We can determine θs for pairs of genes or loci. Next question is how to place them in a genetic map; i.e., grouping loci into linkage groups and ordering sets of 3 or more loci. 1. Grouping loci into linkage groups The question beyond determining linkage of any two loci is the ordering of the loci into a reasonable genetic map. Ordering can be done using the MLE of θ, determined via a two-point...

Expressed sequence tag (EST) markers were developed for Ambystoma tigrinum tigrinum (Eastern tiger salamander) and for A. mexicanum (Mexican axolotl) to generate the first comprehensive linkage map for these model amphibians. We identified 14 large linkage groups (125.5-836.7 cM) that presumably correspond to the 14 haploid chromosomes in the Ambystoma genome. The extent of genome coverage for ...

The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises...