Supplement 1. Colonize: a tool to estimate the number of individuals colonizing a new habitat.

File List All files at once colonize_linux.zip -- all files for Linux at once colonize_windows.zip -- all files for Windows at once Source code colonize.cpp -- C++ source code Manual colonize_manual.pdf -- manual in portable document format Example files example.dat -- example file Executables colonize -- executable for Linux operating systems colonize.exe -- executable for Windows operating systems Readme files readme_linux.txt -- installation instructions for Linux readme_windows.txt -- installation instructions for Windows Description We provide the source code and executables for Windows and Linux operating systems, and a short description of the program. The software program Colonize was developed to estimate the range of colonizers allowed to account for the observed allele frequencies in a sampled focal population given the observed allele frequencies in a sampled source population. This is done by creating random samples based on source and target population samples and given a number of colonists, and comparing the observed differences in allelic composition with the difference between the original samples. In this way probabilities are calculated for the minimum and maximum number of individuals colonizing the focal population. These probabilities can then be combined in a joint probability for each number of colonizers. There are a few assumptions to be met: there is no gametic linkage disequilibrium among the analyzed loci, and there has been no substantial genetic drift in source nor target population between the time of colonization and the moment of sampling. The program is available in a Windows and Linux version from [e-mail] and from the website http://bio.kuleuven.be/eco/colonize, as well as in the Ecological Archives Supplements.