Population structure of CFM in the Canadian Prairies
We found little overall geographic structuring related to either canola
production or soil zone in the 16 populations included in this study,
although nuclear SNP analyses recovered substantially more population
structure than COI haplotype analysis (Fig. 1). Both PCA and
Structure analyses using SNPs recovered only four markedly divergent
populations (Swan River and Portage la Prairie in Manitoba, and
Athabasca and Sangudo in Alberta), located near the edges of canola
production in those regions (Fig. 1, Fig. 2). While this may be
indicative of an edge effect (sensu Cook 1961), other populations were
also sampled near the edges of canola production but were not
genetically distinct. The Portage la Prairie population is a possible
exception to this, as these individuals were sampled from a research
farm (Canada-Manitoba Crop Diversification Centre) located in the city
of Portage la Prairie, and as a result may have reduced opportunities
for gene flow with other CFM populations located on more rural farmland.
The remaining 12 central populations formed a large genetic cluster
spanning eastern Alberta, Saskatchewan, and western Manitoba. Within
this central cluster, Structure analysis indicated two distinct sources
of genetic ancestry that were not clearly related to sampling geography
(Fig. 1, Fig. 2D), and which was particularly pronounced in the Fairy
Glen and Preeceville populations. Pairwise FSTwas also low between these central populations (Table 1), and IBD
analysis was non-significant (Fig. 3C) suggesting few geographic
barriers to gene flow. This is consistent with the homogenous landscape
throughout much of the Canadian Prairies, and the high level of
contemporary canola inventory in the sampling region of this study (Fig.
1A).
COI haplotype diversity was relatively low overall, and the four
divergent populations in the SNP-based analyses were not distinct forCOI . These results are consistent with contemporary, widespread
gene flow facilitated by large-scale canola production in the Canadian
Prairies. It is possible that differences in recovered population
structure between SNPs and COI are due to temporal differences in
habitat connectivity resulting from year-over-year changes in canola
inventory, and/or changes in effective population sizes of CFM due to
regional and temporal differences in insecticide use. The COIgene represents only a single haploid marker, and if our sampling
coincided with a period of greater effective population size and
connectivity, we may expect to have less population structure in one or
a few markers compared to thousands of diploid nuclear SNPs (Dussexet al. 2016; Liu et al. 2019). Data for historical
year-over-year canola inventory production numbers or insecticide spray
records are unavailable over this broad geographic range, so we cannot
test this hypothesis.