Effective species conservation and management requires comprehensive biomonitoring, enhanced by combining traditional and newer methodologies, such as environmental DNA (eDNA) analyses. A seasonal pulse of spawning adult Atlantic salmon ( Salmo salar ) was detected by normalised eDNA 12S reads from metabarcoding, which facilitated estimation of spatial patterns in salmon biomass. A strong relationship was found between normali...

Understanding the processes that shape community assembly is a critical focus of ecology. Marine benthic meiofauna, microscopic invertebrates inhabiting sediment environments, play important roles in ecosystem functioning but have been largely overlooked in metacommunity studies due to the lack of community data. In this study, we quantify the relative contributions of environmental filtering, spatial processes, and biotic ass...

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide‐ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative fra...

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning...

Generalist species are core components of ecological networks and crucial for the maintenance of biodiversity. Generalist species and networks are expected to be more resilient, and therefore understanding the dynamics of specialization and generalization in ecological networks is a key focus in a time of rapid global change. Whilst diet generalization is frequently studied, our understanding of how it changes over time is lim...

The response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate c...

Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous and ecologically important inhabitants of benthic marine ecosystems. Their high species richness and rapid response to environmental change make them promising targets for ecological and biomonitoring studies. However, diversity patterns of benthic marine meiofauna remain poorly known due to challenges in species identification using classical morpholog...

Aim Landmasses have been continuously modified by tectonic activity, the breakup and collision of landmasses is thought to have generated or suppressed ecological opportunities, altering the rates of speciation, dispersal and extinction. However, the extent to which the signatures of past geological events are retained in modern biodiversity patterns—or obliterated by recent ecological dynamics—remains unresolved. We aim to id...

Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon ‐like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodive...

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad app...

High‐throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability an...

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome‐wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta a...

Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on‐going and future climate change on biodiversity and function...

To establish if fishes’ consumption of jellyfish changes through the year, we conducted a molecular gut‐content assessment on opportunistically sampled species from the Celtic Sea in October and compared these with samples previously collected in February and March from the Irish Sea. Mackerel Scomber scombrus were found to feed on hydrozoan jellyfish relatively frequently in autumn, with rare consumption also detected in sard...

Diversification and speciation of terrestrial organisms are anticipated in oceanic islands such as Macaronesia, a group of Atlantic islands that have remained unconnected to continental landmasses. Hitherto, the diversification of marine organisms in oceanic islands, especially those with low vagility, has received little direct empirical analysis using molecular markers. Here, we focus on such a case study, through applying a...

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and me...

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“ HTS ”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA ” or “ eDNA ”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “ eDNA metabarcoding” and offers a powerful molecular tool capable of noninv...

Aim Meiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life‐history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological tax...

Despite the high number of species and ecological diversity of pandalid shrimps, there has been no previous attempt to resolve evolutionary relationships of several genera using molecular tools. Although mitochondrial DNA cytochrome oxidase I ( COI ) is widely used in barcoding studies to delimit species boundaries, additional insights into phylogenetic affinities can be obtained, especially when used in combination with data...