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Aim Our aim was to determine the combined impacts of Pleistocene climatic oscillations and glacial periods with recognized biogeographical barriers on the evolutionary history of huemul deer ( Hippocamelus bisulcus). Location Southern Chile and Argentina's Andean forest, and Patagonian fjords. Methods We examined the phylogeography of huemul using 772 bp of the mitochondrial DNA control region sequence from 275 samples (29 locations) collected throughout the distributional range of the species. We grouped samples into clusters based on Bayesian genetic and spatial structure analyses and reconstructed the species' phylogeographical and demographic history. Results We observed 63 haplotypes that grouped into three clusters (Central Chile, North Patagonia and South Patagonia). All but five haplotypes in North and South Patagonia were distributed locally. Bayesian skyline plots showed that population sizes remained fairly constant until an increase during and after the Last Glacial Maximum. Genetic diversity was generally low, except in three populations in the eastern Andes and on Wellington Island (Patagonian fjords). Main conclusions Our results suggest that the biogeographical separation of huemul into phylogeographical groups has been heavily influenced by Pleistocene glacial stages, and more recently by habitat fragmentation and isolation. This provides the first evidence that the region west of the Cordilleran ice field was a refugium for at least one species of large mammal during the Pleistocene in southern South America. These results have direct implications for the conservation and management of this endangered deer species. [ABSTRACT FROM AUTHOR]

Although guanacos (Lama guanicoe) are widely distributed throughout much of their historic range, they are often restricted to small, isolated populations that are at risk of inbreeding and loss of genetic diversity. Here we document and interpret baseline patterns of genetic variation in a guanaco population inhabiting in the Bolivian Chaco that is threatened by hunting and habitat degradation. The region, once open grasslands, is dominated by dense shrubs, the result of livestock grazing. The most-recent census identified only 74 individuals and is designated as at 'risk of extinction' by the Bolivian government. We assessed the population's genetic health and uniqueness from the genetic patterns of 16 microsatellite loci, the Hyper-variable Domain I of the mitochondrial Control Region and SRY gene with 29 fecal samples. We identified 19 male and 10 female unique individuals. Microsatellite variation (Ho = 0.64) was similar to larger, less-isolated populations. However, the estimated effective population size was low and consistent with the continuing loss of allelic variation. The two observed mtDNA haplotypes are common in other L. g. guanicoe populations. Although we documented moderate genetic diversity, gene flow among Bolivian and Paraguayan guanaco Chaco populations should be assessed and integrated into explicit conservation management plans. [ABSTRACT FROM AUTHOR]