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 recolonization 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 a larger mammalian community 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.

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome.

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

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

We focus on a case study along an English canal comparing environmental DNA (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.

A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad.

Typically anadromous, the twaite shad (Alosa fallax) can become landlocked and adapt to a fully freshwater life. The only landlocked shad population in Northwestern Europe is found in a lake in Ireland, Lough Leane. The Killarney shad, Alosa killarnensis (or Alosa fallax killarnensis, as it is mostly referred to) displays a level of morphological divergence that indicates a long-term isolation in the lake. Microsatellites and mtDNA control region sequences were used within a coalescent framework (BEAST and Approximate Bayesian Computation (ABC)) to investigate its colonization history and to clarify its taxonomic status. Results indicate that the lake was likely colonized in two independent events, the first coinciding with the retreat of the ice sheet from the area after the Last Glacial Maximum and the second after the Younger Dryas. Microsatellite data has shown that these two landlocked lineages have completely admixed within the lake, and have started diverging significantly from their closest ancestor, the twaite shad. We argue that our molecular results (together with the life-history and physiological divergence between Killarney and twaite shad) are conspicuous enough to view the landlocked population as a new species, and one whose future existence would certainly not be insured by its sister taxon.

Towards vibrant fish populations and sustainable fisheries that benefit all: learning from the last 30 years to inform the next 30 years.

A common goal among fisheries science professionals, stakeholders, and rights holders is to ensure the persistence and resilience of vibrant fish populations and sustainable, equitable fisheries in diverse aquatic ecosystems, from small headwater streams to offshore pelagic waters. Achieving this goal requires a complex intersection of science and management, and a recognition of the interconnections among people, place, and fish that govern these tightly coupled socioecological and sociotechnical systems. The World Fisheries Congress (WFC) convenes every four years and provides a unique global forum to debate and discuss threats, issues, and opportunities facing fish populations and fisheries. The 2021 WFC meeting, hosted remotely in Adelaide, Australia, marked the 30th year since the first meeting was held in Athens, Greece, and provided an opportunity to reflect on progress made in the past 30 years and provide guidance for the future. We assembled a diverse team of individuals involved with the Adelaide WFC and reflected on the major challenges that faced fish and fisheries over the past 30 years, discussed progress toward overcoming those challenges, and then used themes that emerged during the Congress to identify issues and opportunities to improve sustainability in the world's fisheries for the next 30 years. Key future needs and opportunities identified include: rethinking fisheries management systems and modelling approaches, modernizing and integrating assessment and information systems, being responsive and flexible in addressing persistent and emerging threats to fish and fisheries, mainstreaming the human dimension of fisheries, rethinking governance, policy and compliance, and achieving equity and inclusion in fisheries. We also identified a number of cross-cutting themes including better understanding the role of fish as nutrition in a hungry world, adapting to climate change, embracing transdisciplinarity, respecting Indigenous knowledge systems, thinking ahead with foresight science, and working together across scales. By reflecting on the past and thinking about the future, we aim to provide guidance for achieving our mutual goal of sustaining vibrant fish populations and sustainable fisheries that benefit all. We hope that this prospective thinking can serve as a guide to (i) assess progress towards achieving this lofty goal and (ii) refine our path with input from new and emerging voices and approaches in fisheries science, management, and stewardship.

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding.

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between ß-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

Evidence of stock connectivity, hybridization, and misidentification in white anglerfish supports the need of a genetics-informed fisheries management framework.

Understanding population connectivity within a species as well as potential interactions with its close relatives is crucial to define management units and to derive efficient management actions. However, although genetics can reveal mismatches between biological and management units and other relevant but hidden information such as species misidentification or hybridization, the uptake of genetic methods by the fisheries management process is far from having been consolidated. Here, we have assessed the power of genetics to better understand the population connectivity of white (Lophius piscatorius) and its interaction with its sister species, the black anglerfish (Lophius budegassa). Our analyses, based on thousands of genome-wide single nucleotide polymorphisms, show three findings that are crucial for white anglerfish management. We found (i) that white anglerfish is likely composed of a single panmictic population throughout the Northeast Atlantic, challenging the three-stock based management, (ii) that a fraction of specimens classified as white anglerfish using morphological characteristics are genetically identified as black anglerfish (L. budegassa), and iii) that the two Lophius species naturally hybridize leading to a population of hybrids of up to 20% in certain areas. Our results set the basics for a genetics-informed white anglerfish assessment framework that accounts for stock connectivity, revises and establishes new diagnostic characters for Lophius species identification, and evaluates the effect of hybrids in the current and future assessments of the white anglerfish. Furthermore, our study contributes to provide additional evidence of the potentially negative consequences of ignoring genetic data for assessing fisheries resources.

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach.

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine-scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April-September), factoring in larval duration and interannual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean F ST = 0.021) within a relatively fine spatial scale in the north-west Atlantic. Environmental association analysis indicates that oceanographic currents and geographic proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperature extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographic scale.

Connectivity and Dispersal Patterns of Protected Biogenic Reefs: Implications for the Conservation of Modiolus modiolus (L.) in the Irish Sea.

Biogenic reefs created by Modiolus modiolus (Linnaeus, 1758) (horse mussel reefs) are marine habitats which support high levels of species biodiversity and provide valuable ecosystem services. Currently, M. modiolus reefs are listed as a threatened and/or declining species and habitat in all OSPAR regions and thus are highlighted as a conservation priority under the EU Marine Strategy Framework Directive (MSFD). Determining patterns of larval dispersal and genetic connectivity of remaining horse mussel populations can inform management efforts and is a critical component of effective marine spatial planning (MSP). Larval dispersal patterns and genetic structure were determined for several M. modiolus bed populations in the Irish Sea including those in Wales (North Pen Llyn), Isle of Man (Point of Ayre) and Northern Ireland (Ards Peninsula and Strangford Lough). Simulations of larval dispersal suggested extant connectivity between populations within the Irish Sea. Results from the genetic analysis carried out using newly developed microsatellite DNA markers were consistent with those of the biophysical model. Results indicated moderately significant differentiation between the Northern Ireland populations and those in the Isle of Man and Wales. Simulations of larval dispersal over a 30 day pelagic larval duration (PLD) suggest that connectivity over a spatial scale of 150km is possible between some source and sink populations. However, it appears unlikely that larvae from Northern Ireland will connect directly with sites on the Llyn or Isle of Man. It also appears unlikely that larvae from the Llyn connect directly to any of the other sites. Taken together the data establishes a baseline for underpinning management and conservation of these important and threatened marine habitats in the southern part of the known range.

Ancient divergence in the trans-oceanic deep-sea shark Centroscymnus crepidater.

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements.