Prospects for nuclear gene phylogeography

umail.umd.edu Over the past decade, phylogeography grew as a discipline because allelic phylogenies provided explicitly historical tools for the study of geographical subdivision among populations1.Analysing the relative ages and historical relationships of alleles in a geographical context could distinguish ongoing processes such as GENE FLOW (see Glossary) from previous events such as range expansion. The temporal resolution offered by genealogies was previously unavailable through classical population genetic analyses (e.g. hierarchical partitioning of variation using F-statistics)2. In addition, using alleles rather than populations as the basic unit in phylogenetic clustering promoted integrated analyses of history above and below the species level without the need to make a priori taxonomic distinctions. Animal mitochondrial (mt)DNA and chloroplast (cp)DNA have been the primary data sources making phylogeography such a productive empirical approach. Extending and generalizing phylogeography by using nuclear HAPLOTYPE data has been a desirable goal in efforts to test ever more sophisticated historical models. However, given the potential for technical and biological complications when analysing nuclear haplotype data at the intraspecific level, it has been uncertain whether a phylogeographical study design could generally be extended to noncytoplasmic markers1. An evaluation of achievements made to date in nuclear phylogeography arguably provides the most practical guide to its future potential. A gene tree for a single cytoplasmic or nuclear (nDNA) LOCUS provides a slim and sometimes misleading representation of the population histories through which alleles were transmitted3,4. Because cytoplasmic loci are usually inherited uniparentally, they will not have genealogical patterns that are representative of the entire population history, especially when sex biases have affected fitness or dispersal behavior5. Loci under selection can also have genetic patterns that deviate from expectations based on population history and demography, yet the selected patterns often mimic alternative demographic histories. Testing alternative hypotheses about evolutionary forces must ultimately rely on the fact that selection acts locally within a genome, whereas population demography leaves a common signature across all neutral loci1,6. In phylogeography,an empirical focus on gene lineages enables the history of