Species tree inference in the age of genomics

Trends in Evolutionary Biology

Volumn 3, Issue 1, 2011, Pages 23-28

  Whelan, Nathan V ^a  

^a UNIVERSITY OF ALABAMA   (United States)

Author keywords

Coalescence; Phylogenomics; Species tree

Indexed keywords

EID: 84865306773     PISSN: 20362641     EISSN: 2036265X     Source Type: Journal    
DOI: 10.4081/eb.2011.e5     Document Type: Review

References (72)

1. Barracloough TG, Volger AP. Detecting the geographical pattern of species from species-level phylogenies. American Naturalist 2000;155:419-34.
2. Wiley EO. Phylogenetics: the theory and practice of phylogenetic systematics. Wiley, 1981, p. 439.
3. Carstens BC, Dewey TA. Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Systematic Biology 2010;58:400-14.
4. Leaché AD, Fujita MK. Bayesian species delimitation in West African forest geckos. Proceeding of the Royal Society B 2010; 277:3071-7.
5. Yang Z, Rannala B. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences. 2010;107:9264-9.
6. Kembel SW, Hubbell SP. The phylogenetic structure of a neotropical forest tree community. Ecology 2006;Supplement:S86-S99.
7. Vamosi SM, Heard SB, Vamosi JC, Webb CO. Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 2009;18:572-92.
8. Agnarsson I, Kuntner M, May-Collado LJ. Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora. Molecular Phylogenetics and Evolution 2010;54:726-45.
9. Douglas ME, Douglas MR, Schuett GW, et al. Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach. Mole-cular Phylogenetics and Evolution 2010;55: 153-67.
10. Perez KE, Minton RL. Practical applications for systematics and taxonomy in North American freshwater gastropod conservation. Journal of the North American Benthological Society 2008;27:471-83.
11. Laurance WF. Have we overstated the tropical biodiversity crisis? Trends in Ecology and Evolution 2007;22:65-70.
12. Felsenstein J. Phylogenies and the comparative method. American Naturalist 1985;125:1-15.
13. Giribet G. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. Acta Zoologica 2009;91:11-9.
14. Funk DJ, Omland KE. Species-level paraphyly and polyphyly: frequency, causes, and consequences with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics 2003; 34:397-423.
15. Maddison WP. Gene trees in species trees. Systematic Biology. 1997;3:523-36.
16. Edwards SV. Natural selection and phylogenetic analysis. Proceedings of the National Academy of Sciences 2009;106: 8799-800.
17. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology 2009;58: 130-45.
18. Degnan JH, Rosenberg NA. Discordance of species trees with their most likely gene trees. PLoS Genetics 2006;2:e68.
19. Townsend TM, Mulcahy DG, Noonna BP, et al. Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concattenated and species-tree approaches for an ancient, rapid radiation. Molecular Phylogenetics and Evolution 2011;61:263-80.
20. Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Computational Biology 2009;5:e1000262.
21. de la Torre-Bárcena JE, Kolokotronis S-O, Lee EK, et al. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS ONE 2009;4:e5764.
22. Sanderson MJ, McMahon MM, Steel M. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 2010;10:1-13.
23. Pollock DD, Zwickl DJ, Jimmy A M, Hillis DM. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 2002;51:664-71.
24. Townsend JP, Lopez-Giraldez F. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Systematic Biology 2010;59:446-57.
25. Dunn CW, Hejnol A, Matus DQ, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008;452:745-9.
26. Burleigh JG, Bansal MS, Eulenstein O, et al. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Systematic Biology 2011;60:117-25.
27. Jacobsen F, Omland KE. Species tree infer-ence in a recent radiation of orioles (Genus Icterus): Multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Molecular Phylogenetics and Evolution 2011;61:460-69.
28. Horvath JE, Weisrock DW, Embry SL, et al. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genome Research. 2008;18:489-99.
29. Knowles LL, Kubatko LS, eds. Estimating species trees: practical and theoretical aspects. Hoboken, New Jersey, Wiley-Blackwell, 2010.
30. Knowles LL. Sampling strategies for species tree estimation. In: LL Knowles, LS Kubatko, editors. Estimating species trees: pracitical and theoretical aspects. Hoboken, New Jersey, Wiley-Blackwell, 2010, p. 163-73.
31. McCormack JE, Huang H, Knowles LL. Maximum likelihood estimates of species trees: how accracy of phylogenetic inference depends upon divergence history and sampling design. Systematic Biology 2009;58:501-8.
32. Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450: 203-18.
33. Shedlock AM, James DE, Edwards SV. Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. In: WJ Murphy WJ, ed. Methods in molecular biology: phylogenomics. Totowa, NJ, Humana Press Inc., 2008.
34. Thomson RC, Shedlock AM, Edwards SV, Bradeley S. Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles. Molecular Phylogenetics and Evolution 2008;49:514-25.
35. Parfrey LW, Grant J, Tekle YI, et al. Broadly sampled multigene analyses yield a wellresolved Eukaryotic tree of life. Systematic Biology 2010;59:518-33.
36. Leaché AD, Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Systematic Biology 2011;60:126-37.
37. Kubatko LS, Degnan JH. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biolo-gy 2009;56:17-24.
38. Liu L, Pearl DK. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 2007;56:504-14.
39. Heled J, Drummond AJ. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 2010;27: 570-80.
40. Rannala B, Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 2003;164: 1645-56.
41. Liu L. BEST: bayesian estimation of species trees under the coalescent model. Bioinformatics 2008;24:2542-3.
42. Kubatko LS, Carstens BC, Knowles LL. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009;25:971-3.
43. Larget B, Kotha SK, Dewey CN, Ané C. BUCKy: gene tree / species tree reconciliation with the Bayesian concordance analysis. Bioinformatics. 2010;26:2910-1.
44. Ané C, Larget B, Baum DA, et al. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 2007;24:412-26.
45. Chung Y, Ané C. Comparing two bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Systematic Biology 2011;60:261-75.
46. Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Systematic Biology 2009;58:468-77.
47. Liu L, Yu L. Estimating species trees from unrooted gene trees. Systematic Biology 2011;60:661-7.
48. Liu L, Yu L, Pearl DK. Maximum tree: a consistent estimator of the species tree. Journal of Mathematical Biology 2010;60: 96-106.
49. Liu J, Yu L, Edwards SV. A maximum pseudolikelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology 2010;10: 302.
50. Oliver JC. AUGIST: inferring species trees while accommodating gene tree uncertainty. Bioinformatics 2008;24:2932-3.
51. Maddison WP, Knowles LL. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 2006;55:21-30.
52. Chaudhary R, Bansal MS, Wehe A, et al. iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioninformatics 2010;11:574.
53. O'Meara BC. New heuristic methods for joint species delimitation and species tree inference. Systematic Biology 2010;59:59-73.
54. Huang H, He Q, Kubatko LS, Knowles LL. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Systematic Biology 2010;59:573-83.
55. Keck BP, Near TJ. A young clade repeating an old pattern: diversity in Nothonotus darters (Teleostei:Percidae) endemic to the Cumberland River. Molecular Ecology 2010;19:5030-42.
56. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-8.
57. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004;32:1792-7.
58. Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008;320:1632-5.
59. Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science 2008;319:473-6.
60. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 2007;56:564-77.
61. Kumar S, Filipski A. Multiple sequnece alignment: in pursuit of homologous DNA positions. Genome Research 2007;17:127-35.
62. Sullivan J, Joyce P. Model selection in phylogenetics. Annual Review of Ecology, Evolution and Systematics 2005;36:445-66.
63. Kelchner SA, Thomas MA. Model use in phylogenetics: nine key questions. Trends in Ecology and Evolution 2007;22:87-94.
64. Posada D. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 2008;25:1253-6.
65. Nylander JA. MrModeltest v. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, 2004.
66. Pickett KM, Randle CP. Strange bayes indeed: uniform topological priors imply non-uniform clade priors. Molecular Phylogenetics and Evolution 2005;34:203-11.
67. Randle CP, Pickett KM. Are nonuniform clade priors important in Bayesian phylogenetic analysis? A response to Brandley et al. Systematic Biology 2006;55:147-51.
68. Randle CP, Pickett KM. The conflation of ignorance and knowledge in the inference of clade posteriors. Cladistics 2010;26: 550-9.
69. Liu L, Pearl DK, Brumfield R, Edwards SV. Estimating species trees using multiple allele data. Evolution 2008;62:2080-91.
70. Willyard A, Wallace LE, Wagner WL, et al. Estimating the species tree for Hawain Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution. Molecular Phylogenetics and Evolution 2011;60:29-48.
71. Kubatko LS, Gibbs HL, Bloomquist EW. Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes. Systematic Biology 2011.
72. Ence DD, Carstens BC. SpedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Resources 2011;11:473-80.