Joost Stéphane, Kalbermatten Michael, Bezault Etienne, Seehausen Ole
Laboratory of Geographic Information Systems (LASIG), Institute of Environmental Engineering (IIE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Methods Mol Biol. 2012;888:295-314. doi: 10.1007/978-1-61779-870-2_17.
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.
在基因组中寻找可能处于选择作用下的基因座时，除了群体遗传学理论模型外，另一种方法是为每个基因座建立等位基因分布模型（ADM），以便直接关联等位基因频率与环境变量，如降水量、温度或太阳辐射。在一个名为MATSAM的计算程序中实现了这种并行实施多个逻辑回归模型的方法。最近，该应用程序得到了改进，以支持定性环境预测因子，并允许识别基因组变异与个体表型之间的关联，从而能够检测涉及多态性状遗传结构的基因座。在这里，我们展示了相应的方法学进展，并在一个实证背景下比较了实施群体遗传学理论模型（DFDIST和BAYESCAN）和ADM（MATSAM）的软件所产生的结果，以检测与维多利亚湖丽鱼科鱼类物种形成相关的基因组分化特征。
