The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Vilela, Roberto V ^a   Machado, Taís ^a,b   Ventura, Karen ^a   Fagundes, Valéria ^c   De J Silva, Maria José ^b   Yonenaga Yassuda, Yatiyo ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b INSTITUTO BUTANTAN   (Brazil)

^c FEDERAL UNIVERSITY OF ESPÍRITO SANTO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CHROMOSOME; CLASSIFICATION; DNA SEQUENCE; FEMALE; GENETICS; KARYOTYPING; MOLECULAR EVOLUTION; PHYLOGENY; PORCUPINE; SEQUENCE ALIGNMENT;

ANIMALS; CHROMOSOMES, MAMMALIAN; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FEMALE; KARYOTYPING; PHYLOGENY; PORCUPINES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 60849105376     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-29     Document Type: Article

References (89)

1. WP Luckett J-L Hartenberger, Evolutionary relationships among rodents: a multidisciplinary analysis New York; London: Plenum Press; in cooperation with NATO Scientific Affairs Division 1985
2. JD Bryant MC McKenna Mongolyn Shinzhl*ekh Ukhaany Akademi, Cranial anatomy and phylogenetic position of Tsaganomys altaicus (Mammalia, Rodentia) from the Hsanda Gol Formation (Oligocene), Mongolia New York: American Museum of Natural History 1995
3. A new giant porcupine (Rodentia, Erethizontidae) from the late Miocene of Argentina. AM Candela, Journal of Vertebrate Paleontology 2004 24 732 741 10.1671/0272-4634(2004)024[0732:ANGPRE]2.0.CO;2
4. B Patterson AE Wood, Rodents from the Deseadan Oligocene of Bolivia and the relationships of the Caviomorpha Cambridge: The Museum of Comparative Zoology at Harvard College 1982
5. L Emmons F Feer, Neotropical rainforest mammals: a field guide Chicago: University of Chicago Press 2 1997
6. RS Voss R Angermann Zoologisches Museum Berlin Germany), Revisionary notes on neotropical porcupines (Rodentia, Erethizontidae). 1, Type material described by Olfers (1818) and Kuhl (1820) in the Berlin Zoological Museum New York: American Museum of Natural History 1997
7. Molecular and karyologic evidence of the taxonomic status of Coendou and Sphiggurus (Rodentia: Hystricognathi). CR Bonvicino V Penna-Firme E Braggio, J Mammal 2002 83 1071 1076 10.1644/1545-1542(2002)083〈1071:MAKEOT〉2.0. CO;2
8. RM Nowak, Walker's mammals of the world Baltimore: Johns Hopkins University Press 6 1999
9. Infraorder Hystricognathi Brandt, 1855. CA Woods CW Kilpatrick, Mammal species of the world: a taxonomic and geographic reference Baltimore, Md.: Johns Hopkins University Press, Wilson DE, Reeder DM, 3 2005 2 1538 1600
10. A new species of prehensile-tailed porcupine, genus Coendou Lacépède, from Brazil. CO Handley Jr RH Pine, Mammalia 1992 56 237 244
11. JF Eisenberg KH Redford, Mammals of the Neotropics Chicago: University of Chicago Press 1999
12. Die Trigonodontie der simplicidentaten Nager. HG Stehlin S Schaub, Schweiz Paläont Abhandl 1951 67 1 385
13. Simplicidentata (= Rodentia). S Schaub, Traité de Paleontologie. Edited by Piveteau J. Paris: Masson et Cie 1958 6 659 818
14. Suborder Hystricognathi. CA Woods, Mammal species of the world: a taxonomic and geographic reference Washington: Smithsonian Institution Press, Wilson DE, Reeder DM, 2 1993 771 806
15. On the systematic position of the Chaetomys subspinosus (Rodentia: Caviomorpha) based on evidence from the incisor enamel microstructure. T Martin, J Mamm Evol 1994 2 117 131 10.1007/BF01464364
16. Substitution of the deciduous premolar Chaetomys subspinosus (Olfers, 1818) (Hystricognathi, Rodentia) and its taxonomic implications Z. Säugetierkunde 65. G Carvalho, Z Sauget 2000 65 187 190
17. MC McKenna SK Bell GG Simpson, Classification of mammals above the species level New York: Columbia University Press 1997
18. Evolution of the cytochrome b gene of mammals. DM Irwin TD Kocher AC Wilson, J Mol Evol 1991 32 128 144 10.1007/BF02515385 1901092
19. Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes. DP Ma A Zharkikh D Graur JL VandeBerg WH Li, J Mol Evol 1993 36 327 334 8315653
20. The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences. MC Lara JL Patton MN da Silva, Mol Phylogenet Evol 1996 5 403 413 10.1006/mpev.1996.0035 8728398
21. An index of substitution saturation and its application. X Xia Z Xie M Salemi L Chen Y Wang, Mol Phylogenet Evol 2003 26 1 7 10.1016/S1055-7903(02) 00326-3 12470932
22. Molecular systematics of Sciurognathi (Rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). C Montgelard S Bentz C Tirard O Verneau FM Catzeflis, Mol Phylogenet Evol 2002 22 220 233 10.1006/mpev.2001.1056 11820843
23. Cladistic Permutation Tests for Monophyly and Nonmonophyly. DP Faith, Syst Zool 1991 40 366 375 10.2307/2992329
24. Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. AR Templeton, Statistical Analysis of DNA Sequence Data New York: Marcel Dekker, Weir BJ, 1983 151 179
25. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. H Kishino M Hasegawa, J Mol Evol 1989 29 170 179 10.1007/BF02100115 2509717
26. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. H Shimodaira M Hasegawa, Mol Biol Evol 1999 16 1114 1116
27. Nine karyomorphs for spiny rats of the genus Proechimys (Echimyidae, Rodentia) from North and Central Brazil. T Machado MJJ Silva ER Leal-Mesquita AP Carmignotto Y Yonenaga-Yassuda, Genet Mol Biol 2005 28 682 692 10.1590/S1415-47572005000500007
28. The Bolivian bamboo rat, Dactylomys boliviensis (Rodentia: Echimyidae), a new record for chromosome number in a mammal. JL Dunnum J Salazar-Bravo TL Yates, Z Sauget 2001 66 121 126
29. Craniometric differentiation and chromosomal speciation of the genus Proechimys (Rodentia, Echimyidae). M Aguilera M Corti, Z Sauget 1994 59 366 377
30. YLR Leite University of California Berkeley. Museum of Vertebrate Zoology, Evolution and systematics of the Atlantic tree rats, genus Phyllomys (Rodentia, Echimyidae) with description of two new species Berkeley: University of California Press 2003
31. The chromosome complement and meiosis of the North American porcupine. K Benirschke, J Hered 1968 59 71 76 5656924
32. Sphiggurus vestitus pruinosus (Mammalia, Rodentia, Erethizontidae): the karyotype and its phylogenetic implications, descriptive notes. JL Concepcián J Molinari, Stud Neotrop Fauna Environm 1991 26 237 241 10.1080/01650529109360858
33. The karyotype of Sphiggurus villosus (Rodentia: Erethizontidae) from Brazil. CR Bonvicino FC Almeida R Cerqueira, Stud Neotrop Fauna Environm 2000 35 81 83 10.1076/0165-0521(200008)35:2;1-9;FT081
34. Hystricomorph chromosomes. W George BJ Weir, Symp Zool Soc Lond 1974 34 79 108
35. Cariátipos em espécies de Dasyproctidae e Erethizontidae, com discussão da evolução cromossômica (Rodentia, Caviomorpha). FS Lima, Braz J Genet Supplement 1994 17 135
36. [Karyotype diversity and systematics in Venezuelan populations of Proechimys (Rodentia, Echimyidae) with additional information of Peruvian and Colombian populations]. OA Reig M Useche, Acta Cient Venez 1976 27 132 140 1020601
37. Estudos citogenéticos em dez espécies de roedores brasileiros da família Echimyidae. ER Leal-Mesquita, Dissertation (Master) Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo 1991
38. TC Hsu K Benirschke, An Atlas of mammalian chromosomes New York, Heidelberg, Berlin: Springer-Verlag 1977
39. Reproductive and chromosomal characters of ctenodactylids as a key to their evolutionary relationships. W George, Evolutionary relationships among rodents: a multidisciplinary analysis New York, London: Plenum Press; in cooperation with NATO Scientific Affairs Division, Luckett WP, Hartenberger J-L, 1985 453 474
40. SJ O'Brien JC Menninger WG Nash, Atlas of mammalian chromosomes Hoboken: John Wiley & Sons 2006
41. Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae). MH Gallardo CA Gonzalez I Cebrian, Genomics 2006 88 214 221 10.1016/j.ygeno.2006.02.010 16580173
42. Beitrage zur nahern Kenntniss der Saugetiere Russlands. JF Brandt, Mem Acad Imp St Petersbourg 1855 9 1 375
43. Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene. MA Nedbal MW Allard RL Honeycutt, Mol Phylogenet Evol 1994 3 206 220 10.1006/mpev.1994.1023 7820285
44. High-level phylogeny of early Tertiary rodents: dental evidence. L Marivaux M Vianey-Liaud J-J Jaeger, Zool J Linn Soc 2004 142 105 134 10.1111/j.1096-3642.2004.00131.x
45. Molecular systematics of hystricognath rodents: the contribution of sciurognath mitochondrial 12S rRNA sequences. FM Catzeflis C Hanni P Sourrouille E Douzery, Mol Phylogenet Evol 1995 4 357 360 10.1006/mpev.1995.1032 8845970
46. From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. D Huchon EJ Douzery, Mol Phylogenet Evol 2001 20 238 251 10.1006/mpev.2001.0961 11476632
47. Arrival and diversification of caviomorph rodents and platyrrhine primates in South america. C Poux P Chevret D Huchon WW de Jong EJ Douzery, Syst Biol 2006 55 228 244 10.1080/10635150500481390 16551580
48. South American mammal molecular systematics, evolutionary clocks, and continental drift. VM Sarich JE Cronin, Evolutionary Biology of the New World Monkeys and Continental Drift New York: Plenum Press, Ciochon RI, Chiarelli AB, 1980 399 421
49. New evidence of hystricognath rodents monophyly from the phylogeny of their pinworms. JP Hugot, Tangled trees: phylogeny, cospeciation, and coevolution Chicago: The University of Chicago Press, Page RDM, 2002 144 174
50. Minimal Values for Reliability of Bootstrap and Jackknife Proportions, Decay Index, and Bayesian Posterior Probability. RH Zander, PhyloInformatics 2004 2 1 13
51. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. D Huchon FM Catzeflis EJ Douzery, Proc Biol Sci 2000 267 393 402 10722222 10.1098/rspb.2000.1014
52. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. D Huchon FM Catzeflis EJ Douzery, Mol Biol Evol 1999 16 577 589 10335651
53. Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited. YL Leite JL Patton, Mol Phylogenet Evol 2002 25 455 464 10.1016/S1055-7903(02)00279-8 12450750
54. Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. RM Adkins AH Walton RL Honeycutt, Mol Phylogenet Evol 2003 26 409 420 10.1016/S1055-7903(02)00304-4 12644400
55. The role of Asia in the origin and diversification of hystricognathous rodents. L Marivaux M Vianey-Liaud J-L Welcomme J-J Jaeger, Zool Scr 2002 31 225 239 10.1046/j.1463-6409.2002.00074.x
56. Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae. RL Honeycutt DL Rowe MH Gallardo, Mol Phylogenet Evol 2003 26 476 489 10.1016/S1055-7903(02) 00368-8 12644405
57. Molecular Relationships Among Octodontidae (Mammalia: Rodentia: Caviomorpha). MH Gallardo JAW Kirsch, J Mamm Evol 2001 8 73 89 10.1023/A:1011345000786
58. A molecular timescale for caviomorph rodents (Mammalia, Hystricognathi). JC Opazo, Mol Phylogenet Evol 2005 37 932 937 10.1016/j.ympev.2005.05.002 16085429
59. Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach. T Galewski JF Mauffrey YL Leite JL Patton EJ Douzery, Mol Phylogenet Evol 2005 34 601 615 10.1016/j.ympev.2004.11.015 15683932
60. Extracting high-quality DNA from shed reptile skins: a simplified method. JW Fetzner Jr, Biotechniques 1999 26 1052 1054 10376138
61. ER Hall, The mammals of North America New York: Wiley 2 1981
62. Multiple sequence alignment with Clustal X. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson, Trends Biochem Sci 1998 23 403 405 10.1016/S0968-0004(98)01285-7 9810230
63. MacClade, version 4.08. DR Maddison WP Maddison, Sinauer Associates 2005
64. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
65. DAMBE: software package for data analysis in molecular biology and evolution. X Xia Z Xie, J Hered 2001 92 371 373 10.1093/jhered/92.4.371 11535656
66. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), version 4b10. DL Swofford, Sinauer Associates 2003 18428704
67. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839
68. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953
69. MrModeltest. JAA Nylander, MrModeltest, version 2. Program distributed by the author 2004
70. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
71. Branch support and tree stability. K Bremer, Cladistics 1994 10 295 304 10.1111/j.1096-0031.1994.tb00179.x
72. MD Sorenson EA Franzosa, TreeRot, version 3 Boston University 2007
73. Relaxed phylogenetics and dating with confidence. AJ Drummond SY Ho MJ Phillips A Rambaut, PLoS Biol 2006 4 e88 16683862 10.1371/journal.pbio.0040088
74. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evol Biol 2007 7 214 17996036 10.1186/1471-2148-7-214
75. A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy. MJ Sanderson, Mol Biol Evol 1997 14 1218 1231
76. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. G Jobb A von Haeseler K Strimmer, BMC Evol Biol 2004 4 18 15222900 10.1186/1471-2148-4-18
77. Revised geochronology of the casamayoran south american land mammal age: climatic and biotic implications. RF Kay RH Madden MG Vucetich AA Carlini MM Mazzoni GH Re M Heizler H Sandeman, Proc Natl Acad Sci USA 1999 96 13235 13240 10557304 10.1073/pnas.96.23.13235
78. The Rodents of the Santa Rosa Local Fauna. CD Frailey KE Campbell Jr, The Paleogene Mammalian Fauna of Santa Rosa, Amazonian Peru Los Angeles: Natural History Museum of Los Angeles County, Science Series, Campbell Jr KE, 2004 40 71 130
79. Review and analysis of the radiation of the South American Hystricognathi (Mammalia, Rodentia). MG Vucetich DH Verzi J-L Hartenberger, C R Acad Sci Paris 1999 329 763 769
80. Relationships among extant and fossil echimyids (Rodentia: Hystricognathi). GAS Carvalho LO Salles, Zool J Linn Soc 2004 142 445 477 10.1111/j.1096-3642.2004.00150.x
81. Nucleotide sequence variation in the mitochondrial 12S rRNA gene and the phylogeny of African mole-rats (Rodentia: Bathyergidae). MW Allard RL Honeycutt, Mol Biol Evol 1992 9 27 40 1552839
82. Evidence from intron 1 of the nuclear transthyretin (Prealbumin) gene for the phylogeny of African mole-rats (Bathyergidae). AH Walton MA Nedbal RL Honeycutt, Mol Phylogenet Evol 2000 16 467 474 10.1006/mpev.2000.0808 10991798
83. Phylogenetic relationships, ecological correlates, and molecular evolution within the cavioidea (mammalia, rodentia). DL Rowe RL Honeycutt, Mol Biol Evol 2002 19 263 277 11861886
84. Diversidad molecular entre cuyes domésticos (Cavia porcellus) y su relacián filogenética cercana con la especie silvestre andina Cavia tschudii. AE Spotorno JP Valladares JC Marin H Zeballos, Rev Chil Hist Nat 2004 77 243 250
85. Ecological constraints drive social evolution in the African mole-rats. CG Faulkes NC Bennett MW Bruford HP O'Brien GH Aguilar JU Jarvis, Proc Biol Sci 1997 264 1619 1627 9404025 10.1098/rspb.1997.0226
86. Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber. CG Faulkes DH Abbott HP O'Brien L Lau MR Roy RK Wayne MW Bruford, Mol Ecol 1997 6 615 628 10.1046/j.1365-294X.1997.00227.x 9226945
87. Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha). MN da Silva JL Patton, Mol Phylogenet Evol 1993 2 243 255 10.1006/mpev.1993.1023 8136924
88. Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach. CH Slamovits JA Cook EP Lessa MS Rossi, Mol Biol Evol 2001 18 1708 1719 11504851
89. The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation. EP Lessa JA Cook, Mol Phylogenet Evol 1998 9 88 99 10.1006/mpev.1997.0445 9479698