Taxonomy and phylogeography of the Arctic char (Salvelinus alpinus) in Ireland

  • Noé Barthelemy Louis

Student thesis: Doctoral ThesisDoctor of Philosophy


A comprehensive analysis of the genetics of the Arctic char Salvelinus alpinus in Irish lakes was undertaken to investigate the taxonomic status of the species in the island of Ireland (hereafter referred to as Ireland) as well as the phylogeographic history and population structuring of contemporary extant populations. Also, it aimed to assess the importance of scientific communication on conservation decisions by policymakers in the context of S. alpinus in Ireland; and how to use the information generated, in addition to other available data, to assist with the development of scientifically sound conservation measures of its populations.S. alpinus representing 37 Irish lakes (i.e., 82% of all lakes where the species is still present) were sampled for analyses. Archived samples were also available from 18 additional lakes where char is now thought to be extinct. Limited samples from Scotland, England and Sweden were added as genetic outgroups. No samples from Wales were available for our study, even though this region hosts many char populations. Historical samples (collected during the late 1800s and early 1900s) were obtained from the biological archive collections held by the Natural History Museum of London and from the National Museum of Ireland. These samples included holotypes and syntypes for each of the species previously described in Ireland by both Günther (1862,1863) and Regan (1908, 1911). Over 3,200 S. alpinus specimens were analysed during this study.Genetic analyses involved nuclear and mitochondrial DNA markers. Both nuclear and mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (SNPs) markers were developed based on a sample set representing 29 char lakes in Ireland in addition to outgroup specimens from England and Scotland.Nuclear SNPs were used to screen of the 3,072 sample set. Results indicated that S. alpinus lakes in Ireland harboured genetically different populations with varying degrees of divergence. No major correlation between geographical and genetic distance was observed. Thus, geography was not always an indicator of genetic similarity. A notable result was that several Irish lakes (e.g., Acoose, Cloonaghlin, Coomaglaslaw, Mask, Corrib, Fad East) appeared to harbour more than one genetically distinct population (i.e., sympatric populations). Sympatric populations were also noted in a sample from England, where they are known to exist (Lake Windermere).Comparative analyses of 342 S. alpinus mitogenomes (248 generated in this study) revealed 173 distinct mtDNA haplotypes. Results indicated that S. alpinus in Ireland’s lakes are represented by four genetically distinct and rich (i.e., represented by several genetic variants) evolutionary lineages.One of these appeared to be endemic in Ireland. The other three lineages, while well represented in Ireland, were also found elsewhere in Great Britain (GB) and in the North Atlantic. In Ireland, most of the mitogenomic diversity was explained by within lake diversity. Similar to that observed from nuclear DNA based SNP analyses, there was no correlation between geography and the presence of these lineages among S. alpinus lakes in Ireland. Results from the screening the 3,072 sample collection, in addition to museum derived samples, for selected mtDNA SNPs, confirmed and extended (i.e., by uncovering additional genetic variants within each of the main lineages) previous findings. In particular, the lack of correlation between geographical location and distribution of the four mtDNA lineages in Ireland and elsewhere. An unusually high number of haplotypes was observed in several lakes. Many of these lakes have been thought to harbour sympatric populations from previous nuclear SNP results. This hypothesis was, thus, supported by the mtDNA results. There was no support for full species status for the Victorian based taxonomy. Overall, combined results from the genetic analyses indicated that most of the contemporary, surprisingly rich mitochondrial DNA diversity (haplotypes) observed among S. alpinus lakes in Ireland is endemic (potentially unique from Ireland), having arisen locally (in isolation) since the end of the last glacial maxima.The results of the environmental economics analyses indicated that policymakers were likely to make significantly different conservation decisions when the unknowns of a conservation context were explicitly mentioned or not. Taking these results into consideration, and using the genetic and morphometric data generated in this study, in combination with other available information on the studied lakes, a prioritisation ranking list for S. alpinus conservation in Ireland was produced based on a simple, transparent and readily applicable point based system. This ranking list was designed to be directly usable by the relevant stakeholders (e.g., policymakers), while allowing them to define their own priorities for conservation between the diversity or level of threat upon Irish S. alpinus populations.

Thesis embargoed until 31st July 2026

Date of AwardJul 2023
Original languageEnglish
Awarding Institution
  • Queen's University Belfast
SponsorsEnvironmental Protection Agency
SupervisorPaulo Prodohl (Supervisor), George Hutchinson (Supervisor) & Rose Hynes (Supervisor)


  • Phylogeography
  • genetics
  • salmonids
  • evolution
  • data analysis
  • taxonomy
  • morphometrics
  • environmental economics

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