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Techniques and statistical data analysis in molecular population genetics

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Abstract

Following the development of PCR methods, molecular techniques have become widely used for detecting genetic variation in natural populations. Most nucleotide changes can be detected by these techniques. Many of these changes probably reflect silent substitutions that are likely to be selectively neutral, making them particularly suitable to population genetic studies. In this paper, we review the published literature on molecular population genetics, with respect to the genome assayed (nuclear, mitochondrial or chloroplast), the organisms studied, the molecular techniques used, and the biological problems addressed. Several molecular techniques are then compared using experimental results obtained from a population genetic study of the Mytilus complex in the North Atlantic and Mediterranean. Finally, the most appropriate theoretical tools to analyse molecular population genetic data are discussed.

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References

  • Allendorf, F. W. & S. R. Phelps, 1981. Use of allelic frequencies to describe population structure. Can. J. Fish. aquat. Sci. 38: 1507–1514.

    Google Scholar 

  • Avise, J. C., 1994. Molecular Markers, Natural History and Evolution. Chapman & Hall, London.

    Google Scholar 

  • Avise, J. C., 1996. Introduction: the scope of conservation genetics. In Avise, J. C. & J. L. Hamrick (eds), Conservation Genetics. Chapman & Hall, New York: 1–9.

    Google Scholar 

  • Avise, J. C. & G. C. Johns, 1999. Proposal for a standardised temporal scheme of biological classification for extant species. Proc. natn. Acad. Sci. U.S.A. 96: 7358–7363.

  • Baker, C. S. & S. R. Palumbi, 1994. Which whales are hunted? A molecular genetic approach to monitoring whaling. Science 265: 1538–1539.

    Google Scholar 

  • Bell, J. & S. B. Friedman, 1994. Genetic structure and diversity within local populations of Bacillus mycoides. Evolution 48: 1698–1714.

    Google Scholar 

  • Bensche, S., D. Hasselquist & T. V. Schants, 1994. Genetic similarity between parents predicts hatching failure: Nonincestuous inbreeding in the great reed warbler? Evolution 48: 317–326.

    Google Scholar 

  • Berry, A. & M. Kreitman, 1993. Molecular analysis of an allozyme cline: Alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America. Genetics 134: 869–893.

    Google Scholar 

  • Beynon, C. M. & D. O. F. Skibinski, 1996. The evolutionary relationships between three species of mussel (Mytilus) based on anonymous DNA polymorphisms. J. exp. mar. Biol. Ecol. 203: 1–10.

    Google Scholar 

  • Block, B. B., A. F. R. Finnerty, A. F. R. Stewart & J. Kidd, 1993. Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny. Science 260: 210–214.

    Google Scholar 

  • Boulding, E. G., J. D. G. Boom & A. T. Beckenbach, 1993. Genetic variation in one bottlenecked and two wild populations of the Japanese scallop (Patinopecten yessoensis): empirical parameter estimates from coding regions of mitochondrial DNA. Can. J. Fish. aquat. Sci. 50: 1147–1157.

    Google Scholar 

  • Brohman, L., A. Rambaut & P. H. Harvey, 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. mol. Evol. 43: 610–621.

    Google Scholar 

  • Cai, Q.-Q. & I. Touitou, 1993. Excess PCR primers may dramatically affect SSCP efficiency. Nucl. Acids Res. 21: 3909–3910.

    Google Scholar 

  • Cavalli-Sforza, L. L. & A. W. F. Edwards, 1967. Phylogenetic analysis: models and estimation procedures. Am. J. hum. Genet. 19: 233–257.

    Google Scholar 

  • Cipriano, F. P. & S. R. Palumbi, 1999. Genetic tracking of a protected whale. Nature 397: 307–308.

    Google Scholar 

  • Clark, A. G., 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111–122.

    Google Scholar 

  • Cluster, P. D. & R. W. Allard, 1995. Evolution of ribosomal DNA (rDNA) genetic structure in colonial Californian populations of Avena barbata. Genetics 139: 941–954.

    Google Scholar 

  • Collins, A. G., 1998. Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence. Proc. natn. Acad. Sci. U.S.A. 95: 15458–15463.

    Google Scholar 

  • Comeron, J., M. Kreitman & M. Aguadé, 1999. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151: 239–249.

    Google Scholar 

  • Côrte-Real, H. B. S. M., D. R. Dixon & P. W. H. Holland, 1994. Intron-targeted PCR: a new approach to survey neutral DNA polymorphism in bivalve populations. Mar. Biol. 120: 407–413.

    Google Scholar 

  • Dowling, T. E., C. Moritz, J. D. Palmer & L. H. Rieseberg, 1996. Nucleic acids III: Analysis of fragments and restriction sites. In Hillis, D. M., C. Moritz & B. K. Mable (eds), Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts: 249–320.

    Google Scholar 

  • Echelle, A. A. & T. E. Dowling, 1992. Mitochondrial DNA variation and evolution of the death valley pupfishes (Cyprinidon, Cyprinodontidae). Evolution 46: 193–206.

    Google Scholar 

  • Edwards, C. A. & D. O. F. Skibinski, 1987. Genetic variation of mitochondrial-DNA in mussel (Mytilus edulis and Mytilus galloprovincialis) populations from south-west England and south Wales. Mar. Biol. 94: 547–556.

    Google Scholar 

  • Edwards, J. H., D. G. Boyd, C. M. Strom, D. Goldman & J. Long, 1995. More on DNA typing dispute. Nature 373: 98–99.

    Google Scholar 

  • Efron, B., 1982. The jackknife, the bootstrap and other resampling plans. Society for Industrial and Applied Mathematics, Philadelphia, Pennsylvania.

    Google Scholar 

  • Elliott, N. G., A. J. Smolenski & R. D. Ward, 1994. Allozyme and mitochondrial DNA variation in orange roughy, Haplostethus atlanticus (Teleostei: Trachichthyidae): little differentiation between Australian and North Atlantic populations. Mar. Biol. 119: 621–627.

    Google Scholar 

  • Fan, E., D. B. Levin, B. W. Glickman & D. M. Logan, 1993. Limitations in the use of SSCP analysis. Mutat. Res. 288: 85–92.

    Google Scholar 

  • Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.

    Google Scholar 

  • Fisher, C. & D. O. F. Skibinski, 1990. Sex-biased mitochondrial DNA heteroplasmy in the marine mussel Mytilus. Proc. r. Soc., Lond. B 242: 149–156.

    Google Scholar 

  • Franklin, I. R. & R. Frankham, 1998. How large must populations be to retain evolutionary potential? Anim. Conserv. 1: 69–70.

    Google Scholar 

  • Fu, Y. X., 1996. Estimating the age of the common ancestor of a DNA sample using the number of segregating sites. Genetics 144: 829–838.

    Google Scholar 

  • Geller, J. B., J. T. Carlton & D. A. Powers, 1994. PCR-based detection of mtDNA haplotypes of native and invading mussels on the northeastern Pacific coast: latitudinal pattern of invasion. Mar. Biol. 119: 243–249.

    Google Scholar 

  • Gillespie, J. H., 1987. Molecular evolution and the neutral allele theory. Oxford Surv. evol. Biol. 4: 10–37.

    Google Scholar 

  • Gillham, N. W., 1994. Organelle Genes and Genomes. Oxford University Press, New York.

    Google Scholar 

  • Goldstein, D. B. & D. D. Pollock, 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J. Hered. 88: 335–342.

    Google Scholar 

  • Goldstein, D. B., A. R. Linares, L. L. Cavalli-Sforza & M. W. Feldman, 1995. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. natn. Acad. Sci. U.S.A. 92: 6723–6727.

    Google Scholar 

  • Goldstein, D. B., G. W. Roemer, D.A. Smith, D. E. Reich, A. Bergman & R. K. Wayne, 1999. The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151: 797–801.

    Google Scholar 

  • Grewe, P. M., C. C. Krueger, C. F. Aquadro, E. Bermingham, H. L. Kincaid & B. May, 1993. Mitochondrial DNA variation among lake trout (Salvelinus namaycush) strains stocked into Lake Ontario. Can. J. Fish. aquat. Sci. 50: 2397–2403.

    Google Scholar 

  • Hall, H., J. Beardmore & D. O. F. Skibinski, 1995. A study of mitochondrial DNA variation in brown trout in Wales. In Sakagawa, G. (ed.), Assessment Methodologies and Management.Proceedings of the World Fisheries Congress, theme 5. Oxford and IBH Publishing, New Delhi: 193–195.

    Google Scholar 

  • Hanfstingl, U., A. Berry, E. A. Kellogg, J. T. Costa III, W. Rudiger & F. M. Ausubel, 1994. Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics 138: 811–828.

    Google Scholar 

  • Harpending, H. C., M. A. Batzer, M. Guiven, M., L. B. Jorde, A. R. Rogers & S. T. Sherry, 1998. Genetic traces of ancient demography. Proc. natn. Acad. Sci. U.S.A. 95: 1961–1967.

    Google Scholar 

  • Hartl, D. L. & A. G. Clark, 1997. Principles of population genetics. Sinauer Associates, Sunderland, Massachusetts.

    Google Scholar 

  • Hayashi, K., 1991. PCR-SSCP: a simple and sensitive method for detection of mutations in the genomic DNA. PCR Meth. Applicat. 1: 34–38.

    Google Scholar 

  • Heath, D. D., P. D. Rawson & T. J. Hilbish, 1995. PCR-based nuclear markers identify alien blue mussel (Mytilus spp.) genotypes on the west coast of Canada. Can. J. Fish. aquat. Sci. 52: 2621–2627.

    Google Scholar 

  • Hedges, S. B., 1992. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol. Biol. Evol. 9: 366–369.

    Google Scholar 

  • Hey, J., 1999. The neutralist, the fly and the selectionist. Trends Ecol. Evol. 14: 35–38.

    Google Scholar 

  • Hillis, D.M. & J. Bull, 1993. An empirical test of bootstrapping as a method for assessing confidence limits in phylogenetic analysis. Syst. Biol. 42: 182–192.

    Google Scholar 

  • Hillis, D. M., C. Moritz & B. K. Mable, 1996a. Molecular Systematics. 2nd edition. Sinauer Associates, Sunderland, Massachusetts.

    Google Scholar 

  • Hillis, D. M., B. K. Mable, A. Larson, S. K. Davis & E. A. Zimmer, 1996b. Nucleic acids IV: Sequencing and cloning. In Hillis, D. M., C. Moritz & B. K. Mable (eds), Molecular Systematics. 2nd edn. Sinauer Associates, Sunderland, Massachusetts: 321–381.

    Google Scholar 

  • Hoech, W. R., K. H. Blakley & W. M. Brown, 1991. Heteroplasmy suggests limited biparental inheritance of Mytilus mitochondrial DNA. Science 251: 1488–1490.

    Google Scholar 

  • Holmes, E. C., M. Worobey & A. Rambaut, 1999. Phylogenetic evidence for recombination in Dengue virus. Mol. Biol. Evol. 16: 405–409.

    Google Scholar 

  • Hughes, A. L. & M. Nei, 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. natn. Acad. Sci. U.S.A. 86: 958–962.

    Google Scholar 

  • Hughes, A. L., M. K. Hughes, C. Y. Howell & M. Nei, 1994. Natural selection at the class II major histocompatibility complex loci of mammals. Phil. Trans. r. Soc. Lond. B 345: 359–367.

    Google Scholar 

  • Hurst, C. D. & D. O. F. Skibinski, 1995. Comparison of allozyme and mitochondrial DNA spatial differentiation in the limpet Patella vulgata. Mar. Biol. 122: 257–263.

    Google Scholar 

  • Innan, H. T. & F. Tajima, 1997. The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population. Genetics. 147: 1431–1444.

    Google Scholar 

  • Jablonski, D., 1986. Larval ecology and macroevolution in marine invertebrates. Bull. mar. Sci. 39: 565–587.

    Google Scholar 

  • Jablonski, D. & R. A. Lutz, 1983. Larval ecology of marine benthic invertebrates: paleobiological implications. Biol. Rev. 58: 21–89.

    Google Scholar 

  • Jackson, J. B. C., 1986. Modes of dispersal of clonal benthic invertebrates: consequences for species' distributions and genetic structure of local populations. Bull. mar. Sci. 39: 58–606.

    Google Scholar 

  • Johannesson, K., B. Johanesson & U. Lundgren, 1995. Strong natural selection causes microscale allozyme variation in a marine snail. Proc. natn. Acad. Sci. U.S.A. 92: 2602–2606.

    Google Scholar 

  • Karl, S. A. & J. C. Avise, 1993. PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: Techniques and applications for population genetics. Mol. Biol. Evol. 10: 342–361.

    Google Scholar 

  • Kasuga, T., J. Cheng & K. R. Mitchelson, 1995. Metastable single-strand DNA conformational polymorphism analysis results in enhanced polymorphism detection. PCR Meth. Applicat. 4: 227–233.

    Google Scholar 

  • Kenchington, E., K. S. Naidu, D. L. Roddick, D. I. Cook & E. Zouros, 1993. Use of biochemical genetic markers to discriminate between adductor muscles of the sea scallop (Placopecten magellanicus) and the Iceland scallop (Chlamys islandica). Can. J. Fish. aquat. Sci. 50: 1222–1228.

    Google Scholar 

  • Kimura, M., 1968. Evolutionary rate at the molecular level. Nature 217: 624–626.

    Google Scholar 

  • Kimura, M., 1995. Limitations of Darwinian selection in a finite population. Proc. natn. Acad. Sci. U.S.A. 92: 2343–2344.

    Google Scholar 

  • Lambert, D. M., C. D. Millar, K. Jack, S. Anderson & J. L. Craig, 1994. Single-and multilocus DNA fingerprinting of communally breeding pukeko: do copulations or dominance ensure reproductive success? Proc. natn. Acad. Sci. U.S.A. 91: 9641–9645.

    Google Scholar 

  • Lander, E. S. & B. Budowle, 1994. DNA fingerprinting dispute laid to rest. Nature 371: 735–738.

    Google Scholar 

  • Lessa, E. P., 1992. Rapid surveying of DNA sequence variation in natural populations. Mol. Biol. Evol. 9: 323–330.

    Google Scholar 

  • Lessa, E. P. & G. Applebaum, 1993. Screening techniques for detecting allelic variation in DNA sequences. Mol. Ecol. 2: 119–129.

    Google Scholar 

  • Lewin, R., 1994. Fact, fiction and fossil DNA. New Scientist 141: 38–41.

    Google Scholar 

  • Lewontin, R. C. & D. L. Hartl, 1994. Forensic DNA typing dispute. Nature 372: 398–399.

    Google Scholar 

  • Lewontin, R. C. & J. L. Hubby, 1966. A molecular approach to the study of genetic heterozygosity in natural populations. II: Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595–609.

    Google Scholar 

  • Lynch, M. & R. Lande, 1998. The critical effective size for a genetically secure population. Anim. Conserv. 1: 70–72.

    Google Scholar 

  • Magoulas, A. & E. Zouros, 1993. Restriction-site heteroplasmy in anchovy (Engraulis encrasicolus) indicates incidental biparental inheritance of mitochondrial DNA. Mol. Biol. Evol. 10: 319–325.

    Google Scholar 

  • McMillan, W. O., R. A. Raff & S. R. Palumbi, 1992. Population genetic consequences of developmental evolution in sea urchins (genus Heliocidaris). Evolution 46: 1299–1312.

    Google Scholar 

  • Morin, P. A., J. J. Moore, R. Chakraborty, L. Jin, J. Goodall & D. S. Woodruff, 1994. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science 265: 1193–1201.

    Google Scholar 

  • Moritz, C., J. W. Wright & W. M. Brown, 1992. Mitochondrial DNA analyses and the origin and relative age of parthenogenetic Cnemidophorus: phylogenetic constraints on hybrid origins. Evolution 46: 184–192.

    Google Scholar 

  • Murphy, R. W., J. W. Sites Jr., D. G. Buth & C. H. Haufler, 1996. Proteins: isozyme electrophoresis. In Hillis, D. M., C. Moritz & B. K. Mable (eds), Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts: 51–120.

    Google Scholar 

  • Nei, M., 1972. Genetic distance between populations. Am. Nat. 106: 283–292.

    Google Scholar 

  • Nei, M., 1973. The theory and estimation of genetic distance. In Norton, N. E. (ed.), Genetic Structure of Populations. University Press of Hawaii, Honolulu: 45–54.

    Google Scholar 

  • Nei, M., 1977. F-statistics and analysis of gene diversity in subdivided populations. Ann. hum. Genet. 41: 225–233.

    Google Scholar 

  • Nei, M., 1983. Genetic polymorphism and the role of mutation in evolution. In Nei, M. & R. Koehn (eds), Evolution of Genes and Proteins. Sinauer Press, Sunderland, Massachusetts: 165–190.

    Google Scholar 

  • Nei, M., 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.

    Google Scholar 

  • Nei, M., 1988. Relative roles of mutation and selection in the maintenance of genetic variability. Phil. Trans. r. Soc., Lond. B 319: 615–629.

    Google Scholar 

  • Nei, M., 1991. Relative efficiencies of different tree-making methods for molecular data. In Miyamoto, M. M. & J. Cracraft (eds), Phylogenetic Analysis of DNA Sequences. Oxford University Press, New York: 90–128.

    Google Scholar 

  • Nei, M., 1996. Phylogenetic analysis in molecular evolutionary genetics. Ann. Rev. Genet. 30: 371–403.

    Google Scholar 

  • Nei, M., J. C. Stephens & N. Saitou., 1985. Methods for computing the standard errors of branching points in an evolutionary tree and their application. Mol. Biol. Evol. 2: 66–85.

    Google Scholar 

  • Nei, M., F. Tajima & Y. Tateno, 1983. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. mol. Evol. 19: 153–170.

    Google Scholar 

  • Nielsen, D. A., A. Novoradovsky & D. Goldman, 1995. SSCP primer design based on single-strand DNA structure predicted by a DNA folding program. Nucl. Acids Res. 23: 2287–2291.

    Google Scholar 

  • Ohresser, M., P. Borsa & C. Delsert, 1997. Intron-length polymorphism at the actin gene locus mac-1: A genetic marker for population studies in the marine mussels Mytilus galloprovincialis Lmk. and M. edulis L. Mol. mar. Biol. Biotechnol. 6: 123–130.

    Google Scholar 

  • Ohta, T., 1974. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature 252: 351–354.

    Google Scholar 

  • Ohta, T., 1992. The nearly neutral theory of molecular evolution. Ann. Rev. Ecol. Syst. 23: 263–286.

    Google Scholar 

  • Oldroyd, B. P., A. J. Smolenski, J.-M. Cornuet & R. H. Crozier, 1994. Anarchy in the beehive. Nature 371: 749.

    Google Scholar 

  • Oldroyd, B. P., J.-M. Cornuet, D. Rowe, T. E. Rinderer & R. H. Crozier, 1995. Racial admixture of Apis mellifera in Tasmania, Australia: similarities and differences with natural hybrid zones in Europe. Heredity 74: 315–325.

    Google Scholar 

  • Olson, R. R. & R. McPherson, 1987. Potential vs. realised larval dispersal: fish predation on larvae of the ascidian Lissoclinum patella (Gottschaldt). J. exp. mar. Biol. Ecol. 110: 245–256.

    Google Scholar 

  • Orr, H. A., 1998. Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics 149: 2099–2104.

    Google Scholar 

  • Ota, T. & M. Nei, 1995. Evolution of immunoglobulin V H pseudogenes in chickens. Mol. Biol. Evol. 12: 94–102.

    Google Scholar 

  • Palumbi, S. R., 1996. Nucleic acids II: the polymerase chain reaction. In Hillis, D. M., C. Moritz & B. K. Mable (eds), Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts: 205–247.

    Google Scholar 

  • Palumbi, S. R. & C. S. Baker, 1994. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol. Biol. Evol. 11: 426–435.

    Google Scholar 

  • Pfennig, D. W. & H. K. Reeve, 1993. Nepotism in a solitary wasp as revealed by DNA fingerprinting. Evolution 47: 700–704.

    Google Scholar 

  • Queller, D. C., J. E. Strassmann & C. R. Hughes, 1993. Microsatellites and kinship. Trends Ecol. Evol. 8: 285–288.

    Google Scholar 

  • Quesada, H., M. Warren & D. O. F. Skibinski, 1999. Nonneutral evolution and differential mutation rate of gender-associated mitochondrial DNA lineages in the marine mussel Mytilus. Genetics 149: 1511–1526.

    Google Scholar 

  • Reich, D. E., M. Feldman & D. B. Goldstein, 1999. Statistical properties of two tests that use multilocus data sets to detect population expansions. Mol. Biol. Evol. 16: 453–466.

    Google Scholar 

  • Ritte, U. & A. Pashtan, 1982. Extreme levels of genetic variability in two Red Sea Cerithium species (Gastropoda: Cerithidae). Evolution 36: 403–407.

    Google Scholar 

  • Rosel, P. E., A. E. Dizon & J. E. Heyning, 1994. Genetic analysis of sympatric morphotypes of commom dolphins (genus Delphinus).Mar. Biol. 119: 159–167.

    Google Scholar 

  • Russo, C. A. M., 1997. Efficiencies of different statistical tests in supporting a known vertebrate phylogeny. Mol. Biol. Evol. 14: 1078–1080.

    Google Scholar 

  • Russo, C. A. M., A. M. Solé-Cava & J. P. Thorpe, 1994. Population structure and genetic variation in two tropical sea anemones (Cnidaria, Actiniidae) with different reproductive strategies. Mar. Biol. 119: 267–276.

    Google Scholar 

  • Rzhetsky, A. & M. Nei, 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9: 945–967.

    Google Scholar 

  • Rzhetsky, A. & M. Nei, 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10: 1073–1095.

    Google Scholar 

  • Saiki, R., D. H. Gelfand, S. Stoffel, S. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis & H. A. Erlich, 1988. Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491.

    Google Scholar 

  • Saitou, N. & T. Imanishi, 1989. Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6: 514–525.

    Google Scholar 

  • Saitou, N. & M. Nei, 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.

    Google Scholar 

  • Sanger, S., S. Nicklen & A. R. Coulson, 1977. DNA sequencing with chain-terminating inhibitors. Proc. natn. Acad. Sci. U.S.A. 74: 5463–5467.

    Google Scholar 

  • Silberman, J. D. & P. J. Walsh, 1994. Population genetics of the spiny lobster, Panulirus argus. Bull. mar. Sci. 54: 1084.

    Google Scholar 

  • Silva, E. P., 1998. Population genetic studies of the mussel Mytilus using nuclear DNA. Unpublished Ph.D. thesis. University of Wales, Swansea.

    Google Scholar 

  • Sitnikova, T., A. Rzhetsky & M. Nei, 1995. Interior branch and bootstrap tests of phylogenetic trees. J. mol. Evol. 12: 319–333.

    Google Scholar 

  • Skibinski, D. O. F., 1994. The potential of DNA techniques in the population and evolutionary genetics of aquatic invertebrates. In Beaumont, A. R. (ed.), Genetics and Evolution of Aquatic Organisms. Chapman & Hall, London: 177–199.

    Google Scholar 

  • Skibinski, D. O. F., C. Gallagher & C. M. Beynon, 1994a. Mitochondrial-DNA inheritance. Nature 368: 817–818.

    Google Scholar 

  • Skibinski, D. O. F., C. Gallagher & C. M. Beynon, 1994b. Sex-limited mitochondrial DNA transmission in the marine mussel Mytilus edulis. Genetics 138: 801–809.

    Google Scholar 

  • Slade, R. W., C. Moritz, A. R. Hoelzel & H. R. Burton, 1998. Molecular population genetics of the southern elephant seal Mirounga leonina. Genetics 149: 1945–1957.

    Google Scholar 

  • Slatkin, M., 1985. Rare alleles as indicators of gene flow. Evolution 39: 53–65.

    Google Scholar 

  • Sneath, P. H. A. & R. R. Sokal, 1973. Numerical taxonomy. W. F. Freeman, San Francisco.

    Google Scholar 

  • Solé-Cava, A. M. & J. P. Thorpe, 1990. High levels of genetic variation in marine sponges. In Rutzler, K. (ed.), New Perspectives in Sponge Biology. Smithsonian Institution Press, Washington: 332–337.

    Google Scholar 

  • Solé-Cava, A. M. & J. P. Thorpe, 1991. High levels of genetic variation in natural populations of marine lower invertebrates. Biol. J. linn. Soc. 44: 65–80.

    Google Scholar 

  • Sturmbauer, C., J. C. Levinton & J. Christy, 1996. Molecular phylogeny analysis of fiddler crabs: test of the hypothesis of increasing behavioral complexity in evolution. Proc. natn. Acad. Sci. U.S.A. 93: 10855–10857.

    Google Scholar 

  • Swanson, W. J. & V. D. Vacquier, 1995. Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. Proc. natn. Acad. Sci. U.S.A. 92: 4957–4961.

    Google Scholar 

  • Takezaki, N. & M. Nei, 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389–399.

    Google Scholar 

  • Tanaka, T. & M. Nei, 1989. Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Mol. Biol. Evol. 6: 447–459.

    Google Scholar 

  • Thorpe, J. P., 1983. Enzyme variation, genetic distance and evolutionary divergence in relation to levels of taxonomic separation. In Oxford, R. S. & D. Rollison (eds), Protein Polymorphism: Adaptive and Taxonomic Significance. Academic Press, London: 131–152.

    Google Scholar 

  • Thorpe, J. P. & A. M. Solé-Cava, 1994. The use of allozyme electrophoresis in invertebrate systematics. Zool. Scr. 23: 3–18.

    Google Scholar 

  • Tufto, J. R., A. F. Raybould, K. Hindar & S. Engen, 1998. Analysis of genetic structure and dispersal patterns in a population of sea beet. Genetics 149: 1975–1985.

    Google Scholar 

  • Van Dongen, S., 1994. How should we bootstrap allozyme data? Heredity 74: 445–447.

    Google Scholar 

  • Varvio, S. L., R. Chakraborty & M. Nei, 1986. Genetic variation in subdivided populations and conservation genetics. Heredity 57: 189–192.

    Google Scholar 

  • Vuorinen, J. A., R. A. Bodaly, J. D. Reist, L. Bernatchez & J. J. Dodson, 1993. Genetic and morphological differentiation between dwarf and normal size forms of lake whitefish (Coregonus clupeaformis) in Como Lake, Ontario. Can. J. Fish. aquat. Sci. 50: 210–216.

    Google Scholar 

  • Wang, D. Y.-C., S. Kumar & S. B. Hedges, 1999. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. r. Soc., Lond. B 266: 163–171.

    Google Scholar 

  • Weiss, G. H. & A. Von Haesler, 1998. Inference of population history using a likelihood approach. Genetics 149: 1539–1546.

    Google Scholar 

  • Welsh, J. & M. McClelland, 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 18: 7213–7218.

    Google Scholar 

  • Wetton, J. H., T. Burke, D. T. Parkin & E. Cairns, 1995. Single-locus DNA fingerprinting reveals that male reproductive sucess increases with age through extra-pair paternity in the house sparrow (Passer domesticus). Proc. r. Soc., Lond. B 260: 91–98.

    Google Scholar 

  • Williams, J. G. K., A. R. Kubelik, K. J. Livak, J. A. Rafalski & S. V. Tingey, 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetics markers. Nucl. Acids Res. 18: 6531–6535. 135

    Google Scholar 

  • Wright, S., 1978. Evolution and the genetics of populations. Vol. 4. Variability within and among natural populations. University of Chicago Press, London.

    Google Scholar 

  • Zhang, J. & M. Nei, 1996. Evolution of antennapedia-class homeo-box genes. Genetics 142: 295–303.

    Google Scholar 

  • Zink, R. M., 1994. The geography of mitochondrial DNA variation, population structure, hybridization, and species limits in the fox sparrow (Passerella iliaca). Evolution 48: 96–111.

    Google Scholar 

  • Zink, R. M. & D. L. Dittmann, 1993. Gene flow, refugia and evolution of geographic variation in the song sparrow (Melospiza melodia). Evolution 47: 717–729.

    Google Scholar 

  • Zouros, E., A. O. Ball, C. Saavedra & K. R. Freeman, 1994a. Mitochondrial DNA inheritance. Nature 368: 817–818.

    Google Scholar 

  • Zouros, E., A. O. Ball, C. Saavedra & K. R. Freeman, 1994b. An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus. Proc. natn. Acad. Sci. U.S.A. 91: 7463–7467.

    Google Scholar 

  • Zouros, E., K. R. Freeman, A. O. Ball & G. H. Pogson, 1992. Direct evidence for extensive paternal mitochondrial-DNA inheritance in the marine mussel Mytilus. Nature 359: 412–414.

    Google Scholar 

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Authors and Affiliations

  1. Lab. Genética Marinha, Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil

    E. P. Silva

  2. Lab. Biodiversidade Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil

    C. A. M. Russo

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  1. E. P. Silva
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Silva, E.P., Russo, C.A.M. Techniques and statistical data analysis in molecular population genetics. Hydrobiologia 420, 119–135 (2000). https://doi.org/10.1023/A:1003993824352

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