Saenz, C. | bioRxiv Science

bioRxiv2026

Whole genomes reveal how Andean climate history shapes genetic diversity and modern conservation risk in South American pumas

Climatic oscillations in the Andes have repeatedly reshaped habitats over millions of years, yet their long-term genomic consequences for wide-ranging carnivores remain unclear. We generated whole-genome sequences from pumas (Puma concolor) across ecologically distinct regions of Ecuador to test how paleoclimate shaped population structure, demography, and genetic load. We show that northwestern forest pumas persisted in long-term isolation within humid refugia, whereas northern Andean and southern Pacific populations reconnected intermittently during warm interglacial periods. Southern coastal pumas maintained persistently small effective population sizes, leading to elevated runs of homozygosity and increased burdens of homozygous loss-of-function variants. In contrast, northern populations historically remained larger but exhibit early signs of inbreeding in one individual, marked by long runs of homozygosity and a kinked tail phenotype. Our findings indicate that recent fragmentation may be disrupting historical connectivity. Restoring corridors around the western foothills could reestablish gene flow and reduce inbreeding risk, while targeted genetic rescue may support chronically isolated southern populations. By integrating paleoclimate history with genome-wide data, we provide a framework for region-specific conservation strategies that balance connectivity restoration with the preservation of local adaptation.

genomics↗

bioRxiv2023

Domestic dogs in indigenous Amazonian communities: key players in Leptospira cycling and transmission?

BackgroundLeptospirosis is the worlds most common zoonotic disease. Mitigation and control rely on pathogen identification and understanding the roles of potential reservoirs in cycling and transmission. Underreporting and misdiagnosis obscure the magnitude of the problem and confound efforts to understand key epidemiological components. Difficulties in culturing hamper the use of serological diagnostics and delay the development of DNA detection methods. As a result, especially in complex ecosystems, we know very little about the importance of different mammalian host species in cycling and transmission to humans. Methodology/Principal FindingsWe sampled five indigenous Kichwa communities living in the Yasuni National Park in the Ecuadorian Amazon basin. Blood and urine samples from domestic dogs were collected to assess the exposure of these animals to Leptospira, and to identify the circulating species. Microscopic Agglutination Tests with a panel of 22 different serovars showed anti-leptospira antibodies in 36 sampled dogs (75%), and 10 serotypes were detected. Two DNA-based detection assays revealed pathogenic Leptospira DNA in 18 of 19 dog urine samples (94.7%). Amplicon sequencing and phylogenetic analysis of 16s rDNA and SecY genes from 15 urine samples revealed genetic diversity within two of three different Leptospira species: noguchii (n=7), santarosai (n=7), and interrogans (n=1). Conclusions/SignificanceThe high prevalence of antibodies and Leptospira DNA provides strong evidence for high rates of past and current infections. Such high prevalence has not been previously reported for dogs. These dogs live in the peridomestic environment in close contact with humans, yet they are free-ranging animals that interact with wildlife. This complex web of interactions may explain the diverse types of pathogenic Leptospira observed in this study. Our results suggest that domestic dogs are likely to play an important role in the cycling and transmission of Leptospira. Future studies in areas with complex ecoepidemiology will enable better parsing of the significance of genotypic, environmental, and host characteristics. Author SummaryPeople around the world interact with a wide range of animals, but one of the closest is the domestic dog. Dogs can be reservoirs of several zoonotic infectious diseases, including leptospirosis. The frequent ecological interactions between people, dogs and wildlife in indigenous communities living in the Amazon basin might increase the complexity of leptospirosis transmission, in comparison with what has been described for other settings. In the Amazon basin, wild animals and domestic animals may act as reservoirs of the pathogen, excreting the bacteria through their urine. In this work we analyzed serum and urine samples from dogs living with Kichwa communities from the Yasuni National Park in Ecuador. Serum samples were analyzed with MAT and urine samples with a qPCR that detect the presence of pathogenic Leptospira. Our results suggest that a high percentage of dogs are shedding the pathogen and we identified three different Leptospira species. Our serological analysis suggests the presence of ten serovars in dogs and their high exposure to Leptospira. These findings provide important insights into the epidemiology of leptospirosis in this ecosystem, suggesting that dogs are likely to play a critical role in the transmission of the disease.

microbiology↗