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Survival rate is usually the greatest contributor to population growth in long‐lived species, and its accurate estimation along with the evaluation of the factors influencing it is therefore essential for effective conservation. Here, we studied the survival of breeding eastern imperial eagles Aquila heliaca in Hungary between 2011 and 2022 and investigated the effect of poisoning, the leading known anthropogenic cause of mortality. We used the Cormack‐Jolly‐Seber mark‐recapture model to estimate annual apparent survival and encounter probabilities based on the capture histories of 208 males and 411 females. We obtained encounter data from the DNA profiles of shed feathers collected at the nest sites, which we also supplemented with presences inferred from parentage analysis. The most supported model estimated a constant 91.6% annual survival over the study period, but models including the effect of sex and poisoning rate on survival had similar support. Sex difference in survival was less than 1% on average, but the survival of males decreased more with poisoning rate than the survival of females. However, due to smaller encounter probabilities, the estimates for males were less precise compared to females. Males may be more at risk from poisoning than females not only due to their more active foraging behaviour during incubation and chick‐rearing but also due to their smaller body size. Apart from providing direct practical information for the conservation management of imperial eagles, our results also highlight the importance of long‐term studies for estimating population parameters of birds of prey. [ABSTRACT FROM AUTHOR]

Abundance estimation is frequently an objective of conservation and monitoring initiatives for threatened and other managed populations. While abundance estimation via capture–mark–recapture or spatially explicit capture–recapture is now common, such approaches are logistically challenging and expensive for species such as boreal caribou (Rangifer tarandus), which inhabit remote regions, are widely dispersed, and exist at low densities. Fortunately, the recently developed 'close‐kin mark–recapture' (CKMR) framework, which uses the number of kin pairs obtained within a sample to generate an abundance estimate, eliminates the need for multiple sampling events. As a result, some caribou managers are interested in using this method to generate an abundance estimate from a single, non‐invasive sampling event for caribou populations. We conducted a simulation study using realistic boreal caribou demographic rates and population sizes to assess how population size and the proportion of the population surveyed impact the accuracy and precision of single‐survey CKMR‐based abundance estimates. Our results indicated that abundance estimates were biased and highly imprecise when very small proportions of the population were sampled, regardless of the population size. However, the larger the population size, the smaller the required proportion of the population surveyed to generate both accurate and reasonably precise estimates. Additionally, we also present a case study in which we used the CKMR framework to generate annual female abundance estimates for a small caribou population in Jasper National Park, Alberta, Canada, from 2006 to 2015 and compared them to existing published capture–mark–recapture‐based estimates. Both the accuracy and precision of the annual CKMR‐based abundance estimates varied across years and were sensitive to the proportion of pairwise kinship comparisons which yielded a mother–offspring pair. Taken together, our study demonstrates that it is possible to generate CKMR‐based abundance estimates from a single sampling event for small caribou populations, so long as a sufficient sampling intensity can be achieved. [ABSTRACT FROM AUTHOR]

Current diagnostic methods for Bovine tuberculosis (TB) and Paratuberculosis (pTB) involve invasive sampling methods that require handling and restraining causing stress and pain to the animals along with days required for the interpretation of test results. By the 3Rs ethical principle and animal welfare, an alternative non-invasive sampling method to screen herds could be a better option. Milk may be a major source for the large-scale spread of tuberculosis and to a considerable extent of paratuberculosis bacilli in humans. Keeping this in view, milk samples were utilized for the screening of herds employing acid-fast staining microscopic examination to determine the presence of Mycobacterium and other acid-fast bacilli (AFB). For the study, a total of 150 milk samples collected randomly from dairy herds of five major gaushalas of the Vrindavan and Mathura region of Uttar Pradesh, India were screened. Microscopic examination reveals the presence of AFB in 18 samples from 3 out of the 5 herds under study. In conclusion, the presence of the AFB in the milk being used for feeding calves and human consumption is alarming for both animal and human health aspects and requires confirmation on a large scale to control the further spread. Also, the study indicates the importance of milk samples microscopic examination for AFB as an alternative non-invasive procedure for initial screening of dairy herds for TB and pTB.

The ongoing expansion of wolf (Canis lupus) populations in Europe has led to a growing demand for up‐to‐date abundance estimates. Non‐invasive genetic sampling (NGS) is now widely used to monitor wolves, as it allows individual identification and abundance estimation without physically capturing individuals. However, NGS is resource‐intensive, partly due to the elusive behaviour and wide distribution of wolves, as well as the cost of DNA analyses. Optimisation of sampling strategies is therefore a requirement for the long‐term sustainability of wolf monitoring programs. Using data from the 2020–2021 Italian Alpine wolf monitoring, we investigate how (i) reducing the number of samples genotyped, (ii) reducing the number of transects, and (iii) reducing the number of repetitions of each search transect impacted spatial capture‐recapture population size estimates. Our study revealed that a 25% reduction in the number of transects or, alternatively, a 50% reduction in the maximum number of repetitions yielded abundance estimates comparable to those obtained using the entire dataset. These modifications would result in a 2046 km reduction in total transect length and 19,628 km reduction in total distance searched. Further reducing the number of transects resulted in up to 15% lower and up to 17% less precise abundance estimates. Reducing only the number of genotyped samples led to higher (5%) and less precise (20%) abundance estimates. Randomly subsampling genotyped samples reduced the number of detections per individual, whereas subsampling search transects resulted in a less pronounced decrease in both the total number of detections and individuals detected. Our work shows how it is possible to optimise wolf monitoring by reducing search effort while maintaining the quality of abundance estimates, by adopting a modelling framework that uses a first survey dataset. We further provide general guidelines on how to optimise sampling effort when using spatial capture‐recapture in large‐scale monitoring programmes. [ABSTRACT FROM AUTHOR]

Non‐invasive genetic sampling is an increasingly common approach in wildlife research. It allows the gathering of first‐hand data on wild mammalian populations without capturing or handling individuals. For this reason, it has proved to be particularly useful when applied to elusive species living at low population densities and/or hard to identify in the field. The European wildcat represents an interesting case study in this respect. Several papers have been produced in the last decades, in which non‐invasive genetic sampling has been applied. Nevertheless, evidence from different case studies presents a complex scenario, where the efficiency of the method can vary considerably. This paper aimed to analyse possible interpretations of such differences and to identify potential drivers and barriers. 20 papers on the subject have been reviewed and compared, although differences in several details reported in the examined papers limited an in‐depth comparison. The review showed that the overlap of the study period with the reproductive season does not affect the final results of lure stick hair sampling research on the European wildcat. Moreover, valerian lure sticks generally provided positive results in the Continental ecoregion, whereas, in the Mediterranean and Atlantic regions, outcomes were absent or very scarce. Most of the other working hypotheses remain still plausible, despite not yet being definitely provable. Setting up future wildcat monitoring schemes based on effective non‐invasive genetic sampling in different biogeographical regions of Europe is certainly a scope to be pursued. Some suggestions are provided in this respect (e.g. the set of parameters needed to allow further comparisons; the need to test other types of attractants, to make the application of the method possible where the use of valerian was proven to be inefficient or scarcely efficient, in order to allow a better comparison of future results). [ABSTRACT FROM AUTHOR]

Early detection of cancer via biomarkers is vital for improving patient survival rates. In the case of skin cancers, low-molecular-weight biomarkers can penetrate the skin barrier, enabling non-invasive sampling at an early stage. This study focuses on detecting tryptophan (Trp) and kynurenine (Kyn) on the surface of reconstructed 3D melanoma and melanocyte models. This is examined in connection with IDO-1 and IL-6 expression in response to IFN-γ or UVB stimulation, both crucial factors of the melanoma tumor microenvironment (TME). Using a polystyrene scaffold, full-thickness human skin equivalents containing fibroblasts, keratinocytes, and melanocytes or melanoma cells were developed. The samples were stimulated with IFN-γ or UVB, and Trp and Kyn secretion was measured using HPLC-PDA and HPLC-MS. The expression of IDO-1 and IL-6 was measured using RT-qPCR. Increased Trp catabolism to Kyn was observed in IFN-γ-stimulated melanoma and melanocyte models, along with higher IDO-1 expression. UVB exposure led to significant changes in Kyn levels but only in the melanoma model. This study demonstrates the potential of skin surface Trp and Kyn monitoring to capture TME metabolic changes. It also lays the groundwork for future in vivo studies, aiding in understanding and monitoring skin cancer progression. [ABSTRACT FROM AUTHOR]

Mesocarnivores are major components of carnivore assemblages, and they play important roles in structuring communities and regulating community dynamics. In Southwest China, many apex predators have been extirpated, and this has potentially resulted in the ecological release of mesocarnivores. Estimating the sizes of mesocarnivore populations is challenging. We used DNA derived from hairs and spatial capture–mark–recapture techniques to estimate the population size of masked palm civets (Paguma larvata) in Laohegou Nature Reserve in the Minshan Mountains of Sichuan Province, China. In the fall of 2014 and the spring of 2015, we collected 144 and 230 hair samples, respectively, at 30 baited stations. We used 16S rRNA fragments, microsatellite genotyping, and sexing to determine that 191 samples were derived from 44 masked palm civet individuals (24 males and 20 females). Using spatially explicit capture–recapture analysis, we estimated that there were 82 ± 13 masked palm civets in the study area, with a density of 1.7 individuals/km2. This is the first study to estimate the population size of masked palm civets in the wild. Our data provide important new information on the density of masked palm civets. [ABSTRACT FROM AUTHOR]

Current diagnostic methods for Bovine tuberculosis (TB) and Paratuberculosis (pTB) involve invasive sampling methods that require handling and restraining causing stress and pain to the animals along with days required for the interpretation of test results. By the 3Rs ethical principle and animal welfare, an alternative non-invasive sampling method to screen herds could be a better option. Milk may be a major source for the large-scale spread of tuberculosis and to a considerable extent of paratuberculosis bacilli in humans. Keeping this in view, milk samples were utilized for the screening of herds employing acid-fast staining microscopic examination to determine the presence of Mycobacterium and other acid-fast bacilli (AFB). For the study, a total of 150 milk samples collected randomly from dairy herds of five major gaushalas of the Vrindavan and Mathura region of Uttar Pradesh, India were screened. Microscopic examination reveals the presence of AFB in 18 samples from 3 out of the 5 herds under study. In conclusion, the presence of the AFB in the milk being used for feeding calves and human consumption is alarming for both animal and human health aspects and requires confirmation on a large scale to control the further spread. Also, the study indicates the importance of milk samples microscopic examination for AFB as an alternative non-invasive procedure for initial screening of dairy herds for TB and pTB. [ABSTRACT FROM AUTHOR]

Abstract Acquiring sufficient blood for hormone analysis in mice can be a limiting step. Hormone analysis techniques using non‐invasive sample collection have been vigorously developed for endangered species, from whom blood sampling is prohibited, or from species that are otherwise difficult to handle in a laboratory setting. Because there are interactions between glucocorticoids and thyroid hormones (T3 and T4), reducing the animal's “distress” during sample collection is imperative. Measurement of fecal T3 provides less sensitive, baseline information regarding thyroid function while permitting a non‐invasive technique for more frequent sampling. We demonstrated that using a methanol extraction protocol produced the most reliable fecal T3 measurement in an enzyme‐linked immunosorbent assay (ELISA). We found that during a thyroid hormone‐treated state, fecal and plasma T3 measurements from mice are directly related, while during a methimazole‐treated state, fecal and plasma T3 measurements from mice are inversely related. Fecal samples are a useful way to monitor thyroid hormone function in laboratory mice.

Abstract Survival rate is usually the greatest contributor to population growth in long‐lived species, and its accurate estimation along with the evaluation of the factors influencing it is therefore essential for effective conservation. Here, we studied the survival of breeding eastern imperial eagles Aquila heliaca in Hungary between 2011 and 2022 and investigated the effect of poisoning, the leading known anthropogenic cause of mortality. We used the Cormack‐Jolly‐Seber mark‐recapture model to estimate annual apparent survival and encounter probabilities based on the capture histories of 208 males and 411 females. We obtained encounter data from the DNA profiles of shed feathers collected at the nest sites, which we also supplemented with presences inferred from parentage analysis. The most supported model estimated a constant 91.6% annual survival over the study period, but models including the effect of sex and poisoning rate on survival had similar support. Sex difference in survival was less than 1% on average, but the survival of males decreased more with poisoning rate than the survival of females. However, due to smaller encounter probabilities, the estimates for males were less precise compared to females. Males may be more at risk from poisoning than females not only due to their more active foraging behaviour during incubation and chick‐rearing but also due to their smaller body size. Apart from providing direct practical information for the conservation management of imperial eagles, our results also highlight the importance of long‐term studies for estimating population parameters of birds of prey.

Abstract Abundance estimation is frequently an objective of conservation and monitoring initiatives for threatened and other managed populations. While abundance estimation via capture–mark–recapture or spatially explicit capture–recapture is now common, such approaches are logistically challenging and expensive for species such as boreal caribou (Rangifer tarandus), which inhabit remote regions, are widely dispersed, and exist at low densities. Fortunately, the recently developed ‘close‐kin mark–recapture’ (CKMR) framework, which uses the number of kin pairs obtained within a sample to generate an abundance estimate, eliminates the need for multiple sampling events. As a result, some caribou managers are interested in using this method to generate an abundance estimate from a single, non‐invasive sampling event for caribou populations. We conducted a simulation study using realistic boreal caribou demographic rates and population sizes to assess how population size and the proportion of the population surveyed impact the accuracy and precision of single‐survey CKMR‐based abundance estimates. Our results indicated that abundance estimates were biased and highly imprecise when very small proportions of the population were sampled, regardless of the population size. However, the larger the population size, the smaller the required proportion of the population surveyed to generate both accurate and reasonably precise estimates. Additionally, we also present a case study in which we used the CKMR framework to generate annual female abundance estimates for a small caribou population in Jasper National Park, Alberta, Canada, from 2006 to 2015 and compared them to existing published capture–mark–recapture‐based estimates. Both the accuracy and precision of the annual CKMR‐based abundance estimates varied across years and were sensitive to the proportion of pairwise kinship comparisons which yielded a mother–offspring pair. Taken together, our study demonstrates that it is possible to generate CKMR‐based abundance estimates from a single sampling event for small caribou populations, so long as a sufficient sampling intensity can be achieved.

Acquiring up-to-date information on the distribution of a species is an issue of paramount importance to set up proper conservation strategies and to assess its conservation status over time. The European wildcat has recently expanded its distribution in different parts of its range in Italy, including the Northern Apennines area. The current study represents the first wildcat systematic monitoring in the central part of Northern Apennines. Non-invasive genetic sampling—based both on valerian and catnip lures—was applied, integrated with camera trapping within two Regional Parks. This approach is needed in order to obtain hair samples to be genetically analyzed, since cross-breeding with domestic cats can make wildcat identification based only on coat characteristics misleading. Videos obtained from camera traps allowed the identification of several individuals (image capture rate of 1.04/100 trap-nights), including at least one female. Hair samples were only collected in April–May using catnip as an attractant, whereas the valerian-based solution used did not yield the expected results (i.e., attracting wildcats and stimulating their rubbing behavior to allow hair collection). These results allowed for the first time the genetic confirmation of a pure wildcat in the study area. Domestic cat presence (image capture rate of 1.4/100 trap-nights) was also assessed in the same locations, posing a possible threat for wildcat conservation at the expanding margin of its distribution. Our findings confirm the effectiveness of the integration of multiple monitoring techniques for wildcat detection and highlight the need for a continued monitoring of the species, especially in newly colonized areas. [ABSTRACT FROM AUTHOR]

Przewalski's horse (Equus ferus) is a national protected species in China. It first became extinct in the wild in 1976, and was reintroduced to the Kalamaili National Park (KNP) in Xinjiang, China in 2001. This study aimed to analyze the genetic diversity and structure of the reintroduced population of Przewalski's horse in KNP. Here, we developed and designed microsatellite molecular markers using 48 feces samples and combined this with published genomic data from the species. A preliminary analysis of genetic diversity within the Przewalski's horse population in the KNP was conducted using 16 pairs of simple sequence repeat (SSR) markers with high levels of polymorphism and high stability. A total of 199 alleles were amplified using 16 SSR primer pairs, averaging 12.438 at each locus. In the sample of 48 genomes, the average effective number of alleles detected was 2.695, the average expected heterozygosity was 0.577 and the inbreeding coefficient was 0.232. Twelve loci showed significant deviation from Hardy–Weinberg equilibrium following Bonferroni sequential corrections. Our research finds that the genetic diversity of the Przewalski's horse population in the KNP remains high. This is the first research using newly developed SSR markers to describe the genetic diversity and structure of the reintroduced Przewalski's horse population in KNP, China. As such, it can inform future reintroductions of the species and conservation measures. [ABSTRACT FROM AUTHOR]

Sampling the DNA of rare animal species should have minimal impacts on individual health. This can be accomplished through non-lethal/non-invasive sampling. Few of these methods have been developed for invertebrates, including the Mollusca, which are in global decline. Tissue clipping the foot is a common non-lethal method for gastropods. However, it causes permanent damage and is inappropriate for smaller snails. This study used Flinders Technology Associates (FTA) cards to sample DNA from snail mucus for species of different sizes and habitat types, and across evolutionarily distant lineages. In a survival assay, the death rate of individuals sampled with FTA cards (12.1%) was greater than in the controls (3.7%), but the difference was not significant. Of 224 individuals representing 27 snail species (17 Hawaiian native, ten non-native) sampled using both FTA cards and tissue clipping, 80.4% of FTA samples and 91.6% of tissue samples amplified for COI, a significant difference. COI sequencing success did not differ significantly between the two methods. For individuals that failed to produce a COI sequence, an attempt was made to sequence 16S. For 16S, amplification and sequencing rates did not differ significantly between FTA and tissue samples. Habitat type and shell size did not affect FTA sampling success. Phylogenetically basal taxa exhibited lower success rates, but this may have been because of difficulty in sampling operculate taxa, and not because of identity. These results indicate that the FTA sampling is a viable non-lethal alternative to tissue clipping and can be used for diverse gastropods. [ABSTRACT FROM AUTHOR]

Abstract The ongoing expansion of wolf (Canis lupus) populations in Europe has led to a growing demand for up‐to‐date abundance estimates. Non‐invasive genetic sampling (NGS) is now widely used to monitor wolves, as it allows individual identification and abundance estimation without physically capturing individuals. However, NGS is resource‐intensive, partly due to the elusive behaviour and wide distribution of wolves, as well as the cost of DNA analyses. Optimisation of sampling strategies is therefore a requirement for the long‐term sustainability of wolf monitoring programs. Using data from the 2020–2021 Italian Alpine wolf monitoring, we investigate how (i) reducing the number of samples genotyped, (ii) reducing the number of transects, and (iii) reducing the number of repetitions of each search transect impacted spatial capture‐recapture population size estimates. Our study revealed that a 25% reduction in the number of transects or, alternatively, a 50% reduction in the maximum number of repetitions yielded abundance estimates comparable to those obtained using the entire dataset. These modifications would result in a 2046 km reduction in total transect length and 19,628 km reduction in total distance searched. Further reducing the number of transects resulted in up to 15% lower and up to 17% less precise abundance estimates. Reducing only the number of genotyped samples led to higher (5%) and less precise (20%) abundance estimates. Randomly subsampling genotyped samples reduced the number of detections per individual, whereas subsampling search transects resulted in a less pronounced decrease in both the total number of detections and individuals detected. Our work shows how it is possible to optimise wolf monitoring by reducing search effort while maintaining the quality of abundance estimates, by adopting a modelling framework that uses a first survey dataset. We further provide general guidelines on how to optimise sampling effort when using spatial capture‐recapture in large‐scale monitoring programmes.

Abstract Aquaculture industries face challenges in fish production, primarily due to disease occurrence. Clinical manifestations of these diseases often indicate a considerable advancement in the pathological process. Infected fish often experience morbidity, leading to compromised welfare and substantial economic losses for production facilities. Therefore, prophylaxis and early detection of the pathogens could allow the facility managers to intervene or treat the disease before clinical disease signs occur. For the first time, environmental DNA/RNA (collectively eNA) was used to detect the salmonid pathogen Aeromonas salmonicida subsp. salmonicida in the water hosting rainbow trout (Oncorhynchus mykiss). This took place under controlled experimental conditions, before the occurrence of clinical outcome and mortality. The concentration of bacteria in the water was determined by using a standard curve. To determine the window of possible intervention, bacterial concentration was measured from an early stage of disease and throughout when fish became moribund. Furthermore, the acute phase protein, serum amyloid A produced by rainbow trout, was detected in the water and was found to be up‐regulated 4 days post challenge. It was thereby shown that it is possible to detect strong immune responses in the fish in a non‐invasive manner. The detection of eNA from the water can be used as a tool to detect pathogens in the early phase of infection before the disease becomes severe. This will facilitate interventions to limit the disease and increase the welfare of the fish, which is becoming a requirement for a more sustainable and ethical animal production.

The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non‐invasive and allows for longitudinal sampling. Yet it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In wildlife studies, research on the sampling methodology is limited. In this study focusing on amphibians, we characterize and compare the microbiota (small intestine, large intestine, and feces) of two Hong Kong stream‐dwelling frog species: Lesser Spiny Frog (Quasipaa exilispinosa) and Hong Kong Cascade Frog (Amolops hongkongensis). We found that the microbiota of both species are similar at the level of phylum and family, but diverge at the level of genus. When we assessed the performance of fecal microbiota in representing the intestinal microbiota in these two species, we found that (1) the microbiota of the small and large intestine differs significantly, (2) feces are not an appropriate proxy of either intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our findings raise caution equating fecal and intestinal microbiota in stream‐dwelling frogs. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over‐extrapolation and interpret results carefully. [ABSTRACT FROM AUTHOR]

Non-invasive sampling methods, such as scat sampling, have facilitated genetic studies for conservation genetics researchers, however, the quality and quantity of extracted DNA have always been the main issues with these methods. In the current study, the genetic variation and population structure of wild sheep (Ovis gmelini) in Bamou National Park (Fars, Iran) were evaluated using the swabbing technique and eight microsatellites. The sampling method used showed high efficiency in genotyping individuals and can be considered for use with other species. Expected and observed heterozygosity ranged from 0.502 to 0.943 and 0.950 to 1.00, respectively, and the mean allele richness was 8.87, indicating considerable genetic variation in the population. In addition, inbreeding coefficient across all loci was 0.052. There was no evidence of a bottleneck in the population in the recent past. Despite the high level of genetic variation, the lack of gene flow between populations, and global threats such as climate change, highlight the necessity of implementing reintroduction programs to maintain the evolutionary potential of the species. [ABSTRACT FROM AUTHOR]

High‐resolution mass spectrometry and ion mobility spectrometry provide additional confidence in biological marker discovery and elucidation by adding additional peak capacity through physiochemical separation orthogonal to chromatography. Sophisticated analytical techniques have proved valuable in the identification of human skin surface chemicals used by vector mosquitoes to find their human host. Polydimethylsiloxane (PDMS) was used as a non‐invasive passive wearable sampler to concentrate skin surface non‐volatile and semi‐volatile compounds prior to solvent desorption directly in an LC vial, thereby simplifying the link between extraction and analysis. Ultra‐performance liquid chromatography with ion mobility spectrometry coupled with high‐resolution mass spectrometry (UPLC‐IMS‐HRMS) was used for compound separation and detection. A comparison of the skin chemical profiles between the ankle and wrist skin surface region sampled over a 5‐day period for a human volunteer was done. Twenty‐three biomarkers were tentatively identified with the aid of a collision cross‐section (CCS) prediction tool, seven associated with the ankle skin surface region and 16 closely associated with the wrist skin surface. Ten amino acids were detected and unequivocally identified on the human skin surface for the first time. Furthermore, 22 previously unreported skin surface compounds were tentatively identified on the human skin surface using accurate mass, CCS values and fragmentation patterns. Method limits of detection for the passive skin sampling method ranged from 8.7 (sulfadimethoxine) to 95 ng (taurine). This approach enabled the detection and identification of as‐yet unknown human skin surface compounds and provided corresponding CCS values. [ABSTRACT FROM AUTHOR]

Context. Invasive mammalian predators are a threat to biodiversity and agriculture globally, yet management outcomes for lethal predator control remain difficult to monitor and evaluate. Understanding whether changes in activity indices correspond to true changes in population density will help inform effective monitoring and management programs. Aims. The aim of this study was to evaluate the effect of poison baiting on invasive red fox (Vulpes vulpes) populations using two alternative population metrics: fox activity from camera trap surveys and density estimation from scat genetic analysis. Methods. We conducted before–after control–impact studies in two regions of semi-arid Australia (Wimmera and Mallee) by monitoring paired nontreatment and treatment sites during unbaited and baited periods. We estimated the effects of poison baiting on: (1) a monthly fox activity index, derived from an array of 10 off-road camera traps per site; and (2) fox density. To estimate density, we collected fox scats along 14-km transects, identified individuals using polymorphic microsatellite DNA markers and fitted spatially explicit capture–recapture models. Key results. Fox activity remained consistently low at all sites except the Mallee non-treatment. The top-ranked models of fox activity and density contained an interaction between treatment and period, with an interactive and additive effect of region, respectively. However, there was little evidence that baiting reduced fox activity or density. In the unbaited period, fox densitiesranged from 0.69 (95% CI: 0.47–1.0) to 1.06 (95% CI: 0.74–1.51) foxes km−2 and were similar across regions. Conclusions. Camera traps have the potential to provide continuous index-based measures of fox populations but may not record sufficient observations to detect change. Indices can also be confounded by variations in animal behaviour. Scat genetic analysis is a viable option for providing direct estimates of population change at specific snapshots in time; however, this approach is considerably more expensive, and large sample sizes may be required if genotyping successislow. Implications. Ourstudy presents a rare example of multiple concurrent – and non-invasive – monitoring techniques to evaluate the effectiveness of predator control. We highlight the value of rigorous study designs and high-quality density information for designing predator management and monitoring programs. [ABSTRACT FROM AUTHOR]

Faecal samples are an important source of genetic information for studies of wild animals. The quality and quantity of faecal DNA can, however, be affected by different factors. Our goal was to compare different dung sample storage and DNA extraction methods to optimise the quality and quantity of DNA extracted from forest elephant dung samples. Dung samples (n = 132) of forest elephants were collected in a forest area in Côte d'Ivoire. Each faecal sample was preserved in 50 mL cryotubes using five different methods: Ethanol 70%, formalin 10%, Sodium acetate, acetic acid, and formalin (SAF), dimethyl sulfoxide, and Sodium chloride (20% DMSO), and silica gel. We used the Cetyl Trimethyl Ammonium Bromide (CTAB) cationic detergent and the phenol chloroform DNA extraction procedures for comparison. DNA was successfully obtained from all 132 faecal samples using both DNA extraction methods. Regarding the total DNA extracted independently from the storage buffers, the phenol chloroform method yields a mean DNA concentration (2163.93 ± 918.62 ng/μL) sevenfold higher than that obtained with the optimised CTAB method (338.15 ± 528.54 ng/μL). Our study indicates optimised faecal sample storage and DNA extraction procedures that can help implement conservation strategies for forest elephants. [ABSTRACT FROM AUTHOR]

Over one-third of all elasmobranch species are at risk of extinction worldwide. This study aims to contribute to their conservation worldwide through a case study that combines georeferenced data on species presence and abundance with spatial distribution of human activities, through a Spatial Conflict Risk Index (SCRI). The SCRI pinpoints possible risk areas obtained from the spatial overlap of elasmobranch species abundance and distribution with impacting human activities. Data on species presence and abundance around a Marine Protected Area, the Berlengas Natural Reserve (Portugal) were obtained through four non-invasive methods: Baited Remote Underwater Videos (BRUV), Local Ecological Knowledge (LEK), scientific observers onboard longline commercial fishing vessels and citizen science and social media reports. Human activities were mapped based on LEK. Qualitative abundance and distribution data was obtained for 22 species. SCRI highlighted some high-risk areas due to overlap of areas of frequent occurrence of elasmobranchs with potential high impact activities (e.g. longline fishery). This study highlighted the potential of multi-method approaches to estimate the distribution of rare, highly mobile species in data-limited contexts, and assess their exposure to human activities. The SCRI is a useful tool to support the implementation of effective conservation regulations.

Mesocarnivores are major components of carnivore assemblages, and they play important roles in structuring communities and regulating community dynamics. In Southwest China, many apex predators have been extirpated, and this has potentially resulted in the ecological release of mesocarnivores. Estimating the sizes of mesocarnivore populations is challenging. We used DNA derived from hairs and spatial capture–mark–recapture techniques to estimate the population size of masked palm civets (Paguma larvata) in Laohegou Nature Reserve in the Minshan Mountains of Sichuan Province, China. In the fall of 2014 and the spring of 2015, we collected 144 and 230 hair samples, respectively, at 30 baited stations. We used 16S rRNA fragments, microsatellite genotyping, and sexing to determine that 191 samples were derived from 44 masked palm civet individuals (24 males and 20 females). Using spatially explicit capture–recapture analysis, we estimated that there were 82 ± 13 masked palm civets in the study area, with a density of 1.7 individuals/km2. This is the first study to estimate the population size of masked palm civets in the wild. Our data provide important new information on the density of masked palm civets.

Abstract Background The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus). Results We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery. Conclusion We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.

Abstract The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non‐invasive and allows for longitudinal sampling. Yet it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In wildlife studies, research on the sampling methodology is limited. In this study focusing on amphibians, we characterize and compare the microbiota (small intestine, large intestine, and feces) of two Hong Kong stream‐dwelling frog species: Lesser Spiny Frog (Quasipaa exilispinosa) and Hong Kong Cascade Frog (Amolops hongkongensis). We found that the microbiota of both species are similar at the level of phylum and family, but diverge at the level of genus. When we assessed the performance of fecal microbiota in representing the intestinal microbiota in these two species, we found that (1) the microbiota of the small and large intestine differs significantly, (2) feces are not an appropriate proxy of either intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our findings raise caution equating fecal and intestinal microbiota in stream‐dwelling frogs. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over‐extrapolation and interpret results carefully.

Simple Summary: Our study is one of the few comparative and within-a-species descriptions of microbiomes in wild non-passerine birds. Particularly, it focuses on red-legged partridges, which are medium-sized gamebirds inhabiting open dry countryside and low-intensity cultivations with a mix of fallow and uncultivated areas in southwestern Europe. We wanted to study microbes living in their gut as their occurrence and diversity may affect both survival and reproduction of these birds. We collected fresh red-legged partridge fecal pellets at different sites located on both the western (two) and eastern (one) sides of Elba Island (central Italy). Although most represented bacteria were the same in all the three sites, we found differences between western and eastern Elban subpopulations in terms of microbiome composition and diversity. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. Overall, we suggest that the two partridge subpopulations should be managed separately to avoid any loss or significant variation in their microbiome structure. This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in—among others—habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units. [ABSTRACT FROM AUTHOR]

Reliable assessment of wildlife population parameters is essential to ensure conservation and management. Data on spatio-temporal variations in population density are needed to understand habitat requirements and anthropogenic impacts. We investigated the impact of forest loss and fragmentation on the population density of a forest specialist mammal like the pine marten. We assessed it in two contrasted landscapes, a continuous forest and an agricultural land where forests are fragmented into small woodlots and hedgerows. A non-invasive genetic sampling was carried out over two consecutive years to assess population density using capture-mark-recapture models implemented in CAPWIRE and CAPTURE. Across the different sampling sessions, 86 distinct pine martens could be identified, 59 in the hedged farmland and 27 in the forest site. Contrary to our expectations, the hedged farmland carried a similar level of pine marten density (around 0.85 (95%CI 0.44–1.30) individual/km2) to that estimated in forest (0.64 (95%CI 0.41–1.09) individual/km2) but experienced a high rate of turnover. Consistently with other studies in Europe, we showed that at between 20 and 35% of forest cover, landscapes can carry high-density levels for pine marten populations. This study underlines the need to keep forest patches in agricultural landscapes safe from trapping and hunting to maintain sustainable pine marten populations. [ABSTRACT FROM AUTHOR]

Abstract The use of invertebrate‐derived DNA (iDNA) is a promising non‐invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and sub‐tropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies and mosquitoes‐derived DNA to assess vertebrate diversity in semi‐urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non‐bloodfed mosquitoes were metabarcoded using 108‐bp vertebrate‐specific 12 S rRNA (12 S‐V5) and 94‐bp mammal‐specific 16 S rRNA (16Smam) mitochondrial markers, and individual bloodfed mosquitoes were sequenced using the 340‐bp vertebrate‐specific 12 S rRNA fragment (Mam‐12 S‐340). Most sequencing was only successful for mammal species. From the fly pools, we detected 10 mammal species using 16Smam, and six species using 12 S‐V5. From the non‐bloodfed mosquito pools, we only amplified putative contaminant DNA, indicating that mosquito females without visual signs of a blood meal carry no traces of vertebrate DNA. Finally, in the bloodfed mosquitoes, we identified four mammal species. We did not find significant differences in the proportion of mammal species detected regarding the total available number of species between sampling localities. Fly samples were easier to obtain and more abundant over the sampled localities compared to mosquito samples. We conclude that, while there are a few advantages in using mosquito blood meals, the use of flies in the detection of wildlife in a suburban environment is more effective in terms of collection of samples and detection of vertebrates, although this technique is limited to few mammal species in the urban environment.

Food distribution and abundance can affect intra- and inter-dietary variation in non-human primates, influencing feeding ecology and altering behaviour. Natural and/or human-induced actions can influence the dynamics between primates and the environment, with associated impacts on socio-ecology and demography. This relationship in anthropogenic landscapes, however, is poorly understood. Here, we use DNA metabarcoding to obtain high resolution dietary diversity data, and multivariate generalised linear models to investigate variation in the diet of this threatened primate. We characterise the diet of the western red colobus (Piliocolobus badius) in both the better preserved Gola Rainforest National Park (GRNP, Sierra Leone), and in the fragmented forests of Cantanhez National Park (CNP, Guinea-Bissau), and evaluate biological, ecological and temporal differences. Dietary plant species richness was high in both protected areas, and the type of plants consumed varied significantly across seasons, space, and time. Although we identify dependence on a few key plants, red colobus in CNP consumed a higher average number of plant taxa than in GRNP, and 11% of the diet consisted of cultivated foods (e.g. mango). This is the first time a molecular approach has been used to investigate red colobus diet, and reveal dietary flexibility in degraded forests. Predicting the consequences of dietary change on long-term population persistence, however, remains a significant knowledge gap. Nevertheless, our results provide critical information to inform targeted regional conservation planning and implementation.

Background: The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus). Results: We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery. Conclusion: We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so. [ABSTRACT FROM AUTHOR]

Characterizing patterns and drivers of dispersal is fundamental to our understanding of animal ecology and ultimately informing species conservation and management strategies. In this study, we used microsatellite data from 3941 individual black bears Ursus americanus occupying 73 spatially distinct sampling areas across a large heterogeneous landscape to characterize dispersal via gene flow directionality. We fit spatial models to quantified gene flow to test hypotheses regarding drivers of putative dispersal patterns. Specifically, we tested the relative influence of food productivity gradients, bear density, and bear harvest on dispersal. We also evaluated differences in gene flow patterns within and between sexes to assess sex‐biased dispersal. We found evidence suggestive of positive density‐dependent, male‐biased dispersal. Our data show evidence of a relationship between dispersal and broad food productivity gradients. Specifically, male bears displayed preferential dispersal towards mixed deciduous forests with higher food productivity relative to less productive boreal forests. Given the dense sampling scheme across a continuous population, occupying a large heterogeneous landscape, these results provide key insight as to the likely drivers of dispersal patterns in a wide‐ranging mammal. [ABSTRACT FROM AUTHOR]

Simple Summary: Hormone concentrations derived from hair can inform us of many aspects of an individual's life, such as their reproductive status or social position. Cortisol is often associated with physiological or even psychological stress, while testosterone is strongly associated with male development and reproductive success. This study investigated cortisol and testosterone concentrations of tail hair collected from feral horses living in a naturally established social structure. We compare values of hair derived cortisol (n = 153) and testosterone (n = 48) to an individual's social position as either an Immature male (2–4 years old), physically mature but non-reproductive male (Bachelor), reproductive dominant male (Stallion), or subordinate harem-associated male (tag). Immature males had significantly lower hair cortisol concentrations than adults. Hair testosterone concentrations were significantly higher in Stallions than males in the other social positions when age is accounted for. Bachelors exhibited a positive correlation between the two hormone levels, while among Stallions the association was negative. These findings suggest that patterns in hair hormone concentrations reflect known physiological interactions between cortisol and testosterone in relation to age, dominance, and reproduction, that have been established in the literature. Steroid-hormone concentrations from non-invasively obtained biomarkers, like hair, can provide a representation of circulating hormones diffused over relatively long time periods (e.g., weeks or months). The hormone cortisol is often associated with physiological or even psychological stress, while testosterone is strongly associated with male development and reproductive success. Increasingly, studies are using hormone levels derived from hair to make inferences among both domestic animals and wildlife. For horses, all previous hair hormone analysis has been done on companion or working animals. We evaluated the levels of hair cortisol (n = 153) and testosterone (n = 48) from 136 feral horses living on Sable Island, Canada that have been part of a long-term individual-based study since 2008. This population has been undisturbed and unmanaged for over 50 years, and exhibits the natural social organization for horses, harem defense polygyny. Hair samples were collected in mid to late summer and the segment analyzed corresponds with hair grown during, and following, the peak of the reproductive season. Social position was determined based on the male's role as either a dominant breeding Stallion (Stallion), a non-breeding subordinate male (tag), adult Bachelor (5 years old or older), or Immature male (2–4 years of age). While there was no difference in hair-cortisol concentration among any class of adult males (i.e., Stallion, tag, or Bachelor), Immature males had significantly lower hair cortisol concentrations than the other groups (p = 0.001). Hair testosterone levels among the four social positions were significantly higher among Stallions (p = 0.04). Hair testosterone concentration was also significantly related to the probability of a male being either a Bachelor or Stallion and was the only variable remaining in AICc model selection (p = 0.016, AICc = 32.3, Null AICc = 38.8). While not a significant relationship, Stallions had a negative correlation between hair cortisol concentrations and testosterone (R2 = −0.20, p = 0.383), and Bachelors, conversely, had a positive association (R2 = 0.43, p = 0.246). Our observations of hormone concentrations in relation to physiological, social, or reproductive parameters in this population suggest trends that are similar to what has been established using blood or other matrices. [ABSTRACT FROM AUTHOR]

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Monitoring of odonates has become an important instrument for ecological status assessment of (semi-)aquatic habitats. Besides information on presence and abundance, knowledge about a species´ autochthony at the surveyed waterbody is a significant information within the assessment process. Here, the finding of exuviae represents the ultimate proof of successful reproduction. Although feasible for most odonate species, morphological identification of exuviae is often time consuming, as it relies on small, fragile structures. To facilitate species identification of exuviae, a DNA barcoding approach was developed, including (1) non-destructive extraction of DNA using whole exuviae or their tracheal tubes, and (2) primer systems for long (< 600 bp) and short (< 200 bp) CO1 fragments. A total of 85 exuviae from 33 species were analysed and compared to results of morphological identification. Additionally, factors potentially influencing DNA quality and quantity, as well as PCR and sequencing success were investigated. Eighty-two exuviae matched the morphologically identified genus, and 60 matched at species level. Of the 33 species present in the data set, 82% could be identified to species level via DNA barcoding. The results show how DNA-based approaches can support fast and accurate species identification and therefore enhance monitoring of an ecologically important taxonomic group, with high relevance for conservation and habitat restoration. Moreover, the use of exuviae as DNA resource once more shows that non-invasive sampling offers great potential for molecular species identification, which is essential when studying rare and endangered species. Implications for insect conservation: Our results show how molecular tools, here DNA barcoding of odonate exuviae, can support species monitoring without the need of catching individuals, harming, or even killing them. Obtaining DNA from non-invasive sources can thus be a direct advantage to the conservation of insects, especially when dealing with rare and endangered species and/or populations. Using the example of odonates as bioindicator organisms for aquatic and semi-aquatic habitats, we highlight the importance of non-invasive genetic approaches for population studies and monitoring of insect species and/or species communities for ecosystem assessments and conservation management. [ABSTRACT FROM AUTHOR]

Mesocarnivores play important ecological roles and are valued by diverse stakeholders. These species are often the focus of conservation efforts or are managed for sustainable harvest. Management actions require accurate population monitoring, but such monitoring is challenging because mesocarnivores are elusive and persist at low densities. We addressed this challenge by evaluating 2 monitoring methods (scent stations and motion‐sensitive cameras) using multi‐method modeling. We estimated occurrence probabilities and habitat relationships for 8 mesocarnivore species by fitting occupancy models to data collected at 75 sites from October to December 2021 across a 3,200‐km2 system in New Hampshire, USA. We assessed the relative estimated precision of the methodological approaches and their costs. We also evaluated tradeoffs in occurrence estimation and uncertainty among study designs by analyzing simulations run across various numbers of study sites and 2 study durations. Cameras cost roughly 10 times more than scent stations but strongly outperformed them in terms of species' detectability and parameter estimate precision. Multi‐method models yielded the most precise estimates of occurrence probability and habitat relationships. Parameter estimates were on average twice as precise for camera and multi‐method models compared to scent stations. Additionally, the estimated precision and direction (positive or negative) of habitat relationships varied with the method employed. Longer camera deployments, additional study sites, and multi‐method approaches nearly always reduced uncertainty, but these reductions were species‐specific and generally most pronounced for more rarely detected species. Overall, our results demonstrate the utility of motion‐sensitive cameras traps for monitoring mesocarnivores while revealing the additional benefits of multi‐method modeling. Our results also provide guidance for designing monitoring programs for mesocarnivores while navigating tradeoffs between study design, cost, and uncertainty. Despite its benefits, multi‐method modeling remains uncommon as a general monitoring approach. We suggest managers consider this approach in light of existing datasets and design monitoring programs that integrate traditional methods with emergent technologies. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Hydrobiology is the property of Editorial Department of Journal of Hydrobiology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Society is becoming increasingly critical of animal husbandry due to its environmental impact and issues involving animal health and welfare including scientific experiments conducted on farm animals. This opens up two new fields of scientific research, the development of non- or minimally invasive (1) methods and techniques using faeces, urine, breath or saliva sampling to replace existing invasive models, and (2) biomarkers reflecting a disease or malfunction of an organ that may predict the future outcome of a pig’s health, performance or sustainability. To date, there is a paucity of non- or minimally invasive methods and biomarkers investigating gastrointestinal function and health in pigs. This review describes recent literature pertaining to parameters that assess gastrointestinal functionality and health, tools currently used to investigate them, and the development or the potential to develop new non- and minimally invasive methods and/or biomarkers in pigs. Methods described within this review are those that characterise gastrointestinal mass such as the citrulline generation test, intestinal protein synthesis rate, first pass splanchnic nutrient uptake and techniques describing intestinal proliferation, barrier function and transit rate, and microbial composition and metabolism. An important consideration is gut health, and several molecules with the potential to act as biomarkers of compromised gut health in pigs are reported. Many of these methods to investigate gut functionality and health are considered ‘gold standards’ but are invasive. Thus, in pigs, there is a need to develop and validate non-invasive methods and biomarkers that meet the principles of the 3 R guidelines, which aim to reduce and refine animal experimentation and replace animals where possible.

The identification of discrete intraspecific units, such as genetically informed management units (MUs), is important to effectively develop and implement conservation strategies for protected species. Harbour seals (Phoca vitulina) occurring in Irish waters are currently viewed as a single nationwide panmictic population (and hence MU), although this assumption is not based on any knowledge of population structure because of the lack of available genetic data.Thus, the present study used mitochondrial control region sequences and between nine and 11 microsatellite loci from harbour seals from Ireland and Northern Ireland (up to n = 123) and adjacent UK/European waters (up to n = 289) to provide insights into the genetic population structure and diversity of harbour seals in the areas studied.Within the island of Ireland, genetic analyses revealed the presence of three genetically distinct local populations, characterized by high genetic diversity, hereby defined as: East Ireland (EI), North‐west & Northern Ireland (NWNI), and South‐west Ireland (SWI).Using previously published and newly generated data, a subsequent wider scale analysis revealed that the EI and SWI local populations were genetically distinct from neighbouring UK/European areas, whereas seals from the NWNI area could not be distinguished from a previously identified Northern UK metapopulation. Migration rate estimates showed that NWNI receives migrants from North‐west Scotland, with NWNI acting as a genetic source for both SWI and EI.The present study provides the most comprehensive genetic assessment of harbour seals in European waters to date, with findings indicating that conservation strategies for harbour seals in Irish waters should be amended to accommodate at least three genetically distinct local populations/MUs. The use of approaches considering both ecological and genetic parameters is recommended for future assessments and delineation of units of ecological relevance for conservation management purposes. [ABSTRACT FROM AUTHOR]

Wolves are currently recolonising their historic range in France. The collection of scats is a widely used a non-invasive survey method to monitor wolf population size. However, seasonal changes in wolf faecal deposition paterns might afect the results of surveys. We used a detection dog and camera trapping (CT) to compare wolf scat detectability during winter and the nursing season. We collected 113 scats deposited by adult wolves at 29 marking sites on forest roads in the Sainte-Baume Regional Park, Provence, France. After parturition, the mean number of adult wolf scats increased by 160% inside the nursing territory and decreased by 80% outside of it. Around the time the pups are born, changes in faecal deposition patterns of adults make it easier to find scats around the wolf den (87% probability per wolf marking site) and harder to find scats outside the nursing territory (11% probability). During winter, the chance to find scats is equal (38 to 40% probability per wolf marking site) inside vs. outside the nursing territory. The combined use of a detection dog and camera traps allowed us to gather data on wolf defecation patterns non-invasively. Detectability of adult wolf scats during the nursing season is highly variable compared to winter due to seasonal behavioural changes affecting scat location. We conclude that surveys to collect samples and estimate wolf population size should be conducted exclusively during winter to avoid sampling biases. [ABSTRACT FROM AUTHOR]

Red pandas (Ailurus fulgens) are taxonomically unique mammals in the order Carnivora that evolved to an arboreal and herbivorous existence in the mountainous regions of south east-central Asia. Now endangered, they have a precarious future in nature due to ever-changing environmental conditions and increasing anthropogenic threats. This study reports on an early mitochondrial DNA survey successfully accomplished by fecal sampling of 68 (minimum) wild red pandas in three regional populations of Nepal at the western end of their range. From 383 bp of control region sequences, our study identified 17 haplotypes, relatively high haplotype diversity (Hd = 0.83) but low nucleotide diversity (π = 0.010) overall with both measures decreasing from east to west, a comparatively close phylogenetic relationship between mtDNA-defined subspecies, differentiation of one population, and the discovery of a haplotype in two samples that belongs to the purported subspecies previously recorded only from the eastern end of their range. We argue for caution in elevating taxonomic rank without incorporating other species-defining criteria, suggest reconsidering subspecies' boundaries and investigating hybridization in the contact zone, provide some evolutionary hypotheses for the genetic distribution exposed, propose specific applications for conservation management, and stress inclusion of nuclear markers to complement future research. This study presents valuable information on red panda population genetics from the western end of their range in Nepal, essential for recovery programs like the IUCN Green Status of Species, to establish an historical baseline for future genetic monitoring and decision-making in the conservation of a rare but iconic endangered species. [ABSTRACT FROM AUTHOR]

This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in—among others—habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units.

Skin disease alters cutaneous lipid mediator metabolism, and if skin secretions contain evidence of these changes, they may constitute useful clinical matrices with low associated subject burden. The influences of skin diseases on sebum lipid mediators are understudied. Here, sebum oxylipins, endocannabinoids, sphingolipids, and fatty acids were quantified from the non-lesional bilateral cheeks of subjects with and without quiescent atopic dermatitis (AD) using LC-MS/MS and GC-MS. AD decreased C36 [NS] and [NdS] ceramide concentrations. Compared to males, females demonstrated increased concentrations of oxylipin alcohols and ketones, and saturated and monounsaturated non-esterified fatty acids, as well as decreased concentrations of C42 [NS] and [NdS] ceramides. Additionally, contemporaneously collected sweat lipid mediator profiles were distinct, with sebum showing higher concentrations of most targets, but fewer highly polar lipids. Therefore, AD and gender appear to alter sebum lipid metabolism even in non-lesional skin of quiescent subjects.

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non‐invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free‐ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non‐invasive samples. [ABSTRACT FROM AUTHOR]

Acquiring sufficient blood for hormone analysis in mice can be a limiting step. Hormone analysis techniques using non-invasive sample collection have been vigorously developed for endangered species, from whom blood sampling is prohibited, or from species that are otherwise difficult to handle in a laboratory setting. Because there are interactions between glucocorticoids and thyroid hormones (T3 and T4), reducing the animal's "distress" during sample collection is imperative. Measurement of fecal T3 provides less sensitive, baseline information regarding thyroid function while permitting a non-invasive technique for more frequent sampling. We demonstrated that using a methanol extraction protocol produced the most reliable fecal T3 measurement in an enzyme-linked immunosorbent assay (ELISA). We found that during a thyroid hormone-treated state, fecal and plasma T3 measurements from mice are directly related, while during a methimazole-treated state, fecal and plasma T3 measurements from mice are inversely related. Fecal samples are a useful way to monitor thyroid hormone function in laboratory mice., (© 2024 The Author(s). Physiological Reports published by Wiley Periodicals LLC on behalf of The Physiological Society and the American Physiological Society.)

Abstract Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non‐invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free‐ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non‐invasive samples.

Steroid-hormone concentrations from non-invasively obtained biomarkers, like hair, can provide a representation of circulating hormones diffused over relatively long time periods (e.g., weeks or months). The hormone cortisol is often associated with physiological or even psychological stress, while testosterone is strongly associated with male development and reproductive success. Increasingly, studies are using hormone levels derived from hair to make inferences among both domestic animals and wildlife. For horses, all previous hair hormone analysis has been done on companion or working animals. We evaluated the levels of hair cortisol (n = 153) and testosterone (n = 48) from 136 feral horses living on Sable Island, Canada that have been part of a long-term individual-based study since 2008. This population has been undisturbed and unmanaged for over 50 years, and exhibits the natural social organization for horses, harem defense polygyny. Hair samples were collected in mid to late summer and the segment analyzed corresponds with hair grown during, and following, the peak of the reproductive season. Social position was determined based on the male’s role as either a dominant breeding Stallion (Stallion), a non-breeding subordinate male (tag), adult Bachelor (5 years old or older), or Immature male (2–4 years of age). While there was no difference in hair-cortisol concentration among any class of adult males (i.e., Stallion, tag, or Bachelor), Immature males had significantly lower hair cortisol concentrations than the other groups (p = 0.001). Hair testosterone levels among the four social positions were significantly higher among Stallions (p = 0.04). Hair testosterone concentration was also significantly related to the probability of a male being either a Bachelor or Stallion and was the only variable remaining in AICc model selection (p = 0.016, AICc = 32.3, Null AICc = 38.8). While not a significant relationship, Stallions had a negative correlation between hair cortisol concentrations and testosterone (R2 = −0.20, p = 0.383), and Bachelors, conversely, had a positive association (R2 = 0.43, p = 0.246). Our observations of hormone concentrations in relation to physiological, social, or reproductive parameters in this population suggest trends that are similar to what has been established using blood or other matrices.

Biomarkers of oxidative stress (OS) are useful in addressing a wide range of research questions, but thus far, they have had limited application to wild mammal populations due to a reliance on blood or tissue sampling. A shift toward non‐invasive measurement of OS would allow field ecologists and conservationists to apply this method more readily. However, the impact of methodological confounds on urinary OS measurement under field conditions has never been explicitly investigated. We combined a cross‐sectional analysis with a field experiment to assess the impact of four potential methodological confounds on OS measurements: (1) time of sampling, (2) environmental contamination from foliage; (3) delay between sample collection and flash‐freezing in liquid nitrogen; and (4) sample storage of up to 15 months below −80°C. We measured DNA oxidative damage (8‐hydroxy‐2′‐deoxyguanosine, 8‐OHdG), lipid peroxidation (malondialdehyde, MDA), total antioxidant capacity (TAC), and uric acid (UA) in 167 urine samples collected from wild Zanzibar red colobus (Piliocolobus kirkii). We found that MDA was higher in samples collected in the morning than in the afternoon but there were no diurnal patterns in any of the other markers. Contamination of samples from foliage and length of time frozen at −80°C for up to 15 months did not affect OS marker concentrations. Freezing delay did not affect OS levels cross‐sectionally, but OS values from individual samples showed only moderate‐to‐good consistency and substantial rank‐order reversals when exposed to different freezing delays. We recommend that diurnal patterns of OS markers and the impact of storage time before and after freezing on OS marker concentrations be considered when designing sampling protocols. However, given the high stability we observed for four OS markers subject to a variety of putative methodological confounds, we suggest that urinary OS markers provide a valuable addition to the toolkit of field ecologists and conservationists within reasonable methodological constraints. [ABSTRACT FROM AUTHOR]