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Three ecologically and morphologically distinct forms of Arctic charr (Salvelinus alpinus L.) have been identified in Loch Rannoch, Scotland, whose evolutionary status and origins are incompletely understood. A study was made of restriction fragment length polymorphism (RFLPs) detected variation in the D-loop, ND1 and cytochrome b regions of the mitochondrial genome, encompassing [3500 bp. Eight RFLP haplotypes were identified that clustered into three distinct clans based on restriction differences and into four clans based on sequence differences. Significant differences in RFLP frequencies were found among all morph groups. The pelagic morph was highly divergent from the two benthic forms, with the benthic forms having variants from only one genetic clan while the pelagic was dominated by a single variant from another clan. The relative divergence observed among benthic and pelagic forms is *10 fold greater when nucleotide divergence among the haplotypes, as well as haplotype frequency differences, is taken into account. Sequence divergence between haplotypes in the two main clans is of a similar order to that between haplotypes in these clans and a charr from North America. In contrast, divergence among the two benthic morphs relates entirely to differences in haplotype frequencies. The study confirms the genetic distinctiveness of the pelagic and benthic forms as well as of the two benthic forms. It strongly supports previous evidence that the genetic divergence between the pelagic and benthic populations is allopatric in origin. Additionally, the results strongly suggest that the two benthic populations have undergone peripatric divergence through the sequential colonisation of the two basins by one lineage, followed by their spatial separation and reproductive isolation.

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Three genetically discrete morphs of Arctic charr in Loch Rannoch, Scotland originated from a recent divergence within the lake (in situ) (piscivore and benthivore morphs) and from secondary contact of two older lineages (ex situ; a planktivore-piscivore/ benthivore divergence). To test if the expression of traits with strong functional roles was linked to the age of the divergence, fin and gill anatomy, and dentition were quantified and compared across morphs. Five additional working hypotheses suggesting a rank order of trait expression amongst morphs were also tested. The planktivorous morph had more rays in the dorsal and pectoral fins, longer gill rakers (but not more) as well as a smaller gill cavity than the other two morphs.The piscivorous morph had more palatine teeth and longer teeth on the mandible, pre-maxillary and glossohyal bones, and a larger buccal cavity. These differences indicate a differential response to selection in these functional anatomical features most likely related to morph foraging specialisms. Notably, between-morph divergences in the expression of these traits were not simply linked to the length of divergence between morphs and have arisen equally quickly in the recent (in situ) divergence as they have in older, ex situ divergences.

Polymorphic Arctic charr Salvelinus alpinus populations frequently display distinct differences in habitat use, diet, and parasite communities. Changes to the relative species densities and composition of the wider fish community have the potential to alter the habitat niche of sympatric Arctic charr populations. This study evaluated the temporal stability of the parasite community, diet, and stable isotopes (δ 13 C, δ 15 N) of three sympatric Arctic charr morphs (piscivore, benthivore, and planktivore) from Loch Rannoch, Scotland, in relation to changes to the fish community. All Arctic charr morphs displayed distinct differences in parasite communities, diet, and stable isotope signatures over time, despite the establishment of four new trophically transmitted parasite taxa, and increased fish and zooplankton consumption by the piscivorous and planktivore morphs, respectively. Native parasite prevalence also increased in all Arctic charr morphs. Overall, Loch Rannoch polymorphic Arctic charr morph populations have maintained their distinct trophic niches and parasite communities through time despite changes in the fish community. This result indicates that re‐stocking a native fish species has the potential to induce shifts in the parasite community and diet of Arctic charr morphs.