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International wild Atlantic salmon management priorities have moved from exploitation to conservation since the 1990s, recognizing the need to protect diversity and abundance at individual river levels amid widespread declines. Here we review international salmon-stock assessments and describe a simple, transferable catch-advice framework, established for management of fisheries that conforms to international obligations. The risk assessment approach, applied at the river scale, jointly incorporates uncertainty in estimated and forecasted returning salmon numbers with the level of uncertainty around spawning requirements (Conservation Limits). Outputs include quantification of risk of stocks not attaining conservation limits (CL) and surpluses above CL on stocks able to support sustainable exploitation via total allowable catches (TAC), with monitoring by rod catch or fish counter. Since management implementation and cessation of at-sea mixed-stock fisheries, there has been a deterioration in the performance of many individual stocks, without any sustained increase in fisheries open to harvest. Given declines in mid-latitude Atlantic salmon populations over 30 years, the novel framework presented provides an approach to protect stocks failing to meet spawning thresholds while supporting sustainable exploitation of those achieving them. On-going management policy of adopting scientific advice and allowing exploitation only on stocks exceeding CLs is central to the objective of protecting salmon stocks. [ABSTRACT FROM AUTHOR]

Background: Rabbit haemorrhagic disease virus (RHDV) is a Lagovirus, a subgroup of the family Caliciviridae. RHDV2 is a variant first described in France in 2010, and has since spread globally. It has been reported in several Lagomorph species (rabbits, hares, and their relatives) as well as other mammals including voles and shrews. The disease has raised international concerns for its potential impact on population abundance trajectories, particularly as 25% of Lagomorphs are currently Red-Listed by the International Union for the Conservation of Nature (IUCN). The Irish hare (Lepus timidus hibernicus) is a subspecies of the mountain hare, L. timidus, and is endemic to Ireland, making it an Evolutionarily Significant Unit of intrinsic value. Case presentation: The first case of RHDV2 was detected in a wild Irish hare in July 2019. The individual exhibited atypical neurological behaviour (running in circles) prior to death. On necropsy, pink tinged foam was seen in the trachea and congestion was noted in the lungs, but there was no evidence of haemorrhages in any other organ. Both the liver and spleen were tested by reverse transcription real time qPCR confirming high levels of RHDV2 RNA. Histopathology confirmed multifocal necrotising hepatitis. Conclusion: The Irish hare is susceptible to RHDV2 infection. Further investigation is warranted to explore the clinical, epidemiological, and population biology implications. [ABSTRACT FROM AUTHOR]

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Animal populations at northern latitudes may have cyclical dynamics that are degraded by climate change leading to trophic cascade. Hare populations at more southerly latitudes are characterized by dramatic declines in abundance associated with agricultural intensification. We focus on the impact of historical climatic and agricultural change on a mid‐latitude population of mountain hares, Lepus timidus hibernicus. Using game bag records from multiple sites throughout Ireland, the hare population index exhibited a distinct regime shift. Contrary to expectations, there was a dynamical structure typical of northern latitude hare populations from 1853 to 1908, during which numbers were stable but cyclic with a periodicity of 8 years. This regime was replaced by dynamics more typical of southern latitude hare populations from 1909 to 1970, in which cycles were lost and numbers declined dramatically. Destabilization of the autumn North Atlantic Oscillation (NAO) led to the collapse of similar cycles in the hare population, coincident with the onset of agricultural intensification (a shift from small‐to‐large farms) in the first half of the 20th century. Similar, but more recent regime shifts have been observed in Arctic ecosystems and attributed to anthropogenic climate change. The present study suggests such shifts may have occurred at lower latitudes more than a century ago during the very early 20th century. It seems likely that similar tipping points in the population collapse of other farmland species may have occurred similarly early but went undocumented. As northern systems are increasingly impacted by climate change and probable expansion of agriculture, the interaction of these processes is likely to disrupt the pulsed flow of resources from cyclic populations impacting ecosystem function. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

According to the International Union for Conservation of Nature Red List, 41% of the world's amphibian species are threatened with extinction, making them more threatened than any other vertebrate group nowadays. Given the global amphibian crisis, comprehensive understanding of demographics and population trends of declining and threatened species is essential for effective management and conservation strategies. Counting egg spawns is widely used to assess population abundance in pond breeding anurans. However, it is unknown how such counts translate into robust population size estimations. We monitored the breeding activity of the Natterjack toad (Epidalea calamita), combining egg string counts and individual photo‐identification with Capture‐Mark‐Recapture population size and operational sex ratio estimation. Male Natterjack toads were identified by the pattern of natural markings with repeated ID of the same individual confirmed for 10% of the samples using genetic fingerprinting. We identified 647 unique individuals within a closed study population at Caherdaniel, Co Kerry. Population estimates derived from egg string counts estimated a breeding population of 368 females (95% CI 353–384) and Capture‐Mark‐Recapture estimated a breeding population of 1698 males (95% CI 1000–2397). The female:male sex ratio was conservatively estimated at 1:5 (95% CI 1:3–1:6) where 62% ± 6% of females were assumed to spawn. These substantially departed from any priori assumption of 1:1 which could have underestimated the breeding population by up to 72%. Where amphibian absolute population size estimation is necessary, methods should include empirical survey data on operational sex ratios and not rely on assumptions or those derived from the literature which may be highly population and/or context‐dependent. [ABSTRACT FROM AUTHOR]

Farmland ponds are a highly threatened freshwater habitat which has undergone dramatic losses during the last 200 years due to land drainage schemes and agricultural intensification. Agri‐environment schemes (AES) incentivize farmers to adopt farming methods to benefit biodiversity, yet there are a paucity of data evaluating the success of artificially created AES ponds as analogues of natural ponds in an attempt to recreate lost environments.We examined variation in environmental parameters and aquatic and terrestrial invertebrate communities between 38 natural ponds and 91 artificial ponds that were created in south‐west Ireland (n = 129).Artificial ponds in agricultural grassland did not replicate natural ponds in adjacent semi‐natural habitats differing significantly in size, pH, conductivity, productivity (indicated by submerged and emergent plant cover including algae) and surrounding vegetation structure that is, sward height. These differences significantly influenced aquatic and terrestrial invertebrate community structure with a suite of indicator taxa in both natural and artificial ponds.The conservation value of artificial ponds in agricultural grasslands should not be underestimated as they had 43% higher aquatic species richness and 33% higher aquatic species abundance than natural ponds in adjacent semi‐natural habitats.Synthesis and applications. We demonstrate that artificial agri‐environment scheme ponds created in agricultural grasslands, whilst not direct analogues of natural ponds in adjacent semi‐natural habitats, do fulfil a role in preserving high local biodiversity albeit representing a different community of species. Creation of ponds in farmland as well as in adjacent natural habitats could provide a wider range of environmental conditions and richer associated macroinvertebrate communities, increasing landscape connectivity and further enhancing regional biodiversity. [ABSTRACT FROM AUTHOR]

Following advice fromthe International Council for the Exploration of the Seas and North Atlantic Salmon Conservation Organization, Irish salmon stocks have been managed on a river-by-river basis since 2007 with biological reference points (BRPs) based on maximum sustainable yield (MSY). A method for estimating BRPs at the river scale and the associated variability arising from observed variability in population structures and fecundities is presented here. Calculations of BRPs (referred to as conservation limits, CLs) were updated and their natural variability was included. Angling logbooks provided new river specific weight data to give sea age and fecundity ranges, and improved estimates of river-wetted areas, to account for available nursery habitat for juveniles and river-specific carrying capacities, were introduced. To transport BRPs, Bayesian stock-recruitment analysis was re-run with an updated list of monitored rivers and smolt ages. Results were converted to salmon numbers per river in Monte Carlo simulations incorporating the variability in sea ages and fecundities. Minimum sample size rules were implemented to reduce sampling error effects. Results showed that average total CL increased by 7%, average one sea-winter (1SW) CL decreased by 5%and average multi-sea-winter (MSW) CL increased by 157%.Differences were attributed to increases in wetted areas, MSW proportions, and changes inboth 1SW and MSW fecundities. While some changes were large, we believe that these updated CLs provide more accurate estimates and with associated confidence limits they are more robust, river-specific, and readily incorporated into stock assessments. As a significant improvement on their predecessors, they represent a major development for the conservation and management of salmon stocks. Additionally, the approach described is portable across stocks and has the potential to be implemented in other jurisdictions to improve the management of Atlantic salmon. Finally, this method of incorporating variation has application for the development of BRPs and management of other species. [ABSTRACT FROM AUTHOR]

Throughout the European Union, the EC Habitats Directive requires that member states undertake national surveillance of designated species. Despite biological connections between-populations across-borders, national assessments need not be co-ordinated in any way. We conducted a trans-boundary assessment of the status of Eurasian otters (Lutra lutra) aimed at providing consistency across a single biogeographical unit, i.e. the island of Ireland, comprising two states, i.e. the Republic of Ireland and the United Kingdom (Northern Ireland). Our aim was to ensure consistency with previous assessments conducted separately in each state, and permit each Government to fulfil their separate statutory reporting commitments. The species range increased by 23% from 1996-2006 and 2007-11. The population estimate of 9400 [95%CI 8700-12,200] breeding females during 2010/11 was not significantly different from 8300 [95%CI 7600-9800] breeding females established as a baseline during 1981-82. Modelling of species-habitat associations suggested that available habitat was not limiting and no putative pressures recorded at sites surveyed negatively affected species occurrence. Thus, under the statutory parameters for assessing a species' conservation status, i.e. range, population, habitat and future prospects, the otter was judged to be in 'Favourable' status throughout Ireland and in both discrete political jurisdictions. Thus, we provide a trans-boundary test case for EU member states that share habitats and species across ecoregions, ensuring conservation assessment data are standardised, synchronised, spatially consistent and, therefore, biologically relevant without compromising legal and administrative autonomy within separate jurisdictions. [ABSTRACT FROM AUTHOR]

Ponds are an ephemeral feature of the landscape but their large-scale loss can have profound implications for biodiversity and the persistence of amphibian populations. We quantified rates of pond loss throughout Ireland over a period of approximately 125 yr. Environmental parameters and perceived risk factors associated with the current occurrence and density of the Common Frog, Rana temporaria, were also analyzed. The numbers of farmland ponds declined by 54% between 1887-1913 and 2005-11, with most ponds and the greatest losses in the East, coincident with agricultural intensification and human habitation. The decline of pond numbers was significant but, at approximately 0.5% per annum, was substantially less than losses recorded in other European countries. Losses were coincident with major changes to the agricultural landscape including extensive land drainage. However, losses of pond and natural wetland habitats throughout Ireland may have been partially or wholly mitigated by a synchronous expansion of artificial field margin ditches associated with drainage projects during the mid-20th Century. The ecology of the Common Frog in Ireland was similar to its ecology elsewhere and it appears largely unaffected by pollution and disturbance. Consequently, the conservation status of the frog in Ireland was judged 'favorable' and should remain so for the foreseeable future. [ABSTRACT FROM AUTHOR]

Abstract: Although widespread, the ecology of the whiskered bat, Myotis mystacinus in Europe remains poorly understood. Ireland is positioned at the most western extreme of this species’ range. To ascertain the ecology of M. mystacinus at its geographic range extreme, the roosting behaviour, home range and habitat use of females in a maternity roost in Ireland was investigated by radio-tracking. M. mystacinus were active in a diversity of habitats: namely, mixed woodland, riparian vegetation, arable land and rough grassland. However, only mixed woodland and riparian habitats were selected as core foraging areas. This is in contrast to a previous study from Britain where only pasture was utilised but is in agreement with data from Slovakia, where woodland was also selected, whilst riparian areas were also utilised by this species in Germany. A high degree of overlap in the foraging areas of individuals was observed. A total of seven roosts were utilised by tracked bats and roost switching behaviour was observed. We discuss our contrasting results in respect to range limitations, regional variability in landscape structure and the composition of bat communities. The present results have implications for the conservation of M. mystacinus within Ireland and other parts of its range, highlighting the need for range wide ecological studies. Regional variability in the ecology of bats related to landscape factors is an important consideration for bat conservation and therefore must be incorporated into future management plans. [Copyright &y& Elsevier]

Abstract: The Eurasian otter (Lutra lutra L.) is a top predator in aquatic systems and plays an important role in ecosystem functioning. However, it has undergone dramatic declines throughout Europe as a result of environmental degradation. We examine the putative role of the otter as a bioindicator in Ireland which remains a stronghold for the species and affords a unique opportunity to examine variation in its ecological niche. We describe diet, using spraint contents, along rivers during 2010 and conduct a review and quantitative meta-analysis of the results of a further 21 studies. We aimed to assess variation in otter diet in relation to river productivity, a proxy for natural nutrification and anthropogenic eutrophication, and availability of salmonid prey (Salmo trutta and Salmo salar), to test the hypothesis that otter diet is related to environmental quality. Otter diet did not vary with levels of productivity or availability of salmonids whilst Compositional Analysis suggested there was no selection of salmonid over non-salmonid fish. There was a distinct niche separation between riverine and lacustrine systems, the latter being dominated by Atlantic eel (Anguilla anguilla). Otters are opportunistic and may take insects, freshwater mussels, birds, mammals and even fruit. Otters living along coasts have a greatest niche breath than those in freshwater systems which encompasses a wide variety of intertidal prey though pelagic fish are rarely taken. It is concluded that the ability of the otter to feed on a wide diversity of prey taxa and the strong influence of habitat type, renders it a poor bioindicator of environmental water quality. It seems likely that the plasticity of the habitat and dietary niche of otters, and the extent of suitable habitat, may have sustained populations in Ireland despite intensification of agriculture during the 20th century. [Copyright &y& Elsevier]

Empirical studies of the spatiotemporal dynamics of populations are required to better understand natural fluctuations in abundance and reproductive success, and to better target conservation and monitoring programmes. In particular, spatial synchrony in amphibian populations remains little studied. We used data from a comprehensive three year study of natterjack toad Bufo calamita populations breeding at 36 ponds to assess whether there was spatial synchrony in the toad breeding activity (start and length of breeding season, total number of egg strings) and reproductive success (premetamorphic survival and production of metamorphs). We defined a novel approach to assess the importance of short-term synchrony at both local and regional scales. The approach employs similarity indices and quantifies the interaction between the temporal and spatial components of populations using mixed effects models. There was no synchrony in the toad breeding activity and reproductive success at the local scale, suggesting that populations function as individual clusters independent of each other. Regional synchrony was apparent in the commencement and duration of the breeding season and in the number of egg strings laid (indicative of female population size). Regional synchrony in both rainfall and temperature are likely to explain the patterns observed (e.g. Moran effect). There was no evidence supporting regional synchrony in reproductive success, most likely due to spatial variability in the environmental conditions at the breeding ponds, and to differences in local population fitness (e.g. fecundity). The small scale asynchronous dynamics and regional synchronous dynamics in the number of breeding females indicate that it is best to monitor several populations within a subset of regions. Importantly, variations in the toad breeding activity and reproductive success are not synchronous, and it is thus important to consider them both when assessing the conservation status of pond-breeding amphibians. [ABSTRACT FROM AUTHOR]

Bats of the genus Myotis cannot be identified reliably using conventional acoustic analyses. Here we use morphology of echolocation calls to discriminate between Myotis spp. This method may be used to identify unknown roosts to species level. Echolocation calls of M. daubentonii, M. mystacinus and M. nattereri, were recorded in emergence flights from roosts. Images of echolocation calls were extracted for morphological analysis performed in SHAPE, a program that transforms two-dimensional outline data into Elliptic Fourier Descriptors. Species typical call shapes were described with Mahalanobis models. Discriminant Function Analyses (DFA) were applied with Mahalanobis scores of typical shape alone and with a spectral call parameter, maximum frequency. DFA achieved an overall correct classification rate of 88.9% using typical outline shapes alone. Correct classification of 100% of both M. daubentonii and M. mystacinus was achieved by both typical call outlines. For M. nattereri, 79.6% of calls were correctly classified by call morphology, but the addition of maximum frequency improved this to 96.3%. Shape analyses provide a quick and easy method of distinguishing Myotis species under field conditions and could be extended to include other species of bats that share conventional acoustic parameters. [ABSTRACT FROM AUTHOR]

Amphibian declines are of major conservation concern worldwide. The Natterjack toad (Epidalea calamita) is the rarest amphibian in Ireland, regionally Red-listed as Endangered. The species is at the north-western edge of its European range in Ireland and is subject to substantial conservation efforts, including regular monitoring and surveillance, a pond creation agri-environment scheme, and a head-start and translocation programme to facilitate pond colonisation. We used large-scale intensive monitoring and surveillance data from 2004 to 2018 to quantify temporal trends in egg string production analysing breeding site preferences and occurrence of perceived threats and pressures. Despite substantial conservation efforts, egg string production declined by 23% in Ireland over a 14-year period (−1.6%/year). Twenty-two of 100 artificial ponds had been colonised by 2018, but artificial sites accounted for <10% of eggs laid and had prevented further declines by only 4%. Natterjack toad spawning was associated with ponds with a large surface area, situated in sand dune habitat, with high water conductivity, and a high percentage cover of aquatic vegetation at the substrate with short terrestrial vegetation in the surrounding vicinity. Threats and pressures are related to poor water quality at breeding sites and abandonment of surrounding agricultural land leading to unsuitable terrestrial vegetation. Given the Natterjack toad's population trend in Ireland, continued monitoring and surveillance is vital, while we advocate protection of occupied sand dunes, active engagement with farmers and landowners to ensure compliance with habitat maintenance recommendations and improved habitat connectivity to facilitate colonisation of artificial ponds. [ABSTRACT FROM AUTHOR]