Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea)

Molecular Phylogenetics and Evolution

Volumn 48, Issue 1, 2008, Pages 157-167

  Tinn, Oive ^a   Oakley, Todd H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Divergence times; Evolutionary rates; Fossils; Molecular clock; Ostracoda

Indexed keywords

RIBOSOME DNA; RNA 18S;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; CRUSTACEA; EVOLUTION; FOSSIL; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY;

ANIMALS; CRUSTACEA; DNA, RIBOSOMAL; EVOLUTION; EVOLUTION, MOLECULAR; FOSSILS; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 18S;

CRUSTACEA; HALOCYPRIDA; MANAWA STACEYI; METAZOA; OSTRACODA;

EID: 44949217356     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.03.001     Document Type: Article

References (103)

1. Adamczak F. On kloedenellids and cytherellids (Ostracoda Platycopa) from the Silurian of Gotland. Stockholm Contrib. Geol. 15 (1966) 7-21
2. Akaike, H., 1973. Information theory and an extension of the maximum likelihood principle. Proc. 2nd Int. Symp. Information Theory, Suppl. Problems of Control and Information Theory 267-281.
3. Alroy J. The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. Syst. Biol. 48 (1999) 107-118
4. Angel M.V. The diel migrations and distributions within a mesopelagic community in the Northeast Atlantic 3. Planktonic Ostracods a stable component in the community. Prog. Oceanogr. 13 (1984) 319-352
5. Apostolescu V. Ostracodes du Lias du Bassin de Paris. Rev. Inst. Fran. Petrol. Ann. Combust. Liquides 14 (1959) 795-826
6. Avise J.C., and Johns G.C. Proposal for a standardized temporal scheme of biological classification for extant species. Proc. Natl. Acad. Sci. USA 96 (1999) 7358-7363
7. Bate R.H., and Sheppard L.M. The shell structure of Halocypris inflata (Dana, 1849). In: Bate R.H., Robinson E., Sheppard L.M., and Donovan D.T. (Eds). Fossil and Recent Ostracoda (1982), Ellis Horwood, Chichester 25-50
8. Bell C.D., and Donoghue M.J. Dating the dipsacales: comparing models, genes, and evolutionary implications. Am. J. Bot. 92 (2005) 284-296
9. Bell C.D., Soltis D.E., and Soltis P.S. The age of the angiosperms: a molecular timescale without a clock. Evol. Int. J. Org. Evol. 59 (2005) 1245-1258
10. In: Benton M.J. (Ed). The Fossil Record 2 (1993), Chapman and Hall, London
11. Benton M.J., and Ayala F.J. Dating the tree of life. Science 300 (2003) 1698-1700
12. Benton M.J., and Donoghue P.C. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24 (2007) 26-53
13. Britton T. Estimating divergence times in phylogenetic trees without a molecular clock. Syst. Biol. 54 (2005) 500-507
14. Britton, T., Anderson, C.L., Jaquet, D., Lundquist, S., Bremer, K., 2006. PATHd8 - a new method for estimating divergence times in large phylogenetic trees without a molecular clock. Available at http://www.math.su.se/PATHd8.
15. Britton T., Oxelman B., Vinnersten A., and Bremer K. Phylogenetic dating with confidence intervals using mean path lengths. Mol. Phylogenet. Evol. 24 (2002) 58-65
16. Bromham L., and Penny D. The modern molecular clock. Nat. Rev. Genet. 4 (2003) 216-224
17. Bromham L.D., and Hendy M.D. Can fast early rates reconcile molecular dates with the Cambrian explosion?. Proc. Roy. Soc. Biol. Sci. 267 (2000) 1041-1047
18. Butler G., and Grundel J. Die Ostracoden des Unteren Keupers im Berich des Thuringer Beckens. Bull. Inst. Roy. Sci. Nat. Belgique (Sci. Terre), Ser. C 164 (1963) 33-92
19. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
20. Cohen A., and Morin J.G. Sexual morphology, reproduction and the evolution of bioluminescence in Ostracoda. Paleontol. Soc. Papers 9 (2003) 37-69
21. de Vargas C., Zaninetti L., Hilbrecht H., and Pawlowski J. Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record. J. Mol. Evol. 45 (1997) 285-294
22. Donoghue P.C., and Benton M.J. Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 22 (2007) 424-431
23. Eagar S.H. Myodocopid ostracods from New Zealand collected with a light trap. In: Riha J. (Ed). Ostracoda and Biostratigraphy (1995), Balkema, Rotterdam 399-406
24. Eldredge N., and Gould S.J. Punctuated equilibria: an alternative to phyletic gradualism. In: Schopf T.M. (Ed). Models in Paleobiology (1972), Freeman Cooper, San Francisco 82-115
25. Foote M. The evolution of morphological diversity. Annu. Rev. Ecol. Syst. 28 (1997) 129-152
26. Foote M., and Sepkoski Jr. J.J. Absolute measures of the completeness of the fossil record. Nature 398 (1999) 415-417
27. Gabbott S.E., Siveter D.J., Aldridge R.J., and Theron J.N. The earliest myodocopes: ostracodes from the late Ordovician Soom Shale Lagerstatte of South Africa. Lethaia 36 (2003) 151-160
28. Gillooly J.F., Allen A.P., West G.B., and Brown J.H. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl. Acad. Sci. USA 102 (2005) 140-145
29. Gould S. The Structure of Evolutionary Theory (2002), Belknap Press of Harvard University Press, Cambridge, MA
30. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
31. Herrig E. Vier neue Ostrakoden-Arten aus der Ruegener Schreibkreide (Untermaastricht). Geologie 13 (1964) 1004-1012
32. Higgins D.G., Bleasby A.J., and Fuchs R. CLUSTAL V: Improved software for multiple sequence alignment. Comput. Appl. Biosci. 8 (1992) 189-191
33. Horne D.J., Cohen A.C., and Martens K. Taxonomy, morphology and biology of quaternary and living Ostracoda. In: Holmes J.A., and Chivas A.R. (Eds). The Ostracoda: Applications in Quarternary Research (2002), American Geophysical Union, Washington, DC 5-36
34. Horne D.J., Schon I., Smith R.J., and Martens K. What are Ostracoda? A cladistic analysis of the extant super-families of the subclasses Myodocopa and Podocopa (Crustacea: Ostracoda). In: Koenemann S., and Jenner R.A. (Eds). Crustacea and Arthropod Relationships (2005), Taylor and Francis, Boca Raton
35. Hornibrook N. The New Zealand ostracode family Punciidae. Micropaleontology 9 (1963) 318-320
36. International Commission of Stratigraphy, 2004. Available from .
37. Jaanusson V. Functional morphology of the shell in platycope ostracodes: a study of arrested evolution. Lethaia 18 (1985) 73-84
38. Kidwell S.M. Shell composition has no net impact on large-scale evolutionary patterns in mollusks. Science 307 (2005) 914-917
39. Kornicker L.S. Antarctic and Subantarctic myodocopina (Ostracoda) (1993), Koeltz Scientific Books, Koenigstein
40. Kornicker L.S., and Sohn I.G. Myodocopid Ostracoda from the late Permian of Greece and a basic classification for Paleozoic and Mesozoic myodocopida. Smithsonian Contrib. Paleobiol. 91 (2000) 33
41. Langley C.H., and Fitch W.M. An examination of the constancy of the rate of molecular evolution. J. Mol. Evol. 3 (1974) 161-177
42. Lee M.S. Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 49 (1999) 385-391
43. Lidgard, S., Liow, L.H., In press. Life in the slow lane: prolonged stasis and related concepts from genes to the geologic record. Biol. Rev.
44. Lyubimova P.S. Ostracoda of the Middle Mesozoic formations of the of the central Volga area and the Oshshego Sirta. Trudy VNIGRI 84 (1955) 1-189
45. Maddocks R.F. Living and fossil Macrocyprididae (Ostracoda). Univ. Kansas Paleontol. Contrib. Monogr. 2 (1990) 1-404
46. Magallon S.A., and Sanderson M.J. Angiosperm divergence times: the effect of genes, codon positions, and time constraints. Evol. Int. J. Org. Evol. 59 (2005) 1653-1670
47. Mallatt J.M., Garey J.R., and Shultz J.W. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31 (2004) 178-191
48. Martin A.P., and Palumbi S.R. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90 (1993) 4087-4091
49. Martin G.P.R. Cetacella, eine neue Ostracoden Gattung aus dem Kimmeridge Nordwest-deutschlands. Palaeontol. Z. 32 (1958) 190-196
50. Martin J.W., and Davis G.E. An updated classification of the recent Crustacea. Natural history museum of Los Angeles County. Sci. Ser. 39 (2001) 1-124
51. Moreau C.S., Bell C.D., Vila R., Archibald S.B., and Pierce N.E. Phylogeny of the ants: diversification in the age of angiosperms. Science 312 (2006) 101-104
52. Near T.J., Meylan P.A., and Shaffer H.B. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 165 (2005) 137-146
53. Oakley T.H. Myodocopa (Crustacea:Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism. Hydrobiologia 538 (2005) 179-192
54. Oakley T.H., and Cunningham C.W. Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proc. Natl. Acad. Sci. USA 99 (2002) 1426-1430
55. Park L.E., Martens K., and Cohen A.S. Phylogenetic relationships of Gomphocythere (Ostracoda) in Lake Tanganyika, East Africa. J. Crustacean Biol. 22 (2002) 15-27
56. Perez-Losada M., Hoeg J.T., and Crandall K.A. Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Syst. Biol. 53 (2004) 244-264
57. Pisani D., Poling L.L., Lyons-Weiler M., and Hedges S.B. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2 (2004) 1
58. Pokorny V. Ostracodes. In: Haq B.U., and Boersma A. (Eds). Introduction to Marine Micropaleontology (1998), Elsevier 109-149
59. Pond S.L., Frost S.D., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
60. Porter M.L., Perez-Losada M., and Crandall K.A. Model-based multi-lsocus estimation of decapod phylogeny and divergence times. Mol. Phylogenet. Evol. 37 (2005) 355-369
61. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
62. Pulquerio M.J., and Nichols R.A. Dates from the molecular clock: how wrong can we be?. Trends Ecol. Evol. 22 (2007) 180-184
63. Rambaut A., and Drummond A. Tracer. MCMC Trace Analysis Tool (2003), University of Oxford, Oxford
64. Roe H.S.J. Observations on the diurnal vertical migrations of an ocean animal community. Mar. Biol. 28 (1974) 99-113
65. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
66. Rutschmann F., Eriksson T., Salim K.A., and Conti E. Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points. Syst. Biol. 56 (2007) 591-608
67. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
68. Sanderson M.J. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19 (2003) 301-302
69. Schallreuter R. Zwei weitere ordovizische Cytheracea; Ostracoda, Podocopida. Two more Ordovician Cytheracea; Ostracoda, Podocopida. Neues Jahrb. Geol. P.A. 9 (1978) 567-576
70. Schneider H., Schuettpelz E., Pryer K.M., Cranfill R., Magallon S., and Lupia R. Ferns diversified in the shadow of angiosperms. Nature 428 (2004) 553-557
71. Schoen I., Martens K., Van Doninck K., and Butlin K.R. Evolution in the slow lane: molecular rates of evolution in sexual and asexual ostracods (Crustacea: Ostracoda). Biol. J. Linn. Soc. 79 (2003) 93-100
72. Schon I., and Martens K. No slave to sex. Proc. Roy. Soc. Biol. Sci. 270 (2003) 827-833
73. Schram F.R. Crustacea (1986), Oxford University Press, New York
74. Shneider G. K sistematike iskopaemoi presnovodnoi fauny ostrakod. Doklady Akad. Nauk SSSR 62 (1948) 137-139
75. Simpson G.G. Tempo and Mode in Evolution (1944), Columbia University Press, New York
76. Siveter D.J., Sutton M.D., and Briggs D.E. An ostracode crustacean with soft parts from the Lower Silurian. Science 302 (2003) 1749-1751
77. Siveter D.J., Williams M., and Waloszek D. A phosphatocopid crustacean with appendages from the Lower Cambrian. Science 293 (2001) 479-481
78. Smith A.B., Lafay B., and Christen R. Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 338 (1992) 365-382
79. Smith A.B., and Peterson K.J. Dating the time of origin of major clades: molecular clocks and the fossil record. Annu. Rev. Earth Planet. Sci. 30 (2002) 65-88
80. Smith A.B., Pisani D., Mackenzie-Dodds J.A., Stockley B., Webster B.L., and Littlewood D.T.J. Testing the molecular clock: molecular and Paleontological estimates of divergence times in the Echinoidea (Echinodermata). Mol. Biol. Evol. 23 (2006) 1832-1851
81. Sohn I.G. Latest mississippian (Namurian A) nonmarine ostracodes from West Virginia and Virginia. J. Paleontol. 59 (1985) 446-460
82. Sohn I.G., and Swain F.M. On the superfamily Darwinuloidacea, the type species of Darwinuloidea Mandelstam, 1956, and on the status of Cheikella Sohn and Morris, 1963 (Ostracoda). J. Paleontol. 73 (1999) 159-160
83. Stajich J.E., Block D., Boulez K., Brenner S.E., Chervitz S.A., Dagdigian C., Fuellen G., Gilbert J.G., Korf I., Lapp H., Lehvaslaiho H., Matsalla C., Mungall C.J., Osborne B.I., Pocock M.R., Schattner P., Senger M., Stein L.D., Stupka E., Wilkinson M.D., and Birney E. The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12 (2002) 1611-1618
84. Stokstad E. Invertebrate paleontology. Gutsy fossil sets record for staying the course. Science 302 (2003) 1645
85. Swanson K.M. Distribution, affinities and origin of the Punciidae (Crustacea: Ostracoda). Mem. Queensland Mus. 31 (1991) 77-92
86. Swofford D.L. PAUP*: Phylogenetic Analylsis Using Parsimony (* and Other Methods) (2003), Sinauer Associates, Sunderland, MA
87. Tambareau, Y., 1972. Thanetien superieur et Ilerdien inferieur des Petites Pyrenees, du Plantaurel et des Chainons Audois. Science Naturelles. Universite de Touluse 1-377.
88. Thorne J.L., and Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51 (2002) 689-702
89. Thorne J.L., Kishino H., and Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15 (1998) 1647-1657
90. Tinn O., and Meidla T. Phylogenetic relationships of Early-middle Ordovician ostracods of Baltoscandia. Palaeontology 47 (2004) 199-221
91. Tolmacheva T., Egerquist E., Meidla T., Tinn O., and Holmer L. Faunal composition and dynamics in unconsolidated sediments; a case study from the Middle Ordovician of the East Baltic. Geol. Mag. 140 (2003) 31-44
92. Triebel E. Die Ostracoden der deutschen Kreide; 3, Cytherideinae und Cytherinae aus der unteren Kreide. Senckenbergiana 22 (1940) 160-227
93. Valicenti V.H., and Stephens J.M. Ostracods from the upper Valangilian and upper Hauterivian of the Sundays River Formation, Algoa Basin, South Africa. Rev. Esp. Micropaleontol. 16 (1984) 171-239
94. Wakayama, N., 2007. Embryonic development clarifies polyphyly in ostracod crustaceans. J. Zool.
95. Weaver P.P.E. Ostracoda from the British Lower Chalk and Plenus Marls. Palaeontogr. Soc. Monogr. 135 (1982) 127
96. Webster A.J., Payne R.J., and Pagel M. Molecular phylogenies link rates of evolution and speciation. Science 301 (2003) 478
97. Whatley R., Siveter D., and Boomer I. Arthropoda (Crustacea: Ostracoda). In: Benton M.J. (Ed). The Fossil Record 2 (1993), Chapman and Hall, London 343-357
98. Wiegmann B.M., Yeates D.K., Thorne J.L., and Kishino H. Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Syst. Biol. 52 (2003) 745-756
99. Yamaguchi S. Morphological evolution of cytherocopine ostracods inferred from 18s ribosomal DNA sequences. J. Crustacean Biol. 23 (2003) 131-153
100. Yamaguchi S., and Endo K. Molecular phylogeny of Ostracoda (Crustacea) inferred from 18S ribosomal DNA sequences: implication for its origin and diversification. Mar. Biol. 143 (2003) 23-38
101. Ye, C.H., Gou, Y.S., Hou, Y.T., Coa, M.Z., 1977. Mesozoic and Cenozoic ostracod fauna from Yunnan. In: Palaeontology, N.I.o.G.a., Mesozoic Fossils of Yunnan, Part II. Science Press, Beijing, pp. 153-330.
102. Zuckerkandl E., and Pauling L. In: Pullmann P. (Ed). Horizons in Biochemistry (1962), Academic Press, New York 189-225
103. Zuckerkandl E., and Pauling L. Molecules as documents of evolutionary history. J. Theor. Biol. 8 (1965) 357-366