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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]

A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold-temperate South American environments, the guanaco ( Lama guanicoe) was conducted. Patterns of molecular genetic structure were described using 514 bp of mt DNA sequence and 14 biparentally inherited microsatellite markers from 314 samples. These individuals originated from 17 localities throughout the current distribution across Peru, Bolivia, Argentina and Chile. This confirmed well-defined genetic differentiation and subspecies designation of populations geographically separated to the northwest ( L. g. cacsilensis) and southeast ( L. g. guanicoe) of the central Andes plateau. However, these populations are not completely isolated, as shown by admixture prevalent throughout a limited contact zone, and a strong signal of expansion from north to south in the beginning of the Holocene. Microsatellite analyses differentiated three northwestern and 4-5 southeastern populations, suggesting patterns of genetic contact among these populations. Possible genetic refuges were identified, as were source-sink patterns of gene flow at historical and recent time scales. Conservation and management of guanaco should be implemented with an understanding of these local population dynamics while also considering the preservation of broader adaptive variation and evolutionary processes. [ABSTRACT FROM AUTHOR]