Isolation with differentiation followed by expansion with admixture in the tunicate Pyura chilensis

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Haye, Pilar A ^a,b,c   Muñoz Herrera, Natalia C ^a,b,c  

^a UNIVERSIDAD CATÓLICA DEL NORTE   (Chile)

^b CENTRO DE ESTUDIOS AVANZADOS EN ZONAS ÁRIDAS CEAZA   (Chile)

^c UNIVERSITY OF CONCEPCIÓN   (Chile)

Author keywords

Biofouling; COI; Connectivity; Dispersal potential; Elongation Factor 1 alpha; Genetic structure; Phylogeography; Short lived larvae

Indexed keywords

BIOFOULING; COMMERCIAL SPECIES; DISPERSAL; GENETIC DIFFERENTIATION; GENETIC STRUCTURE; GEOGRAPHICAL DISTRIBUTION; INVERTEBRATE; MITOCHONDRION; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION DISTRIBUTION; POPULATION STRUCTURE;

CHILE;

PYURA CHILENSIS; UROCHORDATA;

CYTOCHROME C OXIDASE; ELONGATION FACTOR 1;

ANIMAL; ARTICLE; BAYES THEOREM; CHILE; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; MITOCHONDRIAL GENE; PHYLOGEOGRAPHY; UROCHORDATA;

ANIMALS; BAYES THEOREM; CHILE; ELECTRON TRANSPORT COMPLEX IV; GENES, MITOCHONDRIAL; GENETIC VARIATION; PEPTIDE ELONGATION FACTOR 1; PHYLOGEOGRAPHY; UROCHORDATA;

EID: 84887517726     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-252     Document Type: Article

References (86)

1. Pyura chilensis Molina 1782 en el Norte del Perú (Ascidacea, Pyuridae). Vásquez JA, Biol Soc Biol Conc 1983 54 171 172
2. Self-fertilization as an alternative mode of reproduction in the solitary tunicate Pyura chilensis. Manríquez PH, Castilla JC, Mar Ecol Prog Ser 2005 305 113 1225
3. Genetic variability and population structure in the tunicate Pyura chilensis Molina, 1782, in the coast of Chile. Astorga MP, Ortiz JC, Rev Chil Hist Nat 2006 79 423 434 (Pubitemid 46469917)
4. Restricted gene flow in Chilean barnacles reflect an oceanographic and biogeographic transition zone. Zakas C, Binford J, Navarrete SA, Wares JP, Mar Ecol Prog Ser 2009 394 165 177
5. Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp. Fraser CI, Thiel M, Spencer HG, Waters JM, BMC Evol Biol 2010 10 203 10.1186/1471-2148-10-203 20594354
6. Does life history predict past and current connectivity for rocky intertidal invertebrates across a marine biogeographic barrier? Ayre DJ, Minchinton TE, Perrin C, Mol Ecol 2009 18 1887 1903 10.1111/j.1365-294X.2009. 04127.x 19434808
7. Population genetics, larval dispersal, and connectivity in marine systems. Weersing K, Toonen RJ, Mar Ecol Prog Ser 2009 393 1 12
8. Genetic structure among 50 species of the northeastern pacific rocky intertidal community. Kelly RP, Palumbi SR, PLoS One 2010 5 8594 10.1371/journal.pone.0008594 20062807
9. The 'expansion-Contraction' model of Pleistocene biogeography: rocky shored suffer a sea change? Marko PB, Hoffman JM, Emme SA, McGovern TM, Keever CC, Cox LN, Mol Ecol 2010 19 146 169 10.1111/j.1365-294X.2009.04417.x 20092033
10. A phylogeographical analysis across three biogeographical provinces of the south-eastern Pacific: the case of the marine gastropod Concholepas concholepas. Cárdenas L, Castilla JC, Viard F, J Biogeo 2009 36 969 981 10.1111/j.1365-2699.2008.02056.x
11. Phylogeographic analyses of the 30°S south-east pacific biogeographic transition zone establish the occurrence of a sharp genetic discontinuity in the kelp Lessonia nigrescens: vicariance or parapatry? Tellier F, Meynard AP, Correa JA, Faugeron S, Valero M, Mol Phylogenet Evol 2009 53 679 693 10.1016/j.ympev.2009.07.030 19647087
12. Heterochronic phenotypic plasticity with lack of genetic differentiation in the southeastern pacific squat lobster pleuroncodes monodon. Haye PA, Salinas P, Acuña E, Poulin E, Evol Dev 2010 12 627 633
13. Genetic diversity and population structure of two South American marine gastropods, Crepipatella dilatata and C. fecunda (Gastropoda: Calytraeidae): distinct patterns based on developmental mode. Guzmán BE, Nuñez JJ, Vejar A, Barriga EH, Gallardo CS, Ital J Zool 2011 78 444 454 10.1080/11250003.2011.576403
14. Spatial pattern of genetic and morphological diversity in the direct developer Acanthina monodon (Gastropoda: Mollusca). Sánchez R, Sepúlveda RD, Brante A, Cárdenas L, Mar Ecol Prog Ser 2011 434 121 131
15. Phylogeography and biogeography concordance in the marine gastropod Crepipatella dilatata (Calyptraeidae) along the Southeastern Pacific coast. Brante A, Fernández M, Viard F, J Hered 2012 103 630 637 10.1093/jhered/ess030 22573790
16. Species replacement along a lineal coastal habitat: phylogeography and speciation in the red alga Mazzaella laminarioides along the south east Pacific. Montencinos A, Broitman B, Faugeron S, Haye PA, Tellier F, Guillermin M-L, BMC Evol Biol 2012 12 97 10.1186/1471-2148-12-97 22731925
17. Phylogeographic insights into cryptic glacial refugia. Provan J, Bennett KD, Trends Ecol Evol 2008 23 564 571 10.1016/j.tree.2008.06.010 18722689
18. Late Pleistocene population expansion of Scylla paramamosain along the coast of China: a population dynamic response to the last Interglacial sea level highstand. He L, Zhang A, Weese D, Zhu C, Jiang C, Qiao Z, J Exp Mar Biol Ecol 2010 385 20 28 10.1016/j.jembe.2010.01.019
19. Genetic evaluation of marine biogeographical barriers: perspectives from two widespread Indo-Pacific snappers (Lutjanus kasmira and Lutjanus fulvus). Gaither MR, Toonen RJ, Robertson DR, Planes S, Bowen BW, J Biogeo 2010 37 133 147
20. Phylogeography of he mottled spinefoot Suganus fuscens: Pleistocene divergence and limited genetic connectivity across the Philippine archipelago. Ravago-Gotanco RG, Juinio-Meñez MA, Mol Ecol 2010 19 4520 4534 10.1111/j.1365-294X.2010.04803.x 20875063
21. Effects of current and historic habitat fragmentation on the genetic structure of the sand goby Pomatoschistus minutus (Osteichthys, Gobiidae). Boissin E, Horeau TB, Berrebi P, Biol J Linn Soc 2011 102 175 198
22. The genetic legacy of the quaternary ice ages. Hewitt GM, Nature 2000 405 907 913 10.1038/35016000 10879524 (Pubitemid 30435039)
23. Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania monus mitochondrial genome and support for the new chordate phylogeny. Singh RS, Tsagkogeorga G, Delsuc F, Blanquart S, Shenkar N, Loya Y, et al. BMC Genomics 2009 10 534 569 10.1186/1471-2164-10-534 19922605
24. The population genomics of a fast evolver: high levels of diversity, functional constraint and molecular adaptation in the tunicate Ciona intestinalis. Tsagkogeorga G, Cahais V, Galtier N, Genome Biol Evol 2012 4 740 749 10.1093/gbe/evs054 22745226
25. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Ho STW, Phillips MJ, Cooper A, Drummond AJ, Mol Biol Evol 2005 22 1561 1568 10.1093/molbev/msi145 15814826 (Pubitemid 40800685)
26. Time-dependent rates of molecular evolution. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, et al. Mol Ecol 2011 20 3087 3101 10.1111/j.1365-294X.2011.05178.x 21740474
27. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Tajima F, Genetics 1989 123 585 595 2513255 (Pubitemid 19274682)
28. Population growth makes waves in the distribution of pairwise genetic differences. Rogers AR, Harpending HC, Mol Biol Evol 1992 9 552 569 1316531
29. Genetic consequences of range expansions. Excoffier L, Foll M, Petit R, Ann Rev Ecol Evol Syst 2009 40 481 501 10.1146/annurev.ecolsys.39.110707.173414
30. A global map of human impact on marine ecosystems. Halpern B, Walbridge S, Selkoe KA, Kappel CV, Micheli F, D'Agrosa C, et al. Science 2008 319 948 952 10.1126/science.1149345 18276889 (Pubitemid 351263764)
31. Sea surface temperature variability in the pacific sector of the southern ocean over the past 700 kyr. Ho SL, Mollenhauers G, Lamy F, Martínez-Garcia A, Mohtadi M, Gersonde R, et al. Paleoceanography 2012 27 4202
32. Timing and duration of the last interglacial: evidence for a restricted interval of widespread coral reed growth. Starling CH, Esat TM, Lambeck K, McCulloch MT, Earth Planet Sci Lett 1998 160 745 762 10.1016/S0012-821X(98) 00125-3 (Pubitemid 29105734)
33. Global sea-level fluctuations during the last interglaciation (MIS 5e). Hearty PJ, Hollin JT, Neumann AC, Leary MJO, McCulloch M, Quaternary Sci Rev 2007 26 2090 2112 10.1016/j.quascirev.2007.06.019 (Pubitemid 350016497)
34. The Phanerozoic record of global sea-level change. Miller KG, Kominz MA, Browning JV, Wright JD, Mountain GS, Katz ME, et al. Science 2005 310 1293 1298 10.1126/science.1116412 16311326 (Pubitemid 41698854)
35. Phylogeography, historical demography and postglacial colonization routes of two amphi-Atlantic distributed amphipods. Krebes L, Blank M, Bastrop R, Syst Biod 2011 9 259 273 10.1080/14772000.2011.604359
36. Phylogeography of the cold-water barnacle Chthamalus challenger in the north-western Pacific: effect of past population expansion and contemporary gene flow. Cheang CC, Tsang LM, Ng WC, Williams GA, Chu KH, Chan KK, J Biogeogr 2012 39 1819 1835 10.1111/j.1365-2699.2012.02742.x
37. Evolutionary history of a widespread Indo-Pacific goby: the role of Pleistocene sea-level changes on demographic contraction/expansion dynamics. Hoareau TB, Boissin E, Berrebi P, Mol Phylogenet Evol 2012 62 566 572 10.1016/j.ympev.2011.10.004 22037473
38. Evaluating signatures of glacial refugia for north Atlantic benthic marine taxa. Maggs CA, Castilho R, Foltz D, Henzler C, Taimour Jolly M, Kelly J, et al. Ecology 2008 89 Suppl 108 S122 19097488
39. The biogeography of mitochondrial and nuclear discordance in animals. Toews DPL, Brelsford A, Mol Ecol 2012 21 3907 3930 10.1111/j.1365-294X.2012. 05664.x 22738314
40. Invasion genetics of the Ciona intestinalis species complex: from regional endemism to global homogeneity. Zhan A, Macisaac HJ, Cristescu ME, Mol Ecol 2010 19 4678 4694 10.1111/j.1365-294X.2010.04837.x 20875067
41. The whereabouts of an ancient wanderer: global phylogeography of the solitary ascidian Styela plicata. Pineda MC, López-Legentil S, Turon X, PLoS One 2011 6 25495 10.1371/journal.pone.0025495 21966535
42. Comparative phylogeography of two colonial ascidians reveals contrasting invasion histories in North America. Lejeusne C, Bock DG, Therriault TW, MacIsaac HJ, Crustescu ME, Biol Invasions 2011 13 635 650 10.1007/s10530-010- 9854-0
43. Extreme genomic variation in a natural population. Small KS, Brudno M, Hill MM, Sidow A, Proc Natl Acad Sci U S A 2007 104 5698 5703 10.1073/pnas.0700890104 17372217 (Pubitemid 47175743)
44. Pathways of spread of the introduced ascidian Styela clava (Tunicata) in Northern Europe, revealed by microsatellite markers. Dupont L, Viard F, Davis MH, Nishikawa T, Bishop JDD, Biol Invasions 2010 12 2707 2721 10.1007/s10530-009-9676-0
45. Regional connectivity and coastal expansion: differentiation pre-border and post-border vectors for the invasive tunicate Styela clava. Goldstein SJ, Schiel DR, Gemmel NJ, Mol Ecol 2011 19 874 885
46. Invasive sea squirts: a growing global problem. Lambert G, J Exp Mar Biol Ecol 2007 342 3 4 10.1016/j.jembe.2006.10.009 (Pubitemid 46186363)
47. Assessing the port to port risk of vessel movements vectoring non-indigenous species within and across domestic Australian borders. Campbell ML, Hewitt CL, Biofouling 2011 6 631 644
48. Vessel biofouling as an inadvertent vector of benthic invertebrates occurring in Brazil. Rocha Farrapeira CM, de OIiviera Tenório D, Duartedo Amaral F, Mar Poll Bull 2011 62 832 839 10.1016/j.marpolbul.2010.12.014
49. Fine- and regional-scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction. Dupont L, Viard F, Dowell MJ, Wood C, Bishop JDD, Mol Ecol 2009 18 442 453 10.1111/j.1365-294X.2008.04045.x 19161467
50. Paradox lost: genetic diversity and the success of aquatic invasions. Roman J, Darling JA, Trends Ecol Evol 2007 22 818 828
51. Sambrook J, Fritsch EF, Maniatis T, Molecular cloning: a laboratory manual New York, NY: Cold Spring Harbor 1989
52. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Folmer O, Black M, Hoeh W, Lutz R, Vrijemhoek R, Mol Mar Biol Biotech 1994 3 294 299
53. Phylogeography: retrospect and prospect. Avise JC, J Biogeo 2009 36 3 15 10.1111/j.1365-2699.2008.02032.x
54. DNA Barcoding of marine metazoan. Bucklin A, Steinke S, Blanco-Bercial L, Ann Rev Mar Sci 2011 3 471 508 10.1146/annurev-marine-120308-080950 21329214
55. Multiple genetic divergences and population expansions of a Mediterranean sandfly, Phlebotomus ariasi, in Europe during the Pleistocene glacial cycles. Mahamdallie SS, Pesson B, Ready PD, Heredity 2011 106 714 726 10.1038/hdy.2010.111 20736970
56. Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian. Aurelle D, Ledoux J-B, Rocher C, Boesa P, Chenuil A, Féral J-P, Genetica 2011 139 855 869 10.1007/s10709-011-9589-6 21739159
57. Genetically separate populations of the ocean-skater Halobates sericeus (Heteroptera: Gerridae) have been maintained since the late Pleistocene. Leo SST, Cheng L, Sperling FA, Biol J Linn Soc 2012 105 797 805
58. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M, Bioinformatics 2005 21 3674 3676 10.1093/bioinformatics/bti610 16081474 (Pubitemid 41264107)
59. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, et al. Geneious v5.4, 2011 2011 [ http://www.geneious.com ]
60. DAMBE: software package for data analysis in molecular biology and evolution. Xia X, Xie Z, J Hered 2001 92 371 373 10.1093/jhered/92.4.371 11535656 (Pubitemid 32848767)
61. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Nei M, Gojobori T, Mol Biol Evol 1986 3 418 426 3444411 (Pubitemid 16010523)
62. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Zhang J, Kumar S, Nei M, Mol Biol Evol 1997 14 1335 1338 10.1093/oxfordjournals.molbev.a025743 9402743
63. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Zhang J, Resenberg HF, Nei M, Proc Natl Acad Sci U S A 1998 95 3708 3713 10.1073/pnas.95.7.3708 9520431 (Pubitemid 28173193)
64. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
65. A new statistical method for haplotype reconstruction from population data. Stephens M, Smith N, Donnelly P, Am J Hum Genet 2001 68 978 989 10.1086/319501 11254454 (Pubitemid 32289743)
66. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Librado P, Rozas J, Bioinformatics 2009 25 1451 1452 10.1093/bioinformatics/ btp187 19346325
67. Swofford DL, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Sunderland, MA, USA: Sinauer Associates 2002
68. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Höhna S, et al. Syst Biol 2011 61 539 542
69. jModelTest: phylogenetic model averaging. Posada D, Mol Biol Evol 2008 25 1253 1256 10.1093/molbev/msn083 18397919 (Pubitemid 351882013)
70. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Raymond M, Rousset F, J Hered 1995 86 248 249
71. Genepop'007: a complete re-implementation of the genepop software for windows and Linux. Rousset F, Mol Ecol Res 2008 8 103 106 10.1111/j.1471-8286. 2007.01931.x (Pubitemid 350231212)
72. Analyzing tables of statistical tests. Rice W, Evolution 1989 43 223 225 10.2307/2409177
73. Arlequin ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Excoffier L, Lischer HEL, Mol Ecol Res 2010 10 564 567 10.1111/j.1755-0998.2010.02847.x
74. Goudet J, FSTAT: A Program to Estimate and Test Gene Diversities and Fixation Indices, Version 2.9.3.2 2002 http://www.unil.ch/Jahia/site/dee/op/ edit/pid/36921
75. Inference of population structure using multilocus genotype data. Pritchard J, Stephens M, Donnelly P, Genetics 2000 155 945 959 10835412 (Pubitemid 30397141)
76. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Falush D, Stephens M, Pritchard JK, Genetics 2003 164 1567 1587 12930761 (Pubitemid 37102217)
77. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Evanno G, Regnaut S, Goudet J, Mol Ecol 2005 14 2611 2620 10.1111/j.1365-294X.2005.02553.x 15969739 (Pubitemid 40886055)
78. A new statistic for detecting genetic differentiation. Hudson RR, Genetics 2000 155 2011 2014 10924493 (Pubitemid 30626415)
79. A simulated annealing approach to define the genetic structure of populations. Dupanloup I, Schneider S, Excoffier L, Mol Ecol 2002 11 2571 2581 10.1046/j.1365-294X.2002.01650.x 12453240 (Pubitemid 35436677)
80. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Rousset F, Genetics 1997 145 1219 1228 9093870 (Pubitemid 27149123)
81. Statistical tests of neutrality of mutations. Fu YX, Li WH, Genetics 1993 133 693 709 8454210
82. Bayesian coalescent inference of past population dynamics from molecular sequences. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, Mol Biol Evol 2005 22 1185 1192 10.1093/molbev/msi103 15703244 (Pubitemid 40577756)
83. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Slatkin M, Hudson RR, Genetics 1991 129 555 562 1743491
84. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Felsenstein J, Genet Res 1992 59 139 147 10.1017/S0016672300030354 1628818
85. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
86. Rambaut A, Drummond AJ, Tracer v1.4 2007 http://beast.bio.ed.ac.uk/Tracer