Reconciling deep calibration and demographic history: Bayesian inference of post glacial colonization patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758)

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Marino, Ilaria A M ^a   Pujolar, Jose Martin ^a   Zane, Lorenzo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE I; UNCLASSIFIED DRUG; MITOCHONDRIAL DNA;

ARTICLE; BAYES THEOREM; CALIBRATION; CARCINUS AESTUARII; CARCINUS MAENAS; CHRONOLOGY; CONTROLLED STUDY; CRAB; ENVIRONMENTAL RECOLONIZATION; EUROPE; EVOLUTION; FLOODING; GENE SEQUENCE; GEOGRAPHIC DISTRIBUTION; GLACIATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION DYNAMICS; SPECIES DIFFERENTIATION; SPECIES REFUGE; ANIMAL; BIOLOGICAL MODEL; BRACHYURA; DEMOGRAPHY; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; SPECIES DIFFERENCE; STATISTICAL MODEL; TIME;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; BRACHYURA; CALIBRATION; DEMOGRAPHY; DNA, MITOCHONDRIAL; EUROPE; EVOLUTION, MOLECULAR; GENETIC VARIATION; GEOGRAPHY; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; SPECIES SPECIFICITY; TIME FACTORS;

EID: 82555185559     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028567     Document Type: Article

References (95)

1. Lovette IJ, (2005) Glacial cycles and the tempo of avian speciation. Trends Ecol Evol 20: 57-59.
2. Hofreiter M, Rabader G, Jaenicke-Despres V, Withalm G, Nagel D, et al. (2004) Evidence for reproductive isolation between cave bear populations. Curr Biol 14: 40-43.
3. Saarma U, Ho SYW, Pybus OG, Kaljuste M, Tumanov IL, et al. (2007) Mitogenetic structure of brown bears (Ursus arctos) in northeastern Europe and a new time frame for the formation of brown bear lineages. Mol Ecol 16: 401-413.
4. Ritten RJ, (1986) Rates of DNA sequence evolution differ between taxonomic groups Science 231: 1393-1398.
5. Hasegawa M, Kishino H, (1989) Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders. Jpn J Genet 64: 243-258.
6. Ayala FJ, (1997) Vagaries of the molecular clock. P Natl Acad Sci USA 94: 7776-7783.
7. Huelsenbeck JP, Larget B, Swofford D, (2000) A compound Poisson process for relaxing the molecular clock. Genetics 154: 1879-1892.
8. Kishino H, Thorne JL, Bruno WJ, (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18: 352-361.
9. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PloS Biol 4: e88.
10. Lepage T, Lawi S, Tupper P, Bryant D, (2006) Continuous and tractable models for the variation of evolutionary rates. Math Biosci 199: 216-233.
11. Rannala B, Yang Z, (2007) Inferring speciation times under an episodic molecular clock. Syst Biol 56: 453-466.
12. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22: 1185-1192.
13. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
14. Ho SYW, (2007) Calibrating molecular estimates of substitution rates and divergence times in birds. J Avian Biol 38: 409-414.
15. Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, et al. (2003) The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet 72: 659-670.
16. Pereira SL, Baker AJ, (2006) A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol Biol Evol 23: 1731-1740.
17. Ho SYW, Phillips MJ, Cooper A, Drummond AJ, (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22: 1561-1568.
18. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, et al. (2011) Time-dependent rates of molecular evolution. Mol Ecol 20: 3087-3101.
19. Burridge CP, Craw D, Fletcher D, Waters JM, (2008) Geological dates and molecular rates: Fish DNA sheds light on time dependency. Mol Biol Evol 25: 624-633.
20. Howell N, Howell C, Elson JL, (2008) Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking. Heredity 101: 107-108.
21. Millar CD, Dodd A, Anderson J, Gibb GC, Ritchie PA, et al. (2008) Mutation and evolutionary rates in Adélie Penguins from the Antarctic. PLoS Genet 4: e1000209.
22. Debruyne R, Poinar HN, (2009) Time dependency of molecular rates in ancient DNA data sets, a sampling artifact? Syst Biol 58: 348-360.
23. Navascués M, Emerson BC, (2009) Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods. Mol Ecol 18: 4390-4397.
24. Ramakrishnan U, Hadly EA, (2009) Do complex population histories drive estimates of substitution rate in phylogenetic reconstructions? Mol Ecol 18: 4341-4343.
25. Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B, (2008) The effect of inappropriate calibration: three case studies in molecular ecology. PLoS One 3: e1615.
26. Penny D, (2005) Evolutionary biology: Relativity for molecular clocks. Nature 436: 183-184.
27. Ho SYW, Larson G, (2006) Molecular clocks: when times are a-changin'. Trends Genet 22: 79-83.
28. Darling JA, Bagley MJ, Roman J, Tepolt CK, Geller JB, (2008) Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus. Mol Ecol 17: 4992-5007.
29. Darling JA, (2011) Interspecific hybridization and mitochondrial introgression in invasive Carcinus shore crabs. PLoS ONE 6: e17828.
30. Rice AL, Ingle RW, (1975) The larval development of Carcinus maenas and C. mediterraneus Czerniavsky (Crustacea, Brachyura, Portunidae) reared in the laboratory. Bull Br Mus Nat Hist 28: 101-119.
31. Bulnheim HP, Bahns S, (1996) Genetic variation and divergence in the genus Carcinus (Crustacea, Decapoda). Int Rev Gesamten Hydrobiol 81: 611-619.
32. Yamada SB, (2001) Global invader: the European green crab. Corvalis OR Oregon State University.
33. Demeusy N, (1958) Recherches sur la mue de puberte du decapode brachyure Carcinus maenas Linne. Arch Zool Exp Gen 95: 253-491.
34. Krijgsman W, Hilgen FJ, Raffi I, Sierro FJ, Wilson DS, (1999) Chronology, causes and progression of the Messinian salinity crisis. Nature 400: 652-655.
35. Por FD, (2010) The new Tethyan ichthyofauna of the Mediterranean- historical background and prospect. In: Golani D, Appelbaum-Golani B, editors. Fish Invasion of the Mediterranean Sea: Change and Renewal Sofia-Moscow Pensoft pp. 13-33.
36. Por FD, Dimentman C, (2006) Mare Nostrum: Neogene and anthropic natural history of the Mediterranean basin with emphasis on the Levant. Sofia-Moscow Pensoft.
37. Geller JB, Walton ED, Grosholz AD, Ruiz GM, (1997) Cryptic invasions of the crab Carcinus detected by molecular plylogeography. Mol Ecol 6: 901-906.
38. Roman J, Palumbi SR, (2004) A global invader at home: population structure of the green crab, Carcinus maenas, in Europe. Mol Ecol 13: 2891-2898.
39. Mona S, Randi E, Tommaseo-Ponzetta M, (2007) Evolutionary history of the genus Sus inferred from cytochrome b sequences. Mol Phylogenet Evol 45: 757-762.
40. Villacorta C, Jaume D, Oromi P, Juan C, (2008) Under the volcano: phylogeography and evolution of the cave-dwelling Palmorchestia hypogaea (Amphipoda, Crustacea) at La Palma (Canary Islands). BMC Biol 6: 7.
41. Zinner D, Groeneveld LF, Keller C, Roos C, (2009) Mitochondrial phylogeography of baboons (Papio spp.)- Indication for introgressive hybridization? BMC Evol Biol 9: 83.
42. Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, et al. (2008) Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biol Letters 4: 370-374.
43. Knowlton N, Weigt LA, (1998) New dates and new rates for divergence across the Isthmus of Panama. P Roy Soc B-Biol Sci 265: 2257-2263.
44. Schubart CD, Diesel R, Hedges SB, (1998) Rapid evolution to terrestrial life in Jamaican crabs. Nature 393: 363-365.
45. Kass RE, Raftery AE, (1995) Bayes Factors. J Am Stat Assoc 90: 773-795.
46. Bucklin A, Frost BW, Bradford-Grieve J, Allen LD, Copley NJ, (2003) Molecular systematics and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Mar Biol 142: 333-343.
47. Patarnello T, Volckaert FAM, Castilho R, (2007) Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break? Mol Ecol 16: 4426-4444.
48. Borrero-Pérez GH, González-Wangüemert M, Marcos C, Pérez-Ruzafa A, (2011) Phylogeography of the Atlanto-Mediterranean sea cucumber Holothuria (Holothuria) mammata: the combined effects of historical processes and current oceanographical pattern. Mol Ecol 20: 1964-1975.
49. Brown J, Hill AE, Fernand L, Horsburgh KJ, (1999) Observation of a seasonal jet-like circulation at the central North Sea cold pool margin. Estuar Coast Shelf S 48: 343-355.
50. Domingues CP, Creer S, Taylor MI, Queiroga H, Carvalho GH, (2010) Genetic structure of Carcinus maenas within its native range: larval dispersal and oceanographic variability. Mar Ecol Prog Ser 410: 111-123.
51. Foss A, Imsland AK, Naevdal G, (1998) Population genetic studies of the Atlantic halibut in the North Atlantic Ocean. J Fish Biol 53: 901-905.
52. Shaw PW, Turan C, Wright JM, O'Connell M, Carvalho GR, (1999) Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses. Heredity 83: 490-499.
53. Hoarau G, Piquet AMT, Van der Veer HW, Rijnsdorp AD, Stam WT, et al. (2004) Population structure of plaice (Pleuronectes platessa) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data. J Sea Res 51: 183-190.
54. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, et al. (2009) The last glacial maximum. Science 325: 710-714.
55. Rögl F, Steininger F, (1983) Vom Zerfall der Tethys zu Mediterran und Paratethys. Ann Nat Hist Mus Wien 85A: 135-163.
56. Dawson AG, (1992) Ice Age Earth: Late Quaternary Geology and Climate. London Routledge.
57. Rögl F, (1999) Mediterranean and Paratethys. Facts and hypotheses of an Oligocene to Miocene paleogeography (short overview). Geol Carpath 50: 339-349.
58. Waelbroeck C, Labeyrie L, Michel E, Duplessy JC, McManus JF, et al. (2002) Sea-level and deep water temperature changes derived from benthic foraminifera isotopic records. Quaternary Sci Rev 21: 295-305.
59. Thiede J, (1978) A glacial Mediterranean. Nature 276: 680-683.
60. Pujolar JM, Marčeta T, Saavedra C, Bressan M, Zane L, (2010) Inferring the demographic history of the Adriatic Flexopecten complex. Mol Phylogenet Evol 57: 942-947.
61. Congiu L, Rossi R, Colombo G, (2002) Population analysis of the sand smelt Atherina boyeri (Teleostei Atherinidae), from Italian coastal lagoons by random amplified polymorphic DNA. Mar Ecol Prog Ser 229: 279-289.
62. Astolfi L, Dupanloup I, Rossi R, Bisol PM, Faure E, et al. (2005) Mitochondrial variability of sand smelt Atherina boyeri populations from north Mediterranean coastal lagoons. Mar Ecol Prog Ser 297: 233-243.
63. Debes PV, Zachos FE, Hanel R, (2008) Mitochondrial phylogeography of the European sprat (Sprattus sprattus, Clupeidae) reveals isolated climatically vulnerable populations in the Mediterranean Sea and range expansion in the northeast Atlantic. Mol Ecol 17: 3873-3888.
64. Maltagliati F, Di Giuseppe G, Barbieri M, Castelli A, Dini F, (2010) Phylogeography and genetic structure of the edible sea urchin Paracentrotus lividus (Echinodermata: Echinoidea) inferred from the mitochondrial cytochrome b gene. Biol J Linn Soc 100: 910-923.
65. Siegert MJ, Dowdeswell JA, (2004) Numerical reconstruction of the Eurasian Ice Sheet and climate during the late Weichselian. Quaternary Sci Rev 23: 1273-1283.
66. Svendsen JIS, Alexanderson H, Astakhov VI, Deminov I, Dowdswell JA, et al. (2004) Late Quaternary ice sheet history of northern Eurasia. Quaternary Sci Rev 23: 1229-1271.
67. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF, (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7: 453-464.
68. Hewitt GM, (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58: 247-276.
69. Gysels ES, Hellemans B, Pampoulie C, Volckaert FAM, (2004) Phylogeography of the common goby, Pomatoschistus microps, with particular emphasis on the colonization of the Mediterranean and the North Sea. Mol Ecol 13: 403-417.
70. Pampoulie C, Stefansson MO, Jorundsdottir TD, Danilowicz BS, Danielsdottir AK, (2008) Recolonization history and large-scale dispersal in the open sea: the case study of the North Atlantic cod, Gadus morhua. Biol J Linn Soc 94: 315-329.
71. Balson PS, Laban C, Frantsen PJ, Parker N, Henriet JP, et al. (1991) Ostend: Sheet 52°N/02°E. Solid Geology, 1:250 000 Series British Geological Survey. Southampton Geological Survey of The Netherlands and Belgian Geological Survey.
72. Van Vliet-Lanoë B, Gu{eth}mundsson Å, Guillou H, Duncan RA, Genty D, et al. (2007) Limited glaciation and very early deglaciation in central Iceland. Implications for climate change. C R Geosci 339: 1-12.
73. Eckert CG, Samis KE, Lougheed SC, (2008) Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Mol Ecol 17: 1170-1188.
74. Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, et al. (2005) Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores islands (Portugal). Mol Biol Evol 22: 1490-1505.
75. Ohta T, (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23: 263-286.
76. Sušnik S, Snoj A, Wilson IF, Mrdak D, Weiss S, (2007) Historical demography of brown trout (Salmo trutta) in the Adriatic drainage including the putative S. letnica endemic to Lake Ohrid. Mol Phylogenet Evol 44: 63-76.
77. Marko PB, Hoffman JM, Emme SA, McGovern TM, Keever CC, et al. (2010) The 'Expansion-Contraction' model of Pleistocene biogeography: rocky shores suffer a sea change? Mol Ecol 19: 146-169.
78. Lecomte F, Grant WS, Dodson JJ, Rodríguez-Sánchez R, Bowen BW, (2004) Living with uncertainty: genetic imprints of climate shifts in East Pacific anchovy (Engraulis mordax) and sardine (Sardinops sagax). Mol Ecol 13: 2169-2182.
79. Zane L, Marcato S, Bargelloni L, Bortolotto E, Papetti C, et al. (2006) Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum. Mol Ecol 15: 4499-4511.
80. Bazin E, Glémin S, Galtier N, (2006) Population size does not influence mitochondrial genetic diversity in animals. Science 312: 570-572.
81. Patwary MU, Kenchington EL, Bird CJ, Zouros E, (1994) The use of random amplified polymorphic DNA (RAPD) markers in genetic studies of the sea scallop Plactopecten magellanicus. J Shellfish Res 13: 547-553.
82. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
83. Librado P, Rozas J, (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
84. McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
85. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
86. Fu YX, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
87. Ramos-Onsins SE, Rozas J, (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19: 2092-2100.
88. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance and Maximum Parsimony methods. Mol Biol Evol 28: 2731-2739.
89. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to mitochondrial DNA restriction data. Genetics 131: 479-491.
90. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
91. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
92. Rannala B, Yang Z, (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43: 304-311.
93. Yang Z, Rannala B, (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 14: 717-724.
94. Rambaut A, Drummond AJ, (2007) Tracer version 1.5. Molecular Evolution, Phylogenetics and Epidemiology website. Available: http://tree.bio.ed.ac.uk/software/tracer. Accessed 2011 Nov 14.
95. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL, (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53: 47-67.