Body size evolution in extant Oryzomyini rodents: Cope's rule or miniaturization?

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Avaria Llautureo, Jorge ^a   Hernández, Cristián E ^a   Boric Bargetto, Dusan ^a   Canales Aguirre, Cristian B ^a   Morales Pallero, Bryan ^a   Rodríguez Serrano, Enrique ^a  

^a UNIVERSITY OF CONCEPCIÓN   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BODY SIZE; CONTROLLED STUDY; EVOLUTION; EVOLUTIONARY ADAPTATION; EXTANT SPECIES; MOLECULAR PHYLOGENY; NONHUMAN; ORYZOMYINI RODENT; PREDICTION; RODENT; SPECIES DIVERSITY; TIME; TREND STUDY; ANIMAL; BAYES THEOREM; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; SIGMODONTINAE; STATISTICAL MODEL; UNCERTAINTY;

MAMMALIA; RODENTIA;

ANIMALS; BAYES THEOREM; BODY SIZE; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; PHYLOGENY; SIGMODONTINAE; TIME FACTORS; UNCERTAINTY;

EID: 84859258155     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034654     Document Type: Article

References (103)

1. Brown JH, (1995) Macroecology Chicago, Illinois University of Chicago Press.
2. Gaston KJ, Chown SL, Mercer RD, (2001) The animal species-body size distribution of Marion Island. Proc Natl Acad Sci U S A 98: 14493-14496.
3. Peters RH, (1983) The ecological implications of body size New York Cambridge University Press.
4. Schmidt-Nielsen K, (1984) Scaling, why is animal size so important? New York Cambridge University Press.
5. Hanken J, Wake DB, (1993) Miniaturization of body size: organismal consequences and evolutionary significance. Annu Rev Ecol Syst 24: 501-519.
6. Sibly RM, Brown JH, (2007) Effects of body size and lifestyle on evolution of mammal life histories. Proc Natl Am Sci 104: 17707-17712.
7. Cope CD, (1887) The origin of the fittest New York Arno Press.
8. Stanley SM, (1973) An explanation for Cope's rule. Evolution 27: 1-26.
9. Alroy J, (1998) Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280: 731-734.
10. Brown JH, Maurer BA, (1986) Body size, ecological dominance and Cope's rule. Nature 324: 248-250.
11. Damuth J, (1993) Cope's rule, the island rule and the scaling of mammalian population density. Nature 365: 748-750.
12. Demetrius L, (2000) Directionality theory and the evolution of body size. Proc Biol Sci 267: 2385-2391.
13. Novack-Gottshall PM, Lanier MA, (2008) Scale-dependence of Cope's rule in body size evolution of Paleozoic brachiopods. Proc Natl Acad Sci U S A 105: 5430-5434.
14. Kingsolver JG, Pfenning DW, (2004) Individual-level selection as a cause of Cope's rule of phyletic size increase. Evolution 58: 1608-1612.
15. Dial KP, Marzluff JM, (1988) Are the smallest organisms the most diverse? Ecology 69: 1620-1624.
16. McShea DW, (1994) Mechanisms of large-scale evolutionary trends. Evolution 48: 1747-1763.
17. Maurer BA, (1998) The evolution of body size in birds. I. Evidence for non-random diversification. Evol Ecol 12: 925-934.
18. Clauset A, Erwin DH, (2008) The evolution and distribution of species body size. Science 321: 399.
19. Rüber L, Kottelat M, Tan HH, Ng PKL, Britz R, (2007) Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world's smallest vertebrate. BMC Evol Biol 7: 38.
20. Yeh J, (2002) The effect of miniaturized body size on skeletal morphology in frogs. Evolution 56 (3): 628-641.
21. Pianka E, (1995) Evolution of body size: varanid lizards as a model system. Am Nat 146: 398-414.
22. Knouft JH, Page LM, (2003) The evolution of body size in extant groups of North American freshwater fishes: speciation, size distributions, and Cope's rule. Am Nat 161: 413-421.
23. Fröbisch NB, Schoch RR, (2009) Testing the impact of miniaturization on phylogeny: Paleozoic dissorophoid amphibians. Syst Biol 58: 312-327.
24. Hanken J, (1992) Life history and morphological evolution. J Evol Biol 5: 549-557.
25. FitzJohn RG, (2010) Quantitative traits and diversification. Syst Biol 59 (6): 619-633.
26. Hone DWE, Benton MJ, (2007) Cope's rule in the Pterosauria, and differing perceptions of Cope's rule at different taxonomic levels. J Evol Biol 20: 1164-1170.
27. Hone DWE, Keesey TM, Pisani D, Purvis A, (2005) Macroevolutionary trends in the Dinosauria: Cope's rule. J Evol Biol 18: 587-595.
28. Smith FA, Boyer AG, Brown JH, Costa DP, Dayan T, et al. (2010) The evolution of maximum body size of terrestrial mammals. Science 330: 1216-1219.
29. Monroe MJ, Bokma F, (2010) Little evidence for Cope's rule from Bayesian phylogenetic analysis of extant mammals. J Evol Biol 23: 2017-2021.
30. McFadden BJ, (1992) Fossil Horses: Systematics, Palaeobiology and Evolution of the Family Equidae New York Cambridge University Press.
31. Huelsenbeck JP, Rannala B, Masly JP, (2000) Accommodating phylogenetic uncertainty in evolutionary studies. Science 288: 2349-2350.
32. Rezende EL, Garland T Jr, (2003) Comparaciones interespecíficas y métodos estadísticos filogenéticos. In: Bozinovic F, editors. Fisiología ecológica y evolutiva. Teoría y casos de estudio en animales Santiago, Chile Ediciones Universidad Católica de Chile pp. 79-98.
33. Schluter D, (1995) Uncertainty in ancient phylogenies. Nature 377: 108-109.
34. Felsenstein J, (2004) Inferring Phylogenies Massachusetts, Sunderland University of Washington, Sinauer Associates Inc.
35. Holder MT, Lewis PO, (2003) Phylogeny estimation: traditional and Bayesian approaches. Nature Rev Genet 4: 275-284.
36. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
37. Larget B, Simon DL, (1999) Markov Chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16: 750-759.
38. Pagel MD, Meade A, (2004) A Phylogenetic Mixture Model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 53 (4): 571-581.
39. Pagel MD, Meade A, (2005) Mixture models in phylogenetic inference. In: Gascuel O, editors. Mathematics of evolution and phylogeny Oxford Oxford University Press pp. 121-142.
40. Huelsenbeck JP, Bollback JP, (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol 50: 351-366.
41. Lutzoni F, Pagel M, Reeb V, (2001) Major fungal lineages derived from lichen-symbiotic ancestors. Nature 411: 937-940.
42. Pagel MD, Lutzoni F, (2002) Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. In: Lässig M, Valleriani A, editors. Biological evolution and statistical physics Berlin Springer-Verlag pp. 148-161.
43. Pagel M, Meade A, (2005) Bayesian estimation of correlated evolution across cultures: A case study of marriage systems and wealth transfer at marriage. In: Mace R, Holden CJ, Shennan S, editors. The evolution of cultural diversity: a phylogenetic approach London University College London Press pp. 235-256.
44. Pagel MD, Meade A, (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am Nat 67: 808-825.
45. Weksler M, Percequillo AR, Voss RS, (2006) Ten new genera of Oryzomyine rodents (Cricetidae:Sigmodontinae). Am Mus Novit 3537: 1-29.
46. Weksler M, (2003) Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon. Mol Phylogenet Evol 29 (2): 331-349.
47. Weksler M, (2006) Phylogenetic relationships of oryzomyine rodents (Muroidea: Sigmodontinae): separate and combined analyses of morphological and molecular data. Bull Am Mus Nat Hist 196: 1-149.
48. Oakley TH, Cunningham CW, (2000) Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54: 397-405.
49. Pagel MD, (2002) Modelling the evolution of continuously varying characters on phylogenetic trees. In: MacLeod N, Foley FL, editors. Morphology, shape and phylogeny London Taylor & Francis pp. 269-286.
50. Ronquist F, (2004) Phylogenetics Series. Bayesian inference of character evolution. Trends Ecol Evol 19: 475-481.
51. Webster AJ, Purvis A, (2001) Testing the accuracy of methods for reconstructing ancestral states of continuous characters. Proc R Soc Lond B 269: 143-149.
52. Moen DS, (2006) Cope's rule in cryptodiran turtles: do they body sizes of extant species reflect a trend of phyletic size increase? J Evol Biol 19: 1210-1221.
53. Alroy J, (2000) New methods for quantifying macroevolutionary patterns and processes. Paleobiology 26 (4): 707-733.
54. Alroy J, (2000) Understanding the dynamics of trends within evolving lineages. Paleobiology 26 (3): 319-329.
55. Gaston KJ, He F, (2002) The distribution of species range size: a stochastic process. Proc R Soc Lond B 269: 1079-1086.
56. Gould SJ, (1988) Trends as changes in variance: a new slant on progress and directionality in evolution. J Paleontol 62: 319-329.
57. Wang SC, (2001) Quantifying passive and driven large-scale evolutionary trends. Evolution 55 (5): 849-858.
58. Trites AW, Pauly D, (1998) Estimating mean body masses of marine mammals from maximum body lengths. Canad J Zool 76: 886-896.
59. GenBank website. Available: http://www.ncbi.nlm.nih.gov/genbank. Accessed 2011 November 10.
60. D'Elia G, (2003) Phylogenetics of Sigmodontinae (Rodentia, Muroidea, Cricetidae), with special reference to the akodont group, and with additional comments on historical biogeography. Cladistics 19: 307-323.
61. D'Elia G, Luna L, González EM, Patterson BD, (2006) On the Sigmodontinae radiation (Rodentia, Cricetidae): An appraisal of the phylogenetic position of Rhagomys. Mol Phylogenet Evol 38: 558-564.
62. Smith MF, Patton JL, (1999) Phylogenetic relationships and the radiation of sigmodontine rodents in South America: Evidence from Cytochrome b. J Mamm Evol 6: 89-128.
63. Engel SR, Hogan KM, Taylor JF, Davis SK, (1998) Molecular systematic and paleobiogeography of the South American sigmodontine rodents. Mol Biol Evol 15 (1): 35-49.
64. Steppan SJ, Adkins RM, Anderson J, (2004) Phylogeny and divergence-date estimates of rapid radiations in Muroid rodents based on multiple nuclear genes. Syst Biol 53: 533-553.
65. Xia X, Xie Z, Salemi M, Chen L, Wang Y, (2003) An index of substitution saturation and its application. Mol Phylogenet Evol 26: 1-7.
66. Xia X, Xie Z, (2001) DAMBE: data analysis in molecular biology and evolution. J Hered 92: 371-373.
67. Xia X, (2000) Data analysis in molecular biology and evolution Boston Kluwer Academic publishers.
68. Xia X, Lemey P, (2009) Assessing substitution saturation with DAMBE. In: Lemey P, Salemi M, Vandamme AM, editors. The phylogenetic handbook: A practical approach to DNA and protein phylogeny Cambridge Cambridge University Press pp. 615-630.
69. Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Ac Research 22: 4673-4680.
70. Test for Punctuational Evolution and the Node-Density Artifact website. Available: http://www.evolution.rdg.ac.uk/pe/index.html. Accessed 2011 October 25.
71. Venditti C, Meade A, Pagel M, (2006) Detecting the node-density artifact in phylogeny reconstruction. Syst Biol 55: 637-643.
72. Drummond AJ, Rambuat A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
73. Palma RE, Rodríguez-Serrano E, Rivera-Milla E, Hernández CE, Salazar-Bravo J, et al. (2010) Phylogenetic relationships of the pygmy rice rats of the genus Oligoryzomys Bangs, 1900 (Rodentia, Sigmodontinae). Zoolog J Linn Soc 160 (3): 551-566.
74. Pardiñas UFJ, D'Elía G, Ortíz PE, (2002) Sigmodontinos fósiles (Rodentia, Muroidea, Sigmodontinae) de América del Sur: estado actual de su conocimiento y prospectiva. Mastozoolog Neotrop 9: 209-252.
75. Rambaut A, Drummond AJ, (2007) Molecular evolution, phylogenetics and epidemiology website. Available: http://beast.bio.ed.ac.uk/Tracer. Accessed 2011 August 10.
76. Gelman A, Carlin JB, Stern HS, Rubin DB, (1995) Bayesian data analysis London Chapman and Hall.
77. Martins EP, Hansen TE, (1997) Phylogenies and the comparative method: general approach to incorporating phylogenetic information into the analysis of interspecific data. Am Nat 149: 646-667.
78. Pagel MD, (1997) Inferring evolutionary processes from phylogenies. Zoolog Scripta 26: 331-348.
79. Pagel MD, (1999) Inferring the historical patterns of biological evolution. Nature 401: 877-884.
80. Pagel MD, (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol 48: 612-622.
81. Freckleton RP, Harvey PH, Pagel M, (2002) Phylogenetic analysis and comparative data: A test and review of evidence. Am Nat 160: 712-726.
82. R Development Core Team (2008) R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria.
83. Rabosky DL, (2010) Extinction rates should not be estimated from molecular phylogenies. Evolution 64: 1816-1824.
84. Percequillo AR, Weksler M, Costa LP, (2011) A new genus and species of rodent from the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini), with comments on oryzomyine biogeography. Zoolog J Linn Soc 161: 357-390.
85. D' Elía G, (2000) Comments on recent advances in understanding sigmodontine phylogeny and evolution. Mastozool Neot 7: 47-54.
86. Jansa SA, Weksler M, (2004) Phylogeny of Muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences. Mol Phylogenet Evol 31: 256-276.
87. McFarlane DA, Debrot AO, (2001) A new species of extinct oryzomyine rodent from the Quaternary of Curaçao, Netherlands Antilles. Carib J Sci 37: 182-184.
88. Pardiñas UFJ, (2008) A new genus of Oryzomyini rodent (Cricetidae: Sigmodontinae) from the Pleistocene of Argentina. J Mammal 89: 1270-1278.
89. Pardiñas UFJ, Deschamps C, (1996) Sigmodontinos (Mammalia, Rodentia) pleistocénicos del sudoeste de la provincia de Buenos Aires (Argentina): aspectos sistemáticos, paleozoogeográficos y paleoambientales. Estud Geolog 52: 367-379.
90. Pardiñas UFJ, Teta P, Cirignoli S, Podestá DH, (2003) Micromamíferos (Didelphimorphia y Rodentia) de norpatagonia extra andina, Argentina: taxonomía alfa y biogeografía. Mastozoolog Neotrop 10 (1): 69-113.
91. Teta P, Loponte D, Acosta A, (2004) Sigmodontinos (Mammalia, Rodentia) del Holoceno tardío del nordeste de la provincia de Buenos Aires (Argentina). Mastozoolog Neotrop 11 (1): 69-80.
92. Turvey ST, Weksler M, Morris EL, Nokkert M, (2010) Taxonomy, phylogeny and diversity of the extinct Lesser Antillean rice rats (Sigmodontinae: Oryzomyini), with description of a new genus and species. Zoolog J Linn Soc 160: 748-772.
93. Voss RS, Weksler M, (2009) On the taxonomic status of Oryzomys curasoae McFarlane and Debrot, 2001, with remarks on the phylogenetic relationships of O. gorgasi Hershkovitz, 1971. Carib J Sci 45: 1-7.
94. Ziljstra JS, Madern PA, van den Hoek Ostende LW, (2010) New genus and two new species of Pleistocene oryzomyines (Cricetidae: Sigmodontinae) from Bonaire, Netherlands Antilles. J Mammal 91 (4): 860-873.
95. Steppan SJ, (1996) A new species Holochilus (Rodentia: Sigmodontinae) from the middle Pleistocene of Bolivia and its phylogenetic significance. J Vert Paleont 16: 522-530.
96. McShea DW, (2000) Matters of the record. Paleobiology 26: 330-333.
97. Raia P, Carotenuto F, Passaro F, Fulgione D, Fortelius M, (2011) Ecological specialization in fossil mammals explain Cope's rule. Am Nat 179 (3): 328-337.
98. Agrawal AA, Dorken ME, (2001) Law of the unspecialized: broken?. Trends Ecol Evol 16 (8): 426.
99. Venditti C, Meade A, Pagel M, (2011) Multiple routes of mammalian diversification. Nature 479: 393-396.
100. Coates AG, Jackson JB, Collins LS, Cronin TM, Dowsett HJ, et al. (1992) Closure of the Isthmus of Panama: the near-shore marine record of Costa Rica and western Panama. Geolog Soc Am Bull 104: 814-828.
101. Ibaraki M, (1997) Closing of the Central American seaway and Neogene coastal upwelling along the Pacific coast of South America. Tectonophysics 281: 99-104.
102. Stadler T, (2011) Mammalian phylogeny reveals recent diversification rate shifts. Proc Natl Acad Sci U S A 108: 6187-6192.
103. Silvestro D, Schnitzler J, Zizka G, (2011) A bayesian framework to estimate diversification rates and their variation through time and space. BMC Evol Biol 11: 311.