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Selective breeding of the guanaco and vicuña indisputably led to the domestic llama and alpaca. However, the place, time and process of domestication remain poorly documented, exacerbated by increased evidence of historic and recent introgression among both domestic populations, especially those involving alpaca. Here, we report the first comprehensive assessment of patterns of microsatellite variation of 13 polymorphic microsatellites in 797 individuals representing 4 species and 2 subspecies to estimate historic and ongoing patterns of gene flow. Our results confirm that llamas were domesticated almost exclusively from the northern subspecies of guanaco (Lama guanicoe cacsilensis), but cluster analyses did not support previous findings that alpacas are solely derived from the northern subspecies of vicuña (Vicugna mensalis), with some more-recent admixture with southern populations. We also confirmed continued gene flow between llama and alpaca, and found evidence for crosses between presumably feral llamas and guanacos in northern Chile. Our results highlight the need to develop and test more-accurate markers and tools for assessing the genetic heritage of individuals, to link phenotypic variation with genetic ancestry, and to conserve historic patterns of unique variation among both the wild and domestic populations. • The dominant herbivores of the arid and semi-arid habitats of South America include wild and domestic species. • The genetic and phenotypic integrity of the domestic llama and alpaca are increasingly being threatened by interbreeding. • Loss of vicuña genetic signal in alpaca is due to hybridization and introgression among South American camelids. [ABSTRACT FROM AUTHOR]

Summary 1. The Chilean National Forestry and Park Service is striving to implement a guanaco management programme of sustained-yield use. To achieve this, the rate, variation and causes of juvenile guanaco mortality must be understood thoroughly. Therefore, we monitored the survival of 409 radio-collared juvenile guanacos in Torres del Paine National Park, Chile, from 1991 to 1996. 2. The Kaplan–Meier product limit estimator of survival for staggered entry was calculated, and survival rates between juvenile males and females and among years were compared using the lifetest procedure in SAS. The Cox proportional hazards model was used to relate mortality rate to explanatory variables such as juvenile sex, birth weight, adult female aggression towards researchers during the capture and tagging of newborns, population density, and mean monthly winter snowfall. 3. Mean juvenile survival rate (ŝ) was 0·38, but varied between 0·31 and 0·55. Survival rates between the sexes were not significantly different, although male survival was lower than that of females. Mortality rate was highest during the first 14 days after birth. Most deaths occurred between birth and 7 months of age. 4. The risk of mortality increased by almost 6% with every 1 cm increase in winter snowfall, whereas the risk of mortality decreased by almost 24% as adult female aggression increased towards researchers. 5. Current management objectives are aimed at the implementation of a rational harvest of guanacos on the Chilean side of the island of Tierra del Fuego. Our results provide improved and updated estimates of juvenile guanaco survival and will aid in the modelling of harvest rates of guanacos in southern Chile. Future proposed harvests from wild populations in southern Chile need to consider the rate and variation of this critical life-history parameter. [ABSTRACT FROM AUTHOR]