IBD (Isolation by Distance): a program for analyses of isolation by distance.

Abstract

The genetic similarity among individuals or populations can be ascertained using a number of statistical techniques (reviewed by Bohonak 1999; Neigel 1997; Roderick 1996; Slatkin 1985). When populations can be defined a priori, one option is to analyze genetic ‘‘isolation by distance’’ (sensu Wright 1943) by plotting the genetic similarity (or distance) among population pairs as a function of the geographic distance between those pairs. Slatkin (1993) suggested the genetic distance M (1/FST 1)/4 as an appropriate similarity measure, although other approaches are possible (e.g., Epperson and Li 1996). Qualitative and statistical analyses of isolation by distance can reveal much about population genetic structure. The primary use for plots of (genetic) isolation by (geographic) distance is to assess whether more distant population pairs are more different genetically. However, these plots can also be used to test the validity of simpler models of population structure (e.g., island or hierarchical island models). Isolation by distance analyses may help separate the effects of population history from ongoing gene flow, and test the explanatory power of alternative dispersal pathways (Slatkin 1994). For example, one might assess whether the distance along a river or a topographic isocline is more biologically relevant than distance ‘‘as the crow flies.’’ The influence of geographic features or specific life-history traits on population differentiation can also be tested. Peterson and Denno (1998) contrasted isolation by distance slopes and intercepts in species with different dispersal abilities. IBD version 1.1 is a program written in C and compiled for Macintosh and Windows that can be used for analyses of isolation by distance. This program provides a number of unique features: isolation by distance slopes and intercepts are calculated using reduced major axis (RMA) regression, confidence intervals are generated based on several different assumptions regarding data structure, and statistical significance is determined using Mantel tests. The program is freely available at http:// www.bio.sdsu.edu/pub/andy/IBD.html.