Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini)

Molecular Phylogenetics and Evolution

Volumn 65, Issue 2, 2012, Pages 621-630

  Perez, S Ivan ^a   Klaczko, Julia ^b   dos Reis, Sérgio F ^b  

^a UNIVERSIDAD NACIONAL DE LA PLATA   (Argentina)

^b UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

*BEAST; America; Gene tree; Molecular datasets; Platyrrhines; Species tree

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; PLATYRRHINI;

ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; PLATYRRHINI;

AOTUS (PRIMATE); CEBIDAE; PITHECIIDAE; PLATYRRHINI; PRIMATES;

EID: 84866165443     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.07.014     Document Type: Article

References (47)

1. Belfiore N.M., Liu L., Moritz C. Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Echimyidae). Syst. Biol. 2008, 57:294-310.
2. Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
3. Clemente-Carvalho R., Klaczko J., Perez S.I., Alves A., Haddad C., dos Reis S.F. Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae). Mol. Phylogenet. Evol. 2011, 61:79-89.
4. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
5. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
6. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
7. Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
8. Felsenstein J. Phylogenies and the comparative method. Am. Nat. 1985, 125:1-15.
9. Felsenstein J. Inferring Phylogenies 2004, Sinauer.
10. Fleagle J.G. Primate Adaptation and Evolution 1999, Academic Press, New York. second ed.
11. Ford S.M. Systematics of the New World monkeys. Systematics, Evolution and Anatomy 1986, vol. 1:73-135. Alan R. Liss, New York. D.R. Swindler, J. Erwin (Eds.).
12. Freckleton R.P., Cooper N., Jetz W. Comparative methods as a statistical fix: the dangers of ignoring an evolutionary model. Am. Nat. 2011, 178:E10-E17.
13. Gavrilets S., Losos J.B. Adaptive radiation: contrasting theory with data. Science 2009, 323:732-737.
14. Goodman M., Porter C.A., Czelusniak J., Page S.L., Schneider H., Shoshani J., Gunnell G., Groves C.P. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 1998, 9:585-598.
15. Hall, T., 2004. BioEdit 7.0.0. http://www.mbio.ncsu.edu/bioedit/bioedit.html.
16. Heled J., Drummond A.J. Bayesian inference of Species Trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
17. Heled, J., Drummond, A.J., Xie, W., 2011. Bayesian inference of Species Trees from multilocus data using *BEAST. http://www.beast.bio.ed.ac.uk/Tutorials.
18. Horovitz I., Zardoya R., Meyer A. Platyrrhine systematics: a simultaneous analysis of molecular and morphological data. Am. J. Phys. Anthropol. 1998, 106:261-281.
19. Kay R.F. The phyletic relationships of extant and fossil Pitheciinae. J. Hum. Evol. 1990, 19:175-208.
20. Knowles L.L., Kubatko L.S. Estimating Species Trees: Practical and Theoretical 2010, Wiley-Blackwell, New York.
21. Leaché A.D., Rannala B. The accuracy of species tree estimation under simulation: A comparison of methods. Syst. Biol. 2011, 60:126-137.
22. Lemey M., Salemi M., Vandamme A.-M. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing 2009, Cambridge University Press, Cambridge.
23. Liu L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 2008, 24:2542-2543.
24. Liu L., Pearl D.K., Brumfield R.T., Edwards S.V. Estimating species trees using multiple-allele DNA sequence data. Evolution 2008, 62:2080-2091.
25. Losos J.B. The limitations of phylogenies in comparative biology. Am. Nat. 2011, 177:709-727.
26. Losos J.B., Mahler D.L. Adaptive radiation: the interaction of ecological opportunity, adaptation, and speciation. Evolution Since Darwin: The First 150Years 2010, 381-420. Sinauer Associates, Sunderland, MA. M.A. Bell, D.J. Futuyma, W.F. Eanes, J.S. Levinton (Eds.).
27. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
28. Norconk M.A., Wright B.W., Conklin-Brittain N.L., Vinyard C.J. Mechanical and nutritional properties of food as factors in Platyrrhine dietary adaptations. South American Primates, Developments in Primatology: Progress and Prospects 2009, 279-319. Springer-Verlag, New York. P.A. Garber, A. Estrada, J.C. Bicca-Marques, E.W. Heymann, K.B. Strier (Eds.).
29. Opazo J.C., Wildman D.E., Prychitko T., Johnson R.M., Goodman M. Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates). Mol. Phylogenet. Evol. 2006, 40:274-280.
30. Perelman P., Johnson W.E., Roos C., Seuánez H.N., Horvath J.E., Moreira M.A.M., Kessing B., Pontius J., Roelke M., Rumpler Y., Schneider M.P.C., Silva A., O'Brien S.J., Pecon-Slattery J. A molecular phylogeny of living Primates. PLoS Genet. 2011, 7:e1001342.
31. Perez S.I., Klaczko J., Rocatti G., dos Reis S.F. Patterns of cranial shape diversification during the phylogenetic branching process of New World monkeys (Primates: Platyrrhini). Evol. Biol. 2011, 24:1826-1835.
32. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
33. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4 software. http://www.beast.bio.ed.ac.uk/Tracer.
34. Rannala B., Yang Z. Phylogenetic inference using whole genomes. Annu. Rev. Genom. Hum. Genet. 2008, 9:217-231.
35. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
36. Rosenberger A.L. Fossil New World Monkeys dispute the molecular clock. J. Hum. Evol. 1984, 13:737-742.
37. Rosenberger A.L. The evolution of feeding niches in New World Monkeys. Am. J. Phys. Anthropol. 1992, 88:525-562.
38. Rosenberger A.L. Platyrrhine paleontology and systematics: the paradigm shifts. The Primate Fossil Record 2002, 151-160. Cambridge University Press, Cambridge. W.C. Hartwig (Ed.).
39. Rosenberger A.L., Tejedor M.F., Cooke S., Halenar L., Pekkar S. Platyrrhine ecophylogenetics, past and present. South American Primates: Comparative Perspectives in the Study of Behavior 2009, 69-113. Ecology and Conservation, Springer, New York. P.A. Garber, A. Estrada, J.C. Bicca-Marques, E.W. Heymann, K.B. Strier (Eds.).
40. Rosenberger, A.L., Tejedor, M.F, in press. The misbegotten: long lineages, long branches and the interrelationships of Aotus, Callicebus and the saki-uakaris. In: Barnett, A.L., Veiga, S., Ferrari, S., Norconk, M.N. (Eds.), Evolutionary Biology and Conservation of Titis, Sakis and Uacaris. Cambridge University Press, Cambridge.
41. Schneider H. The current status of the NewWorld Monkey phylogeny. An. Acad. Bras. Ci. 2000, 72(2).
42. Schneider H., Canavez F.C., Sampaio I., Moreira M.Â.M., Tagliaro C.H., Seuánez H.N. Can molecular data place each neotropical monkey in its own branch?. Chromosoma 2001, 109:515-523.
43. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
44. Tejedor M.F. The origin and evolution of neotropical primates. Arq. Mus. Nac. 2008, 66:251-269.
45. Wiens J.J. Estimating rates and patterns of morphological evolution from phylogenies: lessons in limb lability from Australian Lerista lizards. J. Biol. 2009, 8:19.
46. Wildman D.E., Jameson N.M., Opazo J.C., Yi S.V. A fully resolved genus level phylogeny of neotropical primates (Platyrrhini). Mol. Phylogenet. Evol. 2009, 53:694-702.
47. Wilkinson R.D., Steiper M.E., Soligo C., Martin R.D., Yang Z., Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 2011, 60:16-31.