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The evolution of molecular markers — just a matter of fashion?

Nature Reviews Genetics volume 5, pages 63–69 (2004)Cite this article

Abstract

In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest techniques promise to provide cheap, high-throughput methods for genotyping existing markers, but might other traditional approaches offer better value for some applications?

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Figure 1: Subjective view of the the changing relative importance of different molecular markers.

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Acknowledgements

I am very thankful to R. Achmann, B. Harr, M.-T. Hauser, R. Nielsen, T. Leeb, C. Vogl and two anonymous reviewers for helpful discussion/comments on earlier versions of the manuscript. The laboratory of C.S. is supported by grants from the Fonds zur Förderung der Wissenschaftlichen Forschung and the European Union.

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  1. Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Josef Baumann Gasse 1, Wien, 1210, Austria

    Christian Schlötterer

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DATABASES

FlyBase

Adh

FURTHER INFORMATION

HapMap

Molecular Ecology

Glossary

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM

(AFLP). This marker system uses DNA fragments that are ligated to complementary adaptor oligonucleotides and subsequent rounds of PCR amplification using primers that are complementary to the adaptor sequences. The multiple rounds of amplification reduce the complexity of the PCR product population so that the amplified fragments can be easily resolved by gel electrophoresis.

ADMIXTURE

Gene flow between differentiated populations.

ASCERTAINMENT BIAS

Systematic bias introduced by the criteria used to select individuals and/or loci in which genetic variation is assayed; a pronounced problem for single nucleotide polymorphism (SNP) and restriction fragment length polymorphism (RFLP) analyses.

ASSOCIATION STUDY

A study that aims to identify the joint occurrence of two genetically encoded characteristics in a population. Often, an association between a genetic marker and a phenotype (disease) is assessed.

EUCHROMATIN

Part of an interphase chromosome that stains diffusely; less condensed than the heterochromatin.

F ST

Wright's among-population fixation index. A measure of the extent of population subdivision.

GENE CONVERSION

Non-reciprocal exchange of genetic material among chromosomes.

INTER-RETROTRANSPOSON AMPLIFIED POLYMORPHISM

(IRAP). DNA fragments found between adjacent, oppositely oriented retrotransposons, amplified through PCR, separated by gel electrophoresis and scored for the presence or absence of fragments.

INTER-SIMPLE-SEQUENCE-REPEAT

(ISSR). DNA fragments found between adjacent, oppositely oriented microsatellites, amplified through PCR, separated by gel electrophoresis and scored for the presence or absence of fragments.

LINKAGE DISEQUILIBRIUM

Haplotype frequencies in a population that differ from expectations based on a random combination of alleles at each locus.

PHYLOGENETIC RECONSTRUCTION

Attempt to reconstruct the ancestral relationship among species or populations.

RANDOMLY AMPLIFIED POLYMORPHIC DNA

(RAPD). A marker system that relies on the use of short PCR primers.

RESTRICTION FRAGMENT LENGTH POLYMORPHISM

(RFLP). A fragment length variant that is generated through the presence/absence of a restriction enzyme recognition site. Restriction sites could be gained/lost by base substitutions, insertions or deletions.

STUTTER BANDS

Artifacts that occur by DNA-replication slippage during the PCR amplification of microsatellites. Most stutter bands are shorter than the actual microsatellite allele.

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Schlötterer, C. The evolution of molecular markers — just a matter of fashion?. Nat Rev Genet 5, 63–69 (2004). https://doi.org/10.1038/nrg1249

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