E. Dillane

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

Insights into Genetic Diversity, Parentage, and Group Composition of Atlantic White-Sided Dolphins (Lagenorhynchus acutus) off the West of Ireland Based on Nuclear and Mitochondrial Genetic Markers

The analysis of stranding events and the application of molecular markers can be powerful tools to study cryptic biological aspects of delphinid species that occur mainly in open ocean habitat. In the present study, we investigated nuclear and mitochondrial genetic variability of Atlantic white-sided dolphins that stranded from 1990 to 2006 (n = 42) along the west coast of Ireland, using 8 microsatellite loci and 599 bp of the mitochondrial DNA control region. Results from both classes of markers are concordant with the hypothesis of a large random-mating population of white-sided dolphins along the west coast of Ireland. In addition, the analyses of 2 live mass stranding events (19 and 5 individuals, respectively) revealed that dolphins within each group were mainly unrelated to each other, suggesting dispersal of both sexes from the natal group (i.e., no natal phylopatry). Parentage analyses allowed the identification of mother-offspring pairs but ruled out all adult males as possible fathers. In combination with data on age of individuals, these results confirmed previous knowledge on life-history parameters, with sexually mature females ranging between 11 and 15 years of age and an interbirth interval of at least 2 years. The present study provides novel information on population and group composition of Atlantic white-sided dolphins along the west coast of Ireland, where population and social structure of the species are still poorly understood.

Development and Assessment of a Sensitive and Cost-Effective Polymerase Chain Reaction to Detect Ostreid Herpesvirus 1 and Variants

ABSTRACT Ostreid herpesvirus 1 (OsHV-1) and variants (OsHV-1 var, OsHV-1 µvar, Irish genotype) have had a significant impact on the Pacific oyster, Crassostrea gigas, industry worldwide and on the survival of larvae and juveniles of several other bivalve species in Europe. Diagnostic techniques used to screen for this pathogen include histology, polymerase chain reaction (PCR), and quantitative polymerase chain reaction (qPCR), which allows for quantification of the virus. Techniques used to confirm infection include PCR, in situ hybridization, and transmission electron microscopy, which have variable sensitivity and specificity. In this study, several new primers were designed to amplify the C region in the ORF4 gene of the virus. This region is variable and diagnostic among OsHV-1 and variants. To date, the routinely used C2/C6 primers, which are used to screen for OsHV-1 and variants, amplify a product of 709 bp whereas the new primers described in this study amplify products of 296 bp, 385 bp, and 400 bp. Several C. gigas samples, which had been exposed to herpes virus and variants were screened, and a sample of wild mussels (Mytilus spp.) was used as a negative control. The performance of the new PCR and primers was compared with the performance of the C2/C6 primers and qPCR. The effect of tissue storage and DNA extraction on PCR performance was also examined. The results of this study indicate that the new PCR and primers are more rapid, sensitive, and cost-effective compared with the C2/C6 PCR, and are as sensitive as qPCR. The results also highlight the impact that sample storage, tissue selection, DNA extraction method used, and subsequent storage of DNA have on PCR success or failure.

MHC-mediated spatial distribution in brown trout (Salmo trutta) fry

Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5±(s.e.)21.03m; one allele shared, 222.2±14.49m; two alleles shared, 124.9±23.88m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r=0) (no alleles: 457.6±3.58m; one allele (422.4±3.86 m); two alleles (381.7±10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.

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 F1 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 50 km, 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.

Contrasting levels of genetic differentiation among putative neutral microsatellite loci in Atlantic herring Clupea harengus populations and the implications for assessing stock structure

Microsatellite DNA loci, when used in population genetic studies, are usually assumed to be neutral (unaffected by natural selection, either directly or as a result of tight linkage), but this assumption is rarely tested. Here, the assumption of neutrality is examined using established methods, principally that based on the expected relationship between FST and heterozygosity, at 12 putative neutral microsatellite loci utilised in a study of Atlantic herring Clupea harengus in the north east Atlantic (west of Great Britain and around Ireland) and in the Baltic Sea. All but two of these loci demonstrate relationships that suggest that they may be regarded as neutral genetic markers. Of the other two loci, however, one shows a relationship suggestive of the action of directional selection and the other of balancing natural selection, though other locus-specific effects may operate. Thus, the latter two loci may provide inaccurate inference if used in phylogeographic studies and also demonstrate the danger of assuming neutrality at all microsatellite loci without explicit testing. However, such loci, particularly those affected by directional as opposed to balancing selection, may be of great use in stock discrimination studies, and selected loci in general, have considerably potential in studies of adaptation.

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

This work forms part of the SALSEA-Merge research project (Project No. 212529) and was funded by the European Union under theme six of the Seventh Framework programme. It was also co-sponsored by the Atlantic Salmon Trust and the Total Foundation, who we thank for financial support. PMcG and JC were partly supported by the Beaufort Marine Research Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme. The work was also supported under financial support of the program of fundamental research of Presidium of RAS “Searching fundamental scientific investigations in the interests of development of the Arctic zone of Russian Federation.”

Bat collisions with civil aircraft in the Republic of Ireland over a decade suggest negligible impact on aviation safety

Globally, collisions between wildlife and aircraft are a serious threat to aviation safety. While reported collisions have increased in recent years, the impact of these collisions on air safety is rarely quantified. Here, we report all bat collisions (bat strikes) with civil aircraft known to have occurred in the Republic of Ireland over the 10-year interval, 2006–2015. Morphological and/or DNA identification techniques were used to identify chiropteran specimens to species level. In total, carcasses or remains from five bat strikes—three Leisler’s Nyctalus leisleri, one Soprano Pipistrelle Pipistrellus pygmaeus, and one Natterer’s Myotis nattereri—were recovered. The collisions are discussed in the context of (a) the rate of chiropteran strikes in relation to the number of civil aircraft movements and (b) possible damage caused to aircraft. Overall, however, bat strikes with aircraft appear to have a negligible effect on civil aircraft safety.

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 co-habiting S. salar. Recombination was found to be important to population-level divergence. The α1 and α2 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.