Paulo A. Prodohl

The long history of exploitation and overexploitation of the European lobster (Homarus gammarus) underscores the importance of understanding its genetic structure to inform sustainable management. A set of 12 microsatellites was used to investigate population genetic structure across 20 samples (Ntotal = 2 304 individuals) collected throughout most of the species’ range. Results confirmed a previously suggested bottleneck in the Dutch coast together with a pronounced genetic break in the northernmost fringe of the distribution (at 68°N in Stefjord/Tysfjord system). The three samples from the northern area displayed the lowest genetic diversity as well as the highest levels of genetic differentiation relative to all other samples (mean FST = 0.07), exceeding the differentiation across the Atlantic-Mediterranean phylogeographic discontinuity (mean FST = 0.03). This pattern aligns with the expectations under range expansion scenarios, where populations at the leading edge often undergo founder effects resulting in reduced genetic variation and increased genetic differentiation. Some 6% of the non-private alleles—mapping to different loci—significantly contributed to spatial genetic structure and showed signatures compatible with allele surfing where latitude was a better predictor than temperature for their allele frequencies despite certain correlation between both variables (r2 = 0.5). The northern limit of the European lobster’s distribution lies beyond its thermal optimum of 10°C–20°C. Consequently, ongoing climate change—superimposed on already challenging environmental conditions at the species’ expansion front—may intensify the effects of directional selection in the northern populations. Future genomic analyses will therefore be essential to disentangle demographic from selection-driven processes.

Environmental DNA (eDNA) tools are increasingly used for biodiversity monitoring, with most existing assays targeting species‐level identification. However, the use of eDNA to resolve intraspecific genetic variation remains rare and methodologically underdeveloped. This study presents the development and laboratory validation of a novel molecular assay capable of detecting specific phylogeographic lineages, advancing eDNA applications by enabling resolution below the species level. The assay combines Recombinase Polymerase Amplification (RPA) and CRISPR‐Cas12a technologies with a lateral flow platform for field‐ready, on‐site detection. Irish Arctic char ( Salvelinus alpinus ) was selected as the model due to its conservation relevance and post‐glacial lineage diversity in Ireland. Mitochondrial genome sequencing of known Irish lineages identified a Protospacer Adjacent Motif (PAM) site unique to the Atlantic Subclade 1 lineage, allowing clear discrimination from co‐occurring lineages. Two assays were optimised: a species‐specific assay detecting all Arctic char lineages and a lineage‐specific assay targeting Lineage 1. Both showed high sensitivity and specificity under laboratory conditions, with LbCas12a outperforming AsCas12a at optimised buffer concentrations. The lateral flow adaptation, utilising a dual‐labelled FAM‐Biotin probe, enabled portable and rapid detection with minimal equipment. Field validation using eDNA from Irish lakes highlighted the need for improved sampling protocols, as lake‐edge surface samples failed to yield detections. This assay represents the first reported example of a CRISPR‐based eDNA tool for phylogeographic lineage detection in the field. It offers a novel, non‐invasive, and scalable approach to fine‐scale ecological monitoring and establishes a foundation for future conservation tools targeting intraspecific diversity.

Many habitat generalist species exploit habitat patches of differing types and quality, yet the influence of such habitat mosaics on genetic structure remains poorly understood. Here, we tested whether fine‐scale habitat heterogeneity affects the population structure of the European wood mouse ( Apodemus sylvaticus ) by sampling three matched forest parks in Northern Ireland across hedgerow, forest edge, and inner forest habitats. Microsatellite analysis revealed strong genetic differentiation among sites and consistent divergence between habitat types within sites. Stable isotope data showed that hedgerow mice fed at a higher trophic level than inner forest individuals, with forest edge mice intermediate. Mandible shape also differed by habitat and was correlated with δ ¹⁵ N, though differences were subtle and may reflect both drift and plasticity. Together, these results indicate that habitat mosaics can promote repeated, fine‐scale population divergence even in the absence of physical barriers. This highlights the role of ecological heterogeneity in structuring genetic variation in widespread generalists and cautions against assuming panmixia in continuous landscapes.

Studies of fish behaviour and ecology create opportunities for studying piscivores that have been underutilised. A leading example is the widespread use by fish biologists of Passive Integrated Transponder (PIT) tagging for identifying individuals, tracking movements, and estimating population sizes. PIT tags have high physical durability and long electronic lifespans. In consequence, if a piscivore swallows a tagged fish, the tag will almost certainly be excreted intact and subsequently detectable at the location of excretion for years. Accessible nesting or roosting colonies of piscivorous birds adjacent to fish PIT-tagging study sites thus present a potentially rich source of information on feeding habits. However, when such PIT tag surveys are conducted, they typically focus on the biology of the prey and not the predator. Here, we make opportunistic use of a PIT-tagging study of young Salmo spp. salmonids in Ireland to investigate the biology of a widespread and familiar avian piscivore, the Grey Heron Ardea cinerea. We scanned the ground underneath an accessible heronry for tags known to have been fitted to their carriers over four days in May 2019 in an intensively monitored river from which emigration is only possible via a fish trap. We found 48 focal tags in the heronry out of 594 tagged fish. Tags in the heronry were significantly biased towards smaller individuals and S. salar. Data on unpredated fish implies that all putative predation events occurred at least 10.8 km from the heronry despite there being foraging habitat less than 150 m from the colony, and that the majority occurred before the end of June in the year of tagging. We discuss our results in the context of the relatively limited information on breeding-season foraging activity for Grey Herons, optimal foraging considerations and ways to refine the use of PIT tagging of fish for studying piscivores.

Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemiological links between outbreaks. However, they have limited utility owing to low resolution. Conversely, whole-genome sequencing (WGS) provides the highest resolution data available for molecular epidemiology, producing richer outbreak tracing, insights into phylogeography and epidemic evolutionary history. We illustrate these advantages by focusing on a common single lineage of M. bovis (1.140) from Northern Ireland. Specifically, we investigate the spatial sub-structure of 20 years of herd-level multi locus VNTR analysis (MLVA) surveillance data and WGS data from a down sampled subset of isolates of this MLVA type over the same time frame. We mapped 2108 isolate locations of MLVA type 1.140 over the years 2000–2022. We also mapped the locations of 148 contemporary WGS isolates from this lineage, over a similar geographic range, stratifying by single nucleotide polymorphism (SNP) relatedness cut-offs of 15 SNPs. We determined a putative core range for the 1.140 MLVA type and SNP-defined sequence clusters using a 50 % kernel density estimate, using cattle movement data to inform on likely sources of WGS isolates found outside of core ranges. Finally, we applied Bayesian phylogenetic methods to investigate past population history and reproductive number of the 1.140 M. bovis lineage. We demonstrate that WGS SNP-defined clusters exhibit smaller core ranges than the established MLVA type - facilitating superior disease tracing. We also demonstrate the superior functionality of WGS data in determining how this lineage was disseminated across the landscape, likely via cattle movement and to infer how its effective population size and reproductive number has been in flux since its emergence. These initial findings highlight the potential of WGS data for routine monitoring of bTB outbreaks.

Morphological similarities between skates of the genus Dipturus in the north‐eastern Atlantic and Mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as ‘D. batis’). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the ‘common skate’, with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.

Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.

Salmonid (Salmonidae) sympatric diversity is the co‐occurrence, in a lake or river, of two or more reproductively isolated populations/subpopulations, or phenotypes resulting from phenotypic plasticity. Sympatric populations can arise through allopatric and/or sympatric evolution. Subsequently, allopatric lineages can occur in sympatry due to independent colonisation and/or through anthropogenic introduction. Sympatric divergence is often driven by feeding opportunities, with populations segregating as planktivorous, benthivorous and piscivorous ecotypes (“trophic polymorphism”), and further segregation occurring by feeding depth and body size. Subpopulations evolve by natal homing where a water has two or more discrete spawning areas, often resulting in phenotypically and ecologically cryptic sympatry. Most known sympatric populations/phenotypes in trout of the genus Salmo (Eurasian trout aka brown trout) involve sympatric piscivorous (ferox) and lifetime invertivorous trout. Segregation on the benthic–limnetic axis has been poorly studied in Eurasian trout compared with other salmonids but is likely commoner than currently described. While three sympatric populations/species of Eurasian trout are recognised from Lake Ohrid (Albania/North Macedonia), limited ecological information is available and there are only two lakes with three or four sympatric populations with described benthic, limnetic and piscivorous trophic segregation: Lough Melvin (Ireland) and Loch Laidon (Scotland), the latter having the only identified case of a sympatric profundal benthic feeding populations, possibly due to the absence of Arctic charr (Salvelinus alpinus) in the lake. Many thousands of waters are yet to be examined. Some sympatric populations are extinct, and others are vulnerable with conservation action being urgently required. This should ideally be based on populations/conservation units, but the lack of recognition of intraspecific units in most legislations in the native Eurasian trout range necessitates a pragmatic approach, with species classification, where appropriate, based on integrative taxonomy. Some sympatric populations clearly merit species status and should be formally classified as such if a valid previous name is not available.

Although historical records of introductions that trigger successful biological invasions are common, subsequent patterns of dispersal and colonisation routes are unclear. We use microsatellites to examine genetic population structuring of established invasive brown trout (Salmo trutta) populations in Newfoundland, Canada, for evidence of “natural” dispersal, human-mediated introductions, and colonisation routes. We also explored ancestry of contemporary populations relative to presumed progenitors. Results analysed using STRUCTURE, DAPC, a NJ tree and F_ST comparisons support records of historical introductions; current Newfoundland populations are largely descended from Scottish stock, with St. John’s the primary introduction site. Subsequent dispersal of these trout was facilitated principally by anadromy, largely consistent with a classic stepping-stone model, with significant isolation-by-distance. With one exception, dispersal along the north and south coasts of the Avalon peninsula appears to be natural and independent, involving stochastic processes resulting in unique outcomes for population composition. This study is a good example of dispersal patterns during a contemporary invasion underscoring the potential for non-anadromous founders to re-express anadromy, facilitating colonization of distant sites.

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares ( Lepus timidus ) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome-wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area-specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP , a gene previously implicated in introgression-driven winter coat colour variation in mountain and snowshoe hares ( L. americanus ), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species-specific. However, using coalescent simulations we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our work shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post-glacial dynamics of species.