1. 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. 2. We examined variation in environmental parameters and aquatic and terrestrial invertebrate communities between 38 natural ponds and 91 artificial ponds that were created in southwest Ireland (n = 129). 3. 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. 4. 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. 5. 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. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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/km 2 ) 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
Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical RSV surveillance and the lack of predictable RSV seasonal dynamics and limits the public health response. Wastewater-based epidemiology (WBE) has the capacity to determine levels of health-associated biomarkers and has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community. However, the application of genomic WBE for the surveillance of other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, using RT-qPCR and partial sequencing of the G gene to monitor RSV levels and variants in the community across 2 years encompassing two periods of high RSV clinical positivity in Northern Ireland. We report increasing detection of RSV in wastewater concomitant with increasing numbers of RSV positive clinical cases. Furthermore, analysis of wastewater-derived RSV sequences permitted subtyping, genotyping, and identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance efforts and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.
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.
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