Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, ...pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture. Two complementary genome-wide association (GWAS) analyses were conducted: (i) infected-uninfected; and (ii) 2002/06-2009/12. The SNPs with the highest allelic frequency differences between time-periods and TB outcomes were identified and validated in a large dataset. In addition, we quantified the expression levels of some of their closest genes. These analyses highlighted various SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates for host genetic susceptibility. In addition to TB-driven selection, our findings outline the putative role of demographic events in shaping genomic variation in natural populations and how population crashes and drift may impact host genetic susceptibility to TB over time.
Lagomorph Biology Alves, Paulo C; Ferrand, Nuno; Hackländer, Klaus
2007, 2008, 2007-12-07
eBook, Book
Lagomorphs are a mammalian order which includes rabbits, hares and pikas. They are distributed throughout the world and are of both scientific and public interest as they are classified between ...endangered and pest species. In addition, some have a high economic value as important game species. In the last few decades, a huge amount of information was made available to the scientific community and resulted in remarkable advances on all aspects of Lagomorph biology. However, this information is dispersed in multiple scientific and non-scientific journals. This book provides an updated synthesis of the current knowledge on Lagomorph biology.
The European rabbit Oryctolagus cuniculus, a keystone species of Mediterranean ecosystems, is the target of several recovery and management plans throughout the Iberian Peninsula. The majority of ...these plans are limited in time by budget constraints and lack postintervention monitoring of population trends. This study was conducted in south‐west Portugal and aimed to understand the effect of habitat management and its early cessation on rabbit populations. We assessed rabbit presence and relative abundance before management (2007), during the implementation of measures (2008), immediately after (2009) and 3 years after measures ended (2012). We applied a model selection approach, using generalized linear models to determine the relative importance of MANAGED and UNMANAGED habitat features on rabbit presence in each year. We used spatial eigenvector mapping to describe the spatial autocorrelation in rabbit presence and a variation partitioning approach to quantify the relative effects of management‐related variables, unmanaged environmental descriptors and spatial characteristics on rabbit presence. Rabbit presence and abundance increased shortly after the management intervention but decreased 3 years after. Rabbit presence was positively related to the proximity of installed crops and the existence of favorable soils for digging. Habitat management‐related variables explained most of the variation in all models. Habitat improvement actions, particularly the sowing of pastures, contributed to increased rabbit presence. We propose a continued long‐term intervention and the cultivation of crops with auto‐regeneration properties (e.g., subterranean clover—Trifolium subterraneum) with the aim of continuing to increase rabbit presence and abundance in areas where rabbit populations are scarce.
This study, conducted in south‐west Portugal, aimed to understand the effect of habitat management and its early cessation on European rabbit populations. Rabbit presence and abundance increased shortly after the management intervention (2008 and 2009) but decreased, to pre‐management levels, three years after (2012). Habitat improvement actions, particularly the sowing of pastures, contributed to increased rabbit presence and habitat management‐related variables explained most of the variation in all models, although their influence decreased in 2012.
Abstract Costa Rica is within the Mesoamerican biodiversity hotspot and has about 53 native species of small mammals. This high diversity, along with recent records of new species and indications of ...cryptic genetic diversity, suggest that application of the DNA barcoding approach would be worthwhile. Here we used 131 tissue samples of small mammals from multiple localities in Costa Rica and sequenced the complete mitochondrial cytochrome b (1140 bp). These samples represented 17 recognized species and two taxa of uncertain status. The new sequence data were supplemented with previously published data from INSDC. Our phylogenetic analyses are consistent with and extend upon recent revisions in Heteromys , Peromyscus and Reithrodontomys and suggest possible new cryptic forms within what are currently named Melanomys chrysomelas , Nyctomys sumichrasti and Proechimys semispinosus. The previously named “ Heteromys sp” is indeed likely a new species requiring a full taxonomic description. Moreover, we found new localities for previously described species substantiating recent taxonomic surveys and field guides for the small mammals of Costa Rica . To confirm the presence of cryptic species and major genetic forms in Heteromys , Peromyscus , Reithrodontomys , Melanomys , Nyctomys and Proechimys there needs to be greater sampling, additional genetic markers, morphometrics and other studies. Scotinomys also shows interesting phylogenetic subdivision, requiring further investigation.
Hybridisation between domestic and wild taxa can pose severe threats to wildlife conservation, and human-induced hybridisation, often linked to species' introductions and habitat degradation, may ...promote reproductive opportunities between species for which natural interbreeding would be highly unlikely. Using a biome-specific approach, we examine the effects of a suite of ecological drivers on the European wildcat's genetic integrity, while assessing the role played by protected areas in this process. We used genotype data from 1217 putative European wildcat samples from 13 European countries to assess the effects of landcover, disturbance and legal landscape protection on the European wildcat's genetic integrity across European biomes, through generalised linear models within a Bayesian framework. Overall, we found European wildcats to have genetic integrity levels above the wildcat-hybrid threshold (ca. 83%; threshold = 80%). However, Mediterranean and Temperate Insular biomes (i.e., Scotland) revealed lower levels, with 74% and 46% expected genetic integrity, respectively. We found that different drivers shape the level of genetic introgression across biomes, although forest integrity seems to be a common factor promoting European wildcat genetic integrity. Wildcat genetic integrity remains high, regardless of landscape legal protection, in biomes where populations appear to be healthy and show recent local range expansions. However, in biomes more susceptible to hybridisation, even protected areas show limited effectiveness in mitigating this threat. In the face of the detected patterns, we recommend that species conservation and management plans should be biome- and landscape-context-specific to ensure effective wildcat conservation, especially in the Mediterranean and Temperate Insular biomes.
•We investigated factors influencing European wildcat genetic integrity in Europe.•Wildcats in Temperate Continental biomes revealed high genetic integrity.•Peripheral regions exhibited a concerning scenario of lower genetic integrity.•Forest integrity revealed a common positive effect on wildcat genetic integrity.•Protected areas revealed low effectiveness in peripheral regions.
The diet of the Iberian hare (
Lepus granatensis
) was studied through microhistological pellet analysis in two areas from a mountain ecosystem in Central Portugal. Fecal pellets were collected ...monthly in 24 plots spatially distributed throughout the two study areas. For each period, a sample of 15 to 20 pellets was milled and 400 epidermal fragments were identified, by comparison with a reference collection. A wide range of plant species was observed in hare’s diet. Grasses represent the basis of the Iberian hare diet, with frequencies always higher than 50% in both study areas (annual average = 69.98%). Most of the 35 species of grasses assembled for the reference collection (91.43%) were identified in the pellets. Nevertheless, only six of these were consumed in proportions greater than 5%, being
Anthoxanthum odoratum
,
Secale cereale
and
Agrostis
spp. the species ingested in higher frequencies. The rate of grasses consumption reached 80.69% in winter but decreased in summer to around 55%. In this season, a concurrent rise in the ingestion of other plant groups, like herbs and shrubs, and of plant inflorescences was observed. This work provides the first results on the Iberian hare’s diet on mountain ecosystems, and suggests that the Iberian hare diet in a mountain ecosystem is similar to the observed in
L. europaeus
and
L. timidus
.
Although important to guide conservation management, detailed demographic studies on rare or elusive species inhabiting fragmented, human-dominated landscapes are often hampered by the species' low ...densities, and the logistic and ethical constraints in obtaining reliable information covering large areas. Genetic non-invasive sampling (gNIS) provides cost-effective access to demographic information, though its application to small mammals is still scarce. We used gNIS to infer on the demography of an endemic small mammal, the Cabrera vole (Microtus cabrerae), occurring as a spatially-structured population in a 462-ha Mediterranean farmland landscape. We intensively sampled fresh vole feces in four seasons, extracted the DNA, and performed individual identification based on genotypes built using nine microsatellites. We then estimated population size and individual survival relative to environmental variables, controlling for heterogeneity in capture probabilities using capture-mark-recapture modelling. Population size increased during the wet season and decreased during the dry season, while survival remained constant across the study period. Individuals captured along road-verges and around water-bodies survived longer than those captured near agricultural fields. The use of gNIS on a heterogeneous landscape such as our study area allowed us to demonstrate that human land-use activities affect Cabrera vole demographic parameters in Mediterranean farmland, with implications for conservation planning towards its long-term persistence. Our approach can be widely applied to other elusive small mammals of conservation concern, but for which informative demographic data are still scarce.
•Assessing the demography of rare and elusive species is often problematic.•We evaluated population size and survival of a small-mammal using large-scale gNIS.•Population size increased during the wet season and decreased during the dry season.•Survival was higher near road-verges and water-bodies, and lower near farmed areas.•Our approach provides key information for conserving elusive small mammals.
Introgression of mitochondrial DNA (mtDNA) is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive ...considering the key function of enzymes that it encodes in the oxidative-phosphorylation process, which could give rise to hybrid dysfunction. How mtDNA reticulation affects the evolution of metabolic functions is, however, uncertain. Here we investigated how morpho-physiological traits vary in natural populations of a common rodent (the bank vole, Myodes glareolus) and whether this variation could be associated with mtDNA introgression. First, we confirmed that M. glareolus harbour mtDNA introgressed from M. rutilus by analyzing mtDNA (cytochrome b, 954 bp) and nuclear DNA (four markers; 2333 bp in total) sequence variation and reconstructing loci phylogenies among six natural populations in Finland. We then studied geographic variation in body size and basal metabolic rate (BMR) among the populations of M. glareolus and tested its relationship with mtDNA type.
Myodes glareolus and its arctic neighbour, M. rutilus, are reciprocally monophyletic at the analyzed nuclear DNA loci. In contrast, the two northernmost populations of M. glareolus have a fixed mitotype that is shared with M. rutilus, likely due to introgressive hybridization. The analyses of phenotypic traits revealed that the body mass and whole-body, but not mass corrected, BMR are significantly reduced in M. glareolus females from northern Finland that also have the introgressed mitotype. Restricting the analysis to the single population where the mitotypes coexist, the association of mtDNA type with whole-body BMR remained but those with mass corrected BMR and body mass did not. Mitochondrial sequence variation in the introgressed haplotypes is compatible with demographic growth of the populations, but may also be a result of positive selection.
Our results show that the phenotypic traits vary markedly along the north-south axis of populations of M. glareolus. This variation may be related to adaptation to local environments and coincides with the gradient of genome reticulation between M. glareolus and M. rutilus, which was assessed by mtDNA introgression. Introgression of mtDNA may have affected morpho-physiological traits but do not show strong effects on either body mass or basal metabolic rate alone. We discuss the causes and biological meaning of our results and the means to clarify these questions in future research.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Climate changes in the Iberian Peninsula since the Last Glacial Maximum are associated with distributional shifts of major Mediterranean and European temperate species. The dynamic relationship ...between climate and species in the past may be retrieved from the fossil records available in the Iberian Peninsula. We have used an extensive set of pollen records to reconstruct spatial layers (1 kyr interval) of January minimum temperature, July maximum temperature, and annual precipitation over the time period between 15 and 3 ka. A functional principal component analysis was used to summarise the spatial evolution of climate in areas that share similar climate trends. When compared between them, the identified four areas show different climate trends over the studied period and are coherent with the existence of multiple refugial areas within the Iberian Peninsula.
Estimation of the diagnostic performance of serological tests often relies on another test assumed as a reference or on samples of known infection status, yet both are seldom available for emerging ...pathogens in wildlife. Longitudinal disease serological data can be analysed through multi‐event capture–mark–recapture (MECMR) models accounting for the uncertainty in state assignment, allowing us to estimate epidemiological parameters such as incidence and mortality. We hypothesized that by estimating the uncertainty in state assignment, MECMR models estimate the diagnostic performance of serological tests for rabbit haemorrhagic disease virus (RHDV) and myxoma virus (MYXV). We evaluated this hypothesis on longitudinal serological data of three tests of RHDV and one test of MYXV in two populations of the European rabbit (Oryctolagus cuniculus algirus). First, we selected the optimal cut‐off threshold for each test using finite mixture models, a reference method not relying on reference tests or samples. Second, we used MECMR models to compare the diagnostic sensitivity (Se) and specificity (Sp) of the three tests for RHDV. Third, we compared the estimates of diagnostic performance by MECMR and finite mixture models across a range of cut‐off values. The MECMR models showed that the RHDV test employing GI.2 antigens (Se: 100%) outperformed two tests employing GI.1 antigens (Se: 21.7% ± 8.6% and 8.7% ± 5.9%). At their selected cut‐offs (2.0 for RHDV GI.2 and 2.4 for MYXV), the estimates of Se and Sp were concordant between the MECMR and finite mixture models. Over the duration of the study (May 2018 to September 2020), the monthly survival of European rabbits seropositive for MYXV was significantly higher than that of seronegative rabbits (82.7% ± 4.9% versus 61.5% ± 12.7%) at the non‐fenced site. We conclude that MECMR models can reliably estimate the diagnostic performance of serological tests for RHDV and MYXV in European rabbits. This conclusion could extend to other diagnostic tests and host‒pathogen systems. Longitudinal disease surveillance data analysed through MECMR models allow the validation of diagnostic tests for emerging pathogens in novel host species while simultaneously estimating epidemiological parameters.
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