¹Department of Ecology, Montana State University, Lewis Hall, Bozeman, MT, USA

Correspondence: Dr ST Kalinowski, Department of Ecology, Montana State University, 310 Lewis Hall, Bozeman, MT 59717, USA. E-mail: skalinowski@montana.edu

Received 2 September 2008; Revised 10 November 2008; Accepted 23 December 2008; Published online 28 January 2009.

Abstract

Bifurcating evolutionary trees are commonly used to describe genetic relationships between populations, but may not be appropriate for populations that did not evolve in a hierarchical manner. The degree to which bifurcating trees distort genetic relationships between populations can be quantified with R², the proportion the variation in a matrix of genetic distances between populations that is explained by a tree. Computer simulations were used to measure how well the unweighted pair group method with arithmetic mean (UPGMA) and neighbor-joining (NJ) trees depicted population structure for three evolutionary models: a hierarchical model of population fragmentation, a linear stepping-stone model of gene flow and a two-dimensional stepping-stone model of gene flow. These simulations showed that the UPGMA did an excellent job of describing population structure when populations had a bifurcating history of fragmentation, but severely distorted genetic relationships for the linear and two-dimensional stepping-stone models. The NJ algorithm worked well in a broader range of evolutionary histories, including the linear stepping-stone model. A computer program for performing the calculations described in this study is available for download at www.montana.edu/kalinowski.