Phylogeography and Population Genetics of Vicugna vicugna: Evolution in the Arid Andean High Plateau

Abstract

The vicuña ( Vicugna vicugna ) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000–520,000 animals) is the result of population recovery programs established in response to 500 years of overexploitation. Despite the vicuña’s ecosystemic, economic and social importance, studies about their genetic variation and history are limited and geographically restricted. Here, we present a comprehensive assessment of the genetic diversity of vicuña based on samples collected throughout its distribution range corresponding to eleven localities in Peru and five in Chile representing V. v. mensalis , plus four localities each in Argentina and Chile representing V. v. vicugna. Analysis of mitochondrial DNA and microsatellite markers show contrasting results regarding differentiation between the two vicuña types with mitochondrial haplotypes supporting subspecies differentiation, albeit with only a few mutational steps separating the two subspecies. In contrast, microsatellite markers show that vicuña genetic variation is best explained as an isolation by distance pattern where populations on opposite ends of the distribution present different allelic compositions, but the intermediate populations present a variety of alleles shared by both extreme forms. Demographic characterization of the species evidenced a simultaneous and strong reduction in the effective population size in all localities supporting the existence of a unique, large ancestral population (effective size ∼50,000 individuals) as recently as the mid-Holocene. Furthermore, the genetic variation observed across all localities is better explained by a model of gene flow interconnecting them rather than only by genetic drift. Consequently, we propose space “continuous” Management Units for vicuña as populations exhibit differentiation by distance and spatial autocorrelation linked to sex biased dispersal instead of population fragmentation or geographical barriers across the distribution.

Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes

“…Similarly, the genetic diversity measured in terms of haplotype sharing between ancient and modern samples, or the number of haplotypes and total number of substitutions observed in both datasets ( Figure 7 ), also shows that the ancient samples presented significantly more genetic variation than the modern ones, with the vicuña having lost the most genetic variation across time. The latter is consistent with the evidence for bottlenecks in the species ( Wheeler, 1995 ; Casey et al, 2018 ; González et al, 2019 ; Fan et al, 2020 ).…”

“…To elucidate the origin and evolutionary history of camelids, numerous studies have performed DNA analyses on extant specimens (e.g. Fan et al, 2020 ; González et al, 2019 ; Marin et al, 2013 ; Marín et al, 2017 ; Casey et al, 2018 ; Marín et al, 2007a ; Wheeler et al, 2006 ; Kadwell et al, 2001 ; Stanley et al, 1994 ). However, the conclusions drawn from these studies are ambiguous.…”

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

“…The current study identified a total of 82 haplotypes in dromedary camels. This is relatively high when compared to Bactrians, llamas, and vicuñas, which only had 15, 17, and 57 haplotypes, respectively (Ming et al, 2017;Casey et al, 2018;González et al, 2019). However, these numbers might be correlated with the overall population size of the different camelid species, since dromedaries have a much higher population size than these other species (FAO, 2013(FAO, , 2017.…”

Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos)

“…Together with other camelids, alpacas are also of particular biological, biomedical and evolutionary interest due to their adaptations to extreme environments [10,11], unique and unusual features of their adaptive immune system [12][13][14][15] and as a basal clade of Cetartiodactyla in the mammalian phylogenetic tree [16,17]. Furthermore, the evolutionary history, genetic relationships and population structure of the alpaca and other South American camelids (llama, Lama glama; guanaco, Lama guanicoe and vicuña, Vicugna vicugna), continue to be topics of interest and debate [18][19][20].…”