Resolution of the Hylobates phylogeny: Congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological data sets

Molecular Phylogenetics and Evolution

Volumn 45, Issue 2, 2007, Pages 620-628

  Whittaker, Danielle J ^a   Morales, Juan Carlos ^b,c   Melnick, Don J ^b,c  

^a INDIANA UNIVERSITY   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c New York Consortium in Evolutionary Primatology ^*  (United States)

Author keywords

Hylobatidae; mtDNA; Partition homogeneity test; Southeast Asia

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ANIMAL BEHAVIOR; ARTICLE; CHEMISTRY; CLASSIFICATION; CONFORMATION; DEMOGRAPHY; GENETICS; HAPLORHINI; HISTOLOGY; INDONESIA; PHYLOGENY; PHYSIOLOGY; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; BEHAVIOR, ANIMAL; DEMOGRAPHY; DNA, MITOCHONDRIAL; GENETIC SPECIATION; HYLOBATES; INDONESIA; LIKELIHOOD FUNCTIONS; NUCLEIC ACID CONFORMATION; PHYLOGENY;

HAPLORHINI; HYLOBATES; HYLOBATES KLOSSII; HYLOBATES LAR; HYLOBATES MOLOCH; HYLOBATES PILEATUS; HYLOBATIDAE;

EID: 34948905208     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.08.009     Document Type: Article

References (67)

1. Abegg C., and Thierry B. Macaque evolution and dispersal in insular south-east Asia. Biol. J. Linn. Soc. 75 (2002) 555-576
2. Andayani N., Morales J.C., Forstner M.R.J., Supriatna J., and Melnick D.J. Genetic variability in mtDNA of the silvery gibbon (Hylobates moloch): implications for the conservation of a critically endangered species. Conserv. Biol. 15 (2001) 770-775
3. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge
4. Barker F.K., and Lutzoni F.M. The utility of the incongruence length difference test. Syst. Biol. 51 (2002) 625-637
5. Brandon-Jones D., Eudey A.A., Geissmann T., Groves C.P., Melnick D.J., Morales J.C., Shekelle M., and Stewart C.-B. Asian primate classification. Int. J. Primatol. 25 (2004) 97-164
6. Bull J.J., Huelsenbeck J.P., Cunningham C.W., Swofford D.L., and Waddell P.J. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42 (1993) 384-397
7. Chatterjee, H., 2001. Phylogeny and Biogeography of Gibbons, Genus Hylobates. Unpublished Ph.D. Thesis. University of London.
8. Chivers, D.J., 1977. The lesser apes. In: Prince of Monaco Rainier III (Ed.), Primate Conservation. Academic Press, New York, pp. 539-598.
9. Creel N., and Preuschoft H. Systematics of the lesser apes: a quantitative taxonomic analysis of craniometric and other variables. In: Preuschoft H., Chivers D.J., Brockelman W.Y., and Creel N. (Eds). The Lesser Apes: Evolutionary and Behavioral Biology (1984), Edinburgh University Press, Edinburgh 562-613
10. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 14 (1997) 733-740
11. Cunningham C.W. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46 (1997) 464-476
12. DeSalle R., and Brower A.V.Z. Process partitions, congruence, and the independence of characters: inferring relationships among closely related Hawaiian Drosophila from multiple gene regions. Syst. Biol. 46 (1997) 751-764
13. Eernisse D.J., and Kluge A.G. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10 (1993) 1170-1195
14. Farris J.S., Källersjö J., Kluge A.G., and Bult C. Constructing a significance test for congruence. Syst. Biol. 44 (1995) 570-572
15. Flynn J.J., and Nedbal M.A. Phylogeny of the Carnivora (Mammalia): congruence vs incompatibility among multiple data sets. Mol. Phylogenet. Evol. 9 (1998) 414-426
16. Garza J.C., and Woodruff D.S. A phylogenetic study of the gibbons (Hylobates) using DNA obtained noninvasively from hair. Mol. Phylogenet. Evol. 1 (1992) 202-210
17. Gautier J.-P. Interspecific affinities among guenons as deduced from vocalizations. In: Gautier-Hion A., Bourliere F., Gautier J.-P., and Kingdon J. (Eds). A Primate Radiation: Evolutionary Biology of the African Guenons (1988), Cambridge University Press, Cambridge 194-226
18. Geissmann, T., 1993. Evolution of Communication in Gibbons (Hylobatidae). Unpublished Ph.D. Thesis. University of Zurich.
19. Geissmann, T., 2002a. Taxonomy and evolution of gibbons. Evol. Anthropol. (Suppl. 1), 28-31.
20. Geissmann T. Duet-splitting and the evolution of gibbon songs. Biol. Rev. 77 (2002) 57-76
21. Geissmann T., and Nijman T. Calling in wild silvery gibbons (Hylobates moloch) in Java (Indonesia): behavior, phylogeny, and conservation. Am. J. Primatol. 68 (2006) 1-19
22. Goloboff P.A. Estimating character weights during tree search. Cladistics 9 (1993) 83-91
23. Gorog A.J., Sinaga M.H., and Engstron M.D. Vicariance or dispersal? Historical biogeography of three Sunda shelf murine rodents (Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi). Biol. J. Linn. Soc. 81 (2004) 91-109
24. Groves C.P. The classification of the gibbons. Z. Saugetierkd. 33 (1968) 239-246
25. Groves C.P. Systematics and phylogeny of gibbons. In: Rumbaugh D.M. (Ed). Gibbon and Siamang (1972), Karger, Basel 1-89
26. Groves, C.P., 2001. Primate Taxonomy, Smithsonian Institution Press, Washington, DC.
27. Haimoff E.H., Chivers D.J., Gittins S.P., and Whitten T. A phylogeny of gibbons (Hylobates spp.) based on morphological and behavioural characters. Folia Primatol. 39 (1982) 213-237
28. Hall L.M., Jones D.S., and Wood B.A. Evolution of the gibbon subgenera inferred from cytochrome b DNA sequence data. Mol. Phylogenet. Evol. 10 (1998) 281-286
29. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21 (1985) 160-174
30. Hayashi, S., Hayasaka, K., Takenaka, O., Horai, S., 1995. Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: preliminary report. J. Mol. Evol. 41, 359-365.
31. Hebert P.D.N., Cywinska A., Ball S.L., and de Waard J.R. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270 (2003) 313-321
32. Hebert, P.D.N., Penton, E.H., Burns, J.M., Janzen, D.H., Hallwachs, W., 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Q11. N23 P7 101, 14812-14817.
33. Hipp A.L., Hall J.C., and Sytsma K.J. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst. Biol. 53 (2004) 81-89
34. Hirai H., Wijayanto H., Tanaka H., Mootnick A.R., Iskandriati D., Perwitasari-Farajallah D., and Sajuthi D. A chromosome landmark separating Sumatran and Bornean agile gibbons. Folia Primatol. 75 (2004) 112
35. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., and Gibson T.J. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23 (1998) 403-405
36. King M. Species Evolution: The Role of Chromosome Change (1993), Cambridge University Press, Cambridge
37. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Q11. N23 P7 86, 6196-6200.
38. Lee M.S.Y. Uninformative characters and apparent conflict between molecules and morphology. Mol. Biol. Evol. 18 (2001) 676-680
39. Marshall, J., Sugardjito, J., 1986. Gibbon Systematics. Comparative Primate Biology. In: Systematics, Evolution, and Anatomy, vol. I. Alan R. Liss, Inc., New York, pp. 137-185.
40. Miller G.S. Seventy new Malayan mammals. Smithsonian Misc. Coll. 45 (1903) 1-73
41. Mootnick A., and Groves C. A new generic name for the hoolock gibbon (Hylobatidae). Int. J. Primatol. 26 (2005) 971-976
42. Moritz C., and Cicero C. DNA barcoding: promises and pitfalls. PLoS Biol. 2 (2004) 1529-1531
43. Oates J.F., Bocian C.M., and Terranova C.J. The loud calls of black-and-white colobus monkeys: their adaptive and taxonomic significance in light of new data. In: Whitehead P.F., and Jolly C.J. (Eds). Old World Monkeys (2000), Cambridge University Press, Cambridge 431-452
44. Omland K. Character congruence between a molecular and a morphological phylogeny for dabbling ducks (Anas). Syst. Biol. 43 (1994) 369-386
45. Palumbi, S.R., 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, Sinauer, Sunderland, MA, pp. 205-247.
46. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
47. Prouty L.A., Buchanan P.D., Pollitzer W.S., and Mootnick A.R. A presumptive new hylobatid subgenus with 38 chromosomes. Cytogenet. Cell Genet. 35 (1983) 141-142
48. Remsen J., and DeSalle R. Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae. Mol. Phylogenet. Evol. 9 (1998) 225-235
49. Roos C., and Geissmann T. Molecular phylogeny of the major hylobatid divisions. Mol. Phylogenet. Evol. 19 (2001) 486-494
50. Sambrook E., Fritsch E.P., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
51. Snowdon C.T., Hodun A., Rosenberger A.L., and Coimbra-Filho A.F. Long-call structure and its relation to taxonomy in lion tamarins. Am. J. Primatol. 11 (1986) 253-261
52. Stanyon R., Sineo L., Chiarelli B., Camperio-Ciani A., Mootnick A.R., Haimoff E.H., and Sutarman D. Banded karyotypes of the 44-chromosome gibbons. Folia Primatol. 48 (1987) 56-64
53. * and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
54. Takacs Z., Morales J.C., Geissmann T., and Melnick D.J. A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-4 gene sequences. Mol. Phylogenet. Evol. 36 (2005) 456-467
55. Tanaka H., Wijayanto H., Mootnick A., Iskandriati D., Perwitasari-Farajallah D., Sajuthi D., and Hirai H. Molecular phylogenetic analysis of subspecific relationships in agile gibbons (Hylobates agilis) using mitochondrial and TSPY gene sequences. Folia Primatol. 75 (2004) 418
56. Tenaza R.R. Songs, choruses and countersinging of Kloss' gibbons (Hylobates klossii) in Siberut Island, Indonesia. Z. Tierpsychol. 40 (1976) 37-52
57. Tenaza R.R., and Hamilton W.J.I. Preliminary observations of the Mentawai Islands gibbon, Hylobates klossii. Folia Primatol. 15 (1971) 201-211
58. Tosi A.J., Morales J.C., and Melnick D.J. Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys. Evolution 57 (2003) 1419-1435
59. van Tuinen P., and Ledbetter D.H. Cytogenetic comparison and phylogeny of three species of Hylobatidae. Am. J. Phys. Anthropol. 61 (1983) 453-466
60. Vigilant, L., Pennington, R., Harpending, H., Kocher, T.D., Wilson, A.C., 1989. Mitochondrial DNA sequences in single hairs from a southern African population. Q11. N23 P7 86, 9350-9354.
61. Vogler A.P., and Pearson D.L. A molecular phylogeny of the tiger beetles (Cicindelidae): congruence of mitochondrial and nuclear rDNA data sets. Mol. Phylogenet. Evol. 6 (1996) 321-338
62. Whittaker, D.J., 2005. Evolutionary Genetics of the Kloss's Gibbon (Hylobates klossii): Systematics, Phylogeography, and Conservation. Unpublished Ph.D. Thesis. City University of New York Graduate Center.
63. Woodruff D.S. Non-invasive genotyping of primates. Primates 34 (1993) 333-346
64. Woodruff D.S., Monda K., and Simmons R.E. Mitochondrial DNA sequence variation and subspecific taxonomy in the white-handed gibbon, Hylobates lar. Nat. Hist. J. Chulalongkorn Univ. Supplement 1 (2005) 71-78
65. Zehr, S.M., 1999. A nuclear and mitochondrial phylogeny of the lesser apes (Primates, genus Hylobates). Unpublished Ph.D. Thesis. Harvard University.
66. Zhang Y. Mitochondrial DNA sequence evolution and phylogenetic relationships of gibbons. Acta Genet. Sin. 24 (1997) 231-237
67. Zimmermann E. Differentiation of vocalizations in bushbabies (Galaginae, Prosimiae, Primates) and the significance for assessing phylogenetic relationships. Z. Zool. Syst. Evol. 28 (1990) 217-239