Abstract
Phylogeographic approaches are commonly used to understand historical-biogeographic patterns in the distribution of haplotypes. However, the emphasis of most tools lies on describing spatial patterns of genetic variation and assess how large are haplotypic differences among populations. An evaluation of the relative influence of environmental factors compared to pure neutral process of haplotypic distribution - a question of great interest for molecular ecologists - is less investigated, in part because appropriate tools are lacking. Here, we introduce HaploVectors, a flexible tool that allows exploring phylogeographical patterns and discriminating biogeographic, neutral and environmental factors acting to shape genetic distribution across space. Haplovectors are variables that summarize the major gradients of haplotypic distribution across a set of localities and allow weighting haplotypic frequencies by the number of mutational steps using a fuzzy weighting approach. HaploVectors is presented as an R package for computing haplotypic eigenvectors and performing null model- based tests. Investigation of HaploVectors using empirical datasets showed that the method is useful to uncover hidden patterns of haplotypic distribution, not easily detected using traditional methods. Using a plant species as study case, we demonstrate by means of HaploVectors that, even though the distribution of plant haplotypes was associated with different biogeographic regions of the Brazilian Cerrado biome, such association was not mediated by evolutionary relationships among haplotypes. The applicability of HaploVectors is broad, ranging from the pure pattern exploration and discrimination of genetic populations, to a hypothesis-testing framework that uses null-models to understand the influence of environmental factors on haplotypic distribution.