In the study of
Species-at-Risk,
the degree to which the loss or
decline of local populations affects others
and threatens species extinction depends critically on the spatial
scale of population differentiation and gene flow.
Phylogeographic analysis of mitochondrial DNA sequences
can provide extremely detailed information on the fine-scale population
structure of species, which can inform decisions about the biological independence of "
Designatable Units" in species that are considered
Endangered,
Threatened or of
Special Concern by
COSEWIC under
SARA.
Single-locus studies may of
mtDNA often lack sufficient detail, and analysis of
complete mtDNA genomes by conventional
methods remains laborious. The use of
microarray "DNA chips" for
"DNA re-sequencing" of new individuals with respect to a reference sequence allows generation of
complete individual mtDNA sequences in a single experiment. Experiments with a first-generation
30Kbp human mtDNA microchip show that the method is efficient, accurate, and cost effective.
We
propose to develop DNA re-sequencing technology as a practical method
for assessing the genetic structure of DFO fisheries species and SARA
Species-at-Risk. As a "
proof of principle" experiment, we will design a
DNA microchip for the
Atlantic cod mtDNA genome, and use it to extend our genomics study of the
stock structure and
phylogeography of Atlantic Cod.
A second-generation,
multi-species "ArkChip" will include
up to 300,000bp on a single chip that accommodates
up to 20 species' mtDNA genomes. Use of the extensive database of
reference mtDNA genomes (n > 400) allows experiments to be standardized; available
nucDNA loci can be incorporated. Costs of each component project (
e.g.,
Wolffish) are reduced proportionately
. A breakthrough into high-throughput genomics would enable
cost-effective, co-ordinated investigation of
multiple species
of interest to Species-at-Risk agencies, managers, and
recovery teams.