Biology subjects

McDevitt, A. D.

Publications and source records attributed to McDevitt, A. D..

10 recordsLinked to original sources

bioRxiv2026

Sedimentary ancient DNA reveals Late Pleistocene faunal connectivity between Ireland and Eurasia

Late Pleistocene sea-level fluctuations and glacial corridors intermittently connected the island of Ireland to Britain and continental Eurasia, shaping patterns of megafaunal dispersal and occupation. However, the scarcity of genetic data from ancient Irish fauna has limited our understanding of their demographic histories and relationships to continental populations. To address this, we generated sedimentary ancient DNA sequences from Castlepook Cave in southwest Ireland, detecting twelve ancient taxa, including two without zooarchaeological records at the site. We recovered the first mitochondrial sequences from Irish cave hyenas and woolly mammoths, providing new insights into their maternal population history: cave hyenas carried mtDNA haplogroup A1, previously identified in Late Pleistocene European populations, while woolly mammoths belonged to clade III/B2, which was replaced in Europe at approximately the same time. We also identify two mitochondrial clades (1b and 2), consistent with pre-Last Glacial Maximum mitochondrial lineage turnover in Ireland. Together, these results indicate that Irish megafauna formed a biogeographical continuum with their conspecifics in Europe, extend the known geographical range of several mtDNA lineages, and support faunal connectivity at the northwestern edge of Europe prior to the Last Glacial Maximum.

evolutionary biology↗

bioRxiv2025

Multi-seasonal eDNA metabarcoding highlights a resurgence in fish diversity across a severely impacted estuarine ecosystem

Aquatic ecosystems have been in an alarming state of decline for decades. Therefore, there is an urgent need for more accessible and rapid monitoring methods that will ultimately allow for restoration programmes to be implemented. In this study, we deployed environmental DNA (eDNA) metabarcoding as a fish monitoring tool in the Mersey estuarine system (UK), where ecosystem productivity has been severely impacted by water quality degradation since the Industrial Revolution. Monthly water samples were collected over a year (2023-2024) throughout the estuary, covering saline, brackish and freshwater zones. Overall, 69 species of fish were detected, increasing the number of known species within the estuary in comparison to both historical and contemporary records (46 and 39, respectively), with a generally higher observed richness within the upper estuary sampled zones where the water chemistry is predominantly freshwater. Notably, we identified several species returning to the system for the first time since pre-industrial times. Peak species richness was recorded during the winter season (December-February). Species compositions varied significantly by month and spatially by zone within months, but not when grouped seasonally. Furthermore, around [~]15% of the species detected were diadromous, with the endangered Atlantic salmon Salmo salar, for example, being frequently detected during its key migratory period. This study highlights the resurgence in fish diversity in a once biologically depleted estuarine ecosystem and demonstrates how eDNA metabarcoding can be implemented for detecting historically absent species, thereby enhancing restoration monitoring efforts globally.

ecology↗

bioRxiv2024

Assessing group size and the demographic composition of unhabituated northern muriqui (Brachyteles hypoxanthus) using non-invasive biomonitoring

Obtaining accurate population measures of endangered species is critical for effective conservation and management actions and to evaluate their success overtime. However, determining the population size and demographic composition of most canopy forest-dwelling species has proven to be challenging. Here, we apply two non-invasive biomonitoring methods, arboreal camera trap and genetic tagging of faecal samples, to estimate the population size of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus), in the Caparao National Park, Brazil. When comparing population sizes between camera trapping and genetic tagging, the genetic tagging survey estimated fewer individuals for one of the muriqui groups studied but showed slightly higher population size estimates for the other group. In terms of the cost-efficiency of both methods, arboreal camera trapping had high initial costs but was more cost-effective in the long-term. Genetic tagging on the other hand did not require expensive equipment for data collection but had higher associated expenses for laboratory consumables and data processing. We recommend the use of both methods for northern muriqui monitoring and provide suggestions for improving the implementation of these non-invasive methods for future routine monitoring. Our findings also highlight the potential of arboreal camera trapping and genetic tagging to other arboreal mammals in tropical forests.

ecology↗

bioRxiv2023

Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificacao Florestal e Agricola (IMAFLORA) near Sao Felix do Xingu, in Para, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORAs shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.

ecology↗

bioRxiv2023

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

AimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. LocationWestern Amazonia TaxonThe uakari monkey (genus Cacajao) MethodsWe performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. ResultsOur continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River at [~]1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. The demographic analysis indicates that C. calvus, C. amuna, and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

evolutionary biology↗

bioRxiv2022

Invasive genetic rescue: Dispersal following repeated culling reinforces the genetic diversity of an invasive mammal

Since its introduction from the United States in 1876 the invasive North American Eastern grey squirrel (Sciurus carolinensis) has contributed to the decline of the native Eurasian red squirrel (Sciurus vulgaris) in Britain. Consequently, grey squirrel populations are often subjected to extensive control efforts in order to reduce local abundance and prevent spread, particularly within habitats containing red squirrels. Grey squirrel removal from the island of Anglesey off the coast of north Wales began in 1998 and was completed in 2013. A parallel successful red squirrel reinforcement translocation project also took place. The narrow sea-channel, road and rail bridge connection has meant that the adjacent mainland grey squirrel population has been controlled in subsequent years to reduce the probability of re-invasion. The aim of this study was to assess the overall impact of repeated culling efforts carried out between 2011 and 2020 on the genetic diversity of the grey squirrel population in north Wales to inform future adaptive management plans. Using a combination of mitochondrial DNA (mtDNA) and microsatellite DNA analysis, we found high genetic diversity in both marker types, with six diverse mtDNA haplotypes found and relatively high levels of nuclear genetic diversity, even after repeated culling efforts. Our results suggest that ongoing culling efforts may not adequately reduce genetic diversity to a level where it contributes to a long-term population decline.

ecology↗

bioRxiv2021

Snapshot of the Atlantic Forest canopy: surveying arboreal mammals in a biodiversity hotspot

The Atlantic Forest of South America supports some of the greatest terrestrial biodiversity on our planet but is now reduced to only a small extent of its original forest cover. It hosts a large number of endemic mammalian species but our knowledge on arboreal mammal ecology and conservation has been hindered by the challenges of observing arboreal species from ground level. Camera trapping has proven to be an effective tool in terrestrial mammal monitoring, but the technique has rarely been used for arboreal species. Here we generated data on the arboreal mammal community based on canopy camera trapping for the first time in the Atlantic Forest, focusing on Caparao National Park, Brazil. We placed 24 infrared camera traps in the forest canopy distributed in seven areas within the Park, operating continuously from January 2017 to June 2019. In this time, they accumulated 4,736 camera-days and generated 2,256 sets of pictures and 30 second videos of vertebrates. Canopy camera traps were able to detect arboreal mammals spanning a wide variety of body sizes. The local mammal assemblage comprised of 15 identifiable species, including the critically endangered northern muriqui (Brachyteles hypoxanthus) and the buffy-headed marmoset (Callithrix flaviceps), and other rare, nocturnal and inconspicuous species. For the first time, we confirmed the occurrence of the thin-spined porcupine (Chaetomys subspinosus) in the Park. Species richness varied across sampling areas and forest types. Our findings demonstrate the potential of canopy camera trapping for future surveying efforts to better inform conservation strategies for mammals.

zoology↗

bioRxiv2020

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe.

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using Genotyping-by-Sequencing (GBS)) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia). In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to an increased mammalian fauna on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

evolutionary biology↗

bioRxiv2019

Phylogeographic structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe.

Southern and northern glacial refugia are considered paradigms that explain the complex phylogeographic patterns and processes of European biota. Although the Eurasian pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae) has been used a model species to study geographic isolation and genetic diversification in Mediterranean peninsulas in the Last Glacial Maximum (LGM), and post-glacial population expansion from cryptic northern glacial refugia in Western and Central Europe, there has been incomplete knowledge about the phylogeographic structure, genetic differentiation and demographic history within these regions. Here, we provide a revisited statistical phylogeographic study of S. minutus with greater sampling coverage in terms of numbers of individuals and geographic range, making it the most comprehensive investigation of this species to date. The results showed support for genetically distinct and diverse phylogeographic groups consistent with southern and northern glacial refugia, as expected from previous studies, but also identified geographical barriers concordant with glaciated mountain ranges during the LGM, early diversification events dated between the Upper Pleistocene and Lower Holocene for the main phylogeographic groups, and recent (post-LGM) patterns of demographic expansions. The results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.

evolutionary biology↗

bioRxiv2018

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

ecology↗