Primate molecular phylogenetics in a genomic era

Molecular Phylogenetics and Evolution

Volumn 66, Issue 2, 2013, Pages 565-568

  Ting, Nelson ^a   Sterner, Kirstin N ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

Coalescent theory; Molecular phylogenetics; Morris Goodman; Multispecies coalescent; Phylogenomics; Primate systematics

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; GENETICS; GENOMICS; METHODOLOGY; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PRIMATE;

ANIMALS; GENOMICS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PRIMATES;

PRIMATES;

EID: 84873082673     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.08.021     Document Type: Article

References (50)

1. Bininda-Emonds O.R.P. The evolution of supertrees. Trends Ecol. Evol. 2004, 19(6):315-322.
2. Burgess R., Yang Z. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 2008, 25:1979-1994.
3. de Queiroz A., Gatesy J. The supermatrix approach to systematics. Trends Ecol. Evol. 2007, 22(1):34-41.
4. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
5. Dutheil J.Y., Ganapathy G., Hobolth A., Mailund T., Uyenoyama M.K., Schierup M.H. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 2009, 183(1):259-274.
6. Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
7. Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(14):5936-5941.
8. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, Massachusetts.
9. Gillespie J.H., Langley C.H. Are evolutionary rates really variable?. J. Mol. Evol. 1979, 13:27-34.
10. Goodman M. The role of immunochemical differences in the phyletic development of human behavior. Hum. Biol. 1961, 33:131-162.
11. Goodman M. Evolution of the immunologic species specificity of human serum proteins. Hum. Biol. 1962, 34:104-150.
12. Goodman M. Immunochemistry of the primates and primate evolution. Ann. N.Y. Acad. Sci. 1962, 102:219-234.
13. Goodman M. Man's place in the phylogeny of the primates as reflected in serum proteins. Classification and Human Evolution 1963, 204-230. Viking Fund Publications in Anthropology, Chicago. S. Washburn (Ed.).
14. Goodman M. Serological analysis of the systematics of recent hominoids. Hum. Biol. 1963, 35:377-436.
15. Goodman M. Epilogue: a personal account of the origins of a new paradigm. Mol. Phylogenet. Evol. 1996, 5:269-285.
16. Goodman M., Czelusniak J., Moore G.W., Romero-Herrera A.E., Matsuda G. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 1979, 28:132-163.
17. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27(3):570-580.
18. Hennig, W., 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, Chicago & London.
19. Hobolth A., Christensen O.F., Mailund T., Schierup M.H. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 2007, 3:e7.
20. Horvath J.E., Weisrock D.W., Embry S.L., Fiorentino I., Balhoff J.P., Kappeler P., Wray G.A., Willard H.F., Yoder A.D. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genome Res. 2008, 18:489-499.
21. Hudson R.R. Testing the constant-rate neutral allele model with protein sequence data. Evolution 1983, 37:203-217.
22. Jameson N.M., Hou Z.C., Sterner K.N., Weckle A., Goodman M., Steiper M.E., Wildman D.E. Genomic data reject the hypothesis of a prosimian primate clade. J. Hum. Evol. 2011, 61:295-305.
23. Kim S.K., Carbone L., Becquet C., Mootnick A.R., Li D.J., de Jong P.J., Wall J.D. Patterns of genetic variation within and between gibbon species. Mol. Biol. Evol. 2011, 28(8):2211-2218.
24. Kingman J.F.C. The coalescent. Stochastic Process Appl. 1982, 13(3):235-248.
25. Knowles L.L. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 2009, 58:463-467.
26. Knowles L.L., Lanier H.C., Klimov P.B., He Q. Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy. Mol. Phylogenet. Evol. 2012, 65:501-509.
27. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
28. Leache A.D. Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data. Mol. Phylogenet. Evol. 2010, 54:162-171.
29. Leache A.D., Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 2011, 60(2):126-137.
30. Liu L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 2008, 24:2542-2543.
31. Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 2009, 53:320-328.
32. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
33. Mailund T., Dutheil J.Y., Hobolth A., Lunter G., Schierup M.H. Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet. 2011, 7:e1001319.
34. McCormack J.E., Huang H., Knowles L.L. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 2009, 58:501-508.
35. McVicker, G., Gordon, D., Davis, C., Green, P., 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5.
36. Meng C., Kubatko L.S. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theor. Popul. Biol. 2009, 75:35-45.
37. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5(5):568-583.
38. Patterson N., Richter D.J., Gnerre S., Lander E.S., Reich D. Genetic evidence for complex speciation of humans and chimpanzees. Nature 2006, 441:1103-1108.
39. Perelman P., Johnson W.E., Roos C., Seuanez H.N., Horvath J.E., Moreira M.A., Kessing B., Pontius J., Roelke M., Rumpler Y., Schneider M.P., Silva A., O'Brien S.J., Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet. 2011, 7:e1001342.
40. Perez S.I., Klaczko J., dos Reis S.F. Species tree estimation for a deep phylogenetic divergence in New World monkeys (Primates: Platyrrhini). Mol. Phylogenet. Evol. 2012, 65:621-630.
41. Scally A., Dutheil J.Y., Hillier L.W., Jordan G.E., Goodhead I., Herrero J., Hobolth A., Lappalainen T., Mailund T., Marques-Bonet T., McCarthy S., Montgomery S.H., Schwalie P.C., Tang Y.A., Ward M.C., Xue Y., Yngvadottir B., Alkan C., Andersen L.N., Ayub Q., Ball E.V., Beal K., Bradley B.J., Chen Y., Clee C.M., Fitzgerald S., Graves T.A., Gu Y., Heath P., Heger A., Karakoc E., Kolb-Kokocinski A., Laird G.K., Lunter G., Meader S., Mort M., Mullikin J.C., Munch K., O'Connor T.D., Phillips A.D., Prado-Martinez J., Rogers A.S., Sajjadian S., Schmidt D., Shaw K., Simpson J.T., Stenson P.D., Turner D.J., Vigilant L., Vilella A.J., Whitener W., Zhu B., Cooper D.N., de Jong P., Dermitzakis E.T., Eichler E.E., Flicek P., Goldman N., Mundy N.I., Ning Z., Odom D.T., Ponting C.P., Quail M.A., Ryder O.A., Searle S.M., Warren W.C., Wilson R.K., Schierup M.H., Rogers J., Tyler-Smith C., Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature 2012, 483:169-175.
42. Siepel A. Phylogenomics of primates and their ancestral populations. Genome Res. 2009, 19:1929-1941.
43. Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics 1983, 105(2):437-460.
44. Townsend T.M., Mulcahy D.G., Noonan B.P., Sites J.W., Kuczynski C.A., Wiens J.J., Reeder T.W. Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Mol. Phylogenet. Evol. 2011, 61:363-380.
45. Wang X.-P., Yu L., Roos C., Ting N., Ping C., Wang J., Zhang Y.-P. Phylogenetic relationships among the colobine monkeys revisited: new insights from analyses of complete mitochondrial genomes and forty-four nuclear non-coding markers. PLoS One 2012, 7(4):e36274.
46. Weisrock D.W., Smith S.D., Chan L.M., Biebouw K., Kappeler P.M., Yoder A.D. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical denomstation of the effect of allele sampling in phylogenetics. Mol. Biol. Evol. 2012, 29(6):1615-1630.
47. 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.
48. Wu C.I. Inferences of species phylogeny in relation to segregation of ancestral piolymorphisms. Genetics 1991, 127:429-435.
49. Yu Y., Than C., Degnan J.H., Nakhleh L. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst. Biol. 2011, 60:138-149.
50. Zinner D., Arnold M.L., Roos C. The strange blood: natural hybridization in primates. Evol. Anthropol. 2011, 20:96-103.