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Habitat fragmentation and loss reduce population size and connectivity, which imperils populations. Functional connectivity is key for species persistence in human-modified landscapes. To inform species conservation management, we investigated spatial genetic structure, gene flow and inferred dispersal between twelve breeding sites of the Natterjack toad (Bufo calamita); regionally Red-Listed as Endangered in Ireland. Spatial genetic structure was determined using both Bayesian and non-Bayesian clustering analysis of 13 polymorphic microsatellite loci genotyping 247 individuals. We tested the influence of geographic distance, climate, habitat, geographical features, and anthropogenic pressure on pairwise genetic distances between breeding sites using Isolation-by-distance and Isolation-by-resistance based on least-cost path and circuit theory models of functional connectivity. There was clear spatial structuring with genetic distances increasing with geographic distance. Gene flow was best explained by Isolation-by-resistance models with coniferous forestry plantations, bog, marsh, moor and heath, scrub, anthropogenic presence (Human Influence Index) and rivers (riparian density) identified as habitats with high resistance to gene flow while metapopulation connectivity was enhanced by coastal habitats (beaches, sand dunes and salt marshes) and coastal grassland. Despite substantial declines in census numbers over the past 15 years and its regional status as Endangered, the Natterjack toad population in Ireland retains high genetic diversity. If declines continue, maintaining habitat connectivity to prevent genetic erosion by management of coastal grasslands, pond construction and assisted migration through translocation will be increasingly important.

Molecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.

Effective monitoring of wildlife populations forms the foundation of modern‐day conservation biology. Without reliable estimates of population size, it is not possible to determine population trends, a key requirement in determining species status under international legislation. Carnivores are one of the more difficult taxonomic groups to monitor due to low population densities and elusive behavior. Here, we compare conventional live trapping and two more modern, noninvasive field methods of population estimation: genetic fingerprinting from hair tube sampling and camera trapping for the pine marten (Martes martes). We apply marked spatial capture–recapture (SCR) models to the genetic and live‐trapping data where individuals were identifiable, and unmarked SCR (uSCR), camera‐trap distance sampling (CT‐DS), and random encounter models (REMs) to the camera‐trap data where individual ID was not possible. All five approaches produced plausible and relatively consistent point estimates (0.49–1.20 individuals/km2) despite differences in precision, cost, and effort being apparent. Genetic fingerprinting produced the most precise estimate out of the two approaches for marked animal populations and had the key benefit of being noninvasive but was the most expensive of all the methods. Live trapping produced the highest point estimate while being cheapest, but the most labor intensive and least precise. The camera‐trapping methods for unmarked animal populations were the most time efficient and precise except uSCR with a moderately informative prior (uSCRm), which produced the second least precise density estimate of all the methods compared. The CT‐DS produced the most precise estimate of all the methods, followed by REM and then uSCR with a strongly informative prior (uSCRs). While choice of method of density estimation depends on objectives and funding constraints, as well as the species of interest, we demonstrate the importance of using a priori knowledge of target species and consideration of planned statistical analysis to produce appropriate experimental designs with critical consideration required regarding trap spacing and spatial extent. Such considerations broaden the comparability and applicability of these methods and will serve to provide key reference estimates for researchers, wildlife managers, and non‐governmental organizations involved in monitoring wildlife populations.

The global amphibian crisis is driven by a range of stressors including disease, habitat loss, and environmental contamination. The role of climate change remains poorly studied and is likely to influence environmental suitability, ranges, reproduction, and phenology. This study aimed to characterize the bioclimatic‐habitat niche space of the Natterjack toad (Epidalea calamita) throughout its European range and to assess the impact of climate on the toad's environmental suitability and breeding behavior in Ireland, where declines in recent decades have resulted in it being regionally Red‐Listed as Endangered. To address these questions, we first identified which climate variables best predict the current bioclimatic niche, fecundity (number of eggs deposit), and phenology. We then used future climate projections for two time periods (2041–2060 and 2061–2080) and two greenhouse gas emission scenarios (RCP 4.5 and RCP 8.5) to predict how the species range, fecundity, and phenology would change. The European range of the species was found to be limited by winter temperatures while its bioclimatic niche varied markedly throughout its range. Species distribution models suggested projected climate change will increase environmental suitability for the species throughout its range, including Ireland, but most notably in Scandinavia and the Baltic. Fecundity in Ireland was greatest during the cool temperatures of spring and after wet winters associated with ephemeral breeding pool availability. Warm, dry summers in the preceding year influenced fecundity the following spring indicative of carryover effects. Initiation of spawning was driven by spring temperatures, not rainfall. Projections suggested future climate change may increase fecundity in Ireland while spawning may commence earlier throughout the 21st century especially under a high greenhouse gas emission scenario (RCP 8.5). Despite recent range contraction and population declines due to habitat deterioration, the Natterjack toad, if subject to a suitable species conservation strategy, has the potential to be a climate change winner, notwithstanding unpredictable habitat and land‐use change, sea‐level rise inducing coastal erosion, changes in invertebrate prey abundance, and disease. In this study, we assessed the impact of climate change on the Natterjack toad's environmental suitability, fecundity and spawning behavior. Our results suggested projected climate change will increase environmental suitability for the species throughout its distribution range and may increase fecundity while spawning may commence earlier. Despite recent range contraction and population declines due to habitat deterioration, the Natterjack toad, if subject to a suitable species conservation strategy, has the potential to be a climate change winner.

The Natterjack toad ( Epidalea calamita ) is the rarest amphibian species in Ireland, regionally Red-Listed as Endangered. We applied an eDNA approach to detect species presence in breeding pond water samples. We developed a species-specific qPCR assay targeting the cytochrome c oxidase subunit I (COI). The assay was tested in silico, in vitro (DNA extracted from tissue) and in vivo (DNA extracted from water samples). Water samples were collected from five ponds with known Natterjack toad presence or absence to validate the sensitivity and specificity of the assay. The assay was shown to be highly specific to the Natterjack toad and tested positive only against toad tissue samples and eDNA samples from ponds with known species presence. We believe this method can be used for rapid assessment of species occurrence.

Amphibians have been declining globally since at least the 1970s and are the most endangered class of vertebrates with over 40% of species threatened with extinction. The Natterjack toad (Epidalea calamita) is the rarest amphibian in Ireland, regionally Red-listed as Endangered. The species is subject to substantial Government conservation efforts, including regular monitoring and surveillance, a Pond Creation Scheme and an ongoing Head-start and Translocation Programme to facilitate new pond colonisation. This thesis aimed to update the Natterjack toad's conservation status in Ireland, establish temporal trends assessing threats and pressures, describe its genetic integrity and population structure and evaluate the efficacy of conservation measures. The new information generated spans habitat selection, spatial ecology, population biology, metapopulation dynamics, genetic diversity, biogeography and effects of climate change. Natterjack toad annual egg string counts suggested a -23% decline in the number of egg strings between 2004 and 2018 with local extirpation at one site. Assessment of perceived threats and pressures suggests that declines are likely driven by poor habitat quality. Conservation programmes failed to significantly arrest decreases in the number of egg strings offsetting further declines by only 4%. Nevertheless, the conservation value of artificially created ponds should not be underestimated as they had 43% higher aquatic macroinvertebrate species richness and 33% higher macroinvertebrate abundance than natural ponds. Mark-recapture using photo ID and genetic fingerprinting suggested that extrapolation of total population estimates from egg strings alone may underestimate the census size by up to 83% due to substantial sex ratio deviation from 1:1 with up to 7 males per female at breeding ponds. Genetic studies indicated high genetic diversity with no evidence of genetic bottlenecks or inbreeding depression despite considerable declines in the number of egg strings. The Natterjack toad population in Ireland displayed significant genetic spatial structuring, best explained by barriers to dispersal and gene flow inhibited by coniferous forestry plantations, bog, marsh, moor and heath, scrub, anthropogenic presence and rivers, and facilitated by sand dunes and coastal grasslands. Suitable bioclimatic-habitat niche space for the species is likely to expand northward and to higher elevations under projected global climate change with models predicting increase in the number of egg strings and earlier spawning by the end of the 21 century. However, limited dispersal capability and ongoing threats and pressures mean potential benefits of climatic change are unlikely to be realised. Continued population monitoring and surveillance is recommended while it is suggested that future research should include: estimation of sex ratio variation between metapopulations, use of acoustic monitoring to assess the male population at breeding sites, use of environmental or eDNA in assessing species presence including colonisation of new ponds and calibration of water DNA densities using population abundance derived from egg strings, a greater focus on disease and pathogens, and investigation of terrestrial habitat use and hibernacula availability. Species conservation strategies should focus on working with landowners and farmers to improve habitat quality, water quality and the availability of breeding ponds to maximise connectivity between breeding sites facilitating dispersal. Recommendations are made to conservation practitioners with respect to genetic structuring and identified genetic entities. A major challenge lies in breaching the boundaries between academic research, Government and conservation management decision making and practical on-the-ground conservation action by various stakeholders (principally landowners and farmers) to make conservation programmes more effective and efficient.

There was a single observation in 2007 in the south of the country. Since 2007, no other successful nesting attempts were recorded (Koonjul 2009). A transect was defined as each 'on-effort' track. [...]on each day there could be several transects of varying length. Transects were conducted opportunistically according to the weather conditions and availability of resources. [...]the surveys were part of a broader Biodiversity Project and sometimes the research vessel followed marine mammals in order to observe their behavior.