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The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready‐to‐use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish‐12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish‐12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta‐Fish‐Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib. [ABSTRACT FROM AUTHOR]

Changes in temporal and spatial composition of the British inshore North Sea fish community are reviewed. Sampling from the cooling water filter screens of power stations bordering the North Sea commenced in the early 1960s. To date, a total of 112 marine fish species have been recorded, a high proportion of the total inshore fish species complement of shallow North Sea British waters. The unrecorded top predators, such as large sharks, swordfish and tuna are not regularly observed in waters < 20 m deep. The greatest species number (92) is reported from fully marine waters in East Anglia. A group of 18 ubiquitous, high abundance, taxa form a core inshore community throughout the region in both estuarine and marine waters. They show a high level of concordance in relative abundance along the British east coast from the 1970s to the present. A second group of 20 species are abundant, but more restricted in habitat. Where they do occur, this group are usually always present and form together with the ubiquitous taxa the local core community. The third group of 67 species, are never abundant and are restricted in occurrence both spatially and temporally. Total species richness declines between 50 and 56°N, probably because high summer temperatures allow the southern North Sea to support summer migrants entering via the English Channel. Since the 1960s there has been a notable recovery in fish diversity and abundance in large industrialised estuaries such as the Thames and the Firth of Forth. Linked to spawning and nursery habitat gain, smelt, Osmerus eperlangus, and bass, Dicentrarchus labrax , have greatly increased in abundance. There is no evidence for a decline in species richness since the 1970s. However, elasmobranch species number has declined while two species Raja clavata and Scyliorhinus canicula have remained abundant and one, Mustelus asterias, has increased in abundance. It is argued that overexploitation and habitat destruction remain, as they have been for the last 300 years, the most serious threats to the health of North Sea inshore fish communities. There are no clear signs that climate change is causing species loss, although it may be influencing relative species abundance as species at the southern edge of their range such as the viviparous blenny, Zoarces viviparous , have declined in the southern British North Sea. Power station water temperature records do not show a warming trend, in some estuarine locations temperature has declined with reduced thermal pollution; the temperature record cannot explain the observed major changes in fish relative abundance observed since the 1970s. [ABSTRACT FROM AUTHOR]

Determining the magnitude of homing behaviour within migratory fish species is essential for their conservation and management. We tested for population genetic structuring in the anadromous alosines, Alosa alosa and A. fallax fallax, to establish fidelity of stocks to spawning grounds in the United Kingdom and Ireland. Considerable genetic differences were present among populations of both species, suggesting strong fidelity to breeding grounds and compatible with homing to natal origins. Moreover, the genetic structure of A. fallax fallax showed a clear pattern of isolation-by-distance, consistent with breeding populations exchanging migrants primarily with neighbouring populations. Spatial genetic differences were on average much greater than temporal differences, indicating relatively stable genetic structure. Comparing anadromous A. fallax fallax populations to the landlocked Killarney shad subspecies, A. fallax killarnensis (Ireland), demonstrated a long history of separation. These results demonstrating regional stock structure within the British Isles will inform practical management of stocks and their spawning habitats. [ABSTRACT FROM AUTHOR]

Abstract: We present the first detailed comparison of extinction rates amongst a wide range of nonmarine groups, using data from Britain. For selected taxa, comparisons are made with rates in the United States and the globe. We estimate the overall extinction rate in Britain is 1–5% of the regional species list per century. Most of the groups of organisms assessed have very similar rates, with high rates in some groups which are aquatic, use dead wood or are on their climatic margin. In Britain, the extinction rate probably rose from the 19th to the 20th Century, and is projected to rise in the 21st Century. Habitat loss is the principal driver of extinctions. In Britain, birds are relatively good indicators of extinction rates and extinction-prone habitats, whilst butterflies are not. At larger scales, such as the USA and globally, birds, freshwater fish and amphibians show potential as indicators. Consideration of ‘Possibly Extinct’ species and monitoring of habitat area may provide more responsive measures of biodiversity loss. [Copyright &y& Elsevier]

Data collected by power station impingement sampling, plus plankton and trawl netting over the last 50 years is used to analyse the dynamics of the whiting, Merlangius merlangus (L.) subpopulation within the Bristol Channel, UK, ecosystem. In Northern Europe, whiting is a dominant member of the inshore community and is commercially exploited. Contemporaneous long-term data for fish and crustacean species gives an exceptional opportunity to explore regulatory interactions for a gadoid fish with high between-year recruitment variability. There is considerable between year variation in whiting recruitment and growth which relates to both biotic and physical variables. However, analysis of a 40-year annual abundance time series detected density-dependent regulation with no long-term trend. Over an extended spawning season, a series of recruitment cohorts travel up estuary to their nursery grounds. The average size at the end of their first year relates to the timing of the dominant cohort within the extended spawning season. Whiting are locked into a web of predator-prey, host-parasite and commensal relationships which act to damp deviations from carrying capacity caused by habitat variability. River flow and seawater temperature change whiting distribution and abundance both directly and via their effects upon prey and predator species. The abundance of two prey, the shrimp, Crangon crangon, and sprat, Sprattus sprattus, positively influence growth and local abundance, conversely, Conger eel, Conger conger , the top predator, has a negative relationship with whiting abundance. During autumn and winter O-group whiting are particularly dependent on C. crangon for food. Whiting appears an ideal candidate for an ecosystem-based fisheries management approach. They are generalist predators eating locally abundant animals smaller than themselves. Carrying capacity likely reflects the total resource base of crustaceans and small fish available. • A 48-year study of the dynamics of whiting, Merlangius merlangus (L.) subpopulation within the Bristol Channel ecosystem is reported. • Whiting is a dominant species within this ecosystem and uses the estuary as a nursery ground. Over an extended spawning season, a series of recruitment waves travel up estuary. • Annual abundance data showed density-dependent regulation with no long-term trend over a 40-year period. • There is considerable between year variation in recruitment and growth which relates to both biotic and physical variables. • Whiting are locked into a web of predator-prey, host-parasite and commensal relationships which act to damp deviations from carrying capacity. [ABSTRACT FROM AUTHOR]

A 26-year time series of monthly samples from the water intake of a power station has been used to analyse the trends exhibited by number of species, total abundance, and composition of the mysids and caridean decapods in the inner Bristol Channel. During this period, annual water temperatures, salinities and the North Atlantic Oscillation Index (NAOI) in winter did not change significantly, whereas annual NAOI declined. Annual mean monthly values for the number of species and total abundance both increased over the 26 years, but these changes were not correlated with any of the measured physico-chemical/climatic factors. As previous studies demonstrated that, during a similar period, metal concentrations in the Severn Estuary and Bristol Channel (into which that estuary discharges) declined and water quality increased, it is proposed that the above changes are due to an improved environment. The fauna was dominated by the mysids Mesopodopsis slabberi and Schistomysis spiritus , which collectively contributed 94% to total abundance. Both species, which were represented by juveniles, males, non-brooding females and brooding females, underwent statistically-indistinguishable patterns of change in abundance over the 26 years. When analysis was based on the abundances of the various species, the overall species composition differed significantly among years and changed serially with year. When abundances were converted to percentage compositions, this pattern of seriation broke down, demonstrating that changes in abundance and not percentage composition were responsible for the seriation. As with the number and abundance of species, changes in composition over the 26 years were not related to any of the physico-chemical/climatic factors tested. Species composition changed monthly in a pronounced cyclical manner throughout the year, due to statistically different time-staggered changes in the abundance of each species. This cyclicity was related most strongly to salinity. [ABSTRACT FROM AUTHOR]