Estimating the abundance or density of populations is fundamental to the conservation and management of species, and as landscapes become more fragmented, maintaining landscape connectivity has ...become one of the most important challenges for biodiversity conservation. Yet these two issues have never been formally integrated together in a model that simultaneously models abundance while accounting for connectivity of a landscape. We demonstrate an application of using capture-recapture to develop a model of animal density using a least-cost path model for individual encounter probability that accounts for non-Euclidean connectivity in a highly structured network. We utilized scat detection dogs (Canis lupus familiaris) as a means of collecting non-invasive genetic samples of American mink (Neovison vison) individuals and used spatial capture-recapture models (SCR) to gain inferences about mink population density and connectivity. Density of mink was not constant across the landscape, but rather increased with increasing distance from city, town, or village centers, and mink activity was associated with water. The SCR model allowed us to estimate the density and spatial distribution of individuals across a 388 km
area. The model was used to investigate patterns of space usage and to evaluate covariate effects on encounter probabilities, including differences between sexes. This study provides an application of capture-recapture models based on ecological distance, allowing us to directly estimate landscape connectivity. This approach should be widely applicable to provide simultaneous direct estimates of density, space usage, and landscape connectivity for many species.
Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non‐invasive genetic studies ...of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non‐invasive genetics, still remains elusive. We present successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR), and for brown bear a sex marker, on a high‐throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear (5/7) and wolf (7/10) than for lynx (4/9), and locus genotyping success was greater for brown bear (0.88). The sex marker was typed in six out of seven brown bear samples. Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non‐invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species‐ and site‐specific sampling conditions, as well as laboratory methods promoting genotyping success, is needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA‐based individual and population‐level studies.
Next-generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and DNA extraction for diet analysis have differed ...from those focusing on target species, even in most studies combining questions on both aspects. We designed an experiment to evaluate two protocols using 11 parameters and select a single one that will generate both target species (Asiatic wild ass, Equus hemionus, in Israel) and diet DNA, as an effective strategy to minimise time, effort, and cost without hampering efficiency. In Protocol A, we swabbed the outer surface of faecal boluses and extracted DNA using a Stool Kit, while for Protocol B, we homogenised faecal matter from inside the bolus followed by extraction using a Powersoil Kit. Protocol A performed significantly better for four parameters, which included, for the target species, microsatellite amplification success and the quantity of the GAPDH gene; and for its diet, the number of exact sequence variants (ESVs) obtained at genus level and plant genus richness. However, there was no significant difference in the amplification success of sex-linked and plant markers, total reads at genus level, number of genera obtained and plant genus composition. Although we chose Protocol A, both protocols yielded results for the target species and its diet, demonstrating that one single protocol can be used for both purposes, although a pilot study is recommended to optimise the protocol for specific systems. This strategy may also be useful for studies combining target species and their gut microbiome and parasitic load.
Research on terrestrial carnivore ecology frequently relies on scat identification and analysis. However, species assignment is commonly based on scat morphology. Potential errors in scat ...identification are rarely accounted for and might contribute to substantial bias of the final results. Using molecular methods, we evaluate the accuracy of species identification based on morphological characteristics of mammalian mesocarnivore scats collected in two areas in the Iberian Peninsula. Our results revealed that error rates in species assignment of scats based on morphology were highly variable, ranging from 14%, for putative red fox Vulpes vulpes samples, to 88%, for putative wildcats Felis silvestris. The developed models revealed that putative species, season, study area and target species abundance are among the factors involved in identification accuracy. However, the low variability explained suggests that unaccounted factors also had significant effects on accuracy rates. The error rates in scat species assignment constitute a potential source of bias in ecological studies, with serious consequences for the management of threatened species, as unrealistic estimates of status and distribution are prone to occur. Our results suggest that scat identification accuracy rates are circumstance‐specific and therefore should not be transferred or extrapolated. We suggest that scat‐based studies should implement measures (molecular or others) that allow researchers to determine their own circumstance‐specific error rates in scat identification, which should be incorporated in subsequent analyses, ensuring reliable ecological inferences.
In heterogeneous landscapes, resource selection constitutes a crucial link between landscape and population‐level processes such as density. We conducted a non‐invasive genetic study of white‐tailed ...deer in southern Finland in 2016 and 2017 using fecal DNA samples to understand factors influencing white‐tailed deer density and space use in late summer prior to the hunting season. We estimated deer density as a function of landcover types using a spatial capture‐recapture (SCR) model with individual identities established using microsatellite markers. The study revealed second‐order habitat selection with highest deer densities in fields and mixed forest, and third‐order habitat selection (detection probability) for transitional woodlands (clear‐cuts) and closeness to fields. Including landscape heterogeneity improved model fit and increased inferred total density compared with models assuming a homogenous landscape. Our findings underline the importance of including habitat covariates when estimating density and exemplifies that resource selection can be studied using non‐invasive methods.
In heterogeneous landscapes, resource selection constitutes a crucial link between landscape and population‐level processes such as density. We studied factors influencing white‐tailed deer density and space use in Finland by using non‐invasively collected fecal DNA samples and Spatial Capture‐Recapture modeling. Here, we underlined the importance of incorporating habitat covariates when estimating density and exemplify that resource selection can be studied using non‐invasive methods.
Estimating the abundance or density of populations is fundamental to the conservation and management of species, and as landscapes become more fragmented, maintaining landscape connectivity has ...become one of the most important challenges for biodiversity conservation. Yet these two issues have never been formally integrated together in a model that simultaneously models abundance while accounting for connectivity of a landscape. We demonstrate an application of using capture–recapture to develop a model of animal density using a least-cost path model for individual encounter probability that accounts for non-Euclidean connectivity in a highly structured network. We utilized scat detection dogs (Canis lupus familiaris) as a means of collecting non-invasive genetic samples of American mink (Neovison vison) individuals and used spatial capture–recapture models (SCR) to gain inferences about mink population density and connectivity. Density of mink was not constant across the landscape, but rather increased with increasing distance from city, town, or village centers, and mink activity was associated with water. The SCR model allowed us to estimate the density and spatial distribution of individuals across a 388 km2 area. The model was used to investigate patterns of space usage and to evaluate covariate effects on encounter probabilities, including differences between sexes. This study provides an application of capture–recapture models based on ecological distance, allowing us to directly estimate landscape connectivity. This approach should be widely applicable to provide simultaneous direct estimates of density, space usage, and landscape connectivity for many species.
Abstract
We characterized the genetic structure of the Eurasian otter (Lutra lutra) meta-population living in the core of its Italian distribution range providing results from 191 fresh spraints, ...collected from 24 watercourses included in Southern Italy. Furthermore, according to ecological corridors and barriers, we discuss the likely ways of movement and possible evolutionary fate of these populations. We genotyped 136 samples using 11 Lut microsatellite nuclear markers amplified from faecal dna. Microsatellites were moderately variable (Ho = 0.45; He = 0.46), with a total number of alleles and average number of alleles per locus in the meta-population of 50 and 4.54, respectively. No significant heterozygosity excess was observed in meta-population suggesting no recent population bottlenecks. Bayesian clustering discriminated a sub-structuring of the meta-population in five putative clusters, indicating that local populations are genetically differentiated: three of these seem to be identifiable with geographically defined sub-populations (from the Cilento, Agri and Basento river basins). The fourth is represented by multiple sub-populations with admixed genotype, that include genotypes from the Lao, Sinni and Abatemaco river basins, living in a landscape with the higher environmental permeability. Landscape genetic analysis could provide evidence of an unexpected ecological corridor: the seacoast, highlighted, for the first time as a new way for the dispersion of the South-Italian otters. Deepening the knowledge of these perspectives is crucial to identify solid strategies aimed at the future health of the populations of the Italian otters, by restoring dispersal corridors and managing the watercourses.
Context
The area-isolation paradigm of metapopulation theory predicts that larger and more connected patches have a higher probability of occupancy. Although it may be too simplistic for generalist ...terrestrial mammals, the area-isolation paradigm may be an effective tool for assessing patch-occupancy for habitat specialists.
Objectives
We tested predictions of the area-isolation paradigm for the endangered salt marsh harvest mouse (
Reithrodontomys raviventris
), a habitat specialist living in highly fragmented salt marsh habitat in the San Francisco Estuary (California, USA).
Methods
We surveyed for salt marsh harvest mice at 47 marsh patches throughout their range using a non-invasive genetic survey technique. We used occupancy modeling to estimate the effects of patch size, patch connectivity, matrix urbanization, and several habitat characteristics on occupancy probabilities. We evaluated occupancy at both coarse (e.g., among patches) and fine (e.g., within patches) spatial scales.
Results
Patch size, connectivity, and matrix urbanization had significant effects on patch-occupancy. Within patches, occupancy was positively related to the presence of high-tide escape vegetation. Our data also revealed the extirpation of several geographically distinct populations, consistent with expectations due to reduced patch sizes and connectivity over the past century.
Conclusions
Patterns of salt marsh harvest mouse patch-occupancy were consistent with the area-isolation paradigm. In addition, our models provide important guidelines of patch size and connectivity that can inform habitat conservation and restoration for this endangered species. Specifically, our data suggests that selecting restoration sites that are well-connected may be more beneficial than selecting larger, isolated sites.
Arthropod populations are constantly changing due to changes in climate and the globalisation of trade and travel. Effective and diverse monitoring techniques are required to understand these ...changes. DNA metabarcoding has facilitated the development of a broad monitoring method to sample arthropod diversity from environmental and faecal samples. In this study, we applied DNA metabarcoding to DNA extracted from bat faecal pellets collected in Ireland from the lesser horseshoe bat,
Rhinolophus hipposideros
, a protected bat species of conservation concern in Europe. From as few as 24 bat faecal pellets, we detected 161 arthropod species from 11 orders, including 38 pest species of which five were determined to be priority pests, highlighting potential ecosystem services provided by
R. hipposideros
which are important for the functioning of healthy ecosystems. We also report the potential identification of 14 species not previously recorded in Ireland, but upon further investigation found that many of these could have been misidentified due to inadequacies in the genetic reference database. Despite the small sample size, we found that male and female diets did not differ significantly. However, sampling location did explain variation within the diet, highlighting how landscape features influence arthropod composition and diversity. We discuss the current limitations of the methodology in Ireland, how these can be overcome in future studies, and how this data can be used for biodiversity monitoring and informing conservation management of protected bat species.
Background
The sambar (
Rusa unicolor
) is one of the largest deer distributed across diverse habitats of India and threatened due to habitat loss, changes in the land-use patterns, illegal poaching, ...and anthropogenic disturbances. Here, we report the first population genetics account of sambar deer from the Western Himalayas.
Methods and results
We observed relatively compromised genetic diversity (π = 0.0008 ± 0.0006 at mtDNA and Ho = 0.499 ± 0.056 at nDNA). We identified 60 unique individuals using a select panel of seven loci (P
ID
sib cum 1.60E-03). Bayesian skyline plot showed a stable demographic history since the past 8 kyr with a decline in recent years. The population lacked genetic structuring, likely due to the contiguous distribution and large dispersal patterns of sambar.
Conclusion
The preliminary findings are valuable in exploring the utility of genetic diversity in monitoring the sambar population, estimating density following capture-recapture analysis, and aid to the conservation planning of sambar in large landscapes.
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