Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama

Molecular Biology and Evolution

Volumn 19, Issue 11, 2002, Pages 2005-2021

  Marko, Peter B ^a  

^a SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^b NATURAL HISTORY MUSEUM OF LOS ANGELES COUNTY   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Bivalves; Calibration; Cytochrome oxidase 1; Fossil record; Histone 3; Molecular clock; Molluscs; Speciation dates; Substitution models

Indexed keywords

CYTOCHROME C OXIDASE; HISTONE H3; HISTONE;

ARCA IMBRICATA; ARCA MUTABILIS; ARTICLE; ATLANTIC OCEAN; BIODIVERSITY; CALIBRATION; ECOLOGICAL SPECIALIZATION; FOSSIL; GENETIC VARIABILITY; GEOLOGICAL TIME; HYPOTHESIS; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PANAMA; SPECIES DIFFERENTIATION; TAXONOMIC IDENTIFICATION; ANIMAL; CLASSIFICATION; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; MOLLUSC; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL; TIME;

ARCA IMBRICATA; ARCA MUTABILIS; ARCIDAE; BIVALVIA; ISTHMIA; MOLLUSCA;

ANIMALS; BASE SEQUENCE; CALIBRATION; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; FOSSILS; HISTONES; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; MOLLUSCA; PANAMA; PHYLOGENY; SPECIES SPECIFICITY; TIME FACTORS;

EID: 0036854283     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004024     Document Type: Article

References (106)

1. Abbott, R. T. 1974. American Seashells. 2nd Edition. Van Nostrand Reinhold Co., New York.
2. Arctander, P. 1995. Comparison of a mitochondrial gene and a corresponding nuclear pseudogene. Proc. R. Soc. Lond. Ser. B Biol. Sci. 262:13-19.
3. Baldwin, J. D., A. L. Bass, B. W. Bowen, and W. H. Clark. 1998. Molecular phylogeny and biogeography of the marine shrimp Penaeus. Mol. Phylogenet. Evol. 10:399-407.
4. Barber, P. H., S. R. Palumbi, M. V. Erdmann, and M. K. Moosa. 2000. Biogeography: A marine Wallace's line? Nature 406:692-693.
5. Bartsch, P. 1931. The West American mollusks of the genus Acar. U.S. Nat. Mus. Proc. 80:1-4.
6. Bermingham, E., and H. A. Lessios. 1993. Rate variation of proteins and mitochondrial DNA evolution as revealed by sea urchins separated by the Isthmus of Panama. Proc. Natl. Acad. Sci. USA 90:2734-2738.
7. Bermingham, E., S. S. McCafferty, and A. P. Martin. 1997. Fish biogeography and molecular clocks: Perspectives from the Panamanian Isthmus. Pp. 113-128 in T. D. Kocher and C. A. Stepien, eds. Molecular Systematics of Fishes. Academic Press, New York.
8. Beu, A. G. 2001. Gradual Miocene to Pleistocene uplift of the Central American Isthmus: Evidence from tropical American tonnoidean gastropods. J. Paleontol. 75:706-720.
9. Buckley, T. R., C. Simon, and G. K. Chambers. 2001. Exploring among-site variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50:67-86.
10. Burton, R. S. 1998. Intraspecific phylogeography across the Point Conception biogeographic boundary. Evolution 52:734-745.
11. Burton, R. S., and B.-N. Lee. 1994. Nuclear and mitochondrial gene geneaologies amd allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proc. Natl. Acad. Sci. USA 91:5197-5201.
12. Chenoweth, S. F., J. M. Hughes, C. P. Keenan, and S. Lavery. 1998. When oceans meet: A teleost shows secondary intergradation at an Indian-Pacific interface. Proc. R. Soc. Lond. Ser. B Biol. Sci. 265:415-420.
13. Coates, A. G., and J. A. Obando. 1996. The geologic evolution of the Central American isthmus. Pp. 21-56 in J. B. C. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and Environment in Tropical America. University of Chicago Press, Chicago.
14. Collins, L. S. 1996. Environmental changes in Caribbean shallow waters relative to the closing tropical American seaway. Pp. 130-167 in J. B. C. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and Environment in Tropical America. University of Chicago Press, Chicago.
15. Collins, T. M. 1989. Rates of Mitochondrial DNA Evolution in Transisthmian Geminate Species. Doctoral dissertation, Yale University, New Haven, Conn.
16. Collins, T. M. 1996. Molecular comparisons of transisthmian species pairs: Rates and patterns of evolution. Pp. 303-334 in J. B. C. Jackson, A. E Budd, and A. G. Coates, eds. Evolution and Environment in Tropical America. University of Chicago Press, Chicago.
17. Collins, T. M., K. Frazer, A. R. Palmer, G. J. Vermeij, and W. M. Brown. 1996. Evolutionary history of northern hemisphere Nucella (Gastropoda, Muricidae): Molecules, ecology, and fossils. Evolution 50:2287-2304.
18. Conrad, T. A. 1869. Descriptions of new fossil Mollusca, principally Cretaceous. Am. J. Conchol. 5:96-103.
19. -. 1870. Notes on recent and fossil shells, with descriptions of new species. Am. J. Conchol. 6:71-78.
20. Cox, L. R. et al. 1969. Superfamily arcacea lamarck, 1809. Pp. 250-264 in L. R. Cox, N. D. Newell, D. W. Boyd, et al., eds. Treatise on Invertebrate Zoology, Part N. Vol. 1. Mollusca, Bivalvia. The Geological Society of America, Boulder, Colo., and the University of Kansas, Lawrence.
21. Cunningham, C. W., and T. M. Collins. 1994. Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates. Pp. 406-433 in B. Schierwater, B. Streit, G. P. Wagner, and R. Desalle, eds. Molecular Ecology and Evolution: Approaches and Applications. Birkhauser Verlag, Basel, Switzerland.
22. Distel, D. L. 2000. Phylogenetic relationships among Mytilidae (Bivalvia): 18S rRNA data suggest convergence in mytilid body plans. Mol. Phylogenet. Evol. 15:25-33.
23. Donaldson, K. A., and R. R. Wilson. 1999. Amphi-panamic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA central region of fishes. Mol. Phylogenet. Evol. 13:208-213.
24. Duffy, J. E. 1996. Resource-associated population subdivision in a symbiotic coral-reef shrimp. Evolution 50:360-373.
25. Duque-Caro, H. 1990a. The Choco Block in the northwestern corner of South America: Structural, tectonostratigraphic, and paleogeographic implications. J. S. Am. Earth Sci. 3:71-84.
26. -. 1990b. Neogene stratigraphy, palaeoceanography, and palaeobiology in northwest South America and the evolution of the Panama seaway. Palaeogeogr. Palaeoclimatol. Palaeoecol. 777:203-234.
27. Eames, F. E. 1967. A new arcid species from Holland. Proc. Malacol. Soc. Lond. 34:299-302.
28. Edwards, S., and P. Beerli. 2000. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
29. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 32:79-81.
30. -. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
31. Folmer, O., M. Black, W. Hoeh, R. Lutz, and R. Vrijen-Hoek. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotech. 3:294-299.
32. Gorman, G. C., Y. J. Kim, and R. Rubinoff. 1976. Genetic relationships of three species of Bathygobius from the Atlantic and Pacific sides of Panama. Copeia 361-364.
33. Hart, M. W., M. Byrne, and M. J. Smith. 1997. Analysis of life-history evolution in Asterinid starfish. Evolution 55:1848-1861.
34. Hellberg, M. E. 1998. Sympatric sea shells along the sea's shore: The geography of speciation in the marine gastropod Tegula. Evolution 52:1311-1324.
35. Hellberg, M. E., G. W. Moy, and V. D. Vacquier. 2000. Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein. Mol. Biol. Evol. 17:458-466.
36. Hellberg, M. E., and V. D. Vacquier. 1999. Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. Mol. Biol. Evol. 16:839-848.
37. Hickerson, M. J., and J. R. P. Ross. 2001. Post-glacial population history and genetic structure of the northern clingfish (Gobbiesox maeandricus), revealed from mtDNA analysis. Mar. Biol. 138:407-419.
38. Hickman, C. S., and J. H. McLean. 1990. Systematic revision and suprageneric classification of trochacean gastropods. Nat. Hist. Mus. Los Angel. Cty. Sci. Ser. 35:1-169.
39. Hillis, D. M., B. K. Mable, and C. Moritz. 1996. Applications of molecular systematics. Pp. 515-530 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular Systematics. Sinauer Associates, Sunderland, Mass.
40. Huelsenbeck, J. P., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
41. Jackson, J. B. C., P. Jung, A. G. Coates, and L. S. Collins. 1993. Diversity and extinction of tropical American mollusks and emergence of the Isthmus of Panama. Science 260:1624-1626.
42. Jackson, J. B. C., P. Jung, and H. Fortunato. 1996. Paciphilia revisited: Transisthmian evolution of the Strombina group (Gastropoda: Columbellidae). Pp. 234-270 in J. B. C. Jackson, A. F. Budd, and A. G. Coates, eds. Evolution and Environment in Tropical America. University of Chicago Press, Chicago.
43. Jordan, D. S. 1908. The law of geminate species. Am. Nat. 42:73-80.
44. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-123 in H. N. Munro, ed. Mammalian Protein Metabolism. Academic Press, New York.
45. Keen, A. M. 1974. Sea Shells of Tropical West America. Stanford University Press, Stanford, Calif.
46. Keigwin, L. D. 1982. Isotopic paleooceanography of the Caribbean and east Pacific: Role of Panama uplift in late Neogene time. Science 217:350-352.
47. Kimura, M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78:454-458.
48. Knowlton, N. 1993. Sibling species in the sea. Annu. Rev. Ecol. Syst. 24:189-216.
49. Knowlton, N., and L. A. Weigt. 1998. New dates and new rates for divergence across the Isthmus of Panama. Proc. R. Soc. Lond. Ser. B Biol. Sci. 265:2257-2263.
50. Knowlton, N., L. A. Weigt, L. A. Solorzano, D. K. Mills, and E. Bermingham. 1993. Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panama. Science 260:1629-1632.
51. Lee, M. S. Y. 1999. Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 49:385-391.
52. Lopez, J., M. Culver, J. C. Stevens, W. E. Johnson, and S. J. O'Brien. 1997. Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol. Biol. Evol. 14:277-286.
53. Lessios, H. 1979. Use of Panamanian sea urchins to test the molecular clock. Nature 280:599-601.
54. Lessios, H. A. 1998. The first stage of speciation as seen in organisms separated by the Isthmus of Panama. Pp. 186-201 in D. Howard and S. Berlocher, eds. Endless Forms: Species and Speciation. Oxford University Press, Oxford.
55. Lessios, H. A., B. D. Kessing, and J. S. Pearse. 2001. Population structure and speciation in tropical seas: Global phylogeography of the sea urchin Diadema. Evolution 55:955-975.
56. 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.
57. Marko, P. B. 1998. Historical allopatry and the biogeography of speciation in the prosobranch snail genus Nucella. Evolution 52:757-774.
58. Marko, P. B., and A. L. Moran. 2002. Correlated evolutionary divergence of egg size and a mitochondrial protein across the Isthmus of Panama. Evolution 56:1303-1309.
59. Marko, P. B., and J. B. C. Jackson. 2001. Patterns of morphological diversity among and within arcid bivalve species pairs separated by the Isthmus of Panama. J. Paleontol. 75:590-606.
60. Marshall, L. G. 1985. Geochronology and land-mammal biochronology of the transamerican faunal interchange. Pp. 49-85 in E G. Stehli and S. D. Webb, eds. The Great American Biotic Interchange. Plenum Press, New York.
61. Marshall, L. G., R. F. Butler, R. E. Drake, G. H. Curtis, and R. H. Telford. 1979. Calibration of the great American interchange. Science 204:272-279.
62. Martin, A. P., G. J. P. Naylor, and S. R. Palumbi. 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357:153-155.
63. Metz, E. C., G. Gomez-Guitierrez, and V. D. Vacquier. 1998. Mitochondrial DNA and bindin gene sequence evolution among allopatric species of the sea urchin genus Arbacia. Mol. Biol. Evol. 15:185-195.
64. Miya, M., and M. Nishida. 1997. Speciation in the open sea. Nature 389:803-804.
65. Nei, M., and W.-H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
66. Nelson, E. T. 1870. On the molluscan fauna of the later Tertiary of Peru. Trans. Conn. Acad. Sci. 2:186-206.
67. Noda, H. 1966. The Cenozoic Arcidae of Japan. Sci. Rep. Tokohu Univ. 2nd Ser. 38:1-161.
68. -. 1986. Origin and migration of Anadara, especially the genus Hawaiarca (Bivalvia). Palaeont. Soc. Jpn. Spec. Pub. 29:57-76.
69. -. 1991. Biogeographic distribution of the genus Anadara (Mollusca: Bivalvia). Saito Ho-on Kai Spec. Pub. 3:283-293.
70. Olsson, A. A. 1961. Molluscs of the Tropical Eastern Pacific, Particularly from the Southern Half of the Panamic-Pacific Faunal Province (Panama to Peru). Panamic-Pacific Pelecypoda. Paleontological Research Institution, Ithaca, NY.
71. Palumbi, S. R. 1994. Genetic divergence, reproductive isolation, and marine speciation. Annu. Rev. Ecol. Syst. 25:547-572.
72. -. 1996. What can molecular genetics contribute to marine biogeography? An urchin's tale. J. Exp. Mar. Biol. Ecol. 203:75-92.
73. Palumbi, S. R., G. Grabowsky, T. Duda, L. Geyer, and N. Tachino. 1997. Speciation and population genetic structure in tropical Pacific sea urchins. Evolution 51:1506-1517.
74. Petuch, E. J. 1981. A relict Neogene caenogastropod fauna from northern South America. Malacologia 20:307-347.
75. Posada, D., and K. A. Crandall. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
76. -. 2001. Selecting models of nucleotide substitution: An application to the human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 18:897-906.
77. Quinteiro, J., R. Vidal, and M. Rey-Mendez. 2000. Phylogeny and biogeographic history of hake (genus Merluccius), inferred from mitochondrial DNA control-region sequences. Mar. Biol. 136:163-174.
78. Reinhart, P. W. 1935. Classification of the pelecypod family Arcidae. Mus. R. d'Hist. Nat. Belgiq. Bull. 11:1-68.
79. -. 1937. Three new species of the pelecypod family Arcidae from the Pliocene of California. J. Paleontol. 11:181-185.
80. -. 1943. Mesozoic and Cenozoic Arcidae from the Pacific slope of North America. Geol. Soc. Am. Spec. Pap. 47:1-117.
81. Richards, H. G. 1958. Cretaceous pelecypoda of New Jersey. Pp. 59-266 in H. G. Richards, ed. The Cretaceous Fossils of New Jersey. Department of Conservation and Economic Development, New Jersey Geological Survey, Trenton, NJ.
82. Rodriguez, F., J. F. Oliver, A. Marin, and J. R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
83. Roopnarine, P. D. 2001. A history of diversification, extinction, and invasion in tropical America as derived from species-level phylogenies of chionine genera (Family Veneridae). J. Paleontol. 75:644-657.
84. Schneider, J. A. 1995. Phylogenetic relationships of transisthmian Cardiidae (Bivalvia) and the use of fossils in reinterpretting the geminate species concept. Geol. Soc. Am. Abstr. Prog. 27(6):A-52.
85. Schubart, C. D., R. Diesel, and S. B. Hedges. 1998. Rapid evolution to terrestrial life in Jamaican crabs. Nature 393:363-365.
86. Sheldon, P. G. 1917. The Atlantic slope Arcas. Paleontogr. Am. 1:1-101.
87. Spieker, E. M. 1922. The palaeontology of the Zorritos formation of the North Peruvian oil fields. Johns Hopkins Univ. Stud. Geol. 3:1-177.
88. Stanley, S. M. 1986. Anatomy of a regional mass extinction: Plio-Pleistocene decimation of the western Atlantic bivalve fauna. Palaios 1:17-36.
89. Stephenson, W. L. 1923. The Cretaceous formations of North Carolina. N. C. Geol. Econ. Surv. 5:1-389.
90. Stillman, J. H., and C. A. Reeb. 2001. Molecular phylogeny of eastern Pacific porcelain crabs, genera Petrolisthes and Pachycheles, based on the mtDNA 16S rDNA sequence: Phylogeographic and systematic implications. Mol. Phylogenet. Evol. 19:236-245.
91. Sturmbauer, C., J. S. Levinton, and J. Christy. 1996. Molecular phylogenetic analysis of fiddler crabs: Test of the hypothesis of increasing behavioral complexity in evolution. Proc. Natl. Acad. Sci. USA 93:10855-10857.
92. Sunnucks, P. D., and F. Hales. 1996. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol. Biol. Evol. 13:510-524.
93. Swofford, D. L. 2001. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Mass.
94. Tringali, M. D., T. M. Bert, S. Seifu, E. Bermingham, and D. Bartolacci. 1999. Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae). Mol. Phylogenet. Evol. 13:193-207.
95. Van Oppen, M. J. H., B. L. Willis, and D. J. Miller. 1999. Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proc. R. Soc. Lond. Ser. B Biol. Sci. 266:179-183.
96. Vawter, A. T., R. Rosenblatt, and G. C. Gorman. 1980. Genetic divergence among fishes of the eastern Pacific and the Caribbean: Support for the molecular clock. Evolution 34:705-711.
97. Vermeij, G. J. 1978. Biogeography and Adaptation. Harvard University Press, Cambridge, Mass.
98. -. 2001. Distribution, history, and taxonomy of the Thais clade (Gastropoda: Muricidae) in the Neogene of tropical America. J. Paleontol. 75:697-705.
99. Vermeij, G. J., and E. J. Petuch. 1986. Differential extinction in tropical American molluscs: Endemism, architecture, and the Panama land bridge. Malacologia 17:29-41.
100. Vokes, H. E. 1946. The pelecypod fauna of the "Olive locality" (Aptian) at Abeih. Bull. Am. Nat. Hist. 87:141-215.
101. Wares, J. P. 2001. Patterns of speciation inferred from mitochondrial DNA in North American Cthamalus (Cirripedia: Balanomorpha: Cthamaloidea). Mol. Phylogenet. Evol. 18:104-116.
102. Webb, S. D. 1985. Late Cenozoic mammal dispersals between the Americas. Pp. 357-386 in F. G. Stehli and S. D. Webb, eds. The Great American Biotic Interchange. Plenum Press, New York.
103. Whitfield, R. P. 1891. Observations on some Cretaceous fossils from the Beyrut district of Syria, in the collections of the American Museum of Natural History. Bull. Am. Nat. Hist. 3:381-441.
104. Williams, S. T., and N. Knowlton. 2001. Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol. Biol. Evol. 18:1484-1493.
105. Yang, Z. 1999. Performance of likelihood ratio tests of evolutonary hypotheses under inadequate substitution models. Mol. Biol. Evol. 16:868-875.
106. Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.