Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in northwest Europe

Abstract

Glacial and postglacial processes are known to be important determinants of contemporary population structuring for many species. In Europe, refugia in the Italian, Balkan and Iberian peninsulas are believed to be the main sources of species colonising northern Europe after the glacial retreat; however, there is increasing evidence of small, cryptic refugia existing north of these for many cold-tolerant species. This study examined the glacial history of Atlantic salmon in western Europe using two independent classes of molecular markers, microsatellites (nuclear) and mitochondrial DNA variation. Alongside the well-documented refuge in the Iberian Peninsula, evidence for a cryptic refuge in northwest France is also presented. Critically, methods utilised to estimate divergence times between the refugia indicated that salmon in these two regions had diverged a long time before the last glacial maximum; coalescence analysis (as implemented in the program IMa2) estimated divergence times at around 60 000 years before present. Through the examination of haplotype frequencies, previously glaciated areas of northwest Europe, that is, Britain and Ireland, appear to have been colonised from salmon expanding out of both refugia, with the southwest of England being the primary contact zone and exhibiting the highest genetic diversity.

Three‐dimensional post‐glacial expansion and diversification of an exploited oceanic fish

“…; Finnegan et al . ). Evidence from mtDNA haplotypes alone suggests that the shallow‐ and deep‐pelagic clades diverged over 22 000 years ago, in correspondence with the last glacial maximum (LGM) .…”

Resolving taxonomic uncertainty in vulnerable elasmobranchs: are the Madeira skate (Raja maderensis) and the thornback ray (Raja clavata) distinct species?

“…Alternatively, this group of haplotypes could have arisen within an additional, unidentified refugium, where R. clavata persisted during the last glacial maxima. There is growing evidence from a number of marine species that many organisms survived in isolated populations much closer to the ice sheets than previously thought (Provan et al 2005;Hoarau et al 2007;Olsen et al 2010;Finnegan et al 2013). This has been suggested in previous studies of R. clavata to explain the diversity of haplotypes present in northern Europe (Chevolot et al 2006), putatively suggesting Hurd Deep (i.e.…”

A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad

“…Mitochondrial and nuclear data both, independently, support this time frame. Interestingly, Finnegan et al (2013) reported that Atlantic salmon also colonized Ireland from two separate refugia after the LGM.…”

“…The origins of Ireland's fauna and flora is still a contentious issue in biogeography; its geographical position as an outlying island in western Europe presents many difficulties in terms of how and when freshwater species in particular colonized it. Only Finnegan et al (2013) thus far has attempted to date the origins of a fish species, the Atlantic salmon (Salmo salar), in Ireland. Clearly, a landlocked population can provide fascinating insights into the origin(s) of Irish freshwater fish, in terms of both timing and source populations.…”