Evolution of South American spiny rats (Rodentia, Echimyidae): The star-phylogeny hypothesis revisited

Molecular Phylogenetics and Evolution

Volumn 25, Issue 3, 2002, Pages 455-464

  Leite, Yuri L R ^a   Patton, James L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; RIBOSOME RNA; RNA 16S; RNA, RIBOSOMAL, 12S;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; PHYLOGENY; RAT; RODENT; SOUTH AMERICA; STATISTICAL MODEL; TIME;

ANIMALS; CYTOCHROME B GROUP; EVOLUTION; LIKELIHOOD FUNCTIONS; PHYLOGENY; RATS; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; RODENTIA; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA; TIME FACTORS;

CAPROMYS; CLYOMYS; DACTYLOMYS; ECHIMYIDAE; ECHIMYS; EURYZYGOMATOMYS; HOPLOMYS; ISOTHRIX; KANNABATEOMYS; LONCHOTHRIX; MAKALATA; MESOMYS; MYOCASTOR; PROECHIMYS; RODENTIA; THRICHOMYS; TRINOMYS;

EID: 0036433758     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00279-8     Document Type: Article

References (50)

1. Amorin, D.S., Pires, M.R.S., 1996. Neotropical biogeography and a method for maximum biodiversity estimation. In: Bicudo, C.E.M., Menezes, N.A. (Eds.), Biodiversity in Brazil: A First Approach. CNPq, São Paulo, pp. 183-219
2. Bremer, K., 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
3. Carvalho, D.A.D., Oliveira Filho, A.T.D., Vilela, E.D.A., Gavilanes, M.L., 1995. Phytosociological structure of a riparian forest of the upper Rio Grande (Bom Sucesso, Minas Gerais, Brazil). Rev. Bras. Bot. 18, 39-49.
4. Carvalho, G.A.S., 1999. Relações Filogenéticas Entre Formas Recentes e Fósseis de Echimyidae (Rodentia: Ystricognathi) e Aspectos da Evolução da Morfologia Dentária. Masters Thesis, Universidade Federal do Rio de Janeiro, Rio de Janeiro.
5. Costa, L.P., 2002. The molecular phylogeographic bridge between the Amazon and the Atlantic Forest: a case study with small mammals. J Biogeography, in press.
6. D'Erchia, A.M., Gissi, C., Pesole, G., Saccone, C., Arnason, U., 1996. The guinea-pig is not a rodent. Nature 381, 597-600.
7. Eisenberg, J.F., Redford, K.H., 1999. Mammals of the Neotropics: the Central Neotropics. University of Chicago Press, Chicago, IL.
8. Emmons, L.H., submitted. A revision of the genera of arboreal Echimyidae (Rodentia: Echimyidae, Echimyinae); with descriptions of two new genera. Am. Mus. Novit.
9. Emmons, L.H., Feer F., 1997. Neotropical Rainforest Mammals: A Field Guide, Second Ed. University Of Chicago Press, Chicago, IL
10. Emmons, L.H., Leite, Y.L.R., Kock, D., submitted. A review of the named forms of Phyllomys (Rodentia, Echimyidae), with taxonomic notes. Am. Mus. Novit.
11. Emmons, L.H., Vucetich, M.G., 1998. The identity of Winge's Lasiuromys villosus and the description of a new genus of echimyid rodent (Rodentia: Echimyidae). Am. Mus. Novit. 3223, 1-12.
12. Eriksson, T., 1998. Autodecay. Version 4.0. Department of Botany, Stockholm University, Stockholm.
13. Felsenstein, J., 1985. Confidence limits on phylogenies: An approach utilizing the bootstrap. Evolution 39, 783-791.
14. Frye, M.S., Hedges, S.B., 1995. Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-valine. Mol. Biol. Evol. 12, 168-176.
15. Goldman, N., Anderson, J.P., Rodrigo, A.G., 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49, 652-670.
16. Gutell, R.R., Gray, M.W., Schnare, M.N., 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acid Res. 21, 3055-3074.
17. Haq, B.U., Hardenbol, J., Vail, P.R., 1987. Chronology of fluctuating sea levels since the Triassic. Science 235, 1156-1167.
18. Huchon, D., Douzery, E.J.P., 2001. From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. Mol. Phylogenet. Evol. 20, 238-251.
19. Lara, M.C., Patton, J.L., 2000. Evolutionary diversification of spiny rats (genus Trinomys, Rodentia: Echimyidae) in the Atlantic Forest of Brazil. Zool. J. Linn. Soc. 130, 661-686.
20. Lara, M.C., Patton, J.L., Da Silva, M.N.F., 1996. The simultaneous diversification of South American echimyid rodents (Hystricogna-thi) based on complete cytochrome b sequences. Mol. Phylogenet. Evol. 5, 403-413.
21. Leite, Y.L.R., 2001. Systematics of the Atlantic Tree Rats, Genus Phyllomys (Rodentia, Echimyidae), and the Evolution of Echimyid Rodents in South America. Ph.D. Dissertation, University of California, Berkeley.
22. Marshall, L.G., Sempere, T., 1993. Evolution of the Neotropical Cenozoic land mammal fauna in its geochronologic, stratigraphic and tectonic context. In: Goldblatt, P. (Ed.), Biological Relationships Between Africa and South America. Yale University Press, New Haven, CT, pp. 329-392.
23. Martin, T., 1994. On the systematic position of Chaetomys subspinosus (Rodentia: Caviomorpha) based on evidence from the incisor enamel microstructure. J. Mammal. Evol. 2, 117-131.
24. McKenna, M.C., Bell, S.K., 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York.
25. Montalvo, C., Vucetich, M.G., Verzi, D.H., 1996. Presencia de Theridomysops parvulus (Rodentia, Echimyidae, Eumysopinae) en la Formacion 3 Cerro Azul, Provincia de La Pampa. Ameghiniana 33, 467.
26. Moojen, J., 1948. Speciation in the Brazilian spiny rats (genus Proechimys, family Echimyidae). Univ. Kans. Publ. Mus. Nat. Hist. 1, 303-401.
27. Mori, S.A., Boom, B.M., Prance, G.T., 1981. Distribution patterns and conservation of eastern Brazilian coastal forest tree species. Brittonia 33, 233-245.
28. Nedbal, M.A., Allard, M.W., Honeycutt, R.L., 1994. Molecular systematic of hystricognath rodents: Evidence from the mito-chondrial 12S rRNA gene. Mol. Phylogenet. Evol. 3, 206-220.
29. Patterson, B., Wood, A.E., 1982. Rodents from the Deseadan Oligocene of Bolivia and the relationships of the Caviomorpha. Bull. Mus. Comp. Zool. 149, 371-543.
30. Patton, J.L., Reig, O.A., 1989. Genetic differentiation among echimyid rodents, with emphasis on spiny rats, genus Proechimys. In: Redford, K.H., Eisenberg, J.F. (Eds.), Advances in Neotropical Mammalogy. Sandhill Crane Press, Inc., Gainesville, NC, pp. 75-96.
31. Patton, J.L., Silva, M.N.F., Malcolm, J.R., 2000. Mammals of the Rio Juruá and the evolutionary and ecological diversification of Amazonia. Bull. Am. Mus. Nat. Hist. 244, 1-306.
32. Posada, D., Crandall, K.A., 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14, 817-818.
33. Reig, O.A., 1989. Karyotypic repatterning as one triggering factor in cases of explosive speciation. In: Fontdevila, A. (Ed.), Evolutionary Biology of Transient Unstable Populations. Springer, Berlin, pp. 246-289.
34. Rodríguez, F., Oliver, J.F., Marín, A., Medina, J.R., 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142, 485-501.
35. Sarich, V.M., Cronin, J.E., 1980. South American mammal molecular systematics evolutionary clocks/and continental drift. In: Ciochon, R.I., Chiarelli, A.B. (Eds.), Evolutionary Biology of the New World Monkeys and Continental Drift. Plenum Press, New York, pp. 399-421.
36. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
37. Silva, M.N.F., 1998. Four new species of spiny rats of the genus Proechimys (Rodentia: Echimyidae) from the western Amazon of Brazil. Proc. Biol. Soc. Wash. 111, 436-471.
38. Simpson, G.G., 1945. The principles of classification and a classifica-tion of mammals. Bull. Am. Mus. Nat. Hist. 85, 1-350.
39. Springer, M.S., Douzery, E., 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J. Mol. Evol. 43, 357-373
40. SwoGord, D.L., 2000. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland.
41. Tate, G.H.H., 1935. The taxonomy of the genera of neotropical hystricoid rodents. Bull. Am. Mus. Nat. Hist. 68, 295-447.
42. Vanzolini, P.E., 1988. Distributional patterns of South American lizards. In: Vanzolini, P.E., Heyer, W.R. (Eds.), Proceedings of a Workshop on Neotropical Distribution Patterns. Academia Brasileira de Ciências, Rio de Janeiro, pp. 317-342.
43. Verzi, D.H., Vucetich, M.G., Montalvo, C.I., 1995. Un nuevo Eumysopinae (Rodentia, Echimyidae) del Mioceno Tardio de la Provincia de La Pampa y consideraciones sobre la historia de la subfamilia. Ameghiniana 32, 191-195.
44. Vié, J.C., Volobouev, V., Patton, J.L., Granjon, L., 1996. A new species of Isothrix (Rodentia: Echimyidae) from French Guiana. Mammalia 60, 393-406.
45. Vucetich, M.G., Verzi, D.H., Hartenberger, J.-L., 1999. Review and analysis of the radiation of the South American Hystricognathi (Mammalia, Rodentia). Comp. Rend. Acad. Sci. Ser. II A 329, 763-769.
46. Wallau, B.R., Schmitz, A., Perry, S.F., 2000. Lung morphology in rodents (Mammalia, Rodentia) and its implications for systematics. J. Morphol. 246, 228-248.
47. Woods, C.A., 1982. The history and classification of South American Hystricognath rodents: reflections on the far away and long ago. In: Mares, M.A., Genoways, H.H. (Eds.), Mammalian Biology in South America, vol.6, Special Publication Series: The Pymatuning Symposia in Ecology. University of Pittsburgh, Pittsburgh, pp. 377-392.
48. Woods, C.A., 1989. The Biogeography of West Indian rodents. In: Woods, C.A. (Ed.), Biogeography of the West Indies: Past, Present, and Future. Sandhill Crane Press, Inc., Gainesville, pp. 741-798.
49. Woods, C.A., 1993. Suborder Hystricognathi. In: Wilson, D.E., Reeder, D.M. (Eds.), Mammal Species of the World: A Taxonomic and Geographic Reference. Smithsonian Institution Press, Wash-ington, pp. 771-806.
50. Woods, C.A., Hermanson, J.W., 1985. Myology of hystrichognath rodents: An analysis of form, function, and phylogeny. In: Lucket, W.P., Hartenberger, J.L. (Eds.), Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis, NATO ASI Series. Series A: Life Sciences, vol. 92. Plenum Press, New York, pp. 515-548.