Ecological diversification and phylogeny of emydid turtles

Biological Journal of the Linnean Society

Volumn 79, Issue 4, 2003, Pages 577-610

  Stephens, Patrick R ^a,b,c   Wiens, John J ^b,c  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b SECTION OF VERTEBRATE PALEONTOLOGY   (United States)

^c STONY BROOK UNIVERSITY   (United States)

Author keywords

Adaptive radiation; Combined analysis; Emydidae; Evolutionary ecology; Molecular systematics; Morphological systematics

Indexed keywords

ADAPTIVE RADIATION; ECOLOGY; MOLECULAR ANALYSIS; PHYLOGENY; TURTLE;

CLEMMYS; EMYDIDAE; TESTUDINES; TRACHEMYS;

EID: 0043023695     PISSN: 00244066     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1095-8312.2003.00211.x     Document Type: Article

References (122)

1. Agassiz L. 1857. Contributions to the natural history of the United States of America. Boston: Little, Brown.
2. Albertson RC, Markert JA, Danley PD, Kocher TD. 1999. Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. Proceedings of the National Academy of Sciences, USA 96: 5107-5110.
3. Baldwin BG, Sanderson MJ. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences, USA 95: 9402-9406.
4. Berlocher SH, Swofford DL. 1997. Searching for phylogenetic trees under the frequency parsimony criterion: an approximation using generalized parsimony. Systematic Biology 46: 211-215.
5. Bertl J, Killebrew FC. 1983. An osteological comparison of Graptemys caglei Haynes and McKown and Graptemys versa Stejneger (Testudines: Emydidae). Herpetologica 39: 375-382.
6. Bickham JW, Lamb T, Minx P, Patton JC. 1996. Molecular systematics of the genus Clemmys and the intergeneric relationships of emydid turtles. Herpetologica 52: 89-97.
7. Bramble DM. 1974. Emydid shell kinesis: biomechanics and evolution. Copeia 1974: 102-109.
8. Brooks DR, McLennan DA. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Chicago: University of Chicago Press.
9. Brown JH, Lomolino MV. 1998. Biogeography, 2nd edn. Sunderland, MA: Sinauer Associates.
10. Burke RL, Leuteritz TE, Wolf AJ. 1996. Phylogenetic relationships of emydine turtles. Herpetologica 52: 572-584.
11. Bury R. 1979. Population ecology of freshwater turtles. In: Harless M, Morlock H, eds. Turtles: perspectives and research. New York: John Wiley and Sons, 571-602.
12. Conant R, Collins JT. 1998. A field guide to reptiles and amphibians of eastern and central North America, 3rd edn. Boston: Houghton Mifflin.
13. Cope ED. 1896. The primary factors of organic evolution. Chicago: Open Court Publishing Co.
14. Diamond J, Case TJ, eds. 1986. Community ecology. New York: Harper & Row.
15. Donoghue MJ. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43: 1127-1156.
16. Ernst CH, Barbour RW. 1989. Turtles of the world. Washington DC: Smithsonian Institution Press.
17. Ernst CH, Lovich JE, Barbour RW. 1994. Turtles of the United States and Canada. Washington DC: Smithsonian Institution Press.
18. Ewert MA. 1979. The embryo and its egg: development and natural history. In: Harless M, Morlock H, eds. Turtles: perspectives and research. New York: John Wiley and Sons, 333-413.
19. Ewert MA, Nelson CE. 1991. Sex determination in turtles: diverse patterns and some possible adaptive values. Copeia 1991: 50-69.
20. Feldman CR, Parham JF. 2002. Molecular phylogenetics of emydine turtles: taxonomic revision and the evolution of shell kinesis. Molecular Phylogenetics and Evolution 22: 388-398.
21. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
22. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
23. Futuyma DJ, Moreno G. 1988. The evolution of ecological specialization. Annual Review of Ecology and Systematics 19: 207-233.
24. Gaffney ES. 1979. Comparative cranial morphology of recent and fossil turtles. Bulletin of the American Museum of Natural History 164: 65-376.
25. Gaffney ES, Meylan PA. 1988. A phylogeny of turtles. In: Benton MJ, ed. The phylogeny and classification of tetrapods, Vol. 1. Amphibians, reptiles, and birds. Oxford: Clarendon Press, 157-219.
26. Garland TG, Midford PE, Ires AR. 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. American Zoologist 39: 374-388.
27. Givnish TJ, Sytsma KJ, eds. .1997. Molecular evolution and adaptive radiation. New York: Cambridge University Press.
28. Grant PR. 1986. Ecology and evolution of Darwin's finches. Princeton: Princeton University Press.
29. Grant PR, Grant BR. 1996. Speciation and hybridization in island birds. Philosophical Transactions of the Royal Society of London B, Biological Sciences 351: 765-772.
30. Gu X, Fu Y-X, Li W-H. 1995. Maximum likelihood estimation of heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution 12: 546-557.
31. Gutell RR, Fox GE. 1988. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Research 16: 175-247.
32. Harvey PH, Pagel MD. 1991. The comparative method in evolutionary biology. Oxford: Oxford University Press.
33. Hasegawa M, Kishino K, Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
34. Hedges SB, Maxson LR. 1996. Molecules and morphology in amniote phylogeny. Molecular Phylogenetics and Evolution 6: 312-314.
35. Hillis DM, Bull JJ. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192.
36. Hillis DM, Huelsenbeck JP. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. Journal of Heredity 83: 189-195.
37. Hillis DM, Wiens JJ. 2000. Molecular versus morphological systematics: conflicts, artifacts, and misconceptions. In: Wiens JJ, ed. Phylogenetic analysis of morphological data. Washington DC: Smithsonian Institution Press, 1-19.
38. Holman JA. 1995. Pleistocene amphibians and reptiles in North America. New York: Oxford University Press.
39. Huelsenbeck JP. 1995. Performance of phylogenetic methods in simulation. Systematic Biology 44: 17-48.
40. Iverson JB. 1992. A revised checklist with distribution maps of the turtles of the world. Homestead, FL: Green Nature Books.
41. Killebrew FC. 1979. Osteological variation between Graptemys flavimaculata and Graptemys nigrinoda (Testudines: Emydidae). Herpetologica 35: 146-153.
42. Lamb T, Avise JC. 1992. Molecular and population genetic aspects of mitochondrial DNA variability in the diamond-back terrapin, Malaclemys terrapin. Journal of Heredity 83: 262-269.
43. Lamb T, Lydeard C, Walker R, Gibbons JW. 1994. Molecular systematics of the map turtles (Graptemys): a comparison of mitochondrial restriction site versus sequence data. Systematic Biology 43: 543-599.
44. Legler J. 1960. Remarks on the natural history of the Big Bend slider, Pseudemys scripta gaigeae Hartweg. Herpetologica 16: 139-140.
45. Legler J. 1990. The genus Pseudemys in Mesoamerica: taxonomy, distribution, and origins. In: Gibbons JW, ed. Life history and ecology of the slider turtle. Washington DC: Smithsonian Institution Press, 82-105.
46. Lenk P, Fritz U, Joger U, Winks M. 1999. Mitochondrial phylogeography of the European pond turtle, Emys orbicularis (Linnaeus 1758). Molecular Ecology 8: 1911-1922.
47. Lindeman PV. 2000a. Resource use of five sympatric turtle species: effects of competition, phylogeny, and morphology. Canadian Journal of Zoology 78: 992-1008.
48. Lindeman PV. 2OOOb. Evolution of the relative width of the head and alveolar surfaces in map turtles (Testudines: Emydidae: Graptemys). Biological Journal of the Linnean Society 2000: 549-576.
49. Losos JB. 1992. The evolution of convergent structure in Caribbean Anolis communities. Systematic Biology 41: 403-420.
50. Losos JB, Jackman TR, Larson A, de Quiroz K, Rodríguez-Schettino. 1998. Contingency and determinism in replicated adaptive radiations of island lizards. Science 279: 2115-2118.
51. Loveridge A, Williams EE. 1957. Revision of the African tortoises and turtles of the suborder Cryptodira. Bulletin of the Museum of Comparative Zoology Harvard 115: 163-557.
52. MacArthur RH, Pianka ER. 1966. On optimal use of a patchy environment. Evolution 100: 602-609.
53. MacArthur RH, Wilson EO. 1967. The theory of island biogeography. Princeton, NJ: Princeton University Press.
54. Maddison WP. 1991. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Systematic Zoology 40: 304-314.
55. Maddison WP. 1993. Missing data versus missing characters in phylogenetic analysis. Systematic Biology 42: 576-581.
56. Maddison WP, Maddison DR. 1992. MacClade. Version 3.0. Analysis of phylogeny and character evolution. Sunderland, MA: Sinauer Associates.
57. Martins EP. 1999. Estimation of ancestral states of continuous characters: a simulation study. Systematic Biology 48: 642-650.
58. Martins EP. 2001. COMPARE, Version 4.4. Computer programs for the statistical analysis of comparative data. Distributed by the author via http://compare.bio.indiana.edu/.DepartmentofBiology. Bloomington, IA: Indiana University.
59. McDowell SB. 1964. Partition of the genus Clemmys and related problems in the taxonomy of the aquatic Testudinidae. Proceedings of the Zoological Society of London 143: 239-279.
60. Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Systematic Biology 48: 138-152.
61. Minx P. 1996. Phylogenetic relationships among the box turties, genus Terrapene. Herpetologica 52: 584-597.
62. Morin PJ. 1999. Community ecology. Malden, MA: Blackwell Science.
63. Nosil P. 2002. Transition rates between specialization and generalization in phytophagous insects. Evolution 56: 1701-1706.
64. Pagel M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London Series B, Biological Sciences 255: 37-45.
65. Pagel M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48: 612-622.
66. Petren K, Grant BR, Grant PR. 1999. A phylogeny of Darwin's finches based on microsatellite DNA length variation. Proceedings of the Royal Society of London Series B, Biological Sciences 266: 321-330.
67. Pianka ER. 2000. Evolutionary ecology. San Francisco: Addison-Wesley Longman, Inc.
68. Poe S, Wiens JJ. 2000. Character selection and the methodology of morphological phylogenetics. In: Wiens JJ, ed. Phylogenetic analysis of morphological data. Washington DC: Smithsonian Institution Press, 20-36.
69. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
70. Posada D, Crandall KA. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50: 580-601.
71. de Queiroz A, Donoghue MJ, Kim J. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics. 26: 657-681.
72. Richman AD, Price TD. 1992. Evolution of ecological differences in the Old World leaf warblers. Nature 355: 817-820.
73. Schlichting CD, Pigliucci M. 1998. Phenotypic evolution: a reaction norm perspective. Sunderland, MA: Sinauer Associates.
74. Schluter D. 1996. Adaptive radiation along genetic lines of least resistance. Evolution 50: 1766-1774.
75. Schluter D. 2000. The ecology of adaptive radiation. Oxford, NY: Oxford University Press.
76. Schluter D, Price T, Mooers AØ, Ludwig D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
77. Schoener TW. 1974. Temporal resource partitioning and the compression hypothesis. Proceedings of the National Academy of Sciences USA 71: 4169-4172.
78. Seidel ME. 1981. A taxonomic analysis of pseudemyd turtles (Testudines: Emydidae) from the New River, and phenetic relationships in the subgenus Pseudemys. Brimleyana 6: 25-44.
79. Seidel ME. 1988. Revision of the West Indian emydid turtles (Testudines). American Museum Novitates 2918: 1-41.
80. Seidel ME. 1994. Morphometric analysis of cooter and red-bellied turtles in the North American genus Pseudemys (Emydidae). Chelonian Conservation Biology 1: 117-130.
81. Seidel ME. 2002. Taxonomic observations on extant species and subspecies of slider turtles, genus Trachemys. Journal of Herpetology 36: 285-292.
82. Seidel ME, Adkins MD. 1987. Biochemical comparisons among West Indian Trachemys (Emydidae: Testudines). Copeia 1987: 485-489.
83. Seidel ME, Fritz U. 1997. Courtship behavior provides additional evidence for a monophyletic Pseudemys, and comments on Mesoamerican Trachemys (Testudines: Emydidae). Herpetological Review 28: 70-72.
84. Seidel ME, Inchaustegui Miranda J. 1984. Status of the trachemyd turtles (Testudines: Emydidae) on Hispaniola. Journal of Herpetology 18: 468-479.
85. Seidel ME, Palmer WM. 1991. Morphological variation in turtles of the genus Pseudemys (Testudines: Emydidae) from central Atlantic drainages. Brimleyana 17: 105-135.
86. Shaffer HB, Meylan P, McKnight ML. 1997. Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Systematic Biology 46: 235-268.
87. Smith HM, Smith RB. 1979. Synopsis of the herpetofauna of Mexico, 6: guide to Mexican Turtles. Bibliographic addendum III. North Bennington, VT: John Johnson.
88. Stephens PR, Wiens JJ. 2003. Explaining species richness from continents to communities: the time-for-speciation-effect in emydid turtles. American Naturalist 161: 112-128.
89. Streelman JT, Alfaro ME, Westneat MW, Bellwood DR, Karl SA. 2002. Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution 56: 961-971.
90. Swofford DL. 2001. PAUP*: phylogenetic analysis using parsimony (* and other methods), Version 4.0b1. Sunderland, MA: Sinauer Associates.
91. Thiele K. 1993. The holy grail of the perfect character: the cladistic treatment of morphometric data. Cladistics 9: 275-304.
92. Thompson JN. 1994. The coevolutionary process. Chicago: University of Chicago Press.
93. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
94. Tilman D. 1997. Mechanisms of plant competition. In: Crawley MJ, ed. Plant ecology. Malden, MA: Blackwell Science, 239-261.
95. Tinkle DW. 1962. Variation in shell morphology of North American turtles I. The carapacial seam arrangements. Tulane Studies in Zoology 9: 331-349.
96. Ultsch GR, Ward GM, LeBerte CM, Kuhajda BR, Stewart ER. 2001. Intergradation and origins of subspecies of the turtle Chrysemys picta: morphological comparisons. Canadian Journal of Zoology 79: 485-498.
97. Vanzolini PE. 1995. A new species of turtle, genus Trachemys, from the state of Maranhão, Brazil (Testudines, Emydidae). Revista Brasileira de Biologia 55: 111-125.
98. Vogt RC, Guzman SG. 1988. Food partitioning in a neotropical freshwater turtle community. Copeia 1988: 37-47.
99. Wainwright PC, Reilly SM, eds. .1994. Ecological morphology: integrative organismal biology. Chicago: University of Chicago Press.
100. Ward JP. 1980. Comparative cranial morphology of the freshwater turtle subfamily Emydinae, an analysis of the feeding mechanisms and the systematics. Unpublished PhD Dissertation, Raleigh, NC: North Carolina State University.
101. Ward JP. 1984. Relationships of chrysemyd turtles of North America (Testudines: Emydidae). Special Publications of the Museum Texas Tech University 21: 1-50.
102. Wiens JJ. 1995. Polymorphic characters in phylogenetic systematics. Systematic Biology 44: 482-500.
103. Wiens JJ. 1998a. Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47: 625-640.
104. Wiens JJ. 1998b. Testing phylogenetic methods with tree congruence: phylogenetic analysis of polymorphic morphological characters in phrynosomatid lizards. Systematic Biology 47: 411-428.
105. Wiens JJ. 1998c. Combining data sets with different phylogenetic histories. Systematic Biology 47: 568-581.
106. Wiens JJ. 1999. Polymorphism in systematics and comparative biology. Annual Review of Ecology and Systematics 30: 327-362.
107. Wiens JJ. 2001. Character analysis in morphological phylogenetics: problems and solutions. Systematic Biology 50: 689-699.
108. Wiens JJ. 2003a. Missing data, incomplete data, and phylogenetic accuracy. Systematic Biology 52: in press.
109. Wiens JJ. 2003b. Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem? Journal of Vertebrate Paleontology 23: 297-310.
110. Wiens JJ, Hollingsworth BD. 2000. War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Systematic Biology 49: 143-159.
111. Wiens JJ, Morris MR. 1996. Character definitions, sexual selection, and the evolution of swordtails. American Naturalist 147: 866-869.
112. Wiens JJ, Reeder TW. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Systematic Biology 44: 548-558.
113. Wiens JJ, Reeder TW. 1997. Phylogeny of the spiny lizards (Sceloporus) based on molecular and morphological evidence. Herpetological Monographs 11: 1-101.
114. Wiens JJ, Reeder TW, Nieto Montes de Oca A. 1999. Molecular phylogenetics and evolution of sexual dichromatism among populations of the Yarrow's spiny lizard (Sceloporus jarrovii). Evolution 53: 1884-1897.
115. Wiens JJ, Servedio MR. 1997. Accuracy of phylogenetic analysis including and excluding polymorphic characters. Systematic Biology 46: 332-345.
116. Wiens JJ, Servedio MR. 1998. Phylogenetic analysis and intraspecific variation: performance of parsimony, distance, and likelihood methods. Systematic Biology 47: 228-253.
117. Wilgenbusch J, de Queiroz K. 2000. Phylogenetic relationships among phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612.
118. Wilkinson M. 1995. A comparison of two methods of character construction. Cladistics 11: 297-308.
119. Williams EE. 1972. The origin of faunas: evolution of lizard congeners in a complex island fauna - a trial analysis. Evolutionary Biology 6: 47-89.
120. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39: 306-314.
121. Zangerl R. 1969. The turtle shell. In: Gans C, Bellairs A d'A, Parsons TS, eds. Biology of the Reptilia, Vol. 1: morphology A. London: Academic Press, 311-339.
122. Zug GR. 1966. The penial morphology and the relationships of cryptodiran turtles. Occasional Papers of the Museum of Zoology of the University of Michigan 647: 1-24.