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The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits ( Lepus townsendii ) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B ( EDNRB ), corin serine peptidase ( CORIN ), and agouti signaling protein ( ASIP ). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats’ predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor’s (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

In a context of disease emergence and faced with the ever-growing evidence of the role of wildlife in the epidemiology of transmissible diseases, efforts have been made to develop wildlife disease surveillance (WDS) programs throughout Europe. Disease monitoring is ideally composed of “numerator data” (number of infected individuals) and “denominator data” (size of the target population). Too often however, information is available for only one. Hence, there is a need for developing integrated and harmonized disease and population monitoring tools for wildlife: integrated wildlife monitoring (IWM). IWM should have three components. Passive disease surveillance improves the likelihood of early detection of emerging diseases, while active surveillance and population monitoring are required to assess epidemiological dynamics, freedom of disease, and the outcome of interventions. Here, we review the characteristics of ongoing WDS in Europe, observe how pathogens have been ranked, and note a need for ranking host species, too. Then, we list the challenges for WDS and draw a roadmap for stepping up from WDS to IWM. There is a need to integrate and maintain an equilibrium between the three components of IWM, improve data collection and accessibility, and guarantee the adaptability of these schemes to each epidemiological context and temporal period. Methodological harmonization and centralization of information at a European level would increase efficiency of national programs and improve the follow-up of eventual interventions. The ideal IWM would integrate capacities from different stakeholder; allow to rapidly incorporate relevant new knowledge; and rely on stable capacities and funding., The author Beatriz Cardoso was supported by the FCT-Fundação para a Ciência e Tecnologia IP [grant number 2020.04872.BD]. The authors are grateful to the MCIU project CGL2017-89866 WildDriver.

Monitoring the occupancy and abundance of wildlife populations is key to evaluate their conservation status and trends. However, estimating these parameters often involves time and resource-intensive techniques, which are logistically challenging or even unfeasible for rare and elusive species that occur patchily and in small numbers. Hence, surveys based on field identification of signs (e.g. faeces, footprints) have long been considered a cost-effective alternative in wildlife monitoring, provided they produce reliable detectability and meaningful indices of population abundance. We tested the use of sign surveys for monitoring rare and otherwise elusive small mammals, focusing on the Cabrera vole (Microtus cabrerae) in Portugal. We asked how sampling intensity affects true positive detection of the species, and whether sign abundance is related to population size. We surveyed Cabrera voles’ latrines in 20 habitat patches known to be occupied, and estimated ‘true’ population size at each patch using DNA-based capture-recapture techniques. We found that a searching rate of ca. 3 min/250m2 of habitat based on adaptive guided transects was sufficient to provide true positive detection probabilities > 0.85. Sign-based abundance indices were at best moderately correlated with estimates of ‘true’ population size, and even so only for searching rates > 12 min/250m2. Our study suggests that surveys based on field identification of signs should provide a reliable option to estimate occupancy of Cabrera voles, and possibly for other rare or elusive small mammals, but cautions should be exercised when using this approach to infer population size. In case of practical constraints to the use of more accurate methods, a considerable sampling intensity is needed to reliably index Cabrera voles’ abundance from sign surveys.

Bats have long been associated with multiple pathogens, including viruses affecting humans such as henipaviruses, filoviruses, bunyaviruses and coronaviruses. The alpha and beta coronaviruses genera can infect most mammalian species. Among them, betacoronavirus SARS-CoV, MERS-CoV and SARS-CoV-2, which have caused the three major pandemics in the last two decades, have been proposed to originate in bats. In this study, 194 oral swabs from 22 bats species sampled in 19 locations of the Iberian Peninsula were analysed and characterized by three different PCR tests (coronavirus generic real-time RT-PCR, multiplex conventional PCR, and SARS-CoV-2 specific real-time RT-PCR) to detect bat coronaviruses. Screening with coronavirus generic PCR showed 102 positives out of 194 oral swabs analysed. Then, metabarcoding with multiplex PCR amplified 15 positive samples. Most of the coronaviruses detected in this study belong to alphacoronavirus (α-CoV) genus, with multiple alphacoronaviruses identified by up to five different genetic variants coexisting in the same bat. One of the positive samples identified in a Miniopterus schreibersii bat positive for the generic coronavirus PCR and the specific SARS-CoV-2 PCR was classified as betacoronavirus (β-CoV) through phylogenetic analysis. These results support the rapid evolution of coronaviruses to generate new genomic potentially pathogenic variants likely through co-infection and recombination., This work was supported by the EFSA [OC/EFSA/ALPHA/2016/01]; UCLM [2020-PREDUCLM-16703 & 2020-UNIVERS-9714/Movilidad]; JCCM [BPLY/19/180501/000321]. AMF is founded by Research Plan of University of Castilla-La Mancha, UCLM, Spain, grant 2020-PREDUCLM-16703 and mobility grant 2020-UNIVERS-9714/Movilidad.

Bagaza virus (BAGV) emerged in Spain, in 2010. Since then, BAGV was not reported in other European countries until September 2021, when BAGV was diagnosed by molecular methods in one corn bunting and several red-legged partridges, after abnormal mortality in Southern Portugal. Sequencing revealed high similarity with strains reported previously.

The conservation of animal populations often requires the estimation of population size. Low density and secretive behaviour usually determine scarce data sources and hampers precise abundance estimations of carnivore populations. However, joint analysis of independent scarce data sources in a common modeling framework allows unbiased and precise estimates of population parameters. We aimed to estimate the density of the European wildcat (Felis silvestris) in a protected area of Spain, by combining independent datasets in a spatially-explicit capture-recapture (SCR) framework. Data from live-capture with individual identification, camera-trapping without individual identification and radio-tracking concurrently obtained were integrated in a joint SCR and count data model. Ten live captures of five wildcats were obtained with an effort of 2034 trap-days, whereas seven wildcat independent events were recorded in camera traps with 3628 camera-days. Two wildcats were radio-tagged and telemetry information on their movements was obtained. The integration of the different data sources improved the precision obtained by the standard SCR model. The mean (± SD) density estimated with the integrated model (0.038 ± 0.017 wildcats/km2, 95% highest posterior density 0.013–0.082) is among the lowest values ever reported for this species, despite corresponding to a highly protected area. Among the likely causes of such low density, low prey availability could have triggered an extinction vortex process. We postulate that the estimated low density could represent a common situation of wildcat populations in the southern Iberia, highlighting the need for further studies and urgent conservation actions in the furthermost southwestern range of this species in Europe., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature., Funding was provided by Organismo Autónomo Parques Nacionales, Project OAPN 352/2011. We are grateful for the support received during this study from the staff of Cabañeros National Park. We also thank the assistance received during the fieldwork from T. Oliveira, I. Vaz and J.C. Zarca, and during data processing from A. Fragoso. F. Díaz-Ruiz was supported by a Juan de la Cierva postdoctoral contract (FJCI-2015-24,949) and is currently supported by a postdoctoral contract from the University of Málaga (I Plan Propio de Investigación y Transferencia, call 2020). P. Monterroso was supported by UID/BIA/50027/2019 with funding from FCT/MCTES through national funds.

Besnoitia besnoiti is an apicomplexan parasite whose life cycle is not completely understood. It is assumed that this parasite might have an indirect life cycle with a carnivore as a definitive host able to shed oocysts after the ingestion of mature cysts in tissues of an infected intermediate host. Cattle and wild cervids on the Iberian Peninsula can act as intermediate hosts of B. besnoiti, and exposure to the parasite has been demonstrated in equids. In this study, we aimed to assess the presence of members of the genera Besnoitia in wild lagomorphs from the Iberian Peninsula and the potential role of these host species in the life cycle of B. besnoiti, as all the animals were sampled from 19 regions of the Iberian Peninsula where cases of bovine besnoitiosis have been previously detected. Serum samples (Oryctolagus cuniculus: n = 552; Lepus europaeus: n = 122) were first analysed by ELISA and subsequently confirmed by Western blot (WB). Specific antibodies against B. besnoiti were not found in any sampled animal by WB. In addition, lung samples from a subset of wild rabbits (n = 16) were tested by PCR and Besnoitia spp. DNA was not detected. These results suggest that Besnoitia spp. are unlikely to circulate in wild lagomorphs in the Iberian Peninsula. Thus, lagomorphs are not expected to play a key role in the biological cycle of B. besnoiti. Further studies are necessary to assess whether different micromammal species, such as rodents, can serve as natural reservoirs of Besnoitia spp. in other European regions.

[Aim]: The role of mitochondrial DNA (mtDNA) in local adaptation has been thoroughly debated, and the ancient pervasive mtDNA introgression from Lepus timidus into Lepus granatensis allows testing of this hypothesis. Here, we study the environmental niche of animals with introgressed mtDNA, to gain insights about the potential selective pressures maintaining the introgressed haplotypes., [Location]: Iberian Peninsula., [Taxon]: Lepus granatensis., [Methods]: We modelled the frequency of the L. timidus mtDNA lineage within the L. granatensis distribution area. The response variable was the presence of the L. timidus lineage at the individual level. Finally, the variation in the introgression frequencies was plotted along the environmental gradients (identified by the models), after controlling for latitude., [Results]: The results showed that (i) the niche of the introgressed populations occupy marginal environmental conditions relative to the complete niche of L. granatensis, (ii) both latitude and environment, and their overlaid effects, explain the variation in the introgression frequencies, and (iii) after controlling for latitude, clines in mtDNA introgression frequency are associated with transitions in the environmental gradients, even when the analyses were restricted to the territory where the introgressed haplotypes occur., [Main Conclusions]: While the strict demographic explanation for mtDNA introgression in L. granatensis implies that geography, resulting from the post-glacial expansion of the species, explains the gradients of introgression, our results show correlations with environmental gradients that are not geographically structured. Our results relate the prevalence of introgressed mtDNA with more extreme climatic conditions in the range of L. granatensis, suggesting that environmental selective pressures could have played a role in determining the spatial maintenance of mtDNA haplotypes originating from the cold-adapted species. These results are thus relevant to understand the response of the species to the ongoing processes of global change, which will alter the selective pressures by reducing the specific niche of the introgressed mtDNA lineage., This work was supported by Fundação para a Ciência e a Tecnologia (EXPL/AAG-MAA/1082/2013 Project; ECOMITO - Unravelling the ecological impact of mitochondrial introgression). Further support was obtained from project NORTE-01-0145-FEDER-000007 supported by the Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). AJC was supported by a “Juan de la Cierva” contract from Universidad Castilla-La Mancha (FJCI-2017-33114). MM-H was funded by Junta de Comunidades de Castilla-La Mancha and the European Regional Development Fund (SBPLY/17/180501/000514). PA received support from UCLM through an extension of Ramon y Cajal contract (RYC-2012-11970). JM-F and RC were supported by Fundação para a Ciência e a Tecnologia, FCT, Portugal (CEECIND/00372/2018 and DL57/2016/CP1341/CT0001 research contracts respectively).

Madagascar does not have native wild felid species; however, distinct populations of free-ranging “forest cats” of unknown species are known throughout the island, including at Ankarafantsika National Park, Bezà Mahafaly Special Reserve, Makira Natural Park and the Masoala peninsula. Malagasy “forest cats” are commonly considered invasive lemur predators and competitors with endemic carnivores as well as a nuisance exotic species that kill poultry. These cats may be descendants of African wildcats, European wildcats and/or domestic cats; however, no research on their genetic origin has been published. To determine their taxonomic status, genetic data from short tandem repeat markers was assessed for three wild-caught “forest cats” from the Bezà Mahafaly Special Reserve (BMSR) and 27 “forest cats” from Ankarafantsika National Park. Bayesian analyses comparing the Malagasy “forest cats” to approximately 1900 domestic and wildcat sub-species suggest the Malagasy cats are descendents of domestic cats from the Arabian Sea region, including the islands of Lamu and Pate, Dubai, Kuwait and Oman. Additional genetic influences may descend from India and Pakistan. Combined with cultural and historical information, these data suggest that these felid populations are likely descendents from cats that immigrated to the island on trade ships, particularly along early Arab trade routes.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Aim: Reconstructing species' glacial refugial history and demographic changes over time has greatly relied on comparing inferences from multiple methods while not sufficiently acknowledging their limitations. Here, we aim to integrate as fully as possible complementary methods in ecology, genomics and palaeobiology to improve the reconstruction of species biogeographical history. Location: South-western Europe. Taxon: Cabrera vole (Microtus cabrerae). Methods: We compiled and mapped the raw fossil data of the Cabrera vole for the Last Glacial Maximum (LGM) and Mid-Holocene (MH). Alongside, we projected the calibrated ecological niche model (ENM) of the species' current distribution for the LGM, the Younger Dryas and the MH. Complementarily, we used previously obtained Genotyping-by- Sequencing data to evaluate the demographic history and range expansion patterns of all four Evolutionarily Significant Units of the species, in an integrative framework. Results: ENM-inferred refugial areas and genomic modelling consistently supported northern Iberian glacial refugia for the Cabrera vole. This contrasted with the higher fossil abundance of the species in southern and eastern Iberia and southern France from the LGM to the MH. Our results suggest that populations in areas with high fossil abundance went extinct, and were later replaced by northern Iberian populations such that they did not contribute significantly to the current gene pool. Main conclusions: Our integrative approach indicates how the range of the Cabrera vole fluctuated in response to environmental change during and following the LGM. Despite methodological limitations, the ENM and genomic approaches produced generally congruent results. Instead, the fossil record may misrepresent the ancestral distribution of this species and should be considered cautiously for ancestral distribution reconstruction, considering that it also reflects the fossilization conditions. Overall, our study supports the idea that integrative approaches are essential to provide an accurate and well-supported picture of historical refugial areas and range dynamics info:eu-repo/semantics/publishedVersion

Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926Felisspp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (

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.

Coastal sand dunes are dynamic ecosystems, with vegetation and biota responding to continuous changes in its typical environmental severity. Understanding vegetation patterns is relevant to early detect shifts in prevailing coastal dynamics and to refine monitoring strategies, especially in secondary sand dunes, which are under legal protection in Europe. We assessed the diversity patterns and cross-taxa congruence among lichens, bryophytes and vascular plants in secondary sand dunes under contrasting coastal dynamics (i.e. stable versus erosion sites), along a major biogeographic transition (i.e. Eurosiberian versus Mediterranean regions) in Western Europe. Our results show that the diversity patterns of bryophytes, lichens and vascular plants differ between contrasting coastal dynamics, regardless of the biogeographic context. Also, we found the absence of an explicit cross-taxa congruence among the diversity patterns of the three taxonomic groups. These results highlight the importance of taking into account the diversity of vascular plants, lichens and bryophytes, and the inclusion of other factors besides coastal dynamics, such as anthropogenic pressures. By doing so, a complementary view on the diversity patterns in secondary sand dunes can be provided to better guide conservation actions and monitoring strategies.

Information concerning factors regulating Alpine mountain hare (Lepus timidus varronis) populations such as host-parasite interactions is missing as only a few parasitological surveys exist of this subspecies. Parasites are not only dependent on their host but also on suitable environmental conditions for infestation. Abiotic environmental factors have an important regulating role on parasites in mammals. It is estimated that the elevation range of parasites is likely to shift in response to alternate host movement and changes in climate. Here we assess the parasitic infestation in the Alpine mountain hare by analysing the parasites in faeces and comparing the parasite infestation at different elevation ranges and at varied weather conditions for two years in the Austrian Alps. Almost half of the faecal samples were free of parasites (46.2%, n = 52). Most frequent was the infection by Coccidia (46.2%), whereas stomach intestine strongylids, Trichuris spp, and Cestoda were only found in 9.6% of all faeces. Hence, only Coccidia may be prevalent enough to regulate Alpine mountain hare populations in the Austrian Alps. Elevation had a significant positive effect on the infection of animals by Trichuris spp, whereas temperature had a significant negative effect on the infection by any parasite traceable in faeces and, when looking at the parasite groups individually, on Coccidia., Graphical abstract Image 1, Highlights • Almost half of the Alpine mountain hare faecal samples were free of parasites. • Coccidia was more frequent in our hare faeces than in other examined populations. • Stomach intestine strongylids and Cestoda were only found in 9.6% of our samples. • Only Coccidia may be prevalent enough to regulate this hare population. • Temperature had a significant negative effect on the incidence of any parasite in the faecal samples.

To protect native biodiversity and habitats from the negative impacts of biological invasions, comprehensive studies and measures to anticipate invasions are required, especially across countries in a transfrontier context. Species distribution models (SDMs) can be particularly useful to integrate different types of data and predict the distribution of invasive species across borders, both for current conditions and under scenarios of future environmental changes. We used SDMs to test whether predicting invasions and potential spatial conflicts with protected areas in a transfrontier context, under current and future climatic conditions, would provide additional insights on the patterns and drivers of invasion when compared to models obtained from predictions for individual regions/countries (different modelling strategies). The framework was tested with the invasive alien plant Acacia dealbata in North of Portugal/NW Spain Euro-region, where the species is predicted to increase its distribution under future climatic conditions. While SDMs fitted in a transfrontier context and using “the national strategy (with Portugal calibration data) presented similar patterns, the distribution of the invasive species was higher in the former. The transfrontier strategy expectedly allowed to capture a more complete and accurate representation of the species’ niche. Predictions obtained in a transfrontier context are therefore more suitable to support resource prioritisation for anticipation and monitoring impacts of biological invasions, while also providing additional support for international cooperation when tackling issues of global change. Our proposed framework provided useful information on the potential patterns of invasion by A. dealbata in a transfrontier context, with an emphasis on protected areas. This information is crucial for decision-makers focusing on the prevention of invasions by alien species inside protected areas in a transfrontier context, opening a new way for collaborative management of invasions.

Despite growing efforts to halt biodiversity loss, knowledge of species diversity and distribution is highly geographically biased, leaving some areas unexplored. Taxa distributed in remote, desert areas, such as hedgehogs (Mammalia; Eulipotyphla) in North Africa, are good examples of current knowledge gaps in systematics and biogeography. Here we studied the geographical distribution and intraspecific genetic diversity of hedgehogs in North Africa. Specimens belonging to North African and Eurasian species were analysed with mitochondrial (control region, CR) and nuclear (recombination activating gene 1, RAG1) gene fragments. This revealed a broader geographical distribution of Atelerix algirus in south-western Libya and of Paraechinus aethiopicus along the Atlantic Sahara. High intraspecific genetic differentiation was found in A. algirus and A. albiventris at the mitochondrial level, with nuclear haplotype sharing across their ranges. These findings suggest that biogeographical patterns of hedgehogs in North Africa are more complex than previously suggested, highlighting a need for further investigation in this remote and poorly known area.

Background Anastomotic leakage (AL) after colorectal resections is a common surgical experience and the most frequent major adverse outcome. Early recognition of AL is critical to reduce mortality. We aim to evaluate the incidence, diagnostic criteria, morbidity, and mortality related with AL. Methods This is a cohort, descriptive retrospective, single-centred study of consecutive patients who underwent surgery with a colorectal anastomosis due to colorectal cancer, over a 4-year period (2013–2016). Results From 2013 to 2016, a total of 480 patients were included. A total of 37 (7.7%) had an anastomotic leakage. AL was diagnosed after 6.8 days in average (range 2–17), but most frequently on day 5. 25 out of the 37 patients were diagnosed based on clinical criteria, and 12 had a CT scan of the abdomen; 3 (25%) did not show unequivocal signs of AL. From all AL patients, 6 were managed non-operatively. 24 out of 31 patients (64.8%) were submitted to anastomotic takedown and Hartmann-type of procedure. The rate of Clavien-Dindo grade III and IV complications was significantly higher in the AL-patient group (70.2 vs. 7.7%, p