Genetic Stock Identification
Genetic stock identification through microsatellite or SNP markers is a useful technique for assigning stock of origin to unknown origin individuals. This has proven to be a highly useful method, for example in fisheries management to avoid stocks of conservation concern in catches, as well as for conservation biology to understand what the at-sea behaviour and distribution of different stocks are in order to determine what may be influencing population patterns. Complementary approaches, such as parentage-based tagging (PBT), whereby an individual is assigned to its parents, have proven to be effective for monitoring hatchery output in fisheries management. With improved genomic technology and information, more individuals can be characterized using these approaches. High-throughput amplicon panels are now being designed for non-model species for use in understanding population structure as well as mixed-stock applications, for example eulachon (Sutherland et al. 2020).
Genomic and chromosomal context is valuable in interpreting many aspects of genetics, including genome-wide association studies, population genetics, and gene expression. Salmonids underwent an ancestral whole genome duplication, but now have mostly returned to a diploid state with some residual tetraploidy. Working in the lab of Louis Bernatchez with Céline Audet, we developed a high-density genetic map for Brook Charr Salvelinus fontinalis and integrated this map with all other salmonids, providing insight in the large-scale chromosome rearrangements throughout the rediploidization process (Sutherland et al. 2016). This enabled investigation into the changing sex chromosomes in the salmonids (Sutherland et al. 2017). We then characterized gene co-expression networks within Brook Charr to better understand gene regulatory architecture differences between the sexes (Sutherland et al. 2018).
Oyster Genomics and Population Health
Working in the lab of Kristi Miller (Pacific Biological Station, DFO-MPO) and Curtis Suttle (UBC) I am part of a collaboration funded by the Moore Foundation and Hakai to investigate the factors involved with oyster mortality events in the Pacific Northwest. We hope to advance this field by looking into the genetic factors associated with life on a farm, identifying microbes and genetic signatures associated with large-scale die-offs, and exploring the genetic differences that can be identified throughout the range of Pacific Oysters throughout coastal British Columbia.
Environmental DNA (eDNA) and Fisheries
eDNA is a promising new tool for characterizing biodiversity, disturbances, species range changes, or introductions of invasive species. Although metabarcoding (i.e. sequence-based eDNA evaluation) remains only semi-quantitative, there are some interesting new directions to push this technique into a more quantitative state. With the ease of use and the power that outpaces traditional methods, this technique holds great potential. Within Fisheries and Oceans Canada and CanadaC3, we are analyzing samples taken from all three coasts of Canada (see Vancouver Sun article).
Transcriptomics provides an integrative view of the response of an organism to its biotic and abiotic environment. Working in the lab of Prof. Ben Koop I applied this approach to the question of salmon and infective agents such as sea lice or viruses. In collaboration with Simon Jones (DFO), we have demonstrated species- and life stage-specific variation in sea lice infection rates and host responses to infection (Sutherland et al. 2011; Sutherland et al. 2014). Applying these approaches, we have also investigated the louse responses to Pacific and Atlantic salmonids, highlighting the possibility of co-evolution resulting in different infection dynamics in the responses of lice to different species of hosts (Braden, Sutherland et al., 2017). Transcriptomics work has also indicated energetic trade-offs in responses, for example the suppression of the innate immune system during smoltification (Sutherland et al. 2014), or during responses of sea lice to different levels of abiotic stress (Sutherland et al., 2012). Sea lice transcriptomics has also been used to investigate the differences in sexual dimorphism in lice (Poley et al. 2016), different expression patterns associated with antiparasiticide drug resistance (Sutherland et al. 2015) and sea lice responses to a naturally occurring microsporidian parasite (Poley , Sutherland et al. 2017).
Method Development: MapComp
Presentation from Coastwide Salmonid Genetics Meeting (2018)
Method Development: GO Trimming
© Ben J G Sutherland 2018 All rights reserved