Conflict between Farmers and Guanacos (Lama guanicoe cacsilensis): Field Surveys, Remote Sensing, and Interviews Provide Information for Conservation of a Critically Endangered Species in Southern Peru.

The Peruvian guanaco (Lama guanicoe cacsilensis) is classified as being "in critical danger of extinction" by the government. In this study, we evaluate how the conflict between farmers and guanacos in the Susapaya and Estique Districts, Tacna Department (Southern Peru) may represent a threat to their survival. To evaluate the situation, we 1. Conducted field surveys to monitor guanaco presence, 2. Used available remote sensing data to map guanaco movement, and 3. interviewed the impacted farmers concerning their losses. Remote sensing data showed that sedentary guanaco family groups located in prime steppe vegetation habitats never entered agricultural areas, while field surveys showed that bachelor bands and solitary individuals did, perhaps seeking forage due to growing population pressure. Interview data found that 90% of community farmers felt that guanacos were a problem best resolved by better fencing (45%), hunting (19%), or increased security (16%), and 92% saw no value in the conservation of the species. Hunting is illegal, given the critically endangered status of guanacos in Peru, so additional efforts are needed to both educate those who feel guanacos are a menace and involve them in efforts to preserve the species.

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking.

The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.

Diarrheagenic Escherichia coli isolates from neonatal alpacas mainly display F17 fimbriae adhesion gene.

Neonatal domestic South American Camelid llamas and alpacas suffer from an enteric disease complex characterized by abdominal distention, lethargy, dehydration, and eventual fatal septicemia. Analysis of rectal swabs from neonatal alpacas suffering clinical diarrheas has constantly isolated Escherichia coli, mainly the EPEC and EHEC pathotypes. The present communication reports the results of molecular analysis of 226 E. coli strains from neonatal alpaca rectal swabs. The isolates were initially tested by multiple PCR, to identify E. coli virulence genes eae, bfp, Lt, Stx1, Stx2, sta, stab, and lt genes and a similar test to detect F4, F5, F6, F17, and F41fimbriae adhesin genes. Forty-two of the 226 (18.5%) isolates tested positive for at least one pathogenic gene, 25 of the 42 were classified as EPEC (3 positives for only eae and 22 for both eae and bfp) and the remaining 17 were classified as EHEC. Twenty-four (57%) of the 42 isolates tested positive to F17 adhesin while one was positive for both F6 and F17.

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.

BACKGROUND: Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca. RESULTS: Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. CONCLUSIONS: The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.

Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation.

The causes of Late Pleistocene megafaunal extinctions (60,000 to 11,650 years ago, hereafter 60 to 11.65 ka) remain contentious, with major phases coinciding with both human arrival and climate change around the world. The Americas provide a unique opportunity to disentangle these factors as human colonization took place over a narrow time frame (~15 to 14.6 ka) but during contrasting temperature trends across each continent. Unfortunately, limited data sets in South America have so far precluded detailed comparison. We analyze genetic and radiocarbon data from 89 and 71 Patagonian megafaunal bones, respectively, more than doubling the high-quality Pleistocene megafaunal radiocarbon data sets from the region. We identify a narrow megafaunal extinction phase 12,280 ± 110 years ago, some 1 to 3 thousand years after initial human presence in the area. Although humans arrived immediately prior to a cold phase, the Antarctic Cold Reversal stadial, megafaunal extinctions did not occur until the stadial finished and the subsequent warming phase commenced some 1 to 3 thousand years later. The increased resolution provided by the Patagonian material reveals that the sequence of climate and extinction events in North and South America were temporally inverted, but in both cases, megafaunal extinctions did not occur until human presence and climate warming coincided. Overall, metapopulation processes involving subpopulation connectivity on a continental scale appear to have been critical for megafaunal species survival of both climate change and human impacts.

Health impact evaluation of alternative management systems in vicuña (Vicugna vicugna mensalis) populations in Peru.

To determine the impact of farming over vicuña population in Peru, serum samples were collected from 207 vicuñas (126 captive vicuñas and 81 free-ranging vicuñas) and 614 domestic South American camelids (571 alpacas and 43 llamas), in ten Andean communities at the Salinas y Aguada Blanca reserve, province of Arequipa, southern Peru. Samples were tested for the presence of leptospirosis, foot and mouth disease (FMD), bovine viral diarrhea (BVD), bovine herpesvirus type 1 (BHV-1), brucellosis, bluetongue disease (BT), paratuberculosis, and neosporosis. Serological results showed that 1.9% (4/207) of vicuñas, 18.6% (106/571) of alpacas, and 23.3% (10/43) of llamas were positive to one or more Leptospira serovars. One percent of vicuñas (2/207) and 2.4% of domestic camelids (15/614) had Neospora caninum antibodies tested by ELISA, but only two vicuñas and two alpacas were confirmed by Western blot. Epidemiological evaluation found an association of leptospirosis to sex and age (p < 0.001), with female subjects older than 2.5 years at higher risk of infection. Interestingly, antibodies against Leptospira serovars were only found in captive vicuñas. This is the first study where health status of free-ranging and captive vicuñas has been compared. Results indicate minimal to nil presence of FMD, BVD, BHV-1, brucellosis, BT, paratuberculosis, and neosporosis allied to health disorders in our sample. The detection of seropositive animals against Leptospira, however, unveils the likely significance of leptospirosis in wild and domestic South American camelids, the impact of mixed husbandry over vicuña population and the risk to human health.

Contribución al estudio del parasitismo gastrointestinal en guanacos (Lama guanicoe cacsilensis) / Contribution to the study of gastrointestinal parasitism in the guanaco (Lama Guanicoe Cacsilensis)

El propósito del presente estudio fue identificar las especies de parásitos gastrointestinales que afectan al guanaco peruano y determinar los niveles de parasitismo de las poblaciones evaluadas. Se obtuvieron 132 muestras de heces frescas de guanacos silvestres pertenecientes a nueve poblaciones ubicadas en seis departamentos del Perú: Comunidad Campesina de Huallhua (Ayacucho), Reserva Nacional de Calipuy (La Libertad), Comunidad Campesina de Chavín (Ica), Reserva Nacional Salinas y Aguada Blanca y distritos de Machaguay y Yarabamba (Arequipa), distrito de Quilahuani y Comunidad Campesina de Vila Vilani (Tacna), y distrito de La Capilla (Moquegua). Las muestras fueron procesadas mediante técnicas coproparasitológicas de flotación, sedimentación, cultivo de larvas, Baerman y biometría de larvas y ooquistes. Se identificaron ocho especies de nematodos: Graphinema aucheniae, Bunostomun sp., Ostertagia sp., Trichuris sp, Cooperia sp., Nematodirus sp., Mazamastrongylus peruvianus y Trichostrongylus sp. y cuatro especies de Eimeria: E. lamae, E. alpacae, E. punoensis y E. macusaniensis. Todas las poblaciones se encontraban con al menos un guanaco parasitado, presentando en general cargas bajas y variando las frecuencias de parasitismo gastrointestinal de una población a otra, dependiendo del hábitat y de la proximidad a herbívoros domésticos.

The aim of this study was to identify the species of gastrointestinal parasites affecting the Peruvian guanaco and to determine the levels of parasitism in the populations under evaluation. For this purpose, 132 fresh faecal samples were collected from nine populations of wild guanacos located in six departments of Peru: Huallhua Community in Ayacucho; Calipuy National Reserve in La Libertad; Chavín community in Ica; Salinas and Aguada Blanca National Reserve, and Machaguay and Yarabamba districts in Arequipa, Quilahuani district and Vila Vilani community in Tacna, and La Capilla district in Moquegua. Samples were processed by the coproparasitological techniques of flotation, sedimentation, larvae culture, and Baerman, and biometry of larvae and oocysts. Eight species of nematodes were identified: Graphinema aucheniae, Bunostomun spp., Ostertagia spp., Trichuris spp., Cooperia spp., Nematodirus spp., Mazamastrongylus peruvianus and Trichostrongylus spp., and four Eimeria species: E. lamae, E. alpacae, E. punoensis and E. macusaniensis. All guanaco populations had at least one animal with parasites, showing low parasite burden in general, and with a variation in the frequency of gastrointestinal parasitism from one population to another, depending on the habitat and the proximity to other domestic herbivores.

Ancient DNA evidence for Old World origin of New World dogs.

Mitochondrial DNA sequences isolated from ancient dog remains from Latin America and Alaska showed that native American dogs originated from multiple Old World lineages of dogs that accompanied late Pleistocene humans across the Bering Strait. One clade of dog sequences was unique to the New World, which is consistent with a period of geographic isolation. This unique clade was absent from a large sample of modern dogs, which implies that European colonists systematically discouraged the breeding of native American dogs.