Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/

Background: To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.).

The integration of functional traits into vulnerability assessments is a promising approach to quantitatively capture differences in species sensitivity and adaptive capacity to climate change, allowing the refinement of tree species distribution models. In response to a clear need to identify traits that are responsive to climate change and applicable in amanagement context, we review the state of knowledge of the main mechanisms, and their associated traits, that underpin the ability of boreal and temperate tree species to persist and (or) shift their distribution in a changing climate. We aimed to determine whether current knowledge is sufficiently mature and available to be used effectively in vulnerability assessments. Marshalling recent conceptual advances and assessing data availability, our ultimate objective is to guide modellers and practitioners in finding and selecting sets of traits that can be used to capture differences in species’ ability to persist and migrate. While the physiological mechanisms that determine sensitivity to climate change are relatively well understood (e.g., drought-induced cavitation),manyassociated traits have not been systematically documented for North American trees and differences in methodology preclude their widespread integration into vulnerability assessments (e.g., xylem recovery capacity). In contrast, traits traditionally associated with the ability to migrate and withstand fire are generally well documented, but new key traits are emerging in the context of climate change that have not been as well characterized (e.g., age of optimum seed production). More generally, lack of knowledge surrounding the extent and patterns in intraspecific trait variation, as well as co-variation and interaction among traits, limit our ability to use this approach to assess tree adaptive capacity.We conclude by outlining research needs and potential strategies for the development of trait-based knowledge applicable in large-scale modelling efforts, sketching out important aspects of trait data organization that should be part of a coordinated effort by the forest science community