As part of the research program of the Ecogenomics team, we are sequencing and analyzing whole genome sequences of caribou (Rangifer tarandus) to answer questions pertinent to the conservation of the species. So far, we have generated a chromosome scale reference genome and high-quality annotation with Dovetail Genomics, as well as both high coverage (~100) and low coverage (~350) re-sequenced genomes.
Here is an overview of the whole genome sequencing work completed thus far, also see the publications and resources pages for more information:
Assessment of phylogenomic and population structure
We use population and phylogenomic methods to reconstruct evolutionary history and genetic structuring, important for Designatable Unit (DU) decisions as well as understanding caribou intra specific diversity.
Historical effective population size reconstructions
We reconstruct historical Ne to help understand demographic history, responses to past climate changes, and the likelihood of having high genetic variation.
Measures of inbreeding in Runs of Homozygosity
We measure what proportion in the genome is in a Run of Homozygosity (ROH) which tells us how much of the genome is showing a signature of inbreeding, and whether there is any recent inbreeding occurring.
Measures of genetic diversity (heterozygosity)
We measure individual heterozygosity as a measure of how genetically diverse the caribou are, important for adaptive potential and resilience under environmental changes.
Genetic load estimates
We measure genetic load, for example measuring how many variant sites each caribou has which are putatively bad for fitness, to inform about the susceptibility to inbreeding depression upon population declines.
Gene flow (introgression) levels
Introgression is a measure of how much variation is retained in a genome over generations after gene flow has occurred from a different population and can inform about historical connectivity.
Adaptive variation
We measure adaptive variation, including finding molecular pathways with signatures of selection unique to each caribou lineage, to inform about differential adaptive variation.
Genomic assemblies from non invasive samples
We are now successfully sequencing whole genomes from non invasively collected fecal samples, an important step towards the non invasive monitoring of caribou.
