GENERAL RESEARCH THEME

The majority of the research projects conducted in our laboratory are integrated into the research program of the Chaire de Recherche du Canada in Genomics and Conservation of Aquatic Resources. However, many projects are also part of research programs of internationally renowned research centers, namely Québec-Océan (Groupe interinstitutionnel de recherches océanographiques du Québec), Réseau Aquaculture Québec (RAQ) and CIRSA (Centre Interuniversitaire de Recherche sur le Saumon Atlantique). Furthermore, we collaborate with numerous partners of various other projects, such as the study of genetic population structure in the Caribou, Census size estimation in black bears or the determinants of dispersion patterns in the wandering albatross.

The Canadian Research Chair in conservation genetics of aquatic organisms aims to accomplish three general objectives. The first objective is to acquire fundamental knowledge on evolutionary processes responsible for generating and maintaining genetic diversity within and among populations. This will in turn stimulate the long term economic viability and social value of aquatic species in three complementary domains of activity : recreational and commercial exploitation (fisheries), biodiversity conservation, and aquaculture. The second general objective is to foster the training of highly qualified biologists, researchers, and research professionals in areas of high priority for Canada, namely evolutionary genomics and molecular ecology. A third objective is to increase the public awareness of the usefulness university research regarding the improvement of management and conservation practices of natural populations.

The most distinctive character of our research projects lies in the integrative approach that combines the fields of quantitative and functional genomics, population genetics, bioinformatics, and ecology. The integrative nature of these projects is also reflected by the diversity of their topics. For instance, the current issues surrounding fisheries, aquaculture and biodiversity conservation are generally considered distinct with few common links between them. Such a view has most often been a source of conflict among the people that work or research these areas. In contrast, the view that we are promoting through the research chair program lies on the assumption that these three sectors are facing a common problem, which is the genetic erosion of genetic diversity, as well as incomplete knowledge of the fundamental processes that generate and maintain genetic diversity.

OVERVIEW OF ONGOING RESEARCH PROJECTS

Our ongoing research projects can be grouped into five research areas. A summary of each specific project as well as names of collaborators are presented in the « People » section.

The first reasearch area focuses on the comprehension of genotype-environment interactions, particularly in cases of reproductively isolated populations that have diverged to exploit distinct ecological resources. We employ a multidisciplinary approach, using population and quantitative genetics, genetic mapping, functional genomics, behavioural ecology, and physiology. Our principal study systems include lacustrine fish populations (whitefish, genus Coregonus, Salmonidae) that have recently diverged and vary with respect to their level of reproductive isolation in relation to their level of specialization towards distinct ecological niches. Within this research framework, four specific objectives are currently being investigated:

(i) Elucidate the genetic architecture of reproductive isolation and adaptive phenotypic variation between sympatric forms using a linkage mapping and the analysis of transcription profiles of genes by microarrays.

(ii) Test the hypothesis that observed patterns of introgressive hybridization in natural hybrid zones are determined by the intensity of natural selection acting on quantitative trait loci (QTL) and transcription levels of genes responsible for phenotypic differentiation and reproductive isolation.

(iii) Test the hypothesis that the adaptive divergence and reproductive isolation between whitefish ecotypes involve differences in gene structure and regulation that are adapted to distinct life history and have been shpaed by natural selection.

(iv) By combining detailed limnological investigations employing isotopic methods - test the hypothesis that biomass availability within trophic niches is correlated to energy conversion efficiency and ultimately phenotypic specialization and reproductive isolation between genetically distinct whitefish ecotypes.

A second general research area actively investigated in our laboratory is to examine the respective roles of ecologic and genetic factors implicated in the reproductive success of natural fish populations. Specifically, by comparing the reproductive success of fish populations that have adapted unique life-history strategies, the hypothesis that natural selection maintains these adaptive polymorphisms can be tested (e.g. resident versus
anadromous fish, variable time spent at sea by anadromous fish, sneaking versus territorial males). These objectives are being met through the use of hypervariable molecular markers that allow i) accurate deductions of parental assignment between parents and offspring, ii) calculation of heritability estimates for phenotypic traits associated with fitness under natural conditions. Some of the species employed under this framework are the Atlantic salmon (Salmo salar), brook charr (Salvelinus fontinalis), brown trout (Salmo trutta) and three-spined stickleback (Gasterosteus aculeatus)
.

A third objective being pursued is to comprehend the respective roles and impact of historical, contemporary and even anthropogenic factors (such as exploitation, stocking, translocation, domestication and habitat disturbances) on the genetic structure of animal populations, as well as the genetic basis of local adaptation. We employ genetic markers (mitochondrial DNA, microsatellites, AFLP -Amplified Fragment Length Polymorphisms, SNP - Single Nucleotide Polymorphisms, and functional enzymatic loci : allozymes and MHC – major histocompatibility complexes) for testing fine-scale analyses of genetic diversity. We are also using microarrays to document differential transcription profiles within and among recently diverged populations, for instance between domesticated and wild salmonids.

Fourthly, in collaboration with other researchers that are members of the Réseau Aquaculture Québec, we are pursuing a research program aiming at developing innovative practices for improving freshwater fish production. Overall, this research aims to improve the genetic, physiological, nutritional, health, environmental technologies, economical and legal bases of fish production using the brook charr. . This research is also integrated into the research program of Aquanet, Canada’s Research network in Aquaculture. Our specific objectives are :

i) estimating the genetic variance and covariance of important phenotypic traits in aquaculture, as well as the role of environmental variance on the expression of these traits.

ii) the development of genetic maps (including QTL detection) for the brook charr, using AFLP and microsatellite markers.

iii) a functional genomics assessment of the associaiton between growth performance and differential gene expression as a function of environmental variance using microarray technology.

iv) documenting the physiological and funtional genomic bases of heterosis (hybrid vigour) and exploit this phenomenon for improving brook charr produciton.

v) estimating the extent of genetic contamination and phenotypic changes caused by stocking and associate variation in those parameters with the stoking history and environmental heterogeneity.

A fifth research objective is to contribute to the Canadian Barcode of Life Network initiative which aims at applying the concept of genetic barcode with the goal of accelerating the pace of biodiversity surveys and to allow anyone to identify any organisms without ambiguity. The ultmate goal is to develop within the next 20 years a DNA barcode for all eukaryotes found in Canada. We are contributing to this effort first by developing DNA barcodes for al 200 freshwater fishes found in Canada. This project is also part of the Fish-Bol initiative, which is a global effort to coordinate an assembly of a standardised reference sequence library for all fish species. The project is also ntegrated within the Barcoding of life international consortium that aims at promoting the development of molecular tools for identifying and monitoring all living species worldwide.