Application of eDNA metabarcoding in a fragmented lowland river: spatial and methodological comparison of fish species composition

Assessments of fish communities tend to rely on capture-based methods that, due to sampling biases, can underestimate actual species richness. Alternatively, environmental DNA (eDNA) based metabarcoding is a non-capture approach that infers species richness and distribution by collecting and sequencing DNA present in the ecosystem. Here, eDNA metabarcoding was applied to the lower River Severn, a highly modified and impounded river, to identify the species present in the fish assemblage. Using a universal primer for fish (12S mtDNA region), comparisons were made between the species identified as present by eDNA metabarcoding versus long-term data available from fisheries monitoring data based on capture methods. Depending on the stringency of detection thresholds applied, the two methods detected between 15 and 25 fish species present in the river, with the eDNA metabarcoding detecting most species previously reported in the capture surveys, although with differences in the relative abundance of species between the methods. Notably, eDNA metabarcoding detected species of high conservation importance that were never sampled by capture techniques, including native European shads (Alosa spp.). Differences in the similarity indices of species detection were greater between the sampling methods than between sampling sites on each river. These results highlight the high potential of eDNA metabarcoding to provide an effective monitoring tool for biodiversity and conservation in rivers, but also indicate the need for complementary multi-method sampling for robust estimates of fish species richness

Vicariance in a generalist fish parasite driven by climate and salinity tolerance of hosts

Acanthocephalans are parasites with complex lifecycles that are important components of aquatic systems and are often model species for parasite-mediated host manipulation. Genetic characterisation has recently resurrected Pomphorhynchus tereticollis as a distinct species from Pomphorhynchus laevis, with potential implications for fisheries management and host manipulation research. Morphological and molecular examinations of parasites from 7 English rivers across 9 fish species revealed that P. tereticollis was the only Pomphorhynchus parasite present in Britain, rather than P. laevis as previously recorded. A meta-analysis using two genetic regions and all the DNA sequences Abstract: available for P. tereticollis has identified two distinct genetic lineages of P. tereticollis in Britain. One lineage, possibly associated with cold water tolerant fish, potentially spread to the northern parts of Britain from the Baltic region via a northern route across the estuarine area of what is now the North Sea during the last Glaciation. The other lineage, associated with temperate freshwater fish, may have arrived later via the Rhine/Thames fluvial connection during the last glaciation or early Holocene when sea levels were low. These results raise important questions on this generalist parasite and its variously environmentally adapted hosts, and especially in relation to the consequences for parasite vicariance

Plant–animal interactions in the era of environmental DNA (eDNA): a review

Plant–animal interactions (PAI) represent major channels of energy transfer through ecosystems, where both positive and antagonistic interactions simultaneously contribute to ecosystem functioning. Monitoring PAI therefore increases the understanding of environmental health, integrity, and functioning, and studying complex interactions through accurate, cost-effective sampling can aid in the management of detrimental anthropogenic impacts. Environmental DNA (eDNA)-based monitoring represents an increasingly common, nondestructive approach for biodiversity monitoring, which could help to elucidate PAI. Here, we aim to provide an overall discussion on the potential of using eDNA to study PAI. We assessed the existing literature on this subject from 2009 to 2021 using a freely accessible web search tool. The search was conducted by using keywords involving eDNA and PAI, including both species-specific and metabarcoding approaches, recovering 43 studies. We summarized the advantages and current limitations of such approaches, and we outline research priorities to improve future eDNA-based methods for PAI analysis. Among the 43 studies identified using eDNA to measure PAI such as pollination, herbivory, mutualistic, and parasitic relationships, they have often identified higher taxonomic diversity in several direct comparisons with DNA-based gut/bulk sampling and conventional survey methods. Research needs include the following: better understanding of the influencing factors of eDNA detection involved in PAI (e.g., eDNA degradation, origin, and types), methodological standardization (sampling methods and primer development), and more inclusive sequence reference databases. If these research priorities are addressed, it will have a significant impact to enable PAI biodiversity monitoring with eDNA. In the future, the implementation of eDNA methods to study PAI can particularly benefit the scalability of environmental biomonitoring surveys that are imperative for ecosystem health assessments.Environmental BiologyConservation Biolog

Corrigendum to Loss of genetic integrity and biological invasions result from stocking and introductions of Barbus barbus: Insights from rivers in England [Ecology and Evolution (2016), 6 (5), 1280-1292. doi: 10.1002/ece3.1906]

: [This corrects the article DOI: 10.1002/ece3.1906.]

Human-mediated contact zone between endemic and invasive Barbus species (Teleostei, Cyprinidae) in a regulated lowland river: genetic inferences and conservation implications

Genetic surveys of the endemic Padanian barbel Barbus plebejus (Osteichthyes: Cyprinidae) were completed on the lowland Adda River, a heavily regulated Italian Alpine river in which the European Barbus barbus is invasive. Both Barbus species are of the large fluvio-lacustrine ecophenotype and thus they share habitats in the river. Mitochondrial (N = 35) and nuclear (N = 256) DNA sequences were completed with the aim of estimating the extent and genetic consequences of the B. barbus invasion. The phylogenetic analyses, based on cyt b mtDNA, S7 ribosomal protein and growth hormone (GH) nuclear genes, revealed 59 haplotypes as B. plebejus and 37 as B. barbus. Genetic diversity values (H and \u3c0) and the mismatch distribution analyses indicated B. plebejus was still experiencing demographic radiation from a modest number of founders. The B. barbus cyt b haplotypes suggested their original source was the River Danube. Through analysing the nuclear paralog sequences, evidence was provided of consistent genetic admixture between B. plebejus and B. barbus, being recorded in over 40% of the sampled fishes, indicating that their ecological and biological interactions are disrupting the genetic integrity of B. plebejus. Bayesian analysis and factorial correspondence analysis then revealed that the habitat fragmentation of the Adda River is not limiting population connectivity. It was apparent there has been recent and rapid upstream dispersion of B. barbus, with individuals overcoming barriers to their migration through using fish passes and/or through translocation between impounded sections by anglers. The potential conservation implications of this for the endemic Barbus species are discussed

Hybridisation and genetic population structure of Alosa population in United Kingdom

Human-mediated habitat fragmentation has been proposed as the main factor driving hybridization between the sympatric migratory European shads Alosa alosa and Alosa fallax, which has been coincident with substantial population declines in A. alosa. In river systems across Great Britain, shad are negatively affected by navigation weirs constructed in the last 150 years that impede their spawning migrations. Consequently, the aim here was to assess the impact of human disturbances on genetic introgression and population structure of shad in Great Britain through genotyping 119 Alosa spp. using 24 microsatellite loci