Phylogeny and chronology of the major lineages of New World hystricognath rodents: insights on the biogeography of the Eocene/Oligocene arrival of mammals in South America

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• 作者：Carolina M Voloch (1)
  Julio F Vilela (2)
  Leticia Loss-Oliveira (2)
  Carlos G Schrago (3)
  
• 关键词：Caviomorpha ; Phiomorpha ; Platyrrhini ; Mitochondrial genome ; Supermatrix ; Bayesian relaxed clock
• 刊名：BMC Research Notes
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：6
• 期：1
• 全文大小：389KB
• 参考文献：1. Simpson GG: / Spendid isolation: The curious history od South American mammals. New Haven: Yale University Press; 1983.
  2. Flynn JJ, Wyss AR: Recent advances in South American mammalian paleontology. / Trends Ecol Evol 1998,13(11):449鈥?54. CrossRef
  3. Lavocat R: The implications of rodent paleontology and biogeography to the geographical sources and origin of platyrrhine primates. In / Evolutionary Biology of New World Monkeys and Continental Drift. Edited by: Ciochon RL, Chiarelli BA. New York: Plenum Press; 1980:93鈥?03. CrossRef
  4. Huchon D, Douzery EJ: From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. / Mol Phylogenet Evol 2001,20(2):238鈥?51. CrossRef
  5. Antoine PO, Marivaux L, Croft DA, Billet G, Ganerod M, Jaramillo C, Martin T, Orliac MJ, Tejada J, Altamirano AJ: Middle Eocene rodents from Peruvian Amazonia reveal the pattern and timing of caviomorph origins and biogeography. / Proc R Soc B 2012,279(1732):1319鈥?326. CrossRef
  6. Opazo JC: A molecular timescale for caviomorph rodents (Mammalia, Hystricognathi). / Mol Phylogenet Evol 2005,37(3):932鈥?37. CrossRef
  7. Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, Jenkins PD, Brosius J, Schmitz J: Multiple molecular evidences for a living mammalian fossil. / Proc Natl Acad Sci U S A 2007,104(18):7495鈥?499. CrossRef
  8. Rowe DL, Dunn KA, Adkins RM, Honeycutt RL: Molecular clocks keep dispersal hypotheses afloat: evidence for trans-Atlantic rafting by rodents. / J Biogeogr 2010,37(2):305鈥?24. CrossRef
  9. Sallam HM, Seiffert ER, Steiper ME, Simons EL: Fossil and molecular evidence constrain scenarios for the early evolutionary and biogeographic history of hystricognathous rodents. / Proc Natl Acad Sci U S A 2009,106(39):16722鈥?6727. CrossRef
  10. Poux C, Chevret P, Huchon D, de Jong WW, Douzery EJ: Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. / Syst Biol 2006,55(2):228鈥?44. CrossRef
  11. Loss-Oliveira L, Aguiar BO, Schrago CG: Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents. / Evol Bioinforma 2012, 8:127鈥?37.
  12. Vaughan TA, Ryan JM, Czaplewski NJ: / Mammalogy. 5th edition. Sudbury: Jones & Bartlett Publishers; 2010.
  13. Woods CA: The history and classification of South American Hystricognath Rodents: Reflections on the far away and long ago. In / Mammalian Biology in South America. Edited by: Mares M, Genoways H. Pennsylvania: University of Pittsburgh; 1982:377鈥?92.
  14. Blanga-Kanfi S, Miranda H, Penn O, Pupko T, DeBry RW, Huchon D: Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. / BMC Evol Biol 2009, 9:71. CrossRef
  15. DErchia AM, Gissi C, Pesole G, Saccone C, Arnason U: The guinea-pig is not a rodent. / Nature 1996,381(6583):597鈥?00. CrossRef
  16. Tomasco IH, Lessa EP: The evolution of mitochondrial genomes in subterranean caviomorph rodents: Adaptation against a background of purifying selection. / Mol Phylogenet Evol 2011,61(1):64鈥?0. CrossRef
  17. McKenna MC, Bell SK: / Classification of mammals above the species level. New York: Columbia University Press; 1997.
  18. Kishino H, Hasegawa M: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. / J Mol Evol 1989, 29:170鈥?79. CrossRef
  19. Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. / Mol Biol Evol 1999,16(8):1114鈥?116. CrossRef
  20. de Oliveira FB, Molina EC, Marroig G: Paleogeography of the South Atlantic: a Route for Primates and Rodents into the New World? In / South American Primates, Developments in Primatology: Progress and Prospects. Edited by: Garber PA, Estrada A, Bicca-Marques JC, Heymann EW. New York: Springer-Verlag; 2008.
  21. Houle A: The origin of platyrrhines: An evaluation of the Antarctic scenario and the floating island model. / Am J Phys Anthropol 1999,109(4):541鈥?59. CrossRef
  22. Janis CM, Dawson MR, Flynn LJ: Glires summary. In / Evolution of Tertiary Mammals of North America: Volume 2, Small Mammals, Xenarthrans, and Marine Mammals. Edited by: Janis CM, Gunnell GF, Uhen MD. Cambridge: Cambridge University Press; 2008:263鈥?92. CrossRef
  23. Wood AE: The origin of the caviomorph rodents from a source in Middle America: A clue to the area of origin of the platyrrhine primates. In / Evolutionary Biology of the New World Monkeys and Continental Drift. Edited by: Ciochon RL, Chiarelli AB. New York: Plenum Press; 1980:79鈥?1. CrossRef
  24. Lavocat R: La syst茅matique des rongeurs hystricomorphes et la d茅rive des continents. / C R Acad Sci Paris S茅r D 1969, 269:1496鈥?497.
  25. Martin T: Incisor schmelzmuster diversity in South America's oldest rodent fauna and early caviomorph history. / J Mamm Evol 2005, 12:405鈥?17. CrossRef
  26. Landry SO Jr: A proposal for a new classification and nomenclature for the Glires (Lagomorpha and Rodentia). / Mitteilungen des Museums f眉r Naturkunde, Berlin, Zoologische Reihe 1999, 75:283鈥?16.
  27. Perelman P, Johnson WE, Roos C, Seuanez HN, Horvath JE, Moreira MA, Kessing B, Pontius J, Roelke M, Rumpler Y: A molecular phylogeny of living primates. / PLoS Genet 2011,7(3):e1001342. CrossRef
  28. Williams BA, Kay RF, Kirk EC: New perspectives on anthropoid origins. / Proc Natl Acad Sci U S A 2010,107(11):4797鈥?804. CrossRef
  29. Takai M, Anaya F, Shigehara N, Setoguchi T: New fossil materials of the earliest new world monkey, Branisella boliviana, and the problem of platyrrhine origins. / Am J Phys Anthropol 2000,111(2):263鈥?81. CrossRef
  30. Fleagle JG: / Primate Adaptation and Evolution. 2nd edition. Waltham: Academic Press; 1998.
  31. Schrago CG: On the time scale of new world primate diversification. / Am J Phys Anthropol 2007,132(3):344鈥?54. CrossRef
  32. Hodgson JA, Sterner KN, Matthews LJ, Burrell AS, Jani RA, Raaum RL, Stewart CB, Disotell TR: Successive radiations, not stasis, in the South American primate fauna. / Proc Natl Acad Sci U S A 2009,106(14):5534鈥?539. CrossRef
  33. Kay RF, Fleagle JG, Mitchell TR, Colbert M, Bown T, Powers DW: The anatomy of Dolichocebus gaimanensis, a stem platyrrhine monkey from Argentina. / J Hum Evol 2008,54(3):323鈥?82. CrossRef
  34. Vucetich MG, Vieytes EC MEP, Carlini AA: The rodents from La Cantera. In / The Paleontology of Gran Barranca Evolution and Environmental Change through the Middle Cenozoic of Patagonia. Edited by: Madden RH, Carlini AA, Vucetich MG, Kay RF. Cambridge: Cambridge University Press; 2010:193鈥?05.
  35. Bertrand OC, Flynn JJ, Croft DA, Wyss AR: Two New Taxa (Caviomorpha, Rodentia) from the Early Oligocene Tinguiririca Fauna (Chile). / Am Mus Novit 2012, 3750:1鈥?6. CrossRef
  36. Thompson JD, Higgins DG, Gibson TJ: Clustal-W - Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. / Nucleic Acids Res 1994,22(22):4673鈥?680. CrossRef
  37. Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. / Bioinformatics 2003,19(12):1572鈥?574. CrossRef
  38. Pond SLK, Frost SDW, Muse SV: HyPhy: hypothesis testing using phylogenies. / Bioinformatics 2005,21(5):676鈥?79. CrossRef
  39. Yang ZH: PAML 4: Phylogenetic analysis by maximum likelihood. / Mol Biol Evol 2007,24(8):1586鈥?591. CrossRef
  40. dos Reis M, Yang ZH: Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times. / Mol Biol Evol 2011,28(7):2161鈥?172. CrossRef
  41. Rannala B, Yang ZH: Inferring speciation times under an episodic molecular clock. / Syst Biol 2007,56(3):453鈥?66. CrossRef
  42. Gelman A, Rubin DB: Inference from iterative simulation using multiple sequences. / Stat Sci 1992, 7:457鈥?11. CrossRef
  43. Li CK, Ting SY: The paleogene mammals of china. / Bull Carnagie Mus Nat His 1983, 21:1鈥?3.
  44. Benton MJ, Donoghue PC: Paleontological evidence to date the tree of life. / Mol Biol Evol 2007,24(1):26鈥?3. CrossRef
  45. Tassy P, Pickford M: Un nouveau mastodonte zygolophodonte (proboscidea, mammalia) dans le mioccne inf茅rieur d鈥檃frique orientale. / Geobios 1983,16(1):53鈥?7. CrossRef
  46. Seiffert ER, Simons EL, Clyde WC, Rossie JB, Attia Y, Bown TM, Chatrath P, Mathison ME: Basal anthropoids from Egypt and the antiquity of Africa's higher primate radiation. / Science 2005,310(5746):300鈥?04. CrossRef
  47. Rose KD, DeLeon VB, Missiaen P, Rana RS, Sahni A, Singh L, Smith T: Early Eocene lagomorph (Mammalia) from Western India and the early diversification of Lagomorpha. / Proc R Soc B 2008,275(1639):1203鈥?208. CrossRef
  48. Meng J, Hu YM, Li CK: The osteology of Rhombomylus (mammalia, glires): Implications for phylogeny and evolution of glires. / Bull Am Mus Nat Hist 2003, 275:1鈥?47. CrossRef
  49. Marivaux L, Vianey-Liaud M, Jaeger JJ: High-level phylogeny of early Tertiary rodents: dental evidence. / Zool J Linn Soc 2004,142(1):105鈥?34. CrossRef
  50. Shevyreva NS: New early Eocene rodents from the Zaysan Basin. In / Flora i Fauna Zaysanskoi Vpadiny. Tblisi: Akademiya Nauk Gruzinskoy SSR; 1984:77鈥?14.
  51. Jacobs L, Flynn L: Of mice 鈥?again: the Siwalik rodent record, murine distribution, and molecular clocks. In / Interpreting the Past: Essays on Human, Primate, and Mammal Evolution in Honor of David Pilbeam. Leiden: Brill Academic Publishers; 2005:63鈥?0.
  
• 作者单位：Carolina M Voloch (1)
  Julio F Vilela (2)
  Leticia Loss-Oliveira (2)
  Carlos G Schrago (3)
  
  1. Departamento de Gen茅tica, A2-097, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rua Prof. Rodolpho Paulo Rocco, SN Ilha do Fund茫o, Rio de Janeiro, CEP: 21941-617, Brazil
  2. Departamento de Gen茅tica, A2-095, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rua Prof. Rodolpho Paulo Rocco, SN Ilha do Fund茫o, Rio de Janeiro, CEP: 21941-617, Brazil
  3. Departamento de Gen茅tica, A2-092, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rua Prof. Rodolpho Paulo Rocco, SN Ilha do Fund茫o, Rio de Janeiro, CEP: 21941-617, Brazil
  

文摘

Background The hystricognath rodents of the New World, the Caviomorpha, are a diverse lineage with a long evolutionary history, and their representation in South American fossil record begins with their occurrence in Eocene deposits from Peru. Debates regarding the origin and diversification of this group represent longstanding issues in mammalian evolution because early hystricognaths, as well as Platyrrhini primates, appeared when South American was an isolated landmass, which raised the possibility of a synchronous arrival of these mammalian groups. Thus, an immediate biogeographic problem is posed by the study of caviomorph origins. This problem has motivated the analysis of hystricognath evolution with molecular dating techniques that relied essentially on nuclear data. However, questions remain about the phylogeny and chronology of the major caviomorph lineages. To enhance the understanding of the evolution of the Hystricognathi in the New World, we sequenced new mitochondrial genomes of caviomorphs and performed a combined analysis with nuclear genes. Results Our analysis supports the existence of two major caviomorph lineages: the (Chinchilloidea + Octodontoidea) and the (Cavioidea + Erethizontoidea), which diverged in the late Eocene. The Caviomorpha/phiomorph divergence also occurred at approximately 43 Ma. We inferred that all family-level divergences of New World hystricognaths occurred in the early Miocene. Conclusion The molecular estimates presented in this study, inferred from the combined analysis of mitochondrial genomes and nuclear data, are in complete agreement with the recently proposed paleontological scenario of Caviomorpha evolution. A comparison with recent studies on New World primate diversification indicate that although the hypothesis that both lineages arrived synchronously in the Neotropics cannot be discarded, the times elapsed since the most recent common ancestor of the extant representatives of both groups are different.