Phylogenetic relationships of the cuscuses and brushtail possums (Marsupialia : Phalangeridae) using the nuclear gene BRCA1

Australian Journal of Zoology

Volumn 54, Issue 5, 2006, Pages 353-361

  Raterman, Denise ^a   Meredith, Robert W ^a   Ruedas, Luis A ^b   Springer, Mark S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISPERSAL; DIVERGENCE; DNA FINGERPRINTING; GENETIC ANALYSIS; GEOGRAPHICAL DISTRIBUTION; MARSUPIAL; MITOCHONDRIAL DNA; MORPHOLOGY; PHYLOGENETICS; TAXONOMY;

ASIA; EURASIA; SOUTHEAST ASIA;

AILUROPS; AILUROPS URSINUS; METATHERIA; PHALANGER; PHALANGERIDAE; SPILOCUSCUS; STRIGOCUSCUS; STRIGOCUSCUS CELEBENSIS; TRICHOSURUS; WYULDA; WYULDA SQUAMICAUDATA;

EID: 33751099596     PISSN: 0004959X     EISSN: None     Source Type: Journal    
DOI: 10.1071/ZO05067     Document Type: Article

References (45)

1. Arnason, U., Adegoke, J. A., Bodin, K., Born, E. W., Esa, Y. B., Gullberg, A., Nilsson, M., Short, R. V., Xu, X., and Janke, A. (2002). Mammalian mitogenomic relationships and the root of the eutherian tree. Proceedings of the National Academy of Sciences of the United States of America 99, 8151-8156. doi:10.1073/pnas.102164299
2. Brammall, J. R. (1998). A new petauroid possum from the Oligo-Miocene of Riversleigh, northwestern Queensland. Alcheringa 23, 31-50.
3. Bremer, K. (1994). Branch support and tree stability. Cladistics 10, 295-304. doi:10.1111/j.1096-0031.1994.tb00179.x
4. Case, J. A. (1984). A new genus of potoroinae Marsupialia Macropodidae from the Miocene Ngapakaldi Local Fauna South Australia and a definition of the Potoroinae. Journal of Paleontology 58, 1074-1086.
5. Cooke, B. N. (2000). Cranial remains of a new species of balbarine kangaroo (Marsupialia: Macropodoidea) from the Oligo-Miocene freshwater limestone deposits of Riversleigh World Heritage Area, northern Australia. Journal of Paleontology 74, 317-326. doi:10.1666/0022-3360(2000)074〈0317: CROANS〉2.0.CO;2
6. Crosby, K. (2004). Fossil possums in Australasia: discovery, diversity and evolution. In 'The Biology of Australian Possums and Gliders'. (Eds R. L. Goldingay and S. M. Jackson.) pp. 161-176. (Surrey Beatty: Sydney.)
7. Crosby, K., and Norris, C. A. (2003). Periotic morphology in the trichosurin possums Strigocuscus celebensis and Wyulda squamicaudata (Diprotodontia, Phalangeridae) and a revised diagnosis of the tribe Trichosurini. American Museum Novitates 3414, 1-14. doi:10.1206/0003-0082(2003) 414〈0001:PMITTP〉2.0.CO;2
8. Drummond, A. J., and Rambaut, A. (2003). 'BEAST version 1.3.' Available at http://evolve.zoo.ox.ac.uk/beast [Verified June 2006].
9. Drummond, A. J., Ho, S. Y. W., Phillips, M. J., and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology 4, e88. doi:10.1371/journal.pbio.0040088
10. Flannery, T. (1994). 'Possums of the World. A Monograph of the Phalangeroidea.' (GEO Productions: Sydney.)
11. Flannery, T., Archer, M., and Maynes, G. (1987). The phylogenetic relationships of living phalangerids (Phalangeroidea: Marsupialia) with a suggested new taxonomy. In 'Possums and Opossums: Studies in Evolution'. (Ed. M. Archer.) pp. 477-506. (Surrey Beatty & the Royal Zoological Society of New South Wales: Sydney.)
12. Flynn, J. J., and Nedbal, M. A. (1998). Phylogeny of the Carnivora (Mammalia): congruence vs incompatibility among multiple data sets. Molecular Phylogenetics and Evolution 9, 414-426. doi:10.1006/mpev.1998.0504
13. Gatesy, J., Desalle, R., and Wheeler, W. (1993). Alignment - ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution 2, 152-157. doi:10.1006/mpev.1993. 1015
14. George, G. G. (1987). Characterization of the living species of cuscus (Marsupialia: Phalangeridae). In 'Possums and Opossums: Studies in Evolution'. (Ed. M. Archer.) pp. 507-526. (Surrey Beatty & the Royal Zoological Society of New South Wales: Sydney.)
15. Godthelp, H., Wroe, S., and Archer, M. (1999). A new marsupial from the early Eocene Tingamarra Local Fauna of Murgon, southeastern Queensland: a prototypical Australian marsupial? Journal of Mammalian Evolution 6, 289-313. doi:10.1023/A:1020517808869
16. Goldman, N., and Yang, Z. (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11, 725-736.
17. Hall, R. (1996). Reconstructing Cenozoic SE Asia. In 'Tectonic Evolution of Southeast Asia'. Special Publication No. 106. (Eds R. Hall and D. Blundell.) pp. 153-184. (Geological Society of London: London.)
18. Hall, R. (1998). The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. In 'Biogeography and Geological Evolution of SE Asia'. (Eds R. Hall and J. D. Holloway.) pp. 99-131. (Backhuys Publishers: Leiden, the Netherlands.)
19. Hall, R. (2002). Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations. Journal of Asian Earth Sciences 20, 353-431. doi:10.1016/S1367-9120(01)00069-4
20. Hamilton, A. T., and Springer, M. S. (1999). DNA sequence evidence for placement of the ground cuscus, Phalanger gymnotis, in the Tribe Phalangerini (Marsupialia: Phalangeridae). Journal of Mammalian Evolution 6, 1-17. doi:10.1023/A:1020534212504
21. Huelsenbeck, J. P., and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. doi:10.1093/bioinformatics/ 17.8.754
22. Kirsch, J. A. W., and Wolman, M. A. (2001). Molecular relationships of the bear cuscus, Ailurops ursinus (Marsupialia: Phalangeridae). Australian Mammalogy 23, 23-30.
23. Kirsch, J. A. W., Lapointe, F.-J., and Springer, M. S. (1997). DNAhybridization studies of marsupials and their implications for metatherian classification. Australian Journal of Zoology 45, 211-280. doi:10.1071/ZO96030
24. Kishino, H., and Hasegawa, M. (1989). Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea. Journal of Molecular Evolution 29, 170-179. doi:10.1007/BF02100115
25. Kishino, H., Thorne, J. L., and Bruno, W. J. (2001). Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution 18, 352-361.
26. Löytynoja, A., and Milinkovitch, M. C. (2001). SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17, 573-574. doi:10.1093/bioinformatics/17.6.573
27. McKenna, M. C., and Bell, S. K. (1997). 'Classification of Mammals: Above the Species Level.' (Columbia University Press: New York.)
28. Menzies, J. I., and Pernetta, J. C. (1986). A taxonomic revision of cuscuses allied to Phalanger orientalis Marsupialia Phalangeridae. Journal of Zoology Series B 1, 551-618.
29. Murphy, W. J., Eizirik, E., O'Brien, S. J., Madsen, O., and Scally, M., et al. (2001). Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348-2351. doi:10.1126/science.1067179
30. Muse, S. V., and Gaut, B. S. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution 11, 715-724.
31. Myers, T. J., and Archer, M. (1997). Kuterintja ngama (Marsupialia, Ilariidae): a revised systematic analysis based on material from the late Oligocene of Riversleigh, northwestern Queensland. Memoirs of the Queensland Museum 41, 379-392.
32. Norris, C. A. (1994). The periotic bones of possums and cuscuses: cuscus polyphyly and the division of the marsupial family Phalangeridae. Zoological Journal of the Linnean Society 111, 73-98. doi:10.1006/zjls.1994.1018
33. Osborne, M. J., and Christidis, L. (2002). Molecular relationships of the cuscuses, brushtail and scaly-tailed possums (Phalangerinae). Australian Journal of Zoology 50, 135-149. doi:10.1071/ZO01070
34. Posada, D., and Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818. doi:10.1093/bioinformatics/14.9. 817
35. Rambaut, A., and Drummond, A. J. (2003). 'Tracer version 1.2.' Available at http://evolve.zoo.ox.ac.uk [Verified June 2006].
36. Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. doi:10.1093/bioinformatics/btg180
37. Ruedas, L. A., and Morales, J. C. (2005). Evolutionary relationships among genera of Phalangeridae (Metatheria: Diprotodontia) inferred from mitochondrial DNA. Journal of Mammalogy 86, 353-365. doi:10.1644/BER-117.1
38. Sorenson, M. D. (1999). 'TreeRot. Version 2.' (Boston University: Boston, MA.)
39. Springer, M. S., Kirsch, J. A. W., Aplin, K., and Flannery, T. (1990). DNA hybridization, cladistics, and the phylogeny of phalangerid marsupials. Journal of Molecular Evolution 30, 298-311. doi:10.1007/BF02100000
40. Swofford, D. L. (2002). 'PAUP*. Phylogenetic Analysis Using Parsimony (*And Other Methods). Version 4.' (Sinauer Associates: Sunderland, MA.)
41. Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. (1996). Phylogenetic inference. In 'Molecular Systematics'. 2nd edn. (Eds D. M. Hillis, C. Moritz and B. K. Mable.) pp. 407-514. (Sinauer Associates: Sunderland, MA.)
42. Tate, G. H. H. (1945). Results of the Archibold Expeditions. No. 52. The marsupial genus Phalanger. American Museum Novitates 1283, 1-30.
43. Thorne, J. L., and Kishino, H. (2002). Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51, 689-702. doi:10.1080/10635150290102456
44. Thorne, J. L., Kishino, H., and Painter, I. S. (1998). Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15, 1647-1657.
45. Woodburne, M. O., MacFadden, B. J., Case, J. A., Springer, M. S., Pledge, N. S., Power, J. D., Woodburne, J. M., and Springer, K. B. (1993). Land mammal biostratigraphy and magnetostratigraphy of the Etadunna Formation (late Oligocene) of South Australia. Journal of Vertebrate Paleontology 13, 483-515.