Intraspecific genetic consequences of Pleistocene climate change on Lupinus microphyllus (Fabaceae) in the Andes

The role of Pleistocene climate change in shaping patterns of genetic and species diversity has been widely demonstrated. However, tropical mountains remain less explored. In the northern Andes, distributional shifts of the vegetation during the Pleistocene are believed to have promoted plant diversification. In this regard, the role of gene flow and geographic isolation has been intensively debated. Here, we use a population genetic approach, microsatellite markers, and Bayesian statistics to assess the impact of Pleistocene climate change on intraspecific patterns of gene flow and genetic variation, and on the demographic history of the populations. We study Lupinus microphyllus, which belongs to a clade of Andean Lupinus species that has emerged as a model group in studies of plant diversification. We detect signatures of historical gene flow and negligible contemporary gene flow between populations. We find very low within-population genetic diversity and signals of an ancient decline in population size that may be lasting until today. We conclude that, in spite of periods of increased connectivity and gene flow, intraspecific genetic differentiation is mainly driven by periods of geographic isolation, restricted gene flow, and genetic drift. The intraspecific genetic pattern of high-elevation Andean plant species has been also shaped by local environmental factors, such as volcanic activity or glacier coverage, and by species-specific traits, such as the reproductive and dispersal strategies.