Linked vs. unlinked markers: Multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression

Wim J.M. Koopman, Yinghui Li, Els Coart, W. Eric Van De Weg, Ben Vosman, Isabel Roldán-Ruiz, Marinus J.M. Smulders

Research output: Contribution to journalArticlepeer-review


We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F ST based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.

Original languageEnglish
Pages (from-to)243-256
Number of pages14
JournalMolecular Ecology
Issue number2
StatePublished - Jan 2007
Externally publishedYes


  • Conservation
  • Gene flow
  • Haplotype
  • Introgression

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


Dive into the research topics of 'Linked vs. unlinked markers: Multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression'. Together they form a unique fingerprint.

Cite this