Biology subjects

Bean, C. W.

Publications and source records attributed to Bean, C. W..

6 recordsLinked to original sources

bioRxiv2025

Scale dependent temporal and spatial patterns of population change in anadromous sea trout (Salmo trutta) in Scotland over seven decades

The spatial scale at which temporal change in a population is measured has the potential to skew the inferences drawn on patterns of change from monitoring data. This study analysed data from rod catches of anadromous sea trout (Salmo trutta) in Scotland over a period of 72 years and over three spatial scales (National, Regional and District). The pattern of temporal change evident at the national scale mostly did not clearly manifest at Regional or at District spatial scales; which were also generally decoupled (67% of Regions and 80% of Districts exhibited a different pattern from the National pattern). At the National level, very clear and substantive declines over the study period were evident. At Regional levels (N=9) change in rod catches was more nuanced with some Regions showing no change, one Region showing an increase in sea trout caught and 6 (67%) exhibited a different pattern from the National one. At the District levels (N=64) opposing patterns of change were observed over the study period, even in adjacent Districts with 80% of Districts exhibiting a different pattern from the National one. A conclusion of this study is that, as a national resource, sea trout numbers have declined substantively over the last seven decades (by around 50%). However, this general picture is not applicable across all geographic Regions nor all Districts. Two logical inferences derive from these results. Firstly, for best effect, the application of limited resources for management should be focused at smaller scales than at countrywide. Secondly, that monitoring population change at small spatial scales, for example in several index rivers, is unlikely to capture the highly nuanced patterns of change in species with high levels of intra-specific structuring as is commonly exhibited by the Salmonidae.

ecology↗

bioRxiv2025

The historical patterns that have shaped contemporary genetic differentiation across populations of Arctic charr in Scotland

Glacial history is an important contributor to contemporary biogeographic patterns because it caused population fragmentation and consequently diversification. The Arctic charr (Salvelinus alpinus) is a highly diverse non-anadromous salmonid fish species in Britain and Ireland, which likely was anadromous when it colonised around the end of the last ice age. Colonisation history of the species remains largely unexplored and so the potential impact on contemporary patterns of genetic differentiation remains unclear. To address this, we conducted a national-scale genetic study of Arctic charr using a genome-wide dataset of SNPs (24,878 SNPs and 410 individuals) and mitochondrial ND1 sequences (238 sequences). We found several mitochondrial haplotypes were shared across Britain, Ireland, and the wider Holarctic suggesting colonisation by multiple sub-lineages of the Atlantic lineage of the species. Genetic differentiation was not correlated with geographic distance among river catchments, highlighting the effect of spatial isolation and genetic drift. Several populations across different river catchments showed atypical ancestries and evidence for genetic mixing, which we speculate are due to asynchronous ice coverage and the presence of ice-dammed lakes. Our results highlight how glacial history can impact colonisation history and subsequently contemporary patterns of genetic differentiation in this widespread species.

genetics↗

bioRxiv2025

eDNA sampling reveals no negative effects of beaver recolonisation on the catchment-scale distribution of migratory fish

O_LIReintroduction of keystone species is considered part of the solution to the current biodiversity crisis. The Eurasian beaver (Castor fiber) is one such species, shaping its habitat by felling trees, building dams and creating wetlands. However, while the potential benefits to aquatic biodiversity and ecological functioning have been studied on a local scale, the impacts of beavers on catchment-scale processes such as fish migration remain understudied. C_LIO_LISequencing of environmental DNA (eDNA metabarcoding) from water samples is a cost-effective method to study species distributions across large geographical scales. Here, eDNA samples (n=426) were collected from 142 sites across the UKs oldest and largest established wild beaver population, located on Tayside, East Scotland, and analysed using a vertebrate specific metabarcoding assay. We combined presence/absence data from eDNA results with other environmental and anthropogenic variables to model the effects of beaver presence on the distribution of three migratory fish species. C_LIO_LIUsing generalised linear models, we found no effects of the current beaver presence on the distribution of Atlantic salmon or lamprey, but a positive co-occurrence with European eel at the catchment scale. Model outputs also reinforced previous findings on the impact of barriers to migration and other abiotic and biotic factors on fish species, demonstrating the effectiveness of eDNA sampling in rivers for understanding species distributions at a catchment scale. C_LIO_LIThis case study provides novel insights into the co-distribution of beavers and migratory fish, and highlights how catchment-wide eDNA monitoring can be applied by environmental managers to aid decision-making and impact assessment more generally. C_LI

ecology↗

bioRxiv2025

Defining conservation units in a highly diverse species: A case on Arctic charr

Defining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (Salvelinus alpinus), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories, and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (N=64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability with latitude and distance to the sea suggesting that more southern and more inland populations are more vulnerable to loss due to climate change. Additionally, patterns of vulnerability across several additional metrics identified further populations that may be at high vulnerability to loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.

genomics↗

bioRxiv2022

Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish populations are the study subject, such as the Arctic charr (Salvelinus alpinus L.) populations in Windermere (Cumbria, UK). Arctic charr populations have been studied in this lake since the 1940s, and the locations and characteristics of spawning grounds have been described in detail using techniques such as hydroacoustics, as well as physical and visual surveys of the lake bottom. Here, in conjunction with established netting surveys, we added an environmental DNA (eDNA) metabarcoding approach to assess the spatial distribution of Arctic charr in the lake throughout the year to test whether this tool could allow us to identify spawning locations and activity. Sampling was carried out between October 2017 and July 2018 at three locations in the lake, covering putative and known spawning sites. eDNA metabarcoding provided accurate spatial and temporal characterisation of Arctic charr spawning events. Peaks of Arctic charr read counts from eDNA metabarcoding were observed during the spawning season and at specific locations of both putative and known spawning sites. Net catches of mature Arctic charr individuals confirmed the association between the Arctic charr spawning activity and the peaks of eDNA metabarcoding read counts. This study demonstrates the ability of eDNA metabarcoding to effectively and efficiently characterize the spatial and temporal nature of fish spawning in lentic systems.

molecular biology↗

bioRxiv2020

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals. eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.

molecular biology↗