We performed a combined analysis of mitochondrial DNA (mtDNA) and microsatellite loci among lake whitefish (Coregonus clupeaformis) populations in order to assess the levels of congruence between both types of markers in defining patterns of genetic structuring, introgressive hybridization and inferring population origins in the hybrid zone of the St. John River basin. A second objective was to test the hypothesis that secondary contact between glacial lineages always resulted in the occurrence of sympatric dwarf and normal whitefish ecotypes. Fish were sampled from 35 populations and polymorphism was screened at mtDNA and six microsatellite loci for a total of 688 and 763 whitefish, respectively. Four lakes harbouring a single whitefish population of normal ecotype admixed with mtDNA haplotypes of different lineages were found. This confirmed that secondary contact between whitefish evolutionary lineages did not always result in the persistence of reproductively isolated ecotypes. Microsatellites further supported the definition of distinct glacial lineages by identifying lineage-specific allelic size groups. They also further supported the hypothesis that ecotypes originated from either a single founding lineage (sympatric divergence) or following secondary contacts between lineages (allopatric divergence), depending on the lake. In general, however, the pattern of population differentiation and introgressive hybridization observed at microsatellites was in sharp contrast with that depicted by mtDNA variation. Both factorial correspondence analysis and analysis of admixture proportion revealed a much more pronounced pattern of introgressive hybridization than depicted by mtDNA analyses. Variable levels of introgression indicated that environmental differences may be as important as the historical contingency of secondary contact in explaining the persistence of sympatric ecotypes and the differential pattern of introgressive hybridization among lakes. Whitefish populations from the St. John River basin hybrid zone represent a rare illustration of a continuum of both morphological and genetic differentiation within a given taxon, spanning from complete introgression to possibly complete reproductive isolation, depending on lakes. Thus, each lake may be viewed as a different temporal snapshot taken throughout the gradual process of speciation.

Seasonal and daily vertical activity of lake whitefish Coregonus clupeaformis was studied in Clear Lake, Maine (253 ha), using acoustic telemetry from November 2004 to June 2009. Twenty adult lake whitefish were tagged with acoustic tags that had either a depth sensor or both depth and temperature sensors to assess vertical habitat use at a seasonal and daily resolution. Vertical habitat selection varied seasonally and was strongly influenced by temperature. Between December and April, when the lake was covered with ice, surface temperature was below 2°C and tagged individuals occupied deep areas of the lake (∼15 m). After ice‐out, fish ascended into shallow waters (∼5 m), responding to increased water temperature and possibly to greater foraging opportunity. When surface water temperatures exceeded 20°C, fish descended below the developing thermocline (∼9 m), where they remained until surface temperatures fell below 20°C; fish then ascended into shallower depths, presumably for feeding and spawning. Through the winter, fish remained in thermal habitats that were warmer than the surface temperatures; in the summer, they selected depths with thermal habitats below 15°C. Though the amplitude varied greatly across seasons, lake whitefish displayed a strong diurnal pattern of activity as measured by vertical velocities. Fish were twofold more active during spring, summer, and fall than during winter. Lake whitefish exhibited diel vertical migrations, rising in the water column during nighttime and occupying deeper waters during the day. This pattern was more pronounced in the spring and fall and far less prominent during winter and summer. The strong linkage between temperature and habitat use may limit the current range of lake whitefish and may be directly impacted by climatic change.