ORIGINAL ARTICLE Joint inferences from cytoplasmic DNA and fossil data provide evidence for glacial vicariance and contrasted post-glacial dynamics in tamarack, a transcontinental conifer Emile Warren 1 , Guillaume de Lafontaine 1,a ,S ebastien G erardi 1 , Sauphie Senneville 1 , Jean Beaulieu 1,2 , Martin Perron 3 , Juan Pablo Jaramillo-Correa 4 and Jean Bousquet 1 * 1 Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute of Systems and Integrative Biology, Universit  e Laval, Quebec, QC, Canada G1V0A6, 2 Canadian Wood Fibre Centre, Natural Resources Canada, Quebec, QC, Canada G1V4C7, 3 Direction de la recherche foresti  ere, Minist  ere des For ^ ets, de la Faune et des Parcs du Qu ebec, Quebec, QC, Canada G1P3W8, 4 Departamento de Ecolog  ıa Evolutiva, Instituto de Ecolog  ıa, Universidad Nacional Aut onoma de M exico, Mexico City, Mexico *Correspondence: Jean Bousquet, Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute of Systems and Integrative Biology, 1030 Avenue de la M edecine, Universit  e Laval, Qu ebec, QC, Canada G1V0A6. E-mail: jean.bousquet@sbf.ulaval.ca a Present address: Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA. ABSTRACT Aim Tamarack (Larix laricina) is an early-successional transcontinental boreal conifer occurring within the spruce-fir dominated forest. The aim was to infer the species biogeographical history and to assess the putative genetic imprint left by interspecific competition during post-glacial migration, using cytoplas- mic DNA and fossil data. Location Forty-five locations were sampled across the transcontinental range spanning the North American boreal forest. Methods A total of 621 trees were scanned for mitochondrial and chloroplast DNA polymorphisms to reveal geographical patterns of genetic diversity, differ- entiation, and population structure throughout the species range. Published pollen records were analysed to assess the chronology of post-glacial coloniza- tion of Larix sp. relative to more competitive tree taxa, Picea sp. and Abies sp.. Results Genotyping resulted in two mitotypes (one locus) and 24 chlorotypes (three cpSSR loci). Bayesian assignment test based on cpDNA data detected three groups: eastern North America, western North America and Alaska. CpDNA population differentiation was higher in the western part of the range relative to the eastern part. Post-glacial colonization chronology derived from fossil data indicated that Larix colonized western North America at least 4000 years after Picea and Abies, but shortly preceded them in eastern North America. Main conclusions Cytoplasmic and fossil data provided support for four dis- tinct glacial lineages. Two lineages would have persisted south of the Lauren- tide ice sheet, while the two remaining ones likely originate from northern refugia located in Beringia and Labrador. Larix establishment was possibly hin- dered by earlier establishment of more competitive taxa in western North America, which resulted in high genetic differentiation among western popula- tions. These results provide support for a putative role of interspecific competi- tion in structuring the standing genetic variation at the time of post-glacial colonization. Keywords chloroplast DNA, conifers, genetic diversity, glacial refugia, interspecific com- petition, Larix laricina, microsatellites, mitochondrial DNA, phylogeography, pollen analysis, post-glacial colonization ª 2016 John Wiley & Sons Ltd http://wileyonlinelibrary.com/journal/jbi 1227 doi:10.1111/jbi.12675 Journal of Biogeography (J. Biogeogr.) (2016) 43, 1227–1241