Phylogenetic relationships among the colobine monkeys revisited: New insights from analyses of complete mt genomes and 44 nuclear non-coding markers

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Wang, Xiao Ping ^a   Yu, Li ^a   Roos, Christian ^b   Ting, Nelson ^c   Chen, Cui Ping ^a   Wang, Jing ^a   Zhang, Ya Ping ^a,d  

^a YUNNAN UNIVERSITY   (China)

^b GERMAN PRIMATE CENTER   (Germany)

^c UNIVERSITY OF OREGON   (United States)

^d KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COLOBINAE; GENE; HYBRIDIZATION; MITOCHONDRIAL GENOME; MOLECULAR PHYLOGENY; MONOPHYLY; NASALIS; NONHUMAN; NUCLEAR NONCODING GENE; NUCLEOTIDE SEQUENCE; PARAPHYLY; PILIOCOLOBUS; PRESBYTIS; PYGATHRIX; RHINOPITHECUS; SEMNOPITHECUS; TRACHYPITHECUS; UNINDEXED SEQUENCE; ANIMAL; CELL NUCLEUS; FEMALE; GENETIC MARKER; GENETICS; GENOMICS; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; PHYLOGENY;

COLOBINAE; COLOBUS; MAMMALIA; NASALIS; PILIOCOLOBUS; PRESBYTIS; PRIMATES; PYGATHRIX; SEMNOPITHECUS; TRACHYPITHECUS;

ANIMALS; CELL NUCLEUS; COLOBINAE; EVOLUTION, MOLECULAR; FEMALE; GENES, MITOCHONDRIAL; GENETIC MARKERS; GENOME, MITOCHONDRIAL; GENOMICS; PHYLOGENY;

EID: 84860458557     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036274     Document Type: Article

References (71)

1. Davies AG, Oates JF, (1994) Colobine monkeys: their ecology, behavior, and evolution Cambridge Cambridge University Press.
2. Groves CP, (2001) Primate Taxonomy Washington Smithsonian Institution Press.
3. Brandon-Jones D, Eudey AA, Geissmann T, Groves CP, Melnick DJ, et al. (2004) Asian primate classification. Int J Primatol 25: 97-164.
4. Groves CP, (1989) A Theory of Human and Primate Evolution Oxford Oxford University Press.
5. Jablonski NG, (1993) Quaternary environments and the evolution of primates in East Asia, with notes on two new specimens of fossil Cercopithecidae from China. Folia Primatol 60: 118-132.
6. Napier JR, Napier PH, (1970) Old World Monkeys New York Academic Press.
7. Szalay FS, Delson E, (1979) Evolutionary History of the Primates New York Academic Press.
8. Peng Y, Pan R, Ye Z, Wang H, (1991) Comparative study on cranioface and brain case in Asian colobines. Acta Anthropol Sin 10: 346-356.
9. Pan R, (2007) Dental variation among Asian colobines, with specific reference to the macaques on the same continent. Zool Res 28: 569-579.
10. Bigoni F, Stanyon R, Wimmer R, Schempp W, (2003) Chromosome painting shows that the proboscis monkey (Nasalis larvatus) has a derived karyotype and is phylogenetically nested within Asian colobines. Am J Primatol 60: 85-93.
11. Bigoni F, Houck M, Ryder O, Wienberg J, Stanyon R, (2004) Chromosome painting shows that Pygathrix nemaeus has the most basal karyotype among Asian Colobinae. Int J Primatol 25: 679-688.
12. Perelman P, Johnson WE, Roos C, Seuanez HN, Horvath JE, et al. (2011) A molecular phylogeny of living primates. PLoS Genet 7: e1001342.
13. Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, et al. (2011) Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol 11: 77.
14. Sterner KN, Raaum RL, Zhang YP, Stewart CB, Disotell TR, (2006) Mitochondrial data support an odd-nosed colobine clade. Mol Phylogenet Evol 40: 1-7.
15. Weitzel V, Yang CM, Groves CP, (1988) A catalogue of primate in the Singapore Zoological Reference Collection. Raffles Bull Zool 36: 1-166.
16. Meyer D, Rinaldi ID, Ramlee H, Perwitasari-Farajallah D, Hodges JK, et al. (2011) Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation. Mol Phylogenet Evol 59: 311-319.
17. Osterholz M, Walter L, Roos C, (2008) Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups. BMC Evol Biol 8: 58.
18. Ting N, Tosi AJ, Li Y, Zhang YP, Disotell TR, (2008) Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys. Mol Phylogenet Evol 46: 466-474.
19. Li M, Wei F, Huang C, Pan R, Ruiter JD, (2004) Phylogeny of snub-nosed monkeys inferred from Mitochondrial DNA, Cytochrome B, and 12S rRNA sequences. Int J Primatol 25: 861-873.
20. Wang W, Forstner MRJ, Zhang YP, Liu ZM, Wei Y, et al. (1997) A phylogeny of Chinese leaf monkeys using mitochondrial ND3-ND4 gene sequences. Int J Primatol 18: 305-320.
21. Zhang YP, Ryder OA, (1998) Mitochondrial cytochrome b gene sequences of Old World monkeys: with special reference on evolution of Asian colobines. Primates 39: 39-49.
22. Chatterjee HJ, Ho SY, Barnes I, Groves C, (2009) Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol Biol 9: 259.
23. Fabre PH, Rodrigues A, Douzery EJ, (2009) Patterns of macroevolution among primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol 53: 808-825.
24. Napier JR, Napier JR, (1967) A Handbook of Living Primates London Academic Press.
25. Ting N, (2008) Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys. J Hum Evol 55: 312-325.
26. Groves C, Angst R, Westwood C, (1993) The status of Colobus polykomos dollmani Schwarz. Int J Primatol 14: 573-586.
27. Grubb P, Butynski TM, Oates JF, Bearder SK, Disotell TR, et al. (2003) Assessment of the diversity of African primates. Int J Primatol 24: 1301-1357.
28. Oates JF, Trocco TF, (1983) Taxonomy and phylogeny of black-and-white colobus monkeys: inferences from an analysis of loud call variation. Folia Primatol 40: 83-113.
29. Struhsaker TT, (1981) Vocalizations, phylogeny and palaeogeography of red colobus monkeys (Colobus badius). Afr J Ecol 19: 265-283.
30. Peng ZG, Elango N, Wildman DE, Yi SV, (2009) Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics 10: 247.
31. Delson E, (1975) Evolutionary history of the Cercopithecidae. Contrib Primatol 5: 167-217.
32. Whittaker DJ, Ting N, Melnick DJ, (2006) Molecular phylogenetic affinities of the simakobu monkey (Simias concolor). Mol Phylogenet Evol 39: 887-892.
33. Sambrook E, Fritsch EF, Maniatis T, (1989) Molecular Cloning: A Laboratory Manual Cold Spring Harbor, New York Cold Spring Harbor Press.
34. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
35. Gutell RR, Gray MW, Schnare MN, (1993) A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res 21: 3055-3074.
36. Springer MS, Douzery E, (1996) Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J Mol Evol 43: 357-373.
37. Rokas A, Williams BL, King N, Carroll SB, (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
38. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
39. Swofford DL, (2002) PAUP*: phylogenetic analysis using parsimony (* and other methods). Version 4 Sunderland MA Sinauer Associates.
40. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
41. Akaike H, (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723.
42. Posada D, Buckley TR, (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.
43. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
44. Felsenstein J, (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
45. Stamatakis A, Hoover P, Rougemont J, (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758-771.
46. Larget B, Simon DL, (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16: 750-759.
47. Lartillot N, Philippe H, (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21: 1095-1109.
48. Lartillot N, Lepage T, Blanquart S, (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286-2288.
49. Dutheil J, Boussau B, (2008) Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol 8: 255.
50. Shimodaira H, Hasegawa M, (1999) Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116.
51. Shimodaira H, (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51: 492-508.
52. Shimodaira H, Hasegawa M, (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
53. Zardoya R, Meyer A, (1996) Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 13: 933-942.
54. Russo CA, Takezaki N, Nei M, (1996) Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol 13: 525-536.
55. Miya M, Nishida M, (2000) Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol 17: 437-455.
56. Mueller RL, (2006) Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst Biol 55: 289-300.
57. Yu L, Li YW, Ryder OA, Zhang YP, (2007) Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol 7: 198.
58. Cunha RL, Grande C, Zardoya R, (2009) Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol Biol 9: 210.
59. Yu L, Peng D, Liu J, Luan PT, Liang L, et al. (2011) On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evol Biol 11: 92.
60. Strasser E, Delson E, (1987) Cladistic analysis of cercopithecid relationships. J Hum Evol 16: 81-99.
61. Groves CP, (1970) The forgotten leaf-eaters and the phylogeny of Colobinae. In: Napier JR, Napier PH, editors. Old World Monkeys New York Academic Press pp. 555-586.
62. Jablonski NG, (1998) The evolution of the doucs and snub-nosed monkeys and the question of the phyletic unity of the odd-nosed colobines. In: Jablonski NG, editors. The Natural History of the Doucs and Snub-Nosed Monkeys Singapore World Scientific Press pp. 13-52.
63. Jablonski NG, Peng YZ, (1993) The phylogenetic relationships and classification of the doucs and snub-nosed langurs of China and Vietnam. Folia Primatol 60: 36-55.
64. Oates JF, Davies AG, Delson E, (1994) The diversity of living colobines. In: Davies AG, Oates JF, editors. Colobine Monkeys: Their Ecology, Behavior, and Evolution Cambridge Cambridge University Press pp. 45-74.
65. Benavides E, Baum R, McClellan D, Sites JW Jr, (2007) Molecular phylogenetics of the lizard genus Microlophus (Squamata: Tropiduridae): aligning and retrieving indel signal from nuclear introns. Syst Biol 56: 776-797.
66. Dalebout ML, Steel D, Baker CS, (2008) Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by nuclear introns: implications for the evolution of male tusks. Syst Biol 57: 857-875.
67. Matthee CA, Eick G, Willows-Munro S, Montgelard C, Pardini AT, et al. (2007) Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics. Mol Phylogenet Evol 42: 827-837.
68. Moller-Krull M, Delsuc F, Churakov G, Marker C, Superina M, et al. (2007) Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths). Mol Biol Evol 24: 2573-2582.
69. Yu L, Luan PT, Jin W, Ryder OA, Chemnick LG, et al. (2011) Phylogenetic utility of nuclear introns in interfamilial relationships of Caniformia (order Carnivora). Syst Biol 60: 175-187.
70. Schroder C, Bleidorn C, Hartmann S, Tiedemann R, (2009) Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives. Gene 448: 221-226.
71. Yu L, Wang XP, Ting N, Zhang YP, (2011) Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation. Mitochondrion 11: 497-503.