Genetica

, Volume 127, Issue 1–3, pp 101–120 | Cite as

Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects

Article

Abstract

The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique.

Keywords

biodiversity choice molecular evolution molecular marker practice substitution rate 

Abbreviation

AFLP

Amplification fragment length polymorphism

ARRF

Anonymous rare-cutter restriction fragments

CAPS

Cleaved amplified polymorphic sequence

DALP

Direct amplification of length polymorphism

DGGE

Denaturing gradient gel electrophoresis

ETS

External transcribed spacer (of rDNA)

FISH

Fluorescent in situ hybridization

ILP

Intron length polymorphism

ISSR

Inter-simple sequence repeat

ITS

Internal transcribed spacer

MGM

Molecular genetic marker

ORF

Open reading frame

PCR

Polymerizing chain reaction

RAPD

Random amplified polymorphic DNA

RFLP

Restriction fragment length polymorphism

RSCA

Reference Strand Conformation Analysis

rDNA

Ribosomal DNA

SNP

Single nucleotide polymorphism

SSCP

Single-strand conformation polymorphism

ssDNA

Single-strand DNA

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References

  1. Amann, R.I, Ludwig, W., Schleifer, K.H. 1995Phylogenetic identification and in situ detection of individual microbial cells without cultivationMicrobiol Rev59143169PubMedGoogle Scholar
  2. Atarhouch, T., Rami, M., Cattaneo-Berrebi, G., Ibanez, C., Augros, S., Boissin, E., Dakkak, A., Berrebi, P. 2003Primers for EPIC amplification of intron sequences for fish and other vertebrate population genetic studiesBiotechniques35676682Google Scholar
  3. Atienzar, F., Evenden, A., Jha, A., Savva, D., Depledge, M. 2000Optimized RAPD analysis generates high-quality genomic DNA profiles at high annealing temperatureBiotechniques285254PubMedGoogle Scholar
  4. Avise, J.C. 1994Molecular markers, Natural history and EvolutionChapman & HallNew-York-LondonGoogle Scholar
  5. Bierne, N., Lehnert, S.A., Bedier, E., Bonhomme, F., Moore, S.S. 2000Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCRMol Ecol9233235PubMedCrossRefGoogle Scholar
  6. Bois, P.J.A. 1999Minisatellite instability and germline mutationCell Mol Life Sci5516361648PubMedCrossRefGoogle Scholar
  7. Buonaccorsi, V.P., McDowell, J.R., Graves, J.E. 2001Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue-marlin (Makaira nigricans)Mol Ecol1011791196PubMedCrossRefGoogle Scholar
  8. Caccone, A., Milinkovitch, M.C., Sbordoni, V., Powell, J.R. 1997Mitochondrial DNA rates and biogeography in European newts (genus Euproctus)Syst Biol46126144PubMedGoogle Scholar
  9. Carvalho G.R., 1998. Molecular Ecology: Origins and Approach. In: Carvalho GR (ed) Advances in Molecular Ecology, IOS Press pp 1–16Google Scholar
  10. Chenuil, A., Le Gac, M., Thierry, M. 2003Fast isolation of microsatellite loci of very diverse repeat motifs by library enrichment. Application in echinoderms. (Technical note)Mol Ecol Notes3324327CrossRefGoogle Scholar
  11. Chevaldonné, P., Jollivet, D., Desbruyéres, D., Lutz, R., Vrijenhoek, R. 2002Sister-species of eastern Pacific hydrothermal vent worms (Ampharetidae, Alvinellidae, Vestimentifera) provide new mitochondrial COI clock calibrationCah Biol Mar43367370Google Scholar
  12. Crochet, P-A., Desmarais, E. 2000Slow rate of evolution in the mitochondrial control region of gulls (Ayes:Laridae)Mol Biol Evol1717971806PubMedGoogle Scholar
  13. Davies, N., Villablanca, F.X., Roderick, G.K. 1999Determining the source of individuals:multilocus genotyping in nonequilibrium population geneticsTrends Ecol Evol141721PubMedCrossRefGoogle Scholar
  14. Desmarais, E., Lanneluc, I., Lagnel, J. 1997Direct amplification of length polymorphisms (DALP), or how to get and characterise new genetic markers in many speciesNucleic Acids Res2614581465CrossRefGoogle Scholar
  15. Després, L., Imbert-Establet, D., Combes, C., Bonhomme, F. 1992Molecular evidence linking hominid evolution to recent radiation of Schistosomes (Platyhelminthes:Trematoda)Mol Phyl Evol1295304CrossRefGoogle Scholar
  16. DeWoody, J.A., Avise, J.C. 2000Microsatellite variation in marine, freshwater and anadromous fishes compared with other animalsJ Fish Biol56461473CrossRefGoogle Scholar
  17. Dowling, T.E., Moritz, C., Palmer, J.D., Rieseberg, L.H. 1996

    Nucleic Acids III:Analysis of fragments and restriction sites

    Hillis, D.M.Moritz, C.Mable,  B.K. eds. in Molecular SystematicsSinauer Associates, IncSunderland, Massachusetts249320
    Google Scholar
  18. Ellegren, H. 2000Microsatellite mutations in the germline:implications for evolutionary inferenceTrends Genet16551558PubMedCrossRefGoogle Scholar
  19. Estoup, A., Angers, B. 1998

    Microsatellites and minisatellites for molecular ecology:theoretical and empirical considerations

    Carvalho, G.R. eds. in Advances in molecular ecologyIOS PressAmsterdam5586
    Google Scholar
  20. Féral, J-P. 2002How useful are genetic markers in attempts to understand and manage marine biodiversity?J Exp Mar Biol Ecol268121145CrossRefGoogle Scholar
  21. Fridolfsson, A-K., Ellegren, H. 2000Molecular evolution of the avian CHD1 genes on the Z and W sex chromosomesGenetics15519031912PubMedGoogle Scholar
  22. Gerber, S., Mariette, S., Streiff, R., Bodenes, C., Kremer, A. 2000Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysisMol Ecol910371048PubMedCrossRefGoogle Scholar
  23. Gielly, L., Taberlet, P. 1994The use of chloroplast DNA to resolve plant phylogenies:noncoding versus rbcL sequencesMol Biol Evol11769777PubMedGoogle Scholar
  24. Goldman, J., Madrigal, J. 1997Complementary strand analysis:a new approach for allelic separation in complex polyallelic genetic systemsNucleic acids Res2522362238PubMedCrossRefGoogle Scholar
  25. Graur, D, Li, W.-H. 2000Fundamentals of Molecular EvolutionSinauer Associates, IncSunderland, MassachussetsGoogle Scholar
  26. Hauser, M.-T., Adhami, F., Dorner, M., Fuchs, E., Gössl, J. 1998Generation of co-dominant PCR-based markers by duplex analysis on high resolution gelsPlant J19117125CrossRefGoogle Scholar
  27. Hillis, D.M., Dixon, M.T. 1991Ribosomal DNA:molecular evolution and phylogenetic inferenceQ Rev Biol66411427PubMedCrossRefGoogle Scholar
  28. Jarman, S.N., Ward, R.D., Elliott, N.G. 2002Oligonucleotide primers for PCR amplification of coelomate intronsMar Biotechnol4347355PubMedCrossRefGoogle Scholar
  29. Kayser, M., Roewer, L., Hedman, M., Henke, L., Henke, J., Brauer, S., Kruger, C., Krawczak, M., Nagy, M., Dobosz, T., Szibor, R., Knijff, P., Stoneking, M., Sajantila, A. 2000Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairsAm J Hum Genet6615801588PubMedCrossRefGoogle Scholar
  30. Konieczny, A., Ausubel, F.M. 1993A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-bases markersPlant J4403410PubMedCrossRefGoogle Scholar
  31. Kwok, P.-Y., Chen, X. 2003Detection of Single Nucleotide PolymorphismCurr Issues Mol Biol54360PubMedGoogle Scholar
  32. Laporte, V., Charlesworth, D. 2001Non-sex linked, nuclear cleaved amplified polymorphic sequences in Silene latifolia J Hered92357359PubMedCrossRefGoogle Scholar
  33. Lessios, H.A., Kessing, B.D., Robertson, D.R., P.G.,  1999Phylogeography of the pantropical sea urchin Eucidaris in relation to land barriers and ocean currentsEvolution53806817CrossRefGoogle Scholar
  34. Linder, C.R., Goertzen, L.R., Heuvel, B.V., Francisco-Ortega, J., Jansen, R.K. 2000The complete external transcribed spacer of 18S-26S rDNA:amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied familiesMol Phyl Evol14285303CrossRefGoogle Scholar
  35. Luikart, G., England, P.R. 1999Statistical analysis of microsatellite DNA dataTrends Ecol Evol14632638Google Scholar
  36. Martin, P.G., Dowd, J.M. 1991A comparison of 18S ribosomal RNA and rubisco large subunit sequences for studying angiosperm phylogenyJ Mol Evol33274282PubMedCrossRefGoogle Scholar
  37. Myers, R.M., Maniatis, T., Lerman, L.S. 1987Detection and localization of single base changes by denaturing gradient gel electrophoresisMethods Enzymol155501527PubMedCrossRefGoogle Scholar
  38. Nagai, K. 2001Molecular evolution of Sry and Sox geneGenetics270161169Google Scholar
  39. Nielsen, R. 2001Statistical tests of selective neutrality in the age of genomicsHeredity86641647PubMedCrossRefGoogle Scholar
  40. Ohresser, M., Borsa, P., Delsert, C. 1997Intron-length polymorphism at the actin locus Mac-1:a genetic marker for population studies in the marine mussels Mytilus galloprovincialis Lmk. and M. edulis LMol Mar Biol Biotechnol6123130PubMedGoogle Scholar
  41. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., Sekiya, T. 1989Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphismsProc Natl Acad Sci USA8627662770PubMedCrossRefGoogle Scholar
  42. Palmer, J.D., Adams, K.L., Cho, Y., Parkinson, C.L., Qiu, Y.L., Song, K. 2000Dynamic evolution of plant mitochondrial genomes:mobile genes and introns and highly variable mutation ratesProc Natl Acad Sci U S A9769606966PubMedCrossRefGoogle Scholar
  43. Palumbi, A.R., Cipriano, F., Hare, M.H. 2001Predicting nuclear gene coalescence from mitochondrial data:the three-times ruleEvolution55859868PubMedCrossRefGoogle Scholar
  44. Palumbi, S.R. 1996

    Nucleic Acids II:The polymerase chain reaction

    Hillis, D.M.Moritz, C.Mable.,  B.K. eds. in Molecular systematicsSinauerSunderland, Massachussetts205247
    Google Scholar
  45. Pamilo, P., Bianchi, N.O. 1993Evolution of the Zfx and Zfy genes:rates and interdependence between the genesMol Biol Evol10271281PubMedGoogle Scholar
  46. Pamilo, P., O’Neill, R.J. 1997Evolution of the Sry genesMol Biol Evol144955PubMedGoogle Scholar
  47. Pelandakis, M., Solignac, M. 1993Molecular phylogeny of Drosophila based on ribosomal RNA sequencesJ Mol Evol37525543PubMedCrossRefGoogle Scholar
  48. Pesole, G., Gissi, C., Chirico, A., Saccone, C. 1999Nucleotide substitution rate of mammalian mitochondrial genomesJ Mol Evol48427434PubMedCrossRefGoogle Scholar
  49. Poteaux, C., Bonhomme, F., Berrebi, P. 1999Microsatellite polymorphism and genetic impact of restocking in Mediterranean brown trout (Salmo trutta L.)Heredity82645653PubMedCrossRefGoogle Scholar
  50. Provan, J., Soranzo, N., Wilson, NJ., Goldstein, DB., Powell, W. 1999A low mutation rate for chloroplast microsatellitesGenetics153943947PubMedGoogle Scholar
  51. Prugnolle, F., Mee\^u, T. 2002Inferring sex-based dispersal from population genetic tools:a reviewHeredity88161165PubMedCrossRefGoogle Scholar
  52. Qu L.H., 1986. Structuration et evolution de I’ARN ribosomique 28S chez Ies eucaryotes. Etude systématique de la région 5’ terminale. Ph<D, Paul Sabatier de ToulouseGoogle Scholar
  53. Roger, A., Sandblom, O., Ford Doolittle, W., Philippe, H. 1999An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotesMol Biol Evol16218233PubMedGoogle Scholar
  54. Rokas, A., Nylander, J.A., Ronquist, F., Stone, G.N. 2002A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera:Cynipidae):implications for insect phylogenetic studiesMol Phylogenet Evol22206219PubMedCrossRefGoogle Scholar
  55. Sambrook, J., Fritsch, E.F., Maniatis, T. 1989Molecular cloning. A laboratory manual2Cold Spring Harbor Laboratory PressUSAGoogle Scholar
  56. Slattery, J.P., O’Brien, S.J. 1998Patterns of Y and X chromosome DNA sequence divergence durign the Felidae radiationGenetics14812451255Google Scholar
  57. Sorhannus, U. 1996Higher ribosomal RNA substitution rates in Bacillariophyceae and Dasycladales than in Mollusca, Echinodermata, and Actinistia-TetrapodaMol Biol Evol1310321038PubMedGoogle Scholar
  58. Sunnucks, P. 2000Efficient genetic markers for population biologyTrends Ecol Evol15199203PubMedCrossRefGoogle Scholar
  59. Sunnucks, P., Wilson, A.C., Beheregaray, L.B., Zenger, K., French, J., Taylor, A.C. 2000SSCP is not so difficult:the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecologyMol Ecol916991710PubMedCrossRefGoogle Scholar
  60. Templeton, A. 1998Nested clade analyses of phylogeographic data:testing hypotheses about gene flow and population historyMol Ecol7381397PubMedCrossRefGoogle Scholar
  61. Tourasse, N.J., Gouy, M. 1997Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimonyMol Biol Evol14287298PubMedGoogle Scholar
  62. Vitalis, R., Couvet, D. 2001Estimation of effective population size and migration rate from one-and two-locus identity measuresGenetics157911925PubMedGoogle Scholar
  63. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M.e.a. 1995AFLP:a new technique for DNA fingerprintingNucleic Acids Res2344074414PubMedGoogle Scholar
  64. Walsh, P.S., Metzger, D.A., Higushi, R. 1991Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic materialBiotechniques10506513PubMedGoogle Scholar
  65. Ward, R.D., Woodwark, M., Skibinski, D.O.F. 1994A comparison of genetic diversity levels in marine, freshwater, and anadromous fihesJ Fish Biol44213232CrossRefGoogle Scholar
  66. Waser, P.M., Strobeck, C. 1998Genetic signatures of interpopulation dispersalTrend Ecol Evol134344CrossRefGoogle Scholar
  67. Wattier, R., Engel, C.R., Saumitou-Laprade, P., Valero, M. 1998Short allele dominance as a source of heterozygote deficiency at microsatellite loci:experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta)Mol Ecol715691573CrossRefGoogle Scholar
  68. White, H.W., Kusukawa, N. 1997Agarose-based system for separation of short tandem repeat lociBiotechniques22976980PubMedGoogle Scholar
  69. Yang, Z., Bielawski, J.P. 2000Statistical methods for detecting molecular adaptationTrends Ecol Evol15496503PubMedCrossRefGoogle Scholar
  70. Zane, L., Bargelloni, L., Patarnello, T. 2002Strategies for microsatellite isolation:a reviewMol Ecol11116PubMedCrossRefGoogle Scholar
  71. Zhang, D.-X., Hewitt, G.M. 2003Nuclear DNA analyses in genetic studies of populations:practice, problems and prospectsMol Ecol12563584PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  1. 1.Centre d’Océanologie de Marseille Laboratoire DIMARUMR CNRS 6540-Université de la Méditerranée Chemin de la batterie des LionsMarseilleFrance

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