Ilaria Coscia

Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic

Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here, we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 expressed sequence tag-linked markers, as well as a portion of the mitochondrial DNA (mtDNA) control region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, although the potential ‘surfing effect’ of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.

Modelled larval dispersal and measured gene flow: seascape genetics of the common cockle Cerastoderma edule in the southern Irish Sea

The role of marine currents in shaping population connectivity in the common cockle Cerastoderma edule was investigated in the southern Irish Sea. C. edule is one of the most valuable and exploited shellfish species in the area, yet very little is known about its population dynamics. In the present study, coupled hydrodynamic and particle tracking models are used in conjunction with genetic data collected at twelve microsatellite loci to estimate the influence of the Celtic Sea front on larval transport between the coasts of Britain and Ireland. Genetic analysis highlights the presence of at least three genetic clusters partitioned within locations, suggesting a contact zone between separate subpopulations. Samples collected from the Irish coast are most similar to each other. On the British coast, the Burry Inlet appears genetically isolated while samples collected from the coast of Pembrokeshire show evidence of connectivity between Britain and Ireland. These results agree with the model’s predictions: away from the coastal zone, residual baroclinic currents develop along tidal mixing fronts and act as conduit systems, transporting larvae great distances. Larvae spawned in south Wales are capable of travelling west towards Ireland due to the Celtic Sea front residual current, confirming the action of the Celtic Sea front on larval transport. Sheltered, flood-dominant estuaries such as the Burry Inlet promote self-recruitment. The validation of the model using genetic data represents progress towards a sustainable future for the common cockle, and paves the way for a more effective approach to management of all Irish Sea shellfisheries.

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.

A highly permeable species boundary between two anadromous fishes

Meristic identification, mitochondrial DNA and a suite of microsatellite markers were employed to estimate the incidence of hybridization in wild populations of anadromous Allis shad Alosa alosa and twaite shad Alosa fallax in southern Irish riverine and estuarine waters. It was shown that 16% of the fishes examined were misclassified using meristic count of gill rakers. Next, a significant proportion of fishes that were robustly assigned to a species using nuclear markers were shown to possess the mtDNA of the other. The genomes of A. alosa and A. fallax in Ireland are extensively introgressed, which suggests a complex history of hybridization between these species, which can only partially be explained by recent man-made habitat changes.

Patterns of genetic structuring in a brown trout ( Salmo trutta L.) metapopulation

One main challenge in conservation biology is to preserve genetic variability and adaptive variation within and among populations. However, constant anthropogenic habitat modifications have severe effects on the evolutionary dynamics shaping wild populations and pose a serious threat to the natural evolution of biodiversity. The aim of the present study was to unravel the genetic structuring of brown trout (Salmo trutta) populations in the largest freshwater catchment in Ireland, whose habitats have experienced major human-mediated changes over at least two centuries. A total of 419 juvenile fish were sampled from nine main rivers in the Corrib catchment and were genotyped using 12 microsatellites. Both Bayesian clustering and FST-based analyses of genetic variance sorted these populations into five main genetically distinct groups, characterized by different extent of genetic differentiation among populations. These groups were also characterized by some degree of admixture, which can be partly explained by recent gene flow. Overall, the study suggests that the Corrib trout may conform to a metapopulation model with local populations that show different degrees of isolation and are interconnected by various level of gene flow. Results add further insights into metapopulation evolutionary dynamics and provide a useful basis to implement appropriate conservation strategies.

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.

New microsatellite loci for the longnose velvet dogfish Centroselachus crepidater (Squaliformes: Somniosidae) and other deep sea sharks

The continuing over-exploitation of traditional coastal stocks has resulted in the shift of commercial fishing towards deep-sea ecosystems in many parts of the world. The effects on target and non-target species have been dramatic; particularly for the deep-sea sharks. With the aim of providing tools that will allow the assessment of population genetic structure of Centroselachus crepidater, novel microsatellite loci have been developed for this deep-sea elasmobranch. Seven of these markers showed between 3 and 7 alleles per locus in two North Atlantic populations, with observed and expected heterozygosities between 0.18–0.95 and 0.25–0.82, respectively. Additionally, ten loci cross-amplify in other Elasmobranch species.

Are wild boars roaming Ireland once more

Wild boars (Sus scrofa) have been increasingly sighted in the wild in Ireland during the last few years, likely due to illegal releases and/or escapees. The species has since been designated an invasive species in Ireland, which is seen as controversial by some because of uncertainties about the historic status of the species in Ireland. However, just as pertinent to the argument is the genetic purity of these individuals currently found in Ireland: are these pure wild boars? We carried out a genetic assessment of 15 wild boars shot in Ireland between 2009 and 2012 using 14 microsatellites and mitochondrial DNA (mtDNA). These were compared to European wild boar, domestic pig breeds and a hybrid population of ‘wild boar’ from England. Microsatellite analysis revealed that almost all the Irish individuals belonged to the ‘domestic pig’ genetic cluster, with only three individuals being classified as hybrids. All but two individuals carried Asian mtDNA haplotypes, indicating a domestic pig origin. It is clear from this study that the individuals currently found in Ireland are not pure wild boars and this result has to be factored into any management/eradication plans.

The origins of Great Spotted Woodpeckers Dendrocopos major colonizing Ireland revealed by mitochondrial DNA

Capsule Although necessarily based on a small number of samples, comparisons of molecular data from the newly established Great Spotted Woodpecker populations in Ireland with those in Britain and continental Europe revealed that Britain was the more likely source area of the Irish populations.

Sex change and effective population size: implications for population genetic studies in marine fish

Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the ‘first’ sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the ‘santer’ sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the ‘slinger’ sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.