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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]

Snow leopards ( Panthera uncia) are elusive endangered carnivores found in remote mountain regions of Central Asia. New methods for identifying and counting snow leopards are needed for conservation and management efforts. To develop molecular genetic tools for individual identification of hair and faecal samples, we screened 50 microsatellite loci developed for the domestic cat ( Felis catus) in 19 captive snow leopards. Forty-eight loci were polymorphic with numbers of alleles per locus ranging from two to 11. The probability of observing matching genotypes for unrelated individuals (2.1 × 10−11) and siblings (7.5 × 10−5) using the 10 most polymorphic loci was low, suggesting that this panel would easily discriminate among individuals in the wild. [ABSTRACT FROM AUTHOR]

Here we describe the development of 18 polymorphic microsatellite markers for the endangered Spanish imperial eagle ( Aquila adalberti). Microsatellites were tested in five other raptor species. These markers were revealed as good molecular tools for genetic population studies, individual identification and parentage assessment in Spanish imperial eagle and closely related species. [ABSTRACT FROM AUTHOR]

Abstract Leopards, Panthera pardus, are widely distributed across southern Asia and sub-Saharan Africa. The extent and phylogeographic patterns of molecular genetic diversity were addressed in a survey of 77 leopards from known geographical locales representing 13 of the 27 classical trinomial subspecies. Phylogenetic analysis of mitochondrial DNA sequences (727 bp of NADH5 and control region) and 25 polymorphic microsatellite loci revealed abundant diversity that could be partitioned into a minimum of nine discrete populations, tentatively named here as revised subspecies: P. pardus pardus, P. p. nimr, P. p. saxicolor, P. p. fusca, P. p. kotiya, P. p. delacouri, P. p. japonensis, P. p. orientalis and P. p. melas. However, because of limited sampling of African populations, this may be an underestimate of modern phylogeographic population structure. Combined phylogeographic and population diversity estimates support an origin for modern leopard lineages 470 000–825 000 years ago in Africa followed by their migration into and across Asia more recently (170 000–300 000 years ago). Recent demographic reductions likely have led to genetic impoverishment in P. p. orientalis and in the island subspecies P. p. kotiya. [ABSTRACT FROM AUTHOR]

Abstract The jaguar (Panthera onca ), the largest felid in the American Continent, is currently threatened by habitat loss, fragmentation and human persecution. We have investigated the genetic diversity, population structure and demographic history of jaguars across their geographical range by analysing 715 base pairs of the mitochondrial DNA (mtDNA) control region and 29 microsatellite loci in ≈40 individuals sampled from Mexico to southern Brazil. Jaguars display low to moderate levels of mtDNA diversity and medium to high levels of microsatellite size variation, and show evidence of a recent demographic expansion. We estimate that extant jaguar mtDNA lineages arose 280 000–510 000 years ago (95% CI 137 000–830 000 years ago), a younger date than suggested by available fossil data. No strong geographical structure was observed, in contrast to previously proposed subspecific partitions. However, major geographical barriers such as the Amazon river and the Darien straits between northern South America and Central America appear to have restricted historical gene flow in this species, producing measurable genetic differentiation. Jaguars could be divided into four incompletely isolated phylogeographic groups, and further sampling may reveal a finer pattern of subdivision or isolation by distance on a regional level. Operational conservation units for this species can be defined on a biome or ecosystem scale, but should take into account the historical barriers to dispersal identified here. Conservation strategies for jaguars should aim to maintain high levels of gene flow over broad geographical areas, possibly through active management of disconnected populations on a regional scale. [ABSTRACT FROM AUTHOR]

Simple Summary: Determining the impacts of human activities on natural populations is important for biodiversity conservation. In this paper, we study the past and more recent effects of urbanization and livestock activity on the genetic diversity and population structure of endemic guanaco populations of the arid Monte and Patagonian Steppe of central Argentina. Our results reveal that urbanization, the installation of fences, and the competition from sheep grazing coincided with the isolation of several guanaco populations, especially in areas with the highest intensity of livestock activity. However, our genetic analyses suggest that a more recent increase in connectivity among groups is occurring. Our results highlight the importance of implementing conservation management plans for natural populations in arid and human-intervened environments. Extensive livestock production and urbanization entail modifications of natural landscapes, including installation of fences, development of agriculture, urbanization of natural areas, and construction of roads and infrastructure that, together, impact native fauna. Here, we evaluate the diversity and genetic structure of endemic guanacos (Lama guanicoe) of the Monte and Patagonian Steppe of central Argentina, which have been reduced and displaced by sheep ranching and other impacts of human activities. Analyses of genetic variation of microsatellite loci and d-loop revealed high levels of genetic variation and latitudinal segregation of mitochondrial haplotypes. There were indications of at least two historical populations in the Monte and the Patagonian Steppe based on shared haplotypes and shared demographic history among localities. Currently, guanacos are structured into three groups that were probably reconnected relatively recently, possibly facilitated by a reduction of sheep and livestock in recent decades and a recovery of the guanaco populations. These results provide evidence of the genetic effects of livestock activity and urbanization on wild herbivore populations, which were possibly exacerbated by an arid environment with limited productive areas. The results highlight the importance of enacting conservation management plans to ensure the persistence of ancestral and ecologically functional populations of guanacos. [ABSTRACT FROM AUTHOR]

Tissue specimens from four species of Neotropical small cats (Oncifelis geoffroyi, N = 38; O. guigna, N = 6; Leopardus tigrinus, N = 32; Lynchailurus colocolo, N = 22) collected from throughout their distribution were examined for patterns of DNA sequence variation using three mitochondrial genes, 16S rRNA, ATP8, and NADH-5. Patterns between and among O. guigna and O. geoffroyi individuals were assessed further from size variation at 20 microsatellite loci. Phylogenetic analyses using mitochondrial DNA sequences revealed monophyletic clustering of the four species, plus evidence of natural hybridization between L. tigrinus and L. colocolo in areas of range overlap and discrete population subdivisions reflecting geographical isolation. Several commonly accepted subspecies partitions were affirmed for L. colocolo, but not for O. geoffroyi. The lack of geographical substructure in O. geoffroyi was recapitulated with the microsatellite data, as was the monophyletic clustering of O. guigna and O. geoffroyi individuals. L. tigrinus forms two phylogeographic clusters which correspond to L.t. oncilla (from Costa Rica) and L.t. guttula (from Brazil) and which have mitochondrial DNA (mtDNA) genetic distance estimates comparable to interspecific values between other ocelot lineage species. Using feline-specific calibration rates for mitochondrial DNA mutation rates, we estimated that extant lineages of O. guigna diverged 0.4 million years ago (Ma), compared with 1.7 Ma for L. colocolo, 2.0 Ma for O. geoffroyi, and 3.7 Ma for L. tigrinus. [ABSTRACT FROM AUTHOR]

The endangered Black-faced Spoonbill Platalea minor has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations. [ABSTRACT FROM AUTHOR]

Abstract: Since 1994 wild vicuñas have been captured and shorn for their wool, yet, there remains a noticeable lack of data regarding the possible influence of capture and shearing upon vicuña biology. Therefore, we assessed post-capture group composition, genetic relatedness, and paternity among animals that were captured for live shearing and release. We captured twenty-six groups (134 animals) on the Chilean Altiplano. Seventy-three percent of Male Groups (designated prior to chase) contained exclusively adult males upon capture, whereas remaining “Male Groups” contained crias and/or adult females and crias. Forty-seven percent of Family Groups (designated prior to chase) contained 1 adult male, adult females, and the number of crias≤the number of adult females. Remaining Family Groups contained no or multiple adult males, and more crias than adult females. Average relatedness among all vicuñas was −0.007. Paternity analysis revealed that 35% of crias were captured with their biological mother and that only 1 cria was captured with both biological parents. Based on previous observations of group composition in the wild, animals from different groups may separate and/or mix during the chasing stage. Improvement of the chasing technique and instituting a post-capture monitoring program may aid in the detection of medium- and long-term impacts regarding group stability, cria survival, and ultimately wool production. [Copyright &y& Elsevier]

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]