A time-calibrated species tree of crocodylia reveals a recent radiation of the true crocodiles

Evolution

Volumn 65, Issue 11, 2011, Pages 3285-3297

  Oaks, Jamie R ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Biogeography; Crocodylus; Dirichlet process; Multispecies coalescent; Relaxed clock

Indexed keywords

CIRCUMPOLAR CURRENT; CONSERVATION GENETICS; CROCODILIAN; ENDANGERED SPECIES; MASS EXTINCTION; MIOCENE; MORPHOLOGY; PHYLOGENETICS; SPECIES CONSERVATION; SPECIES RICHNESS; TAXONOMY;

ALLIGATOR; ANIMAL; ARTICLE; BIOLOGICAL MODEL; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ALLIGATORS AND CROCODILES; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

AFRICA;

ALLIGATOR; CROCODYLIDAE (ALL CROCODILES); CROCODYLUS;

EID: 80053985551     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01373.x     Document Type: Article

References (103)

1. Aggarwal, R., K. Majumdar, J. Lang, and L. Singh, 1994. Generic affinities among crocodilians as revealed by DNA fingerprinting with a BKM-derived probe. Proc. Natl. Acad. Sci. USA 91:10601-10605.
2. Akaike, H., 1974. A new look at the statistical model identification. IEEE Trans. Automat. Contr. 19:716-723.
3. Allen, G. R., 1974. The marine crocodile, Crocodylus porosus, from Ponape, Eastern Caroline Islands, with notes on food habits of crocodiles from the Palau Archipelago. Copeia 1974:553.
4. Barber, P. H., and D. R. Bellwood, 2005. Biodiversity hotspots: evolutionary origins of biodiversity in wrasses (Halichoeres: Labridae) in the Indo Pacific and new world tropics. Mol. Phylogenet. Evol. 35:235-253.
5. Brochu, C. A., 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Syst. Biol. 46:479-522.
6. Brochu, C. A. 1999. Phylogenetics, taxonomy, and historical biogeography of Alligatoroidea. Society Of Vertebrate Paleontology Memoir 6:9-100.
7. Brochu, C. A. 2000a. Congruence between physiology, phylogenetics and the fossil record on crocodylian historical biogeography. Pp. 9-28 in G. Grigg, F. Seebacher, and C. Franklin, eds. Crocodilian biology and evolution. Surrey Beatty and Sons, Chipping Norton, New South Wales, Australia
8. Brochu, C. A. 2000b. Phylogenetic relationships and divergence timing of Crocodylus based on morphology and the fossil record. Copeia 2000:657-673.
9. Brochu, C. A. 2003. Phylogenetic approaches toward crocodylian history. Annu. Rev. Earth. Planet Sci. 31:357-397.
10. Brochu, C. A. 2007. Morphology, relationships, and biogeographical significance of and extinct horned crocodile (Crocodylia, Crocodylidae) from the Quaternary of Madagascar. Zool. J. Linn. Soc. 150:835-863.
11. Brochu, C. A., and L. D. Densmore, 2000. Crocodile phylogenetics: a summary of current progress. Pp. 3-8 in G. C. Grigg, F. S. Seebacher, and C. Franklin, eds. Crocodilian biology and evolution. Surrey Beatty and Sons, Chipping Norton, New South Wales, Australia
12. Brochu, C. A., J. Njau, R. J. Blumenschine, and L. D. Densmore, 2010. A new horned crocodile from the Plio-Pleistocene hominid sites at Olduvai Gorge, Tanzania. PLoS One 5:e9333.
13. Brooks, D. R., 1979. Testing hypotheses of evolutionary relationships among parasites: the digeneans of crocodilians. Am. Zool. 19:1225-1238.
14. Brooks, D. R., and R. T. O'Grady, 1989. Crocodilians and their helminth parasites: Macroevolutionary considerations. Am. Zool. 29:873-883.
15. Bustard, H., and B. Choudhury, 1982. Long distance movement by a saltwater crocodile (Crocodylus porosus). Brit. J. Herpetol. 6:87.
16. Clark, J. R., R. H. Ree, M. E. Alfaro, M. G. King, W. L. Wagner, and E. H. Roalson, 2008. A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages. Syst. Biol. 57:693-707.
17. Delfino, M., and L. Rook, 2008. African crocodylians in the Late Neogene of Europe: a revision of Crocodylus bambolii Ristori, 1890. J. Paleontol. 82:336-343.
18. Delfino, M., and J. De Vos, 2010. A revision of the Dubois crocodylians, Gavialis bengawanicus and Crocodylus ossifragus, from the Pleistocene Homo erectus beds of Java. J. Vertebr. Paleontol. 30:427-441.
19. Delfino, M., M. Böhme, and L. Rook, 2007. First European evidence for transcontinental dispersal of Crocodylus (Late Neogene of southern Italy). Zool. J. Linn. Soc. 149:293-307.
20. Densmore, L. D., 1983. Biochemical and immunological systematics of the order Crocodilia. Pp. 397-496 in M. Hecht, B. Wallace, and G. Prance, eds. Evolutionary biology. Plenum Press, New York
21. Densmore, L. D., and H. Dessauer, 1984. Low levels of protein divergence detected between Gavialis and Tomistoma: evidence for crocodilian monophyly?. Comp. Biochem. Phys. 77B:715-720.
22. Densmore, L. D., and R. Owen, 1989. Molecular systematics of the order Crocodilia. Am. Zool. 29:831-841.
23. Densmore, L. D., and P. S. White, 1991. The systematics and evolution of the Crocodilia as suggested by restriction endonuclease analysis of mitochondrial and nuclear ribosomal DNA. Copeia 1991:602-615.
24. Drummond, A. J., and A. Rambaut, 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
25. Eaton, M. J., A. Martin, J. B. Thorbjarnarson, and G. Amato, 2009. Species-level diversification of African dwarf crocodiles (genus Osteolaemus): a geographic and phylogenetic perspective. Mol. Phylogenet. Evol. 50:496-506.
26. Edwards, A. W. F., 1972. Likelihood. Cambridge Univ. Press, Cambridge, England
27. Elsworth, P., F. Seebacher, and C. Franklin, 2003. Sustained swimming performance in crocodiles (Crocodylus porosus): effects of body size and temperature. J. Herpetol. 37:363-368.
28. Feng, G., X. Wu, P. Yan, and X. Li, 2010. Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny. Amphibia-reptilia 31:299-309.
29. Fitzsimmons, N. N., J. C. Buchan, P. V. Lam, G. Polet, T. T. Hung, N. Q. Thang, and J. Gratten, 2002. Identification of purebred Crocodylus siamensis for reintroduction in Vietnam. J. Exp. Zool. 294:373-381.
30. Gatesy, J., and G. D. Amato, 1992. Sequence similarity of 12s ribosomal segment of mitochondrial DNAs of gharial and false gharial. Copeia 1992:241-243.
31. Gatesy, J., and G. Amato, 2008. The rapid accumulation of consistent molecular support for intergeneric crocodylian relationships. Mol. Phylogenet. Evol. 48:1232-1237.
32. Gatesy, J., R. DeSalle, and W. Wheeler, 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2:152-157.
33. Gatesy, J., G. Amato, M. Norell, R. DeSalle, and C. Hayashi, 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 52:403-422.
34. Gatesy, J., R. H. Baker, and C. Hayashi, 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:342-355.
35. Gratten, J., 2003. The molecular systematics phylogeography and population genetics of Indo Pacific Crocodylus. Ph.D. thesis, University of Queensland, Brisbane St. Lucia, Queensland
36. Griffin, D. L., 2002. Aridity and humidity: two aspects of the late Miocene climate of North Africa and the Mediterranean. Palaeogeogr. Palaeoclim. 182:65-91.
37. Groombridge, B., 1987. The distribution and status of world crocodilians. Pp. 9-21 in G. J. W. Webb, S. C. Manolis, and P. J. Whitehead, eds. Wildlife management: crocodiles and alligators. Surrey Beatty & Sons Pty Ltd, Chipping Norton, Australia
38. Harshman, J., C. J. Huddleston, J. P. Bollback, T. J. Parsons, and M. J. Braun, 2003. True and false gharials: a nuclear gene phylogeny of Crocodylia. Syst. Biol. 52:386-402.
39. Hass, C., M. Hoffman, L. Densmore, and L. Maxson, 1992. Crocodilian evolution: insights from immunological data. Mol. Phylogenet. Evol. 1:193-201.
40. Hekkala, E. R., G. Amato, R. DeSalle, and M. J. Blum, 2010. Molecular assessment of population differentiation and individual assignment potential of Nile crocodile (Crocodylus niloticus) populations. Conserv. Genet. 11:1435-1443.
41. Heled, J., and A. J. Drummond, 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
42. Huelsenbeck, J. P., and M. A. Suchard, 2007. A nonparametric method for accomodating and testing across-site rate variation. Syst. Biol. 56:975-987.
43. Inger, R. F., 1948. The systematics of the crocodile, Osteoblepharon osborni. Copeia 1948:15-19.
44. Janke, A., A. Gullberg, S. Hughes, R. K. Aggarwal, and U. Arnason, 2005. Mitogenomic analyses place the gharial (Gavialis gangeticus) on the crocodile tree and provide pre-K/T divergence times for most crocodilians. J. Mol. Evol. 61:620-626.
45. Kälin, J. A., 1955. Zur stammesgeschichte der Crocodilia. Rev. Suisse. Zool. 62:347-356.
46. Kass, R. E., and A. E. Raftery, 1995. Bayes factors. J. Am. Stat. Assoc. 90:773-795.
47. Kosuch, J., M. Vences, A. Dubois, A. Ohler, and W. Bohme, 2001. Out of Asia: mitochondrial DNA evidence for an Oriental origin of tiger frogs, genus Hoplobatrachus. Mol. Phylogenet. Evol. 21:398-407.
48. Latiolais, J. M., M. S. Taylor, K. Roy, and M. E. Hellberg, 2006. A molecular phylogenetic analysis of strombid gastropod morphological diversity. Mol. Phylogenet. Evol. 41:436-444.
49. Lessios, H. A., B. D. Kessing, G. M. Wellington, and A. Gray-Beal, 1996. Indo Pacific echinoids in the tropical Eastern Pacific. Coral Reefs 15:133-142.
50. Lessios, H. A., B. D. Kessing, and D. R. Robertson, 1998. Massive gene flow across the world's most potent marine biogeographic barrier. Proc. R. Soc. Lond. B 265:583-588.
51. Lessios, H. A., B. D. Kessing, D. R. Robertson, and G. Paulay, 1999. Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currents. Evolution 53:806-817.
52. Li, Y., X. Wu, X. Ji, P. Yan, and G. Amato, 2007. The complete mitochondrial genome of the salt-water crocodile (Crocodylus porosus) and phylogeny of crocodilians. J. Genet. Genom. 34:119-128.
53. Lydekker, R., 1886. Indian tertiary and post-tertiary vertebrata: Siwalik Crocodilia, Lacertilia and Ophidia. Palaeontol. Indica 10:209-240.
54. Man, Z., W. Yishu, Y. Peng, and W. Xiaobing, 2011. Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae. Mol. Phylogenet. Evol. 60:62-67.
55. Markwick, P. J., 1998. Crocodilian diversity in space and time: the role of climate in paleoecology and its implication for understanding K/T extinctions. Paleobiology 24:470-497.
56. McAliley, L. R., R. E. Willis, D. A. Ray, P. S. White, C. A. Brochu, and L. D. Densmore, 2006. Are crocodiles really monophyletic? Evidence for subdivisions from sequence and morphological data. Mol. Phylogenet. Evol. 39:16-32.
57. Mead, J. I., D. W. Steadman, S. H. Bedford, C. J. Bell, and M. Spriggs, 2002. New extinct mekosuchine crocodile from Vanuatu, South Pacific. Copeia 2002:632-641.
58. Mead, J. I., R. Cubero, A. L. V. Zamora, S. L. Swift, C. Laurito, and L. D. Gomex, 2006. Plio-Pleistocene Crocodylus (Crocodylia) form southwestern Costa Rica. Stud. Neotrop. Fauna E 41:1-7.
59. Medem, F., 1981. Los Crocodylia de Sur America. Vol. 1. Los Crocodylia de Colombia. Colciencias, Bogotá, Colombia
60. Meganathan, P. R., B. Dubey, M. A. Batzer, D. A. Ray, and I. Haque, 2010. Molecular phylogenetc analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Mol. Phylogenet. Evol. 57:393-402.
61. Meredith, R. W., E. R. Hekkala, G. Amato, and J. Gatesy, 2011. A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: Evidence for a trans-Atlantic voyage from Africa to the New World. Mol. Phylogenet. Evol. 60:183-191.
62. Miller, K. G., R. G. Fairbanks, and G. S. Mountain, 1987. Tertiary oxygen isotope synthesis, sea level history, and continental margin erosion. Paleoceanography 2:1-19.
63. Miller, W. E., 1980. The late Pliocene Las Tunas local fauna from southernmost Baja California, Mexico. J. Paleontol. 54:762-805.
64. Molnar, P., P. England, and J. Martinod, 1993. Mantle dynamics, uplift of the Tibetan Plateau, and the Indian Monsoon. Rev. Geophys. 31:357-396.
65. Molnar, R. E., 1979. Crocodylus porosus from the Pliocene Allingham formation of North Queensland. Results of the Ray E. Lemley expeditions, part 5. Memoirs Of The Queensland Museum 19:357-365.
66. Molnar, R. E., T. H. Worthy, and P. M. A. Willis, 2002. An extinct Pleistocene endemic mekosuchine crocodylian from Fiji. J. Vertebr. Paleontol. 22:612-628.
67. Mook, C., 1927. The skull characters of Crocodylus megarhinus Andrews. Am. Museum Novitates 289:1-8.
68. Mook, C., 1933. A skull with jaws of Crocodilus sivalensis Lydekker. Am. Museum Novitates 670:1-10.
69. Muller, J., and R. R. Reisz, 2005. Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays 27:1069-1075.
70. Neill, W. T., 1971. The Last of the Ruling Reptiles: Alligators, Crocodiles and their kin. Columbia Univ. Press, New York
71. Nettel, A., and R. S. Dodd, 2007. Drifting propagules and receding swamps: genetic footprints of mangrove recolonization and dispersal along tropical coasts. Evolution 61:958-971.
72. Norell, M. A., 1989. The higher level relationships of the extant Crocodylia. J. Herpetol. 23:325-335.
73. Pagel, M., 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48:612-622.
74. Pagel, M., and A. Meade, 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am. Nat. 167:808-825.
75. Pagel, M., A. Meade, and D. Barker, 2004. Bayesian estimation of ancestral character states on phylogenies. Syst. Biol. 53:673-684.
76. Palumbi, S. R., 1997. Molecular biogeography of the Pacific. Pp. 91-96 in H. A. Lessios and I. G. Macintyre, eds. Proceedings of the 8th International Coral Reef Symposium. Smithsonian Tropical Research Institute, Balboa, Panama.
77. Pidcock, S., L. Taplin, and G. Grigg, 1997. Differences in renal-cloacal function between Crocodylus porosus and Alligator mississippiensis have implications for crocodilian evolution. J. Comp. Physiol. 167B:153-158.
78. Piras, P., P. Colangelo, D. C. Adams, A. Buscalioni, J. Cubo, T. Kotsakis, C. Meloro, and P. Raia, 2010. The Gavialis-Tomistoma debate: the contribution of skull ontogenetic allometry and growth trajectories to the study of crocodylian relationships. Evol. Dev. 12:568-579.
79. Poe, S., 1996. Data set incongruence and the phylogeny of crocodilians. Syst. Biol. 45:393-414.
80. Pope, C. H., 1955. The reptile world: a natural history of the snakes, lizards, turtles, and crocodilians. Alfred A. Knopf, New York
81. Ree, R. H., and S. A. Smith, 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 57:4-14.
82. Roos, J., R. K. Aggarwal, and A. Janke, 2007. Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary boundary. Mol. Phylogenet. Evol. 45:663-673.
83. Ross, J. P., 1998. Crocodiles: status survey and conservation action plan. 2nd ed. International Union for Conservation of Nature and Natural Resources, Gland, Switzerland. Available at.
84. Salisbury, S. W., and P. M. A. Willis, 1996. A new crocodylian from the Early Eocene of Southeastern Queensland and a preliminary investigation of the phylogenetic relationships of crocoyloids. Alcheringa 20:179-227.
85. Salisbury, S. W., R. E. Molnar, E. Frey, and P. M. A. Willis, 2006. The origin of modern crocodyliforms: new evidence from the Cretaceous of Australia. Proc. R. Soc. Lond. B 273:2439-2448.
86. Schmidt, K. P., 1919. Contributions to the herpetology of the Belgian Congo. Part 1. Turtles, crocodiles, lizards and chameleons. Bull. Am. Mus. Nat. Hist. 39:385-624.
87. Schmitz, A., P. Mansfeld, E. Hekkala, T. Shine, H. Nickel, G. Amato, and W. Bohme, 2003. Molecular evidence for species level divergence in African Nile crocodiles Crocodylus niloticus (Laurenti, 1786). Comptes Rendus Palevol 2:703-712.
88. Seebacher, F., and R. S. James, 2008. Plasticity of muscle function in a thermoregulating ectotherm (Crocodylus porosus: biomechanics and metabolism. Am. J. Physiol. 294:R1024-R1032.
89. Shimodaira, H., and M. Hasegawa, 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
90. Sill, W. D., 1968. The zoogeography of the Crocodilia. Copeia 1968:76-88.
91. Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
92. Taplin, L., 1988. Osmoregulation in crocodilians. Biol. Rev. 63:333-377.
93. Taplin, L., and G. Grigg, 1981. Salt glands in the tongue of the estuarine crocodile Crocodylus porosus. Science 212:1045-1047.
94. Taplin, L., and J. Loveridge, 1988. Nile crocodiles, Crocodylus niloticus, and estuarine crocodiles, Crocodylus porosus, show similar osmoregulatory responses on exposure to seawater. Comp. Biochem. Phys. 89A:443-448.
95. Taplin, L., and G. Grigg, 1989. Historical zoogeography of the eusuchian crocodilians: a physiological perspective. Am. Zool. 29:885-901.
96. Taplin, L., G. Grigg, P. Harlow, T. Ellis, and W. Dunson, 1982. Lingual salt glands in Crocodylus acutus and C. johnstoni and their absence from Alligator mississipiensis and Caiman crocodilus. J. Comp. Physiol. 149:43-47.
97. Tchernov, E., 1986. Evolution of the crocodiles in East and North Africa. Editions du Centre national de la recherche scientifique, Paris, France.
98. Van Bocxlaer, I., S. D. Biju, S. P. Loader, and F. Bossuyt, 2009. Toad radiation reveals into India dispersal as a source of endemism in the Western Ghats Sri Lanka biodiversity hotspot. BMC Evol. Biol. 9:131.
99. White, P. S., 1992. Relationships of extant Crocodylia as inferred by sequence analysis of mitochondrial DNA. Ph.D. Thesis, Texas Tech University, Lubbock, Texas, USA
100. White, P. S., and L. D. Densmore, 2000. DNA sequence alignment and data analysis methods: their effect on the recovery of crocodylian relationships. Pp. 29-37 in G. Grigg, F. Seebacher, and C. Franklin, eds. Crocodilian biology and evolution. Surrey Beatty & Sons, Chipping Norton, New South Wales, Australia
101. Willis, P. M. A., 1997. Review of fossil crocodilians from Australasia. Aust. J. Zool. 30:287-298.
102. Willis, R. E., L. R. McAliley, E. D. Neely, and L. D. Densmore, 2007. Evidence for placing the false gharial (Tomistoma schlegelii) into the family Gavialidae: Inferences from nuclear gene sequences. Mol. Phylogenet. Evol. 43:787-794.
103. Zwickl, D. J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. thesis, University of Texas at Austin, Austin, Texas, USA