Selection and phylogenetics of salmonid MHC class I: wild brown trout (Salmo trutta) differ from a non-native introduced strain

We tested how variation at a gene of adaptive importance, MHC class I (UBA), in a wild, endemic Salmo trutta population compared to that in both a previously studied non-native S. trutta population and a co-habiting Salmo salar population ( a sister species). High allelic diversity is observed and allelic divergence is much higher than that noted previously for cohabiting S. salar. Recombination was found to be important to population-level divergence. The alpha 1 and alpha 2 domains of UBA demonstrate ancient lineages but novel lineages are also identified at both domains in this work. We also find examples of recombination between UBA and the non-classical locus, ULA. Evidence for strong diversifying selection was found at a discrete suite of S. trutta UBA amino acid sites. The pattern was found to contrast with that found in re-analysed UBA data from an artificially stocked S. trutta population

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F-1 hybrid crosses between them, in the wild home\u27 environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions

Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

notes: PMCID: PMC2882343© 2010 Griffiths et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.European Union INTERREG IIIB programme (Atlantic Salmon Arc Project [ASAP], Project No. 040)

Fine-scale population structure and connectivity of bottlenose dolphins, Tursiops truncatus, in European waters and implications for conservation

Funding: Fyssen post-doctoral fellowship, Fondation Total, a bridge funding from the School of Biology of the University of St Andrews and People’s Trust for Endangered Species (ML).1. Protecting species often involves the designation of protected areas, wherein suitable management strategies are applied either at the taxon or ecosystem level. Special Areas of Conservation (SACs) have been created in European waters under the Habitats Directive to protect bottlenose dolphins, Tursiops truncatus, which forms two ecotypes, pelagic and coastal. 2. The SACs have been designated in coastal waters based on photo‐identification studies that have indicated that bottlenose dolphins have relatively high site fidelity. However, individuals can carry out long‐distance movements, which suggests potential for demographic connectivity between the SACs as well as with other areas. 3. Connectivity can be studied using genetic markers. Previous studies on the species in this area used different sets of genetic markers and therefore inference on the fine‐scale population structure and demographic connectivity has not yet been made at a large scale. A common set of microsatellite markers was used in this study to provide the first comprehensive estimate of genetic structure of bottlenose dolphins in European Atlantic waters. 4. As in previous studies, a high level of genetic differentiation was found between coastal and pelagic populations. Genetic structure was defined at an unprecedented fine‐scale level for coastal dolphins, leading to identification of five distinct coastal populations inhabiting the following areas: Shannon estuary, west coast of Ireland, English Channel, coastal Galicia, east coast of Scotland and Wales/west Scotland. Demographic connectivity was very low among most populations with <10% migration rate, suggesting no demographic coupling among them. Each local population should therefore be monitored separately. 5. The results of this study have the potential to be used to identify management units for bottlenose dolphins in this region and thus offer a significant contribution to the conservation of the species in European Atlantic waters. Future studies should prioritize obtaining biopsies from free‐living dolphins from areas where only samples from stranded animals were available, i.e. Wales, west Scotland and Galicia, in order to reduce uncertainty caused by sample origin doubt, as well as from areas not included in this study (e.g. Iroise Sea, France). Furthermore, future management strategies should include monitoring local population dynamics and could also consider other options, such as population viability analysis or the incorporation of genetic data with ecological data (e.g. stable isotope analysis) in the designation of management units.PostprintPeer reviewe

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F-1 hybrid crosses between them, in the wild home' environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high

Wintering grounds, population size and evolutionary history of a cryptic passerine species from isotopic and genetic data

Cryptic species pose a particular challenge to biologists in the context of life history investigations because of the difficulty in their field discrimination. Additionally, there is normally a lag in their widespread acceptance by the scientific community once they are formally recognised. These two factors might constrain our ability to properly assess the conservation status of the different species conforming a cryptic complex. In this study, we analysed isotopic and genetic data to shed light into the still unclear wintering grounds, population size and evolutionary history of the Iberian chiffchaff Phylloscopus ibericus, a species included within the common chiffchaff Phylloscopus collybita until two decades ago due to their phenotypic similarity. We used molecular methods to identify spring-migrating Phylloscopus species captured in northern Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips (δ2Hc; which would reflect the signatures of their wintering grounds), we detected that δ2Hc values of Iberian chiffchaffs were similar to willow warblers (Phylloscopus trochilus; a renowned trans-Saharan migrant), and higher than common chiffchaffs (mostly a pre-Saharan migrant). These results strongly support the idea that Iberian chiffchaffs winter in tropical Africa. We additionally reconstructed the phylogeny and evolutionary history of the Iberian chiffchaff's clade using mitochondrial and nuclear markers. Our results revealed relatively high values of nucleotide diversity (and, hence, high Ne) for the species that were greater than the values of the common/Iberian most recent common ancestor. This suggests that the Iberian chiffchaff did not experience strong bottlenecks after diverging from the common chiffchaff approximately one million years ago. Ultimately, our study provides another illustrative example of how isotopic and genetic analysis tools can help to enhance our understanding of avian ecology and evolution.Depto. de Biodiversidad, Ecología y EvoluciónFac. de Ciencias BiológicasTRUEpu

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon

The first recorded occurrence of the Asian hornet (Vespa velutina) in Ireland, genetic evidence for a continued single invasion across Europe

The first record of the Asian/yellow-legged hornet (Vespa velutina) in Ireland was reported in April 2021, when a single female individual was discovered in Dublin. Vespa velutina has been present in mainland Europe since 2004 and in the UK since 2016 and poses an enormous threat to European apiculture and bee-mediated pollination services. Three mitochondrial genes were sequenced from the Irish specimen to determine whether the specimen originated from the established European population or signified a new point of entry from its native range in China. Additionally, specimens from Portugal, Spain, France, Germany, and the Channel Islands were sequenced at these three genes to build on previous studies which have asserted, based solely on Cytochrome Oxidase 1 (COI) analysis, that the entire range of V. velutina in Europe represents a single invasion which has proliferated since the first record in France. Further data were retrieved from GenBank for comparison. Results reveal that the mtDNA lineage observed in Dublin is the same as that seen throughout Europe, and therefore the arrival of this species in Ireland likely represents a further spread of the ongoing European invasion