G<scp>eneland</scp>: a computer package for landscape genetics

TLDR

Geneland is a software that uses georeferenced multilocus genotypes to infer the number of populations and the spatial locations of genetic discontinuities. It models an unknown number of populations as equally likely, assumes Hardy–Weinberg equilibrium within each, represents populations as polygons, and treats allele frequencies as random variables under Dirichlet or Falush models, implementing algorithms that output posterior probabilities. In a simulated dataset, Geneland produced a histogram of inferred population numbers and a map of posterior membership probabilities, demonstrating its inference capabilities.

Abstract

Abstract Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy–Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so‐called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland.