Molecular Ecology (2001) 10, 987–1001 © 2001 Blackwell Science Ltd Blackwell Science, Ltd Mitochondrial DNA phylogeography of lake cisco (Coregonus artedi): evidence supporting extensive secondary contacts between two glacial races J. TURGEON* and L. BERNATCHEZ GIROQ, Département de biologie, Université Laval, Ste-Foy, Québec, Canada G1K 7P4 Abstract The comparative molecular phylogeography of regional fish fauna has revealed the wide distribution of young clades in freshwater fishes of formerly glaciated areas as well as inter- specific incongruences in their refugial origins and recolonization routes. In this study, we employed single-strand conformation polymorphism (SSCP) and sequence analyses to describe mitochondrial DNA (mtDNA) polymorphism among 27 populations of the lake cisco (Coregonus artedi) from its entire range of distribution in order to evaluate the hypothesis of dual glacial refuges proposed by Bernatchez & Dodson against the traditional view that this species is solely of Mississippian origin. Results indicate that this taxon is composed of two closely related groups that are widely distributed and intermixed over most of the sampled range. The estimated level of divergence (0.48%), the contrast in the geographical distribution of each group, as well as the general distribution of C. artedi in North America together support the hypothesis that one group dispersed from a Mississippian refuge via the proglacial lakes, while the other is of Atlantic origin and also took advantages of earlier dispersal routes towards eastern Hudson Bay drainages. However, the signal of past range fragmentation revealed by a nested clade analysis was weak, and did not allow to formally exclude the hypothesis of a single Mississippian origin for both lineages. Comparisons with the phylogeographic patterns of other Nearctic freshwater fishes suggest that the salinity tolerance and thermal sensitivity of lake cisco may have been determinant for its extensive postglacial dispersal. The presence or co-occurrence of sympatric or allopatric eco/morphotypes were not found to be necessarily associated with the presence of both haplotype groups. Keywords: Coregonus artedi, colonization, dispersal, ecotype, refuge, mtDNA, phylogeography Received 7 August 2000; revision received 9 November 2000; accepted 9 November 2000 Introduction It is now well recognized that the Pleistocene glaciations have had profound effects on the extant distribution of Holarctic biota, and that these effects were particularly severe in North America (NA) due to the extent of the last Wisconsinan ice sheet (Pielou 1991). Effects of glaciations were felt beyond the ice margin as the general climate became drier and affected the hydrological networks in southern nonglaciated areas. These, however, were evidently both more direct and drastic in formerly glaciated areas of north temperate NA. In these regions, the restrictive dispersal requirements of freshwater fishes has resulted in distributional patterns that are intimately related to the location of glacial refuges and the variable continental hydrology characterizing the period of ice retreat at the end of the last (Wisconsinan) glaciation. The immense proglacial lakes then provided formidable dispersal avenues for those species able to withstand their changing nature and has resulted in typically larger range sizes for fishes of formerly glaciated areas ( McAllister et al. 1986). Inferences on the refugial origin and postglacial dispersal routes of north temperate freshwater fishes of NA have been obtained by comprehensive biogeographical studies using distribution, geographical variation, fossils and parasites as sources of information (Hocutt & Wiley 1986). Correspondence: Julie Turgeon. *Present address: Department of Biology, Dartmouth College, Hanover, NH 03755 USA. Fax: 603 6461347; E-mail: julie.turgeon@dartmouth.edu