期刊论文详细信息
BMC Evolutionary Biology
Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents
Robert C Vrijenhoek4  Richard A Lutz1  Stephen A Karl2  Shannon B Johnson4  D Katharine Coykendall3 
[1] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA;Hawai`i Institute of Marine Biology, University of Hawai`i, Mānoa, Kāne`ohe, HI, USA;USGS-Leetown Science Center, Aquatic Ecology Branch, Kearneysville, WV, USA;Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
关键词: metapopulations;    vent;    Siboglinidae;    Polychaeta;    Annelida;   
Others  :  1144646
DOI  :  10.1186/1471-2148-11-96
 received in 2010-11-05, accepted in 2011-04-13,  发布年份 2011
PDF
【 摘 要 】

Background

Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift.

Results

Genetic differentiation (FST) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically.

Conclusions

Compared to other vent species, DNA sequence diversity is extremely low in R. pachyptila. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events.

【 授权许可】

   
2011 Coykendall et al; licensee BioMed Central Ltd.

【 预 览 】
附件列表
Files Size Format View
20150330221159575.pdf 2464KB PDF download
Figure 3. 17KB Image download
Figure 2. 18KB Image download
Figure 1. 126KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】
  • [1]Wright S: Breeding structure of populations in relation to speciation. Am Natur 1940, 74:232-248.
  • [2]Slatkin M: Gene flow and genetic drift in a species subject to frequent local extinctions. Theor Popul Biol 1977, 12:253-262.
  • [3]Maruyama T, Kimura M: Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent. Proc Natl Acad Sci USA 1980, 77:6710-6714.
  • [4]Slatkin M: Gene flow and the geographic structure of natural populations. Science 1987, 236:787-792.
  • [5]Wade MJ, McCauley DE: Extinction and recolonization: their effects on the genetic differentiation of local populations. Evolution 1988, 42:995-1005.
  • [6]Whitlock M, McCauley D: Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution 1990, 44:1717-1724.
  • [7]Pannell J, Charlesworth B: Neutral genetic diversity in a metapopulation with recurrent local extinction and recolonization. Evolution 1999, 53:664-676.
  • [8]Emerson BC, Paradis E, Thèbaud C: Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol 2001, 16:707-716.
  • [9]Bazin E, Glemin S, Galtier N: Population size does not influence mitochondrial genetic diversity in animals. Science 2006, 312:570-572.
  • [10]Mulligan CJ, Kitchen A, Miyamoto MM: Comment on "Population size does not influence mitochondrial genetic diversity in animals.". Science 2006, 314:1390a.
  • [11]Wares JP, Barber PH, Ross-Ibarra J, Sotka EE, Toonen RJ: Mitochondrial DNA and population size. Science 2006, 314:1388-1389.
  • [12]Vitalis R, Dawson K, Boursot P: Interpretation of variation across marker loci as evidence of selection. Genetics 2001, 158:1811-1823.
  • [13]Galtier N, Depaulis F, Barton N: Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 2000, 155:981-987.
  • [14]Vrijenhoek RC: Gene flow and genetic diversity in naturally fragmented metapopulations of deep-sea hydrothermal vent animals. J Hered 1997, 88:285-293.
  • [15]Vrijenhoek RC: Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations. Mol Ecol 2010, 19:4391-4411.
  • [16]Shea K, Metaxas A, Young CR, Fisher CR: Processes and interactions in macrofaunal assemblages at hydrothermal vents: a modeling perspective. In Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Centers. Volume 178. Edited by Lowell RP, Perfit MR, Seewald J, Metaxas A. Washington, D.C.: Geophysical Monograph Series; 2009::259-274.
  • [17]Chevaldonné P, Jollivet D, Vangrieshiem A, Desbruyères D: Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific. 1. Influence of vent site distribution, bottom currents, and biological patterns. Limnol Oceanogr 1997, 42:67-80.
  • [18]Shank TM, Fornari DJ, Von Damm KL, Lilley MD, Haymon RM, Lutz RA: Temporal and spatial patterns of biological community development at nascent deep-sea hydrothermal vents (9°50'N East Pacific Rise). Deep Sea Res II 1998, 45:465-515.
  • [19]Juniper SK, Tunnicliffe V: Crustal accretion and the hot vent ecosystem. Philos Trans Math Physic Engin Sci 1997, 355:459-474.
  • [20]Lutz RA, Shank TM, Fornari DJ, Haymon RM, Lilley MD, Von Damm KL, Desbruyères D: Rapid growth at deep-sea vents. Nature 1994, 371:663-664.
  • [21]Marsh AG, Mullineaux LS, Young CM, Manahan DT: Larval dispersal potential of the tubeworm Riftia pachyptila at deep-sea hydrothermal vents. Nature 2001, 411:77-80.
  • [22]Kimura M, Weiss WH: The stepping stone model of genetic structure and the decrease of genetic correlation with distance. Genetics 1964, 49:561-576.
  • [23]Audzijonyte A, Vrijenhoek R: When gaps really are gaps: statistical phylogeography of hydrothermal vent invertebrates. Evolution 2010, 64:2369-2384.
  • [24]Black MB, Lutz RA, Vrijenhoek RC: Gene flow among vestimentiferan tube worm (Riftia pachyptila) populations from hydrothermal vents of the Eastern Pacific. Mar Biol 1994, 120:33-39.
  • [25]Hurtado LA, Lutz RA, Vrijenhoek RC: Distinct patterns of genetic differentiation among annelids of eastern Pacific hydrothermal vents. Mol Ecol 2004, 13:2603-2615.
  • [26]Plouviez S, Shank TM, Faure B, Daguin-thiebaut C, Viard F, Lallier FH, Jollivet D: Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the South. Mol Ecol 2009, 18:3903-3917.
  • [27]Plouviez S, Le Guen D, Lecompte O, Lallier F, Jollivet D: Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana. BMC Evol Biol 2010, 10:220. BioMed Central Full Text
  • [28]Shank TM, Halanych KM: Toward a mechanistic understanding of larval dispersal: insights from genomic fingerprinting of the deep-sea hydrothermal vent tubeworm Riftia pachyptila. Mar Ecol 2007, 28:25-35.
  • [29]Fusaro AJ, Baco AR, Gerlach G, Shank TM: Development and characterization of 12 microsatellite markers from the deep-sea hydrothermal vent siboglinid Riftia pachyptila. Mol Ecol Resources 2008, 8:132-134.
  • [30]Boore J, Brown W: Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics 1995, 141:305-319.
  • [31]Jennings RM, Halanych KM: Mitochondrial genomes of Clymenella torquata (Maldanidae) and Riftia pachyptila (Siboglinidae): Evidence for conserved gene order in Annelida. Mol Biol Evol 2005, 22:210-222.
  • [32]Karl SA, Avise JC: PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics. Mol Biol Evol 1993, 10:342-374.
  • [33]Jarman SN, Ward RD, Elliott NG: Oligonucleotide primers for PCR amplification of coelomate introns. Mar Biotech 2002, 4:347-355.
  • [34]Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001, 68:978-989.
  • [35]Stephens M, Donnelly P: A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 2003, 73:1162-1169.
  • [36]Clement M, Posada D, Crandall KA: TCS: a computer program to estimate gene genealogies. Mol Ecol 2000, 4:331-346.
  • [37]Excoffier , Lischer H: Arlequin ver 3.5: an integrated software package for population genetics data analysis. Swiss Institute of Bioinformatics 2009, 1-174.
  • [38]Watterson GA: On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975, 7:256-276.
  • [39]Fu YX: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
  • [40]Nei M: Molecular Evolutionary Genetics. New York, NY, USA: Columbia University Press; 1987.
  • [41]Kalinowsky S: Hp-Rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 2005, 5:187-189.
  • [42]Raymond M, Rousset F: Genepop (Ver. 1.2): population genetics software for exact tests and ecumenicism. J Hered 1995, 86:248-249.
  • [43]Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
  • [44]Casgrain P, Legendre P: The R Package for Multivariate and Spatial Analysis. [http://www.bio.umontreal.ca/casgrain/en/labo/R/index.html] webciteDépartement de sciences biologiques, Université de Montréal; 2001. v. 4.0 d6 - Users Manual.
  • [45]Smouse PE, Long JC, Sokal RR: Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst Zool 1986, 35:627-632.
  • [46]Beaumont MA, Nichols RA: Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B 1996, 263:1619-1626.
  • [47]Antao T, Lopes A, Lopes R, Beja-Pereira A: Lositan: A workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinform 2008, 9:323. BioMed Central Full Text
  • [48]DeMets C, Gordon RG, Argus DF, Stein S: Current plate motions. Geophys J Int 1990, 101:425-478.
  • [49]DeMets C, Gordon RG, Argus DF, Stein S: Effect of recent revisions to the geomagnetic reversal time scale on estimates of current plate motions. Geophys Res Let 1994, 21:2191-2194.
  • [50]Soudarin L, Cazenave A: Large-scale tectonic plate motions measured with the DORIS space geodesy system. Geophys Res Let 1995, 22:469-472.
  • [51]Birky CWJ, Maruyama T, Fuerst P: An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 1983, 103:513-527.
  • [52]Crochet P: Genetic structure of avian populations--allozymes revisited. Mol Ecol 2000, 9:1463-1469.
  • [53]Reid JL: On the total geostrophic circulation of the South Pacific Ocean: Flow patterns, tracers and transports. Progr Oceanogr 1986, 16:1-61.
  • [54]Slatkin M: Isolation by distance in equilibrium and non-equilibrium populations. Evolution 1993, 47:264-279.
  • [55]Jollivet D, Chevaldonné P, Planque B: Hydrothermal-vent alvinellid polychaete dispersal in the Eastern Pacific. 2. A metapopulation model based on habitat shifts. Evolution 1999, 53:1143-1156.
  • [56]MacDonald KC: Linkages between faulting, volcanism, hydrothermal activity and segmentation on fast spreading centers. In Faulting and Magmatism at Mid-Ocean Ridges. Edited by Buck W, Delaney P, Karson J, Lagabrielle Y. Washington, DC: American Geophysical Union; 1998:27-58.
  • [57]Hey R, Massoth G, Vrijenhoek R, Rona P, Lupton J, Butterfield D: Hydrothermal vent geology and biology at Earth's fastest spreading rates. Mar Geophys Res 2006, 27:137-153.
  • [58]Van Dover CL: Community structure of mussel beds at deep-sea hydrothermal vents. Mar Ecol Prog Ser 2002, 230:137-158.
  • [59]Jollivet D, Lallier FH, Barnay AS, Bienvenue N, Bonnivard N, Briand P, Cambon-Bonavita MA, Comtet T, Cosson R, Daguin C, et al.: The BIOSPEEDO cruise: a new survey of hydrothermal bens along the South East Pacific Rise from 7°24'S to 21°33'S. InterRidge News 2004, 13:20-26.
  • [60]Teixeira S, Cambon-Bonavita MA, Serrão E, Desbruyères D, Arnaud-Haond S: Recent population expansion and connectivity in the hydrothermal shrimp Rimicaris exoculata along the Mid-Atlantic Ridge. J Biogeogr 2010, 38:264-574.
  • [61]Kyuno A, Shintaku M, Fujita Y, Matsumoto H, Utsumi M, Watanabe H, Fujiwara Y, Miyazaki JI: Dispersal and differentiation of deep-sea mussels of the genus Bathymodiolus (Mytilidae, Bathymodiolinae). J Mar Biol 2009. Article ID625672:15 pages
  • [62]Young CR, Fujio S, Vrijenhoek RC: Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae. Mol Ecol 2008, 17:1718-1731.
  • [63]Johnson SB, Young CR, Jones WJ, Warén A, Vrijenhoek RC: Migration, Isolation, and Speciation of Hydrothermal Vent Limpets (Gastropoda; Lepetodrilidae) Across the Blanco Transform Fault. Biol Bull 2006, 210:140-157.
  文献评价指标  
  下载次数:3次 浏览次数:7次