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

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An Erratum to this article was published on 08 December 2006

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.

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Abbreviations

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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  1. Centre d’Océanologie de Marseille Laboratoire DIMAR, UMR CNRS 6540-Université de la Méditerranée Chemin de la batterie des Lions, 13007, Marseille, France

    Chenuil Anne

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An erratum to this article is available at http://dx.doi.org/10.1007/s10709-006-9118-1.

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Anne, C. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects. Genetica 127, 101–120 (2006). https://doi.org/10.1007/s10709-005-2485-1

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