Molecular surveillance of potential SARS-CoV-2 reservoir hosts in wildlife rehabilitation centers.

BACKGROUND: The COVID-19 pandemic, caused by SARS-CoV-2 infection, has become the most devastating zoonotic event in recent times, with negative impacts on both human and animal welfare as well as on the global economy. Although SARS-CoV-2 is considered a human virus, it likely emerged from animals, and it can infect both domestic and wild animals. This constitutes a risk for human and animal health including wildlife with evidence of SARS-CoV-2 horizontal transmission back and forth between humans and wild animals. AIM: Molecular surveillance in different wildlife rehabilitation centers and wildlife associated institutions in Chile, which are critical points of animal-human interaction and wildlife conservation, especially since the aim of wildlife rehabilitation centers is to reintroduce animals to their original habitat. MATERIALS AND METHODS: The survey was conducted in six WRCs and three wildlife associated institutions. A total of 185 samples were obtained from 83 individuals belonging to 15 different species, including vulnerable and endangered species. Each specimen was sampled with two different swabs: one oropharyngeal or nasopharyngeal according to the nostril diameter, and/or a second rectal sample. RNA was extracted from the samples and two different molecular assays were performed: first, a conventional RT-PCR with pan-coronavirus primers and a second SARS-CoV-2 qPCR targeting the N and S genes. RESULTS: All 185 samples were negative for SARS-CoV-2. CLINICAL RELEVANCE: This study constitutes the first report on the surveillance of SARS-CoV-2 from wildlife treated in rehabilitation centers in Chile, and supports the biosafety procedures adopted in those centers.

Puma (Puma concolor) in the Neighborhood? Records Near Human Settlements and Insights into Human-Carnivore Coexistence in Central Chile.

The wildland-urban interface lies at the confluence of human-dominated and wild landscapes-creating a number of management and conservation challenges. Wildlife sightings near human settlements have appeared to increase in the last years. This article reports 51 records of presences, sightings, and livestock attacks of Puma concolor, a large-sized felid, collected from 2012 to 2020 across the O'Higgins region in central Chile. Puma records were concentrated in the east of the region in the Andes Range and foothills (90%). The number of puma records is higher in the last four to six years than in previously studied years. Of the 51 records, 23.5% are between 0 and 999 m from the nearest human settlement (classified as very close), 25.5% are between 1000 and 4999 m (moderately close), and 51% are over 5000 m (distant). Most of the sightings are recorded in the summer (35%) and spring (29%). We identify an area of approximately 9000 km2 of suitable habitat as the most probable corridor effectively connecting pumas moving between eastern and western areas, encompassing the Angostura de Paine mountain range. Our results contribute to the understanding of the presence and movements of P. concolor near urban areas and human settlements, confirming their persistence in and adaptation to human-dominated landscapes. We also provide insights into human-carnivore coexistence in the current global context in the densely populated central Chile.

Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae).

Organisms rapidly diversifying across unstable environments such as mountain tops provide substantial challenges for resolving evolutionary histories and delimiting species. The Liolaemus leopardinus clade is a group of five species of lizards adapted to high altitudes in central Chile, with most species found in the Andes, but one species, L. frassinettii is found in the independent Costa Cordillera. Despite their allopatric distributions, they display shallow mitochondrial divergences, making phylogenetics and species delimitation of this clade hard to resolve. We use an integrative approach to delimit species by considering morphological data (linear and landmark-based), mitochondrial DNA (mtDNA), and nuclear DNA (Sequences and SNPs collected with ddRADseq). We find strong conflicting signals between phylogenetic analyses of the nuclear and mtDNA data. While mtDNA places L. frassinettii as sister to the rest of the clade, the SNPs support a south to north order of divergences, with southernmost species (new taxon described here) as sister to the rest of the clade. Moreover, species delimitation using mtDNA only supports two species (one in the Costa and one in the Andes), whereas combined analyses using the nuclear data and morphology support multiple Andean taxa, including a new one we describe here. Based on these results, population structure analyses and our knowledge of the geological and climatic history of the Andes, we argue that this mito-nuclear discordance is explained by past introgression among the Andean taxa, likely during glacial periods that forced these lizards to lower altitudes where they would hybridize. The complete isolation between the Costa and Andes cordilleras has prevented any further contact between taxa on either mountain chain. Our study highlights the importance of using multiple lines of evidence to resolve evolutionary histories, and the potential misleading results from relying solely on mtDNA.