Nucleotide diversity and Pleistocene population expansion in Atlantic and Mediterranean scallops (Pecten maximus and P. jacobaeus) as revealed by the mitochondrial 16S ribosomal RNA gene

Journal of Experimental Marine Biology and Ecology

Volumn 323, Issue 2, 2005, Pages 138-150

  Saavedra, Carlos ^a   Peña, Juan B ^a  

^a CSIC Instituto de Acuicultura de Torre de la Sal IATS   (Spain)

Author keywords

16S rRNA; Nucleotide diversity; Pecten; Population expansion; Scallop

Indexed keywords

MOLLUSC;

PECTEN; PECTEN JACOBAEUS; PECTEN MAXIMUS; PECTINIDAE;

EID: 26044434355     PISSN: 00220981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jembe.2005.03.006     Document Type: Article

References (55)

1. A.D. Ansell, J.-C. Dao, and J. Mason Three European scallops: Pecten maximus, Chlamys (Aequipecten opercularis, and C. (Chlamys) varia S.E. Shumway Scallops: Biology, Ecology and Aquaculture 1991
2. L. Bargelloni, J.A. Alarcón, M.C. Alvarez, E. Penzo, A. Magoulas, C. Reis, and T. Patarnello Discord in the family Sparidae (Teleostei): divergent phylogeographical patterns across the Atlantic-Mediterranean divide J. Evol. Biol. 16 2003 1149 1158
3. A.R. Beaumont Genetic distances between some scallop species S.E. Sumway P.A. Sandifer An International Compendium of Scallop Biology and Culture 1991 World Aquaculture Society Baton Rouge 151 155
4. A. Beu, and T.A. Darragh Revision of southern Australian Cenozoic fossil Pectinidae (Mollusca: Bivalvia) Proc. R Soc. Victoria 113 2001 1 205
5. A.R. Brand Scallop ecology: distributions and behaviour S.E. Shumway Scallops: Biology, Ecology and Aquaculture 1991 Elsevier Amsterdam 517 583
6. M. Clement, D. Posada, and K.A. Crandall TCS: a computer program to estimate gene genealogies Mol. Ecol. 9 2000 1657 1660
7. P. David, and P. Jarne Context-dependent survival differences among electrophoretic genotypes in natural populations of the marine bivalve Spisula ovalis Genetics 146 1998 335 344
8. L. Excoffier, P.E. Smouse, and J.M. Quatro Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human DNA restriction data Genetics 131 1992 479 491
9. J. Felsenstein Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 1985 783 791
10. Y.-X. Fu, and W.-H. Li Statistical tests of neutrality of mutations Genetics 133 1993 693 709
11. E.M. Gosling Bivalve Molluscs 2003 Fishing News Books Oxford
12. T.A. Hall BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp. Ser. 41 1999 95 98
13. D. Hedgecock Does variance in reproductive success limit effective population sizes of marine organisms? A.R. Beaumont Genetics and Evolution of Aquatic Organisms 1994 Chapman and Hall London 122 134
14. D.A. Heipel, J.D. Bishop, and A.R. Brand Mitochondrial DNA variation among open-sea and enclosed populations of the scallop Pecten maximus in western Britain J. Mar. Biol. Assoc. U.K. 79 1999 687 695
15. J. Hey, and C.A. Machado The study of structured populations-new hope for a difficult and divided science Nat. Rev., Genet. 4 2003 535 543
16. S. Karl, and J.C. Avise Balancing selection at allozyme loci in oysters: implications for nuclear RFLPs Science 256 1992 100 102
17. M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of DNA sequences J. Mol. Evol. 16 1980 111 120
18. R.K. Koehn, R.I. Newell, and F. Immermann Maintenance of an aminopeptidase allele frequency cline by natural selection Proc. Natl. Acad. Sci. U. S. A. 77 1980 5385 5389
19. S. Kumar, K. Tamura, I.B. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 2001 1244 1245
20. S.A. Miller, D.D. Dykes, and H.F. Polesky A simple salting out procedure for extracting DNA from human nucleated cells Nucleic Acids Res. 16 1988 1215
21. M.W. Nachmann, and S.L. Crowell Estimate of the mutation rate per nucleotide in humans Genetics 156 2000 297 304
22. M. Naciri, C. Lemaire, P. Borsa, and F. Bonhomme Genetic study of the Atlantic-Mediterranean transition in sea bass (Dicentrarchus labrax) J. Heredity 90 1999 591 596
23. M. Nei Molecular Evolutionary Genetics 1989 Columbia University Press New York
24. M. Nei, and S. Kumar Molecular Evolution and Phylogenetics 2000 Oxford University Press New York
25. S.R. Palumbi Nucleic acids: II. The polymerase chain reaction D.M. Hillis C. Moritz B.K. Mable Molecular Systematics 2nd ed. 1996 Sinauer Sunderland 205 247
26. F.G. Pannacciulli, J.D. Bishop, and S.J. Hawkings Genetic structure of populations of two species of Chthamalus (Crustacea: Cirripedia) in the north-east Atlantic and Mediterranean Mar. Biol. 128 1997 73 82
27. J.B. Peña, J. Canales, J.M. Adsuara, and M.A. Sos Study of seasonal settlements of five scallop species in the western Mediterranean Aquac. Int. 4 1996 253 261
28. M. Pérez-Losada, A. Guerra, and A. Sanjuán Allozyme differentiation in the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) from the NE Atlantic and Mediterranean Heredity 83 1999 280 289
29. D. Posada, and K.A. Crandall Intraspecific gene genealogies: trees grafting into networks TREE 16 2001 37 45
30. H. Quesada, C. Zapata, and G. Alvarez A multilocus allozyme discontinuity in the mussel Mytilus galloprovincialis: the interaction of ecological and life-history factors Mar. Ecol. Prog. Ser. 116 1995 99 115
31. H. Quesada, C.M. Beynon, and D.O.F. Skibinski A mitochondrial DNA discontinuity in the mussel Mytilus galloprovincialis Lmk: Pleistocene vicariance biogeography and secondary intergradation Mol. Biol. Evol. 12 1995 521 524
32. S.E. Ramos-Onsins, and J. Rozas Statistical properties of new neutrality tests against population growth Mol. Biol. Evol. 19 2002 2092 2100
33. M. Raymond, and F. Rousset An exact test for population differentiation Evolution 49 1995 1280 1283
34. M. Raymond, and F. Rousset GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism J. Heredity 86 1995 248 249
35. A. Renzoni Italy S.E. Shumway Scallops: Biology, Ecology and Aquaculture 1991 Elsevier Amsterdam 777 787
36. A.R. Rogers, and H. Harpending Population growth makes waves in the distribution of pairwise genetic differences Mol. Biol. Evol. 9 1992 552 569
37. C. Ríos, S. Sanz, C. Saavedra, and J.B. Peña Allozyme variation in populations of scallops, Pecten jacobaeus (L.) and P. maximus (L.), across the Almeria-Oran front J. Exp. Mar. Biol. Ecol. 267 2002 223 244
38. A. Rombouts Guidebook to Pecten Shells 1991 Crawford House Press Bathurst
39. J. Rozas, J.C. Sánchez del Barrio, X. Messegué, and J. Rozas DnaSP: DNA polymorphism analysis by the coalescent and other methods Bioinformatics 19 2003 2496 2497
40. C. Saavedra, and J.B. Peña Phylogenetic relationships of commercial European and Australasian scallops (Pecten spp.) based on partial 16S ribosomal RNA gene sequences Aquaculture 235 2004 153 166
41. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
42. S. Schneider, and L. Excoffier Estimation of demographic parameters from the distribution of pairwise differences when mutation rates vary among sites: application of human mitochondrial DNA Genetics 152 1999 1079 1089
43. S. Schneider, D. Roessli, and L. Excoffier Arlequin ver. 2.00: Software for Population Genetic Data Analysis 2000 University of Geneva Geneva
44. S.E. Shumway Scallops: Biology, Ecology and Aquaculture 1991 Elsevier Amsterdam
45. K.L. Simonsen, G.A. Churchill, and C.F. Aquadro Properties of statistical tests of neutrality for DNA polymorphism data Genetics 141 1995 413 429
46. M.P. Small, and R.W. Chapman Intraspecific variation in the 16S ribosomal gene of Crassostrea virginica Mol. Mar. Biol. Biotechnol. 6 1997 189 196
47. F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 1989 585 595
48. N. Takahata Allelic genealogy and human evolution Mol. Biol. Evol. 10 1993 2 22
49. A.R. Templeton, K.A. Crandall, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data: III. Cladogram estimation Genetics 132 1992 619 633
50. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
51. J. Tintoré, P.E. La Violette, I. Blade, and A. Cruzado A study of an intense density front in the eastern Alboran sea the Almeria-Oran front J. Phys. Oceanogr. 1988 1384 1397
52. H.P. Wagner Review of the European Pectinidae (Mollusca: Bivalvia) Vita Mar. 41 1991 1 48
53. J. Wakeley, and T. Takahashi Gene genealogies when the sample size exceeds the effective size of the population Mol. Biol. Evol. 20 2003 208 213
54. T.R. Waller Evolutionary relationships among commercial scallops (Mollusca: Bivalvia: Pectinidae) S.E. Shumway Scallops: Biology, Ecology and Aquaculture 1991 Elsevier Amsterdam 1 73
55. C.S. Wilding, A.R. Beaumont, and J.W. Latchford Are Pecten maximus and Pecten jacobaeus different species? J. Mar. Biol. Assoc. U.K. 79 1999 949 952