Species delimitation using bayes factors: Simulations and application to the sceloporus scalaris species group (Squamata: Phrynosomatidae)

Systematic Biology

Volumn 63, Issue 2, 2014, Pages 119-133

  Grummer, Jared A ^a,b   Bryson, Robert W ^b   Reeder, Tod W ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Bayesian; BEAST; BP P; incomplete lineage sorting; marginal likelihood estimation; Mexico; model choice

Indexed keywords

REPTILIAN PROTEIN;

*BEAST; ANIMAL; ARTICLE; BAYES THEOREM; BAYESIAN; BP&P; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; HISTOLOGY; IGUANIDAE; INCOMPLETE LINEAGE SORTING; MARGINAL-LIKELIHOOD ESTIMATION; MEXICO; MODEL CHOICE; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; SPECIES DIFFERENCE;

*BEAST; BAYESIAN; BP&P; INCOMPLETE LINEAGE SORTING; MARGINAL-LIKELIHOOD ESTIMATION; MEXICO; MODEL CHOICE;

ANIMALS; BAYES THEOREM; COMPUTER SIMULATION; IGUANAS; MARKOV CHAINS; MONTE CARLO METHOD; PHYLOGENY; REPTILIAN PROTEINS; SPECIES SPECIFICITY;

EID: 84894557940     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt069     Document Type: Article

References (70)

1. AlfaroM.E., Zoller S., Lutzoni F. 2003. Bayes or bootstrap?Asimulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
2. Baele G., Lemey P., Bedford T., Rambaut A., Suchard M.A., Alekseyenko A.V. 2012. Improving the accuracy of demographic and molecular clock model comparison while accomodating phylogenetic uncertainty. Mol. Biol. Evol. 29(9):2157-2167.
3. Ballard J.W.O., Whitlock M.C. 2004. The incomplete natural history of mitochondria. Mol. Ecol. 13:729-744.
4. Belfiore N.M., Liu, L., Moritz, C. 2008. Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst. Biol. 57:294-310.
5. Benabib M., Kjer K.M., Sites J.W. Jr. 1997.MitochondrialDNAsequencebased phylogeny and the evolution of viviparity in the Sceloporus scalaris group (Reptilia, Squamata). Evolution 51:1262-1275.
6. Bensch S., Irwin D.E., Irwin J.H., Kvist L., Akesson S. 2006. Conflicting patterns of mitochondrial and nuclearDNAdiversity in Phylloscopus warblers. Mol. Ecol. 15:161-171.
7. Bryant D., Moulton V. 2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:255-265.
8. Bryson R.W., García-Vázquez U.O., Riddle B.R. 2011. Relative roles of Neogene vicariance and Quaternary climate change onthe historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico. Mol. Phylogenet. Evol. 62:447-457.
9. Camargo A., Avila L.J., Morando M., Sites J.W. Jr. 2012a. 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.
10. Camargo A., Morando M., Avila L.J., Sites J.W. Jr. 2012b. Species delimitation withABCand other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66:2834-2849.
11. 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.
12. Creer D.A., Kjer K.M., Simmons D.L., Sites J.W. Jr. 1997. Phylogenetic relationships of the Sceloporus scalaris species group (Squamata). J. Herpetol. 31:353-364.
13. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
14. Eckert A.J., Carstens B.C. 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 49:832-842.
15. Ence D.D., Carstens B.C. 2011. SpedeSTEM: a rapid and accurate method for species delimitation. Mol. Ecol. Resour. 11:473-480.
16. Esselstyn J.A., Evans B.J., Sedlock J.L., Khan F.A.A., Heaney L.R. 2012. Single-locus species delimitation: a test of the mixedYule-coalescent model, with an empirical application to Philippine round-leaf bats. P. Roy. Soc. B Biol. Sci. 279:3678-3686.
17. Fan Y., Wu R., Chen M.H., Kuo L., Lewis P.O. 2011. Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28:523-532.
18. Flores-Villela O., Kjer K.M., Benabib M., Sites J.W. Jr. 2000. Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae). Syst. Biol. 49:713-739.
19. Fujita, M.K., Leaché, A.D., Burbrink, F.T., McGuire, J.A., Moritz, C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol. Evol. 27(9):480-488.
20. Harrington, R.C. and T.J. Near. 2012. Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma). Syst. Biol. 61:63-79.
21. Heled J., Drummond A.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
22. Hillis D.M., Bull J.J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
23. Huelsenbeck J.P., Imennov N.S. 2002. Geographic origin of human mitochondrialDNA: accommodating phylogenetic uncertainty and model comparison. Syst. Biol. 51:155-165.
24. Huson D.H., Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
25. Joly S., Bruneau A. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms frommultiple genes: An example from Rosa in north America. Syst. Biol. 55:623-636.
26. Kass, R.E., Raftery, A.E. 1995. Bayes factors. J. Am. Stat. Assoc. 90(430):773-795.
27. Knowles L.L., Carstens B.C. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56(6):887-895.
28. Lartillot N., Philippe, H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55(2):195-207.
29. Leaché A.D. 2010. Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data. Mol. Phylogenet. Evol. 54:162-171.
30. Leaché A.D., Fujita M.K. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). P. Roy. Soc. Biol. Sci. B 277:3071-3077.
31. Leaché A.D., McGuire J.A. 2006. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for amisleading mitochondrial gene tree. Mol. Phylogenet. Evol. 39:628-644.
32. Leaché, A.D., Harris, R.B., Rannala, B., Yang, Z. 2013. The influence of gene flow on species tree estimation: a simulation study. Syst. Biol. 63:17-30.
33. Li W.L.S., Drummond A.J. 2012. Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 29:751-761.
34. Liu L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24:2542-2543.
35. Liu L., Pearl D.K., Brumfield R.T., Edwards S.V. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080-2091.
36. Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
37. Maddison W.P., Maddison D.R. 2010. Mesquite: a modular system for evolutionary analysis. Version 2.73. Available from: URL http://mesquiteproject. org (last accesed November 27, 2013).
38. McCormack J.E., Heled J., Delaney K.S., Peterson A.T., Knowles L.L. 2011. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 65:184-202.
39. McGuire G.,Wright F. 2000. TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics (Oxford) 16:130-134.
40. Milne I., Lindner D., Bayer M., Husmeier D., McGuire G., Marshall D.F., Wright F. 2009. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics (Oxford) 25:126-127.
41. Mink D.G., Sites J.W. 1996. Species limits, phylogenetic relationships, and origins of viviparity in the scalaris complex of the lizard genus Sceloporus (Phrynosomatidae: Sauria). Herpetologica 52:551-571.
42. Nei M., Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
43. NewtonM.A., RafteryA.E. 1994. Approximate Bayesian-inference with the weighted likelihood bootstrap. J. Roy. Stat. Soc. B 56:3-48.
44. O'Meara B.C. 2010. New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59:59-73.
45. 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.
46. Posada D., Buckley T.R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808.
47. Posada D. 2008. jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
48. Raftery A.E., Newton M.A., Satagopan J.M., Krivitsky P.N. 2007. Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. In: Bernardo J.M., Bayarri M.J., Berger J.O., Dawid A.P., Heckerman D., Smith A.F.M., West M., editors. Bayesian statistics 8. Oxford: Oxford University Press 1-45b Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. In: Bernardo J.M., Bayarri M.J., Berger J.O., Dawid A.P., Heckerman D., Smith A.F.M., West M., editors. Bayesian statistics 8. Oxford: Oxford University Press, p. 1-45.
49. Rambaut A., Grassly, N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
50. Rambaut A., Drummond A.J. 2007. Tracer v1.4. Available from: URL http://beast.bio.ed.ac.uk/Tracer.
51. Rannala B., Yang Z.H. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
52. Reeder T.W., Wiens J.J. 1996. Evolution of the lizard family Phrynosomatidae as inferred from diverse types of data. Herpetol. Monogr. 10:43-84.
53. 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.
54. Smith H.M., Hall W.P. 1974. Contributions to the concepts of reproductive cycles and the systematics of the scalaris group of the lizard genus Sceloporus. Great Basin Nat. 34:97-104.
55. Spiegelhalter D.J., Best N.G., Carlin B.R., van der Linde A. 2002. Bayesian measures of model complexity and fit. J. Roy. Stat. Soc. B 64:583-616.
56. Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
57. Stephens M., SmithN.J., Donnelly P. 2001. A newstatistical method for haplotype reconstruction frompopulation data. Am. J. Hum. Genet. 68:978-989.
58. Suchard M.A., Weiss R.E., Dorman K.S., Sinsheimer J.S. 2002. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst. Biol. 51:715-728.
59. Sullivan J., Joyce P. 2005. Model selection in phylogenetics. Ann. Rev. Ecol. Evol. Syst. 36:445-466.
60. Swofford D.L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sunderland, MA: Sinauer Associates.
61. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
62. Thomas R.A., Dixon J.R. 1976. A re-evaluation of the Sceloporus scalaris group (Sauria: Iguanidae). Southwest. Assoc. Nat. 20:523-536.
63. Ward E.J. 2008. A review and comparison of four commonly used Bayesian and maximum likelihood model selection tools. Ecol. Model. 211:1-10.
64. Wheeler T.J., Kececioglu J.D. 2007. Multiple alignment by aligning alignments. Bioinformatics (Oxford) 23:I559-I568.
65. Wiens J.J., Kuczynski C.A., Arif S., Reeder T.W. 2010. Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus. Mol. Phylogenet. Evol. 54:150-161.
66. Wiens J.J., Reeder T.W. 1997. Phylogeny of the spiny lizards (Sceloporus) based on molecular and morphological evidence. Herpetol. Monogr. 11:1-101.
67. Wilgenbusch J.C., Warren D.L., Swofford D.L. 2004. AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available from: URL http://ceb.csit.fsu.edu/awty.
68. Xie W.G., Lewis P.O., Fan Y., Kuo L., Chen M.H. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60:150-160.
69. Yang Z.H., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl Acad. Sci. USA 107:9264-9269.
70. Zhang C., Zhang D.X., Zhu T.Q., Yang Z.H. 2011. Evaluation of a Bayesian coalescent method of species delimitation. Syst. Biol. 60:747-761.