2012. The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc. Natl. Acad. Sci. USA 109: 16208-16212.
77. Templeton A. 1989. The meaning of species and speciation: a population genetics approach. In: Otte D., Endler J., editors. Speciation and its consequences. Sunderland (MA): Sinauer Associates.
78. Templeton A.R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10:779-791.
79. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.H., Smith H.O. 2004. Environmental genome shotgun sequencing of the Sargasso sea. Science 304:66-74.
80. Wiens J.J., Penkrot T.A. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51:69-91.
81. Will K.W., Rubinoff D. 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20:47-55.
82. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
83. Yang Z., Goldman N., Friday A. 1995. Maximum likelihood trees from DNAsequences: a peculiar statistical estimation problem. Syst. Biol. 44:384-399.
84. Yang Z., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proc.Natl. Acad. Sci. USA 107:9264-9269.