Phylogenetic and phylogeographic patterns in sigmodontine rodents of the genus oligoryzomys

Journal of Heredity

Volumn 100, Issue 3, 2009, Pages 309-321

  Miranda, Gustavo B ^a,c   Oliveira, Luiz F B ^b   Andrades Miranda, Jaqueline ^c   Langguth, Alfredo ^d   Callegari Jacques, Sidia M ^a   Mattevi, Margarete S ^c  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c UNIVERSIDADE LUTERANA DO BRASIL   (Brazil)

^d FEDERAL UNIVERSITY OF PARAÍBA   (Brazil)

Author keywords

Cytochrome b; IRBP; Oligoryzomys; Phylogenetics; Phylogeography; Sigmodontinae

Indexed keywords

CELL NUCLEUS RECEPTOR; CYTOCHROME B; INTERPHOTORECEPTOR RETINOID BINDING PROTEIN;

ARTICLE; CLADISTICS; CONTROLLED STUDY; DNA SEQUENCE; GENUS; MITOCHONDRIAL GENE; MONOPHYLY; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PHYLOGEOGRAPHY; PRIORITY JOURNAL; RAT; RICE RAT; SOUTH AMERICA; UNINDEXED SEQUENCE;

ANIMALS; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GEOGRAPHY; PHYLOGENY; SIGMODONTINAE; SPECIES SPECIFICITY;

OLIGORYZOMYS; ORYZOMYS; RODENTIA; SIGMODONTINAE;

EID: 65349106045     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esn099     Document Type: Article

References (59)

1. Andrades-Miranda J, Oliveira LFB, Lima-Rosa CAV, Nunes AP, Zanchin NIT, Mattevi MS. 2001. Chromosome studies of seven species of Oligoryzomys (Rodentia: Sigmodontinae) from Brazil. J Mammal 82:1080-1091.
2. Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37-48.
3. Bangs O. 1900. List of the mammals collected in the Santa Marta region of Colombia by W.W. Brown Jr. Proc N Engl Zoo Club. 1:87-102.
4. Bertorelle G, Barbujani G. 1995. Analysis of DNA diversity by spatial autocorrelation. Genetics 140:811-819.
5. Carleton MD, Musser GG. 1989. Systematic studies of oryzomyine rodents (Muridae, Sigmodontinae): a synopsis of Microryzomys. Bull Am Mus Nat Hist. 191:1-83.
6. Carroll DS, Mills JN, Montgomery JM, Bausch DG, Blair PJ, Burans JP, Felices V, Gianella A, Iihoshi N, Nichol ST, et al. 2005. Hantavirus pulmonary syndrome in central Bolivia: relationships between reservoir hosts, habitats, and viral genotypes. Am J Trop Med Hyg. 72:42-46.
7. Cerqueira R. 1982. South American landscapes and their mammals. In: Mares MA, Genoways HH, editors. Mammalian biology in South America, the pymatuning symposia in ecology. Pittsburgh (PA). Special publication series, University of Pittsburgh. p. 53-55.
8. Clapperton CM. 1979. Glaciation in Bolivia before 3.27 Myr. Nature 277:375-377.
9. Delfraro A, Clara M, Tomé L, Achaval F, Levis S, Calderón G, Enria D, Lozano M, Russi J, Arbiza J. 2003. Yellow pygmy rice rat (Oligoryzomys flavescens) and hantavirus pulmonary syndrome in Uruguay. Emerg Infect Dis. 9:846-852.
10. Dickerman AW, Yates TL. 1995. Systematics of Oligoryzomys: protein-electrophoretic analyses. J Mammal 76:172-188.
11. Emmons LH, Feer F. 1999. Neotropical rainforest mammals: a field guide. 2nd ed. Chicago (IL): University of Chicago Press.
12. Engel SR, Hogan KM, Taylor JF, Davis SK. 1998. Molecular systematics and paleobiogeography of the South American sigmodontine rodents. Mol Biol Evol. 15:35-49.
13. Farris JS, Källersjö M, Kluge AG, Bult C. 1994. Testing significance of incogruence. Cladistics 10:315-319.
14. Farris JS, Källersjö M, Kluge AG, Bult C. 1995. Constructing a significance test for incongruence. Syst Biol. 44:570-572.
15. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
16. Furtado V. 1981. Diversidade cromossômica em roedores das famílias Cricetidae e Caviidae de Pernambuco, Brasil [D. Phil. Thesis]. Porto Alegre-RS (Brazil): Universidade Federal do Rio Grande do Sul.
17. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Sympos Ser. 41:95-98.
18. Hershkovitz P. 1966. South American swamp and fossorial rats of the scapteromyine group (Cricetinae, Muridae) with comments on the glans penis in murid taxonomy. Z Saugetierkd. 31:81-149.
19. Hershkovitz P. 1972. The recent mammals of the neotropical region: a zoogeographic and ecological review. In: Keast A, Erk FC, Glass B, editors. Evolution, mammals and southern continents. Albany (NY): State University of New York Press. p. 311-431.
20. Hooghiemstra H. 1984. Vegetacional and climatic history of the high plain of Bogota, Colombia. Dissertations Botanicae-Band. 79:337.
21. Hooghiemstra H, Van der Hammen T. 1998. Neogene and quaternary development of the neotropical rain forest: the forest refugia hypothesis, and a literature overview. Earth Sci Rev. 44:147-183.
22. Huelsenbeck JP, Ronquist F. 2001. Mr. Bayes: Bayesian inference of phylogeny. Rochester (NY): Biometrics, Department of Biology, University of Rochester.
23. Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120.
24. Marroig G, Cerqueira R. 1997. Plio-Pleistocene South American history and the Amazon lagoon hypothesis: a piece in the puzzle of Amazonian diversification. J Comp Biol. 2:104-119.
25. Medrano JF, Aasen E, Sharrow L. 1990. DNA extraction nucleated red blood cells. Biotechniques 8:43.
26. Mercer J. 1976. Glacial history of southernmost South America. Q Res. 6:125-166.
27. Milazzo ML, Cajimat MN, Hanson JD, Bradley RD, Quintana M, Sherman C, Velasquez RT, Fulhorst CF. 2006. Catacamas virus, a hantaviral species naturally associated with Oryzomys couesi (coues' Oryzomys) in Honduras. Am J Trop Med Hyg. 75:1003-1010.
28. Muschner VC, Lorenz AP, Cervi AC, Bonatto SL, Souza-Chies TT, Salzano FM, Freitas LB. 2003. A first molecular phylogenetic analysis of Passiflora (Passifloraceae). Am J Bot. 90:1229-1238.
29. Musser GG, Carleton MD. 2005. Super family Muroidea. In: Wilson DE, Reeder DM, editors. Mammal species of the world: a taxonomic and geographic reference. Baltimore (MD): Johns Hopkins University Press, p. 894-1531.
30. Myers P, Lundrigan B, Tucker PK. 1995. Molecular phylogenetics of Oryzomyine rodents: the genus Oligoryzomys. Mol Phylogenet Evol. 4:372-382.
31. Nixon KC. 1999. Winclada (BETA) ver. 0.9.9. Published by the author. Ithaca (NY).
32. Palma RE, Rivera-Milla E, Salazar-Bravo J, Torres-Pérez F, Pardiñas UFJ, Marquet PA, Spotorno AE, Meynard AP, Yates TL. 2005. Phylogeography of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in temperate South America. J Mammal 86:191-200.
33. Patton JL, da Silva MNF. 1995. A review of spiny mouse genus Scolomys (Rodentia: Muridae: Sigmodontinae) with the discription of a new species from the western Amazon of Brazil. Proc Biol Soc Wash 108:319-337.
34. Perini MV, Weimer T, Callegari-Jacques SM, Mattevi MS. 2004. Biochemical polymorphisms and genetic relationships in rodents of the genera Oryzomys and Oligoryzomys (Sigmodontinae) from Brazil. Biochem Gen. 42:317-329.
35. Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioin formatics 14:817-818.
36. Powers AM, Mercer DR, Watts DM, Guzman H, Fulhorst CF, Popov VL, Tesh RB. 1999. Isolation and genetic characterization of a hantavirus (Bunyaviridae: Hantavirus) from a rodent, Oligoryzomys microtis (Muridae), collected in northeastern Peru. Am J Trop Med Hyg. 61:92-98.
37. Reig OA. 1984. Geographic distribution and evolutionary history of South American Muroids (Cricetidae: Sigmodontinae). Braz J Gen. 7:333-365.
38. Reig OA. 1986. Diversity patterns and differentiation of high Andean rodents. In: Vuilleumier F, Monasterio M, editors. High altitude tropical biogeography. New York (NY): Oxford University Press. p. 404-439.
39. Savage JM. 1974. The isthmian link and the evolution of Neotropical Mammals. Contr. Sc. Natural History of the Museum of Los Angeles County. 260:1-51.
40. Sbalqueiro IJ, Mattevi MS, Oliveira LF, Solano MJV. 1991. B chromosome system in populations of Oryzomys flavescens (Rodentia, Cricetidae) from southern Brazil. Act Ther. 36:193-199.
41. Schneider H. 2007. Métodos de análise filogenética: um guia prático. 3rd ed. Ribeirão Preto-SP (Brazil): Holos, Editora Ltda.
42. Schneider S, Roeslli D, Excoffier L. 2000. Arlequim: a software for population genetics data analysis. Version 2.000. Geneva (Switzerland): Genetics and Biometry Laboratory, Departament of Anthropology, University of Geneva.
43. Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 16:1114-1116.
44. Smith MF, Patton JL. 1993. The diversification of South American murid rodents: Evidence from mitochondrial DNA sequence data for the akodontine tribe. Biol J Linn Soc. 50:149-177.
45. Smith MF, Patton JL. 1999. Phylogenetic relationships and the radiation of sigmodontine rodents in South America: evidence from cytochrome b. J Mammal Evol. 6:89-128.
46. Steppan SJ. 1995. Revision of the tribe Phyllotini (Rodentia: Sigmodontinae) with a phylogenetic hypothesis for the Sigmodontinae. Fieldiana: Zoology. New Series 80:1-112.
47. Svartman M. 1989. Levantamento cariotípico de roedores da região do Distrito Federal [MSc Dissertation]. São Paulo-SP (Brazil): Universidade de São Paulo.
48. * and other Methods), Ver. 4.0 b10. Sunderland (MA): Sinauer Associates.
49. 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.
50. Templeton A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37:221-244.
51. Thomas O. 1901. On a collection of mammals from the Kanuku Mountains, British Guiana. Ann Mag Nat Hist, series. 7(8):139-154.
52. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgis DG. 1997. The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nuc Acid Res. 24:4876-4882.
53. Trott AI, Callegari-Jacques SM, Oliveira LFB, Langguth A, Mattevi MS. 2007. Genetic diversity and relatedness within and between species of the genus Oligoryzomys (Rodentia, Sigmodontinae). Braz J Biol. 67:631-637.
54. Weksler M. 2003. Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon. Mol Phylogenet Evol. 29:331-349.
55. Weksler M. 2006. Phylogenetic relationships of oryzomyine rodents (Muroidea: Sigmodontinae): separate and combined analyses of morphological and molecular data. Bull Am Mus Nat Hist. 296:1-149.
56. Weksler M, Bonvicino CR. 2005. Taxonomy of pigmy rice rats genus Oligoryzomys Bangs, 1900 (Rodentia, Sigmodontinae) of the Brazilian
57. Cerrado, with the description of two new species. Arq Mus Nac. 63:113-130.
58. Weksler M, Percequillo AR, Voss RS. 2006. Ten new genera of oryzomyine rodents (Cricetidae: Sigmodontinae). Am Mus Novitates 3537:1-29.
59. Xia X, Xie Z. 2001. DAMBE: data analysis in molecular biology and evolution. J Hered 92:371-373.