Taxonomy and phylogeography of the Irish Arctic char (<i>Salvelinus alpinus</i>). Report No. 444

A comprehensive genetic analysis of Arctic char (Salvelinus alpinus) populations in Irish loughs was undertaken to address several aspects relevant to conservation and management. First, the study aimed to clarify the taxonomic status of this species, investigating whether there is scientific evidence supporting the existence of multiple char species in Ireland. Second, it sought to uncover the phylogeographical history and population structure of contemporary Arctic char populations in Ireland. Third, it assessed the impact of scientific communication on conservation decisions made by policymakers, using an environmental economics analytical framework. Finally, the study aimed to provide insights into the development of effective conservation measures for Arctic char in Ireland, using the genetic data generated in conjunction with other available information.The study involved sampling Arctic char from 37 loughs in Ireland, representing 82% of the loughs where the species has been recorded as naturally present. Archived samples were also available from 18 additional loughs where Arctic char is now thought to be extinct. Limited samples from Scotland (UK), England (UK) and Sweden were included in the dataset for comparison. Historical specimens, collected during the late 1800s and early 1900s, were sourced from the Natural History Museum in London and the National Museum of Ireland. These included holotypes and syntypes associated with species previously described in Ireland by Günther (1862, 1863) and Regan (1908, 1911). In total, over 3200 Arctic char specimens were analysed during the study.The analysis involved the examination of genetic data from both nuclear and mitochondrial DNA (mtDNA), in addition to morphometric data. Single nucleotide polymorphism (SNP) markers were developed for both nuclear DNA and mtDNA, based on a sample set of 288 individuals representing 29 Irish Arctic char loughs, along with specimens from England and Scotland for reference. Nuclear SNP markers were employed to screen the 3072 samples collected for the project. The results revealed that all Arctic char loughs hosted genetically distinct populations, with varying degrees of divergence. There was no major correlation between geographical location and genetic similarity, indicating that geographical proximity is not an indicator of genetic similarity. Several loughs were found to host multiple genetically distinct populations, a phenomenon known as sympatric populations.Comparative analysis of 342 Arctic char mitochondrial genomes unveiled 173 distinct mtDNA haplotypes. Results indicate that Arctic char populations in Ireland’s loughs are represented by four genetically distinct, rich (i.e. represented by several genetic variants) evolutionary lineages. Genetic divergence among these lineages suggests separate evolution in distinct refugia prior to the Last Glacial Maximum. As the ice retreated between 20,000 and 13,000 years ago, these lineages independently colonised Irish freshwater habitats. Two of these lineages appeared to be unique to Ireland, possibly representing the first colonisers following the ice retreat. The remaining lineages were also found in other North Atlantic countries. Within-lough diversity explained most of the mitochondrial genetic diversity, further emphasising the lack of a geographical pattern. The disjunct contemporary geographical distribution of lineages indicates that the recolonisation of Ireland was complex, involving colonisation, extinction, recolonisation, and/or secondary contact and admixture among Arctic char populations representing different lineages.The results of the study challenge the species status of Arctic char populations based on Victorian-era taxonomy. Neither genetic nor morphometric data support the existence of multiple char species in Ireland. While scientific evidence does not substantiate the presence of distinct species, the study highlights the uniqueness, richness and potentially endemic nature of mtDNA diversity among Irish Arctic char. Much of this diversity has evolved in isolation since the Last Glacial Maximum. This unique biodiversity warrants conservation attention and protection. The results of the environmental economics analysis reveal that policymakers’ conservation decisions are influenced by the inclusion or exclusion of uncertainties in the conservation context. Building on these findings, to assist with the development of effective conservation measures, a prioritisation list ranking Arctic char conservation needs in Ireland was devised. This ranking system, based on a straightforward points-based approach, uses the novel genetic and morphometric data generated by the study, combined with other available information on the loughs under investigation. This prioritisation list could be a valuable tool for relevant stakeholders, to assist with the development and implementation of sound conservation measures for Arctic char in Ireland

Development of a novel microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California

The rapid advance of high-throughput sequencing has prompted a transition in wildlife and fisheries genetics from using microsatellites toward markers that are more amenable to genotyping by sequencing. Microhaplotypes are novel multi-allelic genetic markers that utilize a high-throughput genomic amplicon sequencing approach to genotype large numbers of individuals for parentage and kinship analysis and population genetic studies, including applications in monitoring and fisheries management. We describe the development of a panel of microhaplotypes for Oncorhynchus mykiss, a species of high cultural and economic importance both in its native range in the North American and the Kamchatka Peninsula of northeast Asia, and globally through introductions for aquaculture and due to its reputation as a prized sport fish among recreational fishers. The panel includes 124 loci presumed to be neutral, a marker for the sex determination locus (SdY), and 10 loci targeting previously identified adaptive genomic variants associated with important life-history traits in this species. We demonstrate that this panel provides high resolution for phylogeographic and other genetic analysis and provide an initial standardized reference population genetic baseline of California O. mykiss