Landscape genetics is a burgeoning field of interest that focuses on how site-specific factors influence the distribution of genetic variation and the genetic connectivity of individuals and populations. In this manuscript, we focus on two methodological extensions for landscape genetic analyses: the use of conditional genetic distance (cGD) derived from population networks and the utility of extracting potentially confounding effects caused by correlations between phylogeographic history and contemporary ecological factors. Individual-based simulations show that when describing the spatial distribution of genetic variation, cGD consistently outperforms the traditional genetic distance measure of linearized FST under both 1- and 2-dimensional stepping stone models and Cavalli-Sforza and Edward’s chord distance Dc in 1-dimensional landscapes. To show how to identify and extract the effects of phylogeographic history prior to embarking on landscape genetic analyses, we use nuclear genotypic data from the Sonoran desert succulent Euphorbia lomelii (Euphrobiaceae), for which a detailed phylogeographic history has previously been determined. For E. lomelii, removing the effect of phylogeographic history significantly influences our ability to infer both the identity and the relative importance of spatial and bio-climatic variables in subsequent landscape genetic analyses. We close by discussing the utility of cGD in landscape genetic analyses.
The distribution of genetic variation within species is the result of both historical and ongoing demographic and evolutionary processes. Here we examine how genetic variation in Euphorbia lomelii (Euphorbaceae) among populations in Baja Mexico to understand how region-wide historical processes may have influenced this species. Specifically, we examined how the formation of the Sea of Cortéz, separating mainland and peninsular populations, and range expansion caused by Post Pleistocene climate change have influenced genetic variation. Samples were obtained from 37 sites in Baja California and mainland Sonora with a total of 324 individuals genotyped using six nuclear DNA markers. Analysis of genetic structure showed that while there was considerable differentiation among sites (ΦST=0.19) there was no significant difference between mainland and peninsular populations. The genetic structure of E. lomelii also has a gradual change with a northward reduction in heterozygosity, most likely caused by the relatively rapid range expansion during the current interglacial period. This research is important in understanding how genetic structure is influenced by historical processes that have operated on species in this region.
To examine the generality of population-level impacts of ancient vicariance identified for numerous arid-adapted animal taxa along the Baja peninsula, we tested phylogeographical hypotheses in a similarly distributed desert plant, Euphorbia lomelii (Euphorbiaceae). In light of fossil data indicating marked changes in the distributions of Baja floristic assemblages throughout the Holocene and earlier, we also examined evidence for range expansion over more recent temporal scales. Two classes of complementary analytical approaches — hypothesis-testing and hypothesis-generating — were used to exploit phylogeographical signal from chloroplast DNA sequence data and genotypic data from six codominant nuclear intron markers. Sequence data are consistent with a scenario of mid-peninsular vicariance originating c. 1 million years ago (Ma). Alternative vicariance scenarios representing earlier splitting events inferred for some animals (e.g. Isthmus of La Paz inundation, c. 3 Ma; Sea of Cortez formation, c. 5 Ma) were rejected. Nested clade phylo- geographical analysis corroborated coalescent simulation-based inferences. Nuclear markers broadened the temporal spectrum over which phylogeographical scenarios could be addressed, and provided strong evidence for recent range expansions along the north– south axis of the Baja peninsula. In contrast to previous plant studies in this region, however, the expansions do not appear to have been in a strictly northward direction. These findings contribute to a growing appreciation of the complexity of organismal responses to past climatic and geological changes — even when taxa have evolved in the same landscape context.
We developed seven nuclear intron markers for Euphorbia lomelii. New exon-primed intron-crossing (EPIC) oligonucleotides were used for initial amplification and sequencing, then locus-specific primers and restriction fragment length polymorphism genotyping assays were designed. Loci showed no significant deviation from Hardy–Weinberg and linkage equilibrium, and they cross-amplify in at least three congeneric species.