Ruzzante, Daniel E.
Permanent URI for this collectionhttps://hdl.handle.net/10222/22314
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Item Open Access Daniel E. Ruzzante CV(2013-08-29) Ruzzante, Daniel EItem Open Access Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish(2013-04) Bradbury, Ian R.; Hubert, Sophie; Higgins, Brent; Bowman, Sharen; Borza, Tudor; Paterson, Ian G.; Snelgrove, Paul V. R.; Morris, Corey J.; Gregory, Robert S.; Hardie, David; Hutchings, Jeffrey A.; Ruzzante, Daniel Eduardo; Taggart, Christopher T.; Bentzen, PaulAs populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.Item Open Access Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence of fisheries-induced selection?(2011-07) Jakobsdottir, Klara B.; Pardoe, Heidi; Magnusson, Arni; Bjornsson, Hoskuldur; Pampoulie, Christophe; Ruzzante, Daniel Eduardo; Marteinsdottir, GuorunThe intense fishing mortality imposed on Atlantic cod in Icelandic waters during recent decades has resulted in marked changes in stock abundance, as well as in age and size composition. Using a molecular marker known to be under selection (Pan I) along with a suite of six neutral microsatellite loci, we analysed an archived data set and revealed evidence of distinct temporal changes in the frequencies of genotypes at the Pan I locus among spawning Icelandic cod, collected between 1948 and 2002, a period characterized by high fishing pressure. Concurrently, temporal stability in the composition of the microsatellite loci was established within the same data set. The frequency of the Pan I BB genotype decreased over a period of six decades, concomitant with considerable spatial and technical changes in fishing effort that resulted in the disappearance of older individuals from the fishable stock. Consequently, these changes have likely led to a change in the genotype frequencies at this locus in the spawning stock of Icelandic cod. The study highlights the value of molecular genetic approaches that combine functional and neutral markers examined in the same set of individuals for investigations of the selective effects of harvesting and reiterates the need for an evolutionary dimension to fisheries management.Item Open Access Contemporary effective population and metapopulation size (Ne and meta-Ne): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries(2013-03) Gomez-Uchida, Daniel; Palstra, Friso P.; Knight, Thomas W.; Ruzzante, Daniel EduardoWe estimated local and metapopulation effective sizes ((N) over cap (e) and meta-(N) over cap (e)) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that (N) over cap (e) might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in (N) over cap (e) ((N) over cap eOSMP) between species, consistent with a hierarchy of adult population sizes ((N) over cap S-e.salarS-e.fontinalisS-e.fontinalisS-e.alpinus). Using another method based on a measure of linkage disequilibrium (LDNE: (N) over cap eLDNE), we found more finite (N) over cap (e) values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest (N) over cap (e) among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in (N) over cap (e), suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-(N) over cap (e) might be significantly smaller than the sum of local (N) over cap (e)s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One bottom-up' or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-(N) over cap (e) estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local (N) over cap (e)s and meta-(N) over cap (e)s and their relevance in ecology, evolution and conservation.