Format

Send to

Choose Destination
See comment in PubMed Commons below
Methods Mol Biol. 2012;888:295-314. doi: 10.1007/978-1-61779-870-2_17.

Use of qualitative environmental and phenotypic variables in the context of allele distribution models: detecting signatures of selection in the genome of Lake Victoria cichlids.

Author information

1
Laboratory of Geographic Information Systems (LASIG), Institute of Environmental Engineering (IIE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. stephane.joost@epfl.ch

Abstract

When searching for loci possibly under selection in the genome, an alternative to population genetics theoretical models is to establish allele distribution models (ADM) for each locus to directly correlate allelic frequencies and environmental variables such as precipitation, temperature, or sun radiation. Such an approach implementing multiple logistic regression models in parallel was implemented within a computing program named MATSAM: . Recently, this application was improved in order to support qualitative environmental predictors as well as to permit the identification of associations between genomic variation and individual phenotypes, allowing the detection of loci involved in the genetic architecture of polymorphic characters. Here, we present the corresponding methodological developments and compare the results produced by software implementing population genetics theoretical models (DFDIST: and BAYESCAN: ) and ADM (MATSAM: ) in an empirical context to detect signatures of genomic divergence associated with speciation in Lake Victoria cichlid fishes.

PMID:
22665288
DOI:
10.1007/978-1-61779-870-2_17
[Indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Springer
    Loading ...
    Support Center