Tuberculosis is an infectious disease caused by a group of acid-fast bacilli known as
complex (MTC), which has a major impact on humans. Transmission of MTC across the human-animal interface has been ...demonstrated by several studies. However, the reverse zoonotic transmission from humans to animals (zooanthroponosis) has often been neglected.
In this study, we used Nanopore MinION and Illumina MiSeq approaches to sequence the whole genome of
strains isolated from two deceased Asian elephants (
) and one human in Chitwan, Nepal. The evolutionary relationships and drug resistance capacity of these strains were assessed using the whole genome data generated by the stand-alone tool Tb-Profiler. Phylogenomic trees were also constructed using a non-synonymous SNP alignment of 2,596 bp, including 94 whole genome sequences representative of the previously described
lineages from elephants worldwide (lineages 1 and 4) and from humans in Nepal (lineages 1, 2 and 3).
The new genomes achieved an average coverage of 99.6%, with an average depth of 55.67x. These
strains belong to lineage 1 (elephant DG), lineage 2 (elephant PK) and lineage 4 (human), and none of them were found to have drug-resistant variants. The elephant-derived isolates were evolutionarily closely related to human-derived isolates previously described in Nepal, both in lineages 1 and 2, providing additional support for zooanthroponosis or bidirectional transmission between humans and elephants. The human-derived isolate clustered together with other published human isolates from Argentina, Russia and the United Kingdom in the lineage 4 clade. This complex multi-pathogen, multi-host system is challenging and highlights the need for a One Health approach to tuberculosis prevention and control at human-animal interface, particularly in regions where human tuberculosis is highly endemic.
North African ungulates include several threatened and emblematic species, yet are poorly studied mainly due to their remoteness and elusiveness. Noninvasive sampling provides a useful approach to ...obtain ecological and genetic information essential to guide conservation actions. The very first and most important step in conservation planning is to accurately identify species, and molecular genetics has been proved to be a useful tool. Several molecular genetics protocols are available for species identification, even for samples with poor quality DNA, such as faeces, hairs or bones. Most of these protocols use mitochondrial DNA for barcoding despite this marker being especially prone to problems, including mtDNA introgression, nuclear insert copies, high intraspecific diversity or heteroplasmy. In this work, we developed a molecular method based on polymorphisms in small fragments of the mitochondrial cytochrome b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for identifying endangered North African ungulates. These fragments revealed polymorphisms, including species‐specific variation, which allowed species identification of nine ungulate species that co‐occur in North Africa. The method was validated across more than 400 samples, including different types of noninvasive samples collected in the field. The simplicity, high reliability and relative low cost of the described method make it a promising tool to improve ecological studies of the North African ungulates and consequently, the implementation of more efficient management and conservation plans for these endangered ungulates.
Tuberculosis is a major global concern. Tuberculosis in wildlife is a risk for zoonotic transmission and becoming one of the challenges for conservation globally. In elephants, the number of cases is ...likely rising. The aim of this study was to identify proteins related to tuberculosis infection in elephants, which could then be used for the development of diagnostic tools and/or vaccines. A serum proteomics approach was used to characterize differentially represented proteins in response to Mycobacterium tuberculosis in Asian elephants (Elaphas maximus). Blood samples were collected from eight elephants, four of which were antibody positive for tuberculosis and four were antibody negative. Proteomics analysis identified 26 significantly dysregulated proteins in response to tuberculosis. Of these, 10 (38%) were identified as immunoglobulin and 16 (62%) as non-immunoglobulin proteins. The results provided new information on the antibody response to mycobacterial infection and biomarkers associated with tuberculosis and protective response to mycobacteria in Asian elephants. Protective mechanisms included defense against infection (Alpha-1-B glycoprotein A1BG, Serpin family A member 1 SERPINA1, Transthyretin TTR), neuroprotection (TTR), and reduced risks of inflammation, infections, and cancer (SERPINA1, Keratin 10 KRT10). Using a translational biotechnology approach, the results provided information for the identification of candidate diagnostic, prognostic, and protective antigens for monitoring and control of tuberculosis in Asian elephants.
The endangered European wildcat (Felis silvestris silvestris) is represented, today, by fragmented and declining populations whose genetic integrity is considered to be seriously threatened by ...crossbreeding with widespread free-ranging domestic cats. Extensive and recent hybridisation has been described in Hungary and Scotland, in contrast with rare introgression of domestic alleles in Italy and Germany. In Portugal, the wildcat is now listed as VULNERABLE in the Red Book of Portuguese Vertebrates. Nevertheless, genetic diversity of populations and the eventual interbreeding with domestic cats remain poorly studied. We surveyed genetic variation at 12 autosomal microsatellites for 34 wild and 64 domestic cats collected across Portugal. Wild and domestic cats were significantly differentiated both at allele frequencies and sizes (F ST=0.11, R ST = 0.18, P < 0.001). Population structure and admixture analyses performed using Bayesian approaches also showed evidence of two discrete groups clustering wild and domestic populations. Results did not show significant genetic divergence among Northern, Central and Southern wildcats. Six morphologically identified wildcats were significantly assigned to the domestic cluster, revealing some discrepancy between phenotypic and genetic identifications. We detected four hybrids (approximately 14%) using a consensus analysis of different Bayesian model-based software. These hybrids were identified throughout all sampled areas, suggesting that hybridisation is of major concern for the appropriate implementation of wildcat conservation strategies in Portugal.
Abstract
The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and ...the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
•We used ensemble modelling to forecast range shifts of a threatened vole under climate change.•Current distribution data was refined using model-guided non-invasive genetic surveys at the range ...margins.•Models predicted major range contractions under all climate change scenarios.•Less severe contractions were predicted by models including the new field data.•Non-invasive genetic surveys are a powerful tool to improve species distribution models.
Forecasting species range shifts under climate change is critical to adapt conservation strategies to future environmental conditions. Ecological niche models (ENMs) are often used to achieve this goal, but their accuracy is limited when species niches are inadequately sampled. This problem may be tackled by combining ENM with field validation to fine-tune current species distribution, though the traditional methods are often time-consuming and the species ID inaccurate. Here we combine ENM with novel field validation methods based on non-invasive genetic sampling to forecast range shifts in the globally near-threatened Cabrera vole (Microtus cabrerae). Using occurrence records mapped at 10km×10km resolution, we built the first ENM (ENM1) to estimate the current species distribution. We then selected 40 grid squares with no previous data along the predicted range margins, and surveyed suitable habitats through presence-sign searches. Faecal samples visually assigned to the species were collected for genetic identification based on the mitochondrial cytochrome-b gene, which resulted in 19 new grid squares with confirmed presence records. The second model (ENM2) was built by adding the new data, and species distribution maps predicted by each model under current and future climate change scenarios were compared. Both models had high predictive ability, with strong influence of temperature and precipitation. Although current distribution ranges predicted by each model were quite similar, the range shifts predicted under climate change differed greatly when using additional field data. In particular, ENM1 overlooked areas identified as important by ENM2 for species conservation in the future. Overall, results suggest that combining ENM with non-invasive genetics may provide a cost-effective approach in studies regarding species conservation under environmental change.
Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild ...populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.
The 2018 outbreak of myxomatosis in the Iberian hare (Lepus granatensis) has been hypothesized to originate from a species jump of the rabbit‐associated myxoma virus (MYXV), after natural ...recombination with an unknown poxvirus. Iberian hares were long considered resistant to myxomatosis as no prior outbreaks were reported. To provide insights into the emergence of this recombinant virus (ha‐MYXV), we investigated serum samples from 451 Iberian hares collected over two time periods almost two decades apart, 1994–1999 and 2017–2019 for the presence of antibodies and MYXV‐DNA. First, we screened all serum samples using a rabbit commercial indirect ELISA (iELISA) and then tested a subset of these samples in parallel using indirect immunofluorescence test (IFT), competitive ELISA (cELISA) and qPCR targeting M000.5L/R gene conserved in MYXV and ha‐MYXV. The cut‐off of iELISA relative index 10 = 6.1 was selected from a semiparametric finite mixture analysis aiming to minimize the probability of false positive results. Overall, MYXV related‐antibodies were detected in 57 hares (12.6%) including 38 apparently healthy hares (n = 10, sampled in 1994–1999, none MYXV‐DNA positive, and n = 28 sampled in 2017–2019 of which four were also ha‐MYXV‐DNA positive) and 19 found‐dead and ha‐MYXV‐DNA‐positive sampled in 2018–2019. Interestingly, four seronegative hares sampled in 1997 were MYXV‐DNA positive by qPCR, the result being confirmed by sequencing of three of them. For the Iberian hares hunted or live trapped (both apparently health), seroprevalence was significantly higher in 2017–2019 (13.0%, CI95% 9.2–18.2%) than in 1994–1999 (5.4%, CI95% 3.0–9.6%) (p = .009). Within the second period, seroprevalence was significantly higher in 2019 compared to 2017 (24.7 vs 1.7% considering all the sample, p = .007), and lower during the winter than the autumn (p < .001). While our molecular and serological results show that Iberian hares have been in contact with MYXV or an antigenically similar virus at least since 1996, they also show an increase in seroprevalence in 2018–2019. The remote contact with MYXV may have occurred with strains that circulated in rabbits, or with unnoticed strains already circulating in Iberian hare populations. This work strongly suggests the infection of Iberian hares with MYXV or an antigenically related virus, at least 20 years before the severe virus outbreaks were registered in 2018.
The interactions between animals and their environment vary across species, regions, but also with gender. Sex‐specific relations between individuals and the ecosystem may entail different behavioral ...choices and be expressed through different patterns of habitat use. Regardless, only rarely sex‐specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex‐specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use‐availability framework using radio‐telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid‐range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex‐biased behavioral patterns may contribute to the resilience of wildcats’ genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats’ habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex‐related differences in environmental preferences.
Sex‐specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Using resource selection functions, we assessed sex‐specific habitat selection patterns for the European wildcat across its Iberian biogeographic distribution. Our results indicate that females selected higher quality habitats and that the strength of association to habitat features was higher for females than for males. Sex‐biased behavioural patterns may be decisive in the resilience of wildcats’ genetic integrity through influencing the directionality of hybridization with domestic cats and that conservation efforts should focus on conserving high‐quality habitats that may harbor a viable population of female wildcats.
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