Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): A phylogenetic and chronological approach

Molecular Phylogenetics and Evolution

Volumn 34, Issue 3, 2005, Pages 601-615

  Galewski, Thomas ^a   Mauffrey, Jean François ^a,b   Leite, Yuri L R ^c   Patton, James L ^d   Douzery, Emmanuel J P ^a  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b Aix Marseille University Marseille   (France)

^c FEDERAL UNIVERSITY OF ESPÍRITO SANTO   (Brazil)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Arboreality; Echimyidae; Relaxed molecular clock; Vicariance; von Willebrand factor

Indexed keywords

CAPROMYS; CLYOMYS; ECHIMYIDAE; EURYZYGOMATOMYS; HOPLOMYS; MYOCASTOR; PROECHIMYS; RODENTIA; SPINY; THRICHOMYS; TRINOMYS;

EID: 15944424361     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.11.015     Document Type: Article

References (85)

1. F. Bossuyt, and M.C. Milinkovitch Amphibians as indicators of early tertiary "out of India" dispersal of vertebrates Science 292 2001 93 95
2. A. Burk, E.J.P. Douzery, and M. Springer The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach J. Mammal. Evol. 9 2002 225 252
3. Carvalho, G.A.S., 1999. Relações filogenéticas entre formas recentes e fosseis de Echimyidae (Rodentia: Hystricognathi) e aspectos da evolução da morfologia dentària. Masters Thesis. Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
4. G.A.S. Carvalho Substitution of the deciduous premolar in Chaetomys subspinosus (Olfers, 1818) (Hystricognathi, Rodentia) and its taxonomic implications Z. Saugetierkd. 65 2000 187 190
5. F.M. Catzeflis Animal tissue collections for molecular genetics and systematics Trends Ecol. Evol. 6 1991 168
6. G.B. Corbet, and J.E. Hills A World List of Mammalian Species third ed. 1991 British Museum (Natural History) Publications London
7. L.P. Costa The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals J. Biogeogr. 30 2003 71 86
8. M.N.F. Da Silva, and J.L. Patton Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha) Mol. Phylogenet. Evol. 2 1993 243 255
9. C.J. Douady, F. Delsuc, Y. Boucher, W.F. Doolittle, and E.J.P. Douzery Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability Mol. Biol. Evol. 20 2003 248 254
10. E.J.P. Douzery, E.A. Snell, E. Bapteste, F. Delsuc, and H. Philippe The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc. Natl. Acad. Sci. USA 101 2004 15386 15391
11. J.F. Eisenberg, and K.H. Redford Mammals of the Neotropics: The Central Neotropics 1999 University of Chicago Press Chicago
12. L.H. Emmons Morphological, ecological, and behavioral adaptations for arboreal browsing in Dactylomys dactylinus (Rodentia, Echimyidae) J. Mammal. 62 1981 183 189
13. L.H. Emmons, and F. Feer Neotropical Rainforest Mammals. A Field Guide second ed. 1997 University of Chicago Press Chicago, IL
14. L.H. Emmons, Y.L.R. Leite, D. Kock, and L.P. Costa A review of the named forms of Phyllomys (Rodentia: Echimyidae) with a description of a new species from coastal Brazil Am. Mus. Nov. 3380 2002 1 40
15. L.H. Emmons, and M.G. Vucetich The identity of Winge's Lasiuromys villosus and the description of a new genus of Echimyid rodent (Rodentia: Echimyidae) Am. Mus. Nov. 3223 1998 1 12
16. J. Felsenstein PHYLIP (PHYLogeny Inference Package). Version 3.6a2.1 2001 Department of Genome Sciences University of Washington, Seattle
17. S. Guindon, and O. Gascuel A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 52 2003 696 704
18. E.R. Hall The Mammals of North America 1981 Wiley New York
19. B.U. Haq, J. Hardenbol, and P.R. Vail Chronology of fluctuating sea levels since the Triassic Science 235 1987 1156 1167
20. A. Hassanin, and E.J.P. Douzery Molecular and morphological phylogenies of Ruminantia and the alternative position of the Moschidae Syst. Biol. 52 2003 206 228
21. S.B. Hedges Historical biogeography of West Indian vertebrates Annu. Rev. Ecol. Syst. 27 1996 163 196
22. R.L. Honeycutt, D.L. Rowe, and M.H. Gallardo Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae Mol. Phylogenet. Evol. 26 2003 476 489
23. C. Hoorn Marine incursions and the influence of Andean Tectonics on the Miocene depositional history of Northwestern Amazonia-results of a palynostratigraphic study Palaeogeogr. Palaeocl. 105 1993 267 309
24. C. Hoorn Marine incursions and the influence of Andean Tectonics on the depositional history of Northwestern Amazonia-results of a Palynostratigraphic study (Vol. 105, p. 267, 1994) Palaeogeogr. Palaeocl. 108 1994 191 191
25. C. Hoorn Fluvial paleoenvironments in the Intracratonic Amazonas Basin (Early Miocene - Early Middle Miocene, Colombia) Palaeogeogr. Palaeocl. 109 1994 1 54
26. C. Hoorn Miocene deposits in the Amazonian foreland basin Science 273 1996 122 123
27. C. Hoorn, J. Guerrero, G.A. Sarmiento, and M.A. Lorente Andean Tectonics as a cause for changing drainage patterns in Miocene Northern South-America Geology 23 1995 237 240
28. D. Huchon, and E.J.P. Douzery From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents Mol. Phylogenet. Evol. 20 2001 238 251
29. D. Huchon, F.M. Catzeflis, and E.J.P. Douzery Molecular evolution of the nuclear von Willebrand Factor gene in mammals and the phylogeny of rodents Mol. Biol. Evol. 16 1999 577 589
30. D. Huchon, F.M. Catzeflis, and E.J.P. Douzery Variance of molecular datings, evolution of rodents, and the phylogenetic affinities between Ctenodactylidae and Hystricognathi Proc. R. Soc. Lond. B 267 2000 393 402
31. D. Huchon, O. Madsen, M. Sibbald, K. Ament, M.J. Stanhope, F. Catzeflis, W.W. de Jong, and E. Douzery Rodent phylogeny and a timescale for the evolution of glires: evidence from an extensive taxon sampling using three nuclear genes Mol. Biol. Evol. 19 2002 1053 1065
32. M.A. Iturralde-Vinent, and R.D.E. MacPhee Paleogeography of the Caribbean region: implications for Cenozoic biogeography Bull. Am. Mus. Nat. Hist. 238 1999 1 95
33. D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences Comput. Appl. Biosci. 8 1992 275 282
34. H. Kishino, and M. Hasegawa Evaluation of the maximum-likelihood estimate of the evolutionary tree topologies from DNA-sequence data, and the branching order in Hominoidea J. Mol. Evol. 29 1989 170 179
35. H. Kishino, J.L. Thorne, and W.J. Bruno Performance of a divergence time estimation method under a probabilistic model of rate evolution Mol. Biol. Evol. 18 2001 352 361
36. M.C. Lara, and J.L. Patton Evolutionary diversification of spiny rats (genus Trinomys, Rodentia: Echimyidae) in the Atlantic Forest of Brazil Zool. J. Linn. Soc. 130 2000 661 686
37. M.C. Lara, J.L. Patton, and M.N.F. Da Silva The simultaneous diversification of south american Echimyid rodents (Hystricognathi) based on complete cytochrome b sequences Mol. Phylogenet. Evol. 5 1996 403 413
38. Y.L.R. Leite The evolution and systematics of Atlantic tree rats, genus Phyllomys (Rodentia, Echimyidae), with description of two new species UC Publ. Zool. 132 2003 1 118
39. Y.L.R. Leite, and J.L. Patton Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited Mol. Phylogenet. Evol. 25 2002 455 464
40. R. MacPhee, and M. Iturralde-Vinent Origin of the Greater Antillean land mammal fauna. 1. New Tertiary fossils from Cuba and Puerto Rico Am. Mus. Nov. 3141 1995 1 30
41. R.D.E. MacPhee, M.A. Iturralde-Vinent, and E.S. Gaffney Domo de Zaza, an early Miocene vertebrate locality in South-central Cuba, with notes on the Tectonic evolution of Puerto Rico and the Mona passage Am. Mus. Nov. 3394 2003 1 42
42. T. Martin African origin of caviomorph rodents is indicated by incisor enamel microstructure Paleobiology 20 1994 5 13
43. M.C. McKenna, and S.K. Bell Classification of Mammals above the Species Level 1997 Columbia University Press New York
44. J. Moojen Speciation in the Brazilian spiny rats (genus Proechimys, familiy Echimyidae) Univ. Kansas Publ. Mus. Nat. Hist. 1 1948 303 401
45. M.A. Nedbal, M.W. Allard, and R.L. Honeycutt Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene Mol. Phylogenet. Evol. 3 1994 206 220
46. A. Nores An alternative hypothesis for the origin of Amazonian bird diversity J. Biogeogr. 26 1999 475 485
47. R.M. Nowak Walker's Mammals of the World fourth ed. 1991 The John Hopkins University Press Baltimore and London
48. R. Pascual, and E.O. Jaureguizar Evolving climates and mammal faunas in Cenezoic South America J. Hum. Evol. 19 1990 23 60
49. B. Patterson, and A.E. Wood Rodents from the Deseadan Oligocene of Bolivia and the relationships of the Caviomorpha Bull. Mus. Comp. Zool. 149 1982 371 543
50. J.L. Patton, M.N.F. Da Silva, and J.R. Malcolm Gene genealogy and differentiation among arboreal spiny rats (Rodentia: Echimyidae) of the Amazon basin: a test of the riverine barrier hypothesis Evolution 48 1994 1314 1323
51. J.L. Patton, and O.A. Reig Genetic differentiation among echimyid rodents, with emphasis on spiny rats, genus Proechimys K.H. Redford J.F. Eisenberg Advances in Neotropical Mammalogy 1989 Sandhill Crane Press Gainesville 75 96
52. C.G.M. Paxton, and W.G.R. Crampton Miocene deposits in the Amazonian foreland basin Science 273 1996 123
53. H. Philippe MUST: a computer package of management utilities for sequences and trees Nucleic Acids Res. 21 1993 5264 5272
54. A.P. Porter, M. Goodman, and M.J. Stanhope Evidence on mammalian phylogeny from sequences of exon 28 of the von Willebrand Factor gene Mol. Phylogenet. Evol. 5 1996 89 101
55. D. Posada, and K.A. Crandall MODELTEST: testing the model of DNA substitution Bioinformatics 14 1998 817 818
56. M.E. Räsänen, A.M. Linna, J.C.R. Santos, and F.R. Negri Late Miocene tidal deposits in the Amazonian foreland basin Science 269 1995 386 390
57. O.A. Reig Karyotypic repatterning as one triggering factor in cases of explosive speciation A. Fontdevilla Evolutionary Biology of Transient Unstable Populations 1989 Springer Berlin 246 289
58. F. Ronquist, and J.P. Huelsenbeck MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 2003 19:1572 1574
59. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
60. H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
61. M.S. Springer, A. Burk, J.R. Kavanagh, V.G. Waddell, and M.J. Stanhope The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole Proc. Natl. Acad. Sci. USA 94 1997 13754 13759
62. M.S. Springer, R.W. DeBry, C. Douady, H.M. Amrine, O. Madsen, W.W. de Jong, and M.J. Stanhope Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction Mol. Biol. Evol. 18 2001 132 143
63. M.S. Springer, and E. Douzery Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules J. Mol. Evol. 43 1996 357 373
64. C. Steiner, P. Sourrouille, and F. Catzeflis Molecular characterization and mitochondrial sequence variation in two sympatric species of Proechimys (Rodentia: Echimyidae) in French Guiana Biochem. Syst. Ecol. 28 2000 963 973
65. S.J. Steppan, B.L. Storz, and R.S. Hoffmann Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1 Mol. Phylogenet. Evol. 30 2004 703 719
66. D.L. Swofford PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), 4 2002 Sinauer Associates Sunderland, MA
67. J.L. Thorne, H. Kishino, and I.S. Painter Estimating the rate of evolution of the rate of molecular evolution Mol. Biol. Evol. 15 1998 1647 1657
68. D.H. Verzi, M.G. Vucetich, and C.I. Montalvo Octodontid-like Echimyidae (Rodentia): an upper Miocene episode in the radiation of the family Palaeovertebrata 23 1994 199 210
69. D.H. Verzi, M.G. Vucetich, and C.I. Montalvo Un nuevo Eumysopinae (Rodentia, Echimyidae) del Mioceno Tardio de la Provincia de La Pampa y consideraciones sobre la historia de la subfamilia Ameghiniana 32 1995 191 195
70. J.-C. Vié, V. Volobouev, J.L. Patton, and L. Granjon A new species of Isothrix (Rodentia: Echimyidae) from French Guiana Mammalia 60 1996 393 406
71. M.G. Vucetich, and A.G. Kramarz New Miocene rodents from Patagonia (Argentina) and their bearing on the early radiation of the octodontids (Hystricognathi) J. Vertebr. Paleontol. 23 2003 435 444
72. M.G. Vucetich, and D.H. Verzi A peculiar octodontid (Rodentia, Caviomorpha) with terraced molars from the lower Miocene of Patagonia (Argentina) J. Vertebr. Paleontol. 16 1996 297 302
73. M.G. Vucetich, and D.H. Verzi First record of Dasyproctidae (Rodentia) in the Pleistocene of Argentina. Paleoclimatic implication Palaeogeogr. Palaeocl. 178 2002 67 73
74. M.G. Vucetich, D.H. Verzi, and J.-L. Hartenberger Review and analysis of the radiation of the South American Hystricognathi (Mammalia, Rodentia) C. R. Acad. Sci. Paris, Earth Planetary Sci. 329 1999 763 769
75. M.G. Vucetich, D.H. Verzi, and E.P. Tonni Paleoclimatic implications of the presence of Clyomys (Rodentia, Echimyidae) in the Pleistocene of central Argentina Palaeogeogr. Palaeocl. 128 1997 207 214
76. P.J. Waddell, H. Kishino, and R. Ota Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data Genome Inform. 13 2002 82 92
77. D. Webb Biological implications of the middle Miocene Amazon seaway Science 269 1995 361 362
78. C.A. Woods The history and classification of South American Hystricognath rodents: reflections on the far away and long ago M.A. Mares H.H. Genoways Mammalian Biology in South America 1982 University of Pittsburgh Pittsburgh 377 392
79. C.A. Woods The biogeography of West Indian rodents C.A. Woods Biogeography of the West Indies: Past, Present, and Future 1989 Sandhill Crane Press Gainesville 741 798
80. C.A. Woods Suborder Hystricognathi D.E. Wilson D.M. Reeder Mammals Species of the World, A Taxonomic and Geographic Reference 1993 Smithsonian Institution Press Washington 771 806
81. C.A. Woods, and J.W. Hermanson Myology of hystricognath rodents: an analysis of form, function, and phylogeny W.P. Luckett J.-L. Hartenberger Evolutionary Relationships Among Rodents: A Multidisciplinary Analysis 1985 Plenum Press New York and London 515 548
82. A.R. Wyss, J.J. Flynn, M.A. Norell, C.C. Swisher III, R. Charrier, M.J. Novacek, and M.C. McKenna South America's earliest rodent and recognition of a new interval of mammalian evolution Nature 365 1993 434 437
83. Z. Yang Estimating the pattern of nucleotide substitution J. Mol. Evol. 39 1994 105 111
84. Z. Yang Among-site rate variation and its impact on phylogenetic analyses Trends Ecol. Evol. 11 1996 367 372
85. Z.H. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci. 13 1997 555 556