Andrew D. Nunn

Context: Pumping stations pose a threat to fish globally through land use change, habitat fragmentation and entrainment risk, with the catadromous and critically endangered European eel particularly impacted. Objectives/methods: Establish, model, assess and understand the present-day distribution of European eel and resident fishes in 152 pumping station catchments in a once extensive wetland (The Fens) using eDNA metabarcoding (855 samples over two and half years), with specific focus on anthropogenic influences on hydrological connectivity and habitat quality. A removal survey design maximised confidence in negative results while minimising time and consumable costs. Results: Eel occurrence upstream of pumping stations was low (occupancy = 28.3%) and positively associated with catchment area, fish species richness and natural hydrological connectivity (gravity drainage or flooding) and negatively associated with distance from the tidal limit. Fish species richness replaced catchment area and improved model performance, potentially acting as a biotic indicator of habitat quality and connectivity. Pumped catchments with manually operated upstream water transfers had reduced eel presence, potentially linked to the direction of water flow or the timing of operation. By contrast, fish species richness increased in these catchments during summer, suggesting displacement into unsuitable long-term habitats. Physical habitat maintenance had no detectable effect on eel occurrence or fish species richness. Conclusions: This study provides the first landscape-scale assessment of European eel distribution and drivers of occurrence in pumped river catchments. The highly novel and comprehensive insights have implications for European eel conservation as well as infrastructure and catchment management, including compliance with legislation (EC Regulation No. 1100/2007).

Population recovery is a key goal for conservation, but our understanding of how genetic and phenotypic variation, including local adaptation, emerges in recently recolonised or recovering systems is limited. This complicates the conservation of fitness-related traits that support resilience and long-term population viability. We employed single nucleotide polymorphism markers, geometric morphometrics and acoustic telemetry to investigate the recovery of Atlantic salmon ( Salmo salar ) in a large river system, which began more than 40 years ago following presumed extirpation in the mid-1900s. We observed genetic differentiation between Atlantic salmon in different tributaries that may reflect natural recolonisation through straying and/or the recovery of remnant populations previously believed to be extinct. Fine-scale philopatry was found to maintain the genetic divergence between tributaries, as confirmed by genetic assignment and telemetry tracking of returning adults, with some individuals displaying ‘search’ behaviour across tributaries. Despite this population structuring, neither consistent genomic signatures of selection nor morphological divergence were detected, indicating no evidence for early stage local adaptation or for differing selective pressures between tributaries. The patterns instead align with stochastic demographic processes (i.e. founder effects and genetic drift), which was further supported by the low contemporary effective population sizes detected across tributaries. These findings highlight the importance of continued genomic and ecological monitoring during population recovery, as improving environmental conditions may promote the re-establishment of remnant populations and/or facilitate recolonisation. This may, in turn, lead to the formation of reproductively isolated units and, over time, the emergence of locally adapted traits of conservation value for Atlantic salmon and other threatened migratory species.

Anadromous fishes are vulnerable to anthropogenic stressors, especially river fragmentation, with the conservation of iteroparous populations requiring an understanding of survival during their freshwater migrations. Here, spatial, temporal, and biological drivers of mortality were determined during the spawning migrations of iteroparous anadromous twaite shad Alosa fallax in the highly fragmented River Severn basin, western Britain. Acoustic telemetry tracked 393 individuals over seven successive spawning migrations. Shad mortality rates in areas immediately downstream of migration barriers were more than double compared to unimpeded river sections, but the extent of excess mortality varied between individual barriers. In-river mortality differed between years for returning shad, but there were no significant temporal patterns of mortality within migrations. Newly tagged shad and returning individuals had similar survival rates, and increasing size was the only significant biological predictor of mortality, with sex and spawning history not significant. These results suggest that where migration barriers increase mortality rates, the population-stabilizing and resilience benefits of iteroparity may be reduced, so river fragmentation mitigations should focus on both improving passage and reducing hazard exposure.

The habitats used by larval and 0+ year juvenile fishes can significantly influence individual growth rates, nutritional condition and survival, and thus recruitment success and population sizes. The quality, quantity and accessibility of potential nursery habitats are therefore among the most important factors driving the structure and dynamics of fish communities. In European rivers, the majority of species favour relatively shallow and slow‐flowing areas in the early larval period. Such areas minimise the risk of predation by larger fish, are frequently warmer than deeper and faster‐flowing water, maximise the amount of energy that can be allocated to somatic growth and generally support the greatest quantities of planktonic prey. However, improvements in swimming ability and predator and prey detection during development can facilitate species‐specific habitat selection. Furthermore, distinct shifts in habitat use may coincide with key intervals in ontogeny, particularly the transition from the larval to juvenile period. Many species also exhibit seasonal shifts in habitat use, typically moving to deeper, slower‐flowing and/or more structurally complex areas in the winter. In addition, species‐specific diel variations in habitat use may occur, probably as a behavioural response to changes in predation risk, which may change during ontogeny or on a seasonal basis. Environmental management invariably has detrimental impacts on habitat quality or integrity and, thus, larval and juvenile fishes, with the systematic rehabilitation of degraded and fragmented ecosystems therefore essential for the recovery of affected populations.

We present a genome assembly from an individual Rutilus rutilus (Roach; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The genome sequence has a total length of 1 100.18 megabases. Most of the assembly (99.56%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases. Gene annotation of this assembly on Ensembl identified 25 358 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

We present a genome assembly from an individual Leuciscus leuciscus (Dace; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The assembly contains two haplotypes with total lengths of 1 198.36 megabases and 1 179.02 megabases. In haplotype 1, 96.76% of the sequence is scaffolded into 25 chromosomal pseudomolecules, and 97.75% of the haplotype 2 sequence is similarly scaffolded. The mitochondrial genome has also been assembled, with a length of 17.59 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

We present a genome assembly from an individual Scardinius erythrophthalmus (Rudd; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The assembly contains two haplotypes with total lengths of 1 229.65 megabases and 1 189.97 megabases. Most of haplotype 1 (95.02%) is scaffolded into 25 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

We present a genome assembly from a specimen of Abramis brama (bronze bream; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The genome sequence has a total length of 1 108.20 megabases. Most of the assembly (99.13%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases. Gene annotation of this assembly on Ensembl identified 25 268 protein-coding genes.

Riverine barriers can have significant negative impacts on the spawning migrations of anadromous fishes, with barriers of low passage efficiency limiting access to upstream spawning areas. Even fish that pass a barrier can be negatively affected via migration delays and energetic costs. The spawning migrations of 74 twaite shad Alosa fallax were tracked at two head-of-tide weirs on a bifurcated channel in the River Severn’s upper estuary, western England, to test how barriers in tidal areas can affect river entry and incur migration delays. Although the weirs had a combined passage efficiency of 98.9%, median passage time was 19.8 h, with the longest passage time being 16.8 days, and those passing fastest being relatively large fish that approached during spring tides and higher river flows. A higher proportion of fish approached and passed the weir on the larger channel that generally had the dominant flow, yet the weir on the other channel had the higher probability of passage, with the effect of elevated river levels being less important, and individuals approaching this weir were less delayed. With river level being a function of the cyclical nature of the lunar and daily tidal cycles, temporal variation in passage efficiencies was predictable. As the environmental conditions that stimulated the entry of fish into the upper estuary were largely unrelated to the conditions facilitating weir passage, there was a high potential for migration delays at these barriers that potentially incurred considerable energetic costs.

Anthropogenic in‐river structures represent barriers to migrating fishes. Fish pass designs usually focus on passing anadromous salmonids, and fish pass studies usually focus on site‐scale metrics, failing to consider the wider effects. Weir passage metrics and spawning distributions of anadromous iteroparous twaite shad Alosa fallax and semelparous sea lamprey Petromyzon marinus were assessed using acoustic telemetry between 2018 and 2023, within a catchment‐scale reconnection programme on the River Severn (‘Unlocking the Severn’ [UtS]). Reconnection was by fish pass installation (Severn mainstem; 3 deep‐vertical slot (DVS), 1 column bypass) and weir modification (Teme tributary; 1 partial removal/reduced head height, 1 reduced gradient). Time‐to‐event analysis revealed reconnection increased the probability of lamprey passing both the most downstream DVS and modified weir, and virgin shad were more likely than previous spawners to pass the DVS, but not the modified weir. Improvements in the proportion of tagged shad (to 7%) and lamprey (to 48%) passing the most downstream DVS were modest, but shad passage times were significantly reduced (by 20 days). Weir modification resulted in greater improvements in shad (to 58%) and lamprey (to 78%) passage. Reconnection also enabled passage on substantially lower flows; shad passed the most downstream Severn weir (via the DVS) at Q89 versus Q3 prior to construction, and lampreys at Q86 versus Q45. At catchment scales, reconnection significantly increased the proportion of shad passing the pre‐reconnection migration limit. However, the upstream extent of both species in the mainstem was not significantly increased. This was attributed to the limited motivations of individuals to access previously fragmented reaches; returning shad expressed fidelity to previous spawning sites and lamprey lacked pheromone cues from ammocoetes upstream. Passage motivations are predicted to increase subsequently as more individuals' spawn in these reaches. Synthesis and applications. UtS succeeded in facilitating both species to pass weirs under lower flow conditions than before. Weir modification improved passage rates more than fish pass installation, although catchment‐scale benefits currently remain limited. Project legacies include identifying long‐term monitoring needs to measure accumulating catchment‐scale benefits, and information on the suitability of reconnection methods to inform similar reconnection programmes.