Martha J. Robertson

Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re‐evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD‐seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans‐Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD‐seq based approaches for the resolution of complex spatial patterns, resolves a region of trans‐Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

Seasonal Effects of Suspended Sediment on the Behavior of Juvenile Atlantic Salmon

Abstract Short-term increases in suspended sediment levels significantly influenced the behavior of juvenile Atlantic salmon in both fall and winter trials. The initial introduction of sediment (20 mg/L, or ≈15 nephelometric turbidity units [NTU]) increased foraging activity, which subsequently declined at sediment levels greater than 180 mg/L (≈35 NTU). Cover use also declined as fish emerged to forage. No fish returned to cover at sediment levels greater than 60 mg/L (≈22 NTU) in the fall trials, whereas some fish in the winter trials never emerged from cover. A rapid decline in territorial behavior and an avoidance response (i.e., alarm reaction) at sediment levels ranging from 60 to 180 mg/L (≈22-42 NTU) were also noted in fall trials but not winter trials. Seasonal differences in the response of juvenile Atlantic salmon to suspended sediments may be explained by temperature-related changes in diel activity patterns.

Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next‐generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation‐based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

An Ecosystem Approach to Describe the Mercury Issue in Canada: From Mercury Sources to Human Health

It has been decades now since the international scientific community initially raised the issue of mercury (Hg) contamination in the global environment. The presence of Hg in ecosystems is ubiquitous, even in the absence of local/regional contamination point sources. Almost all fish consumers (occasional or frequent) are exposed to this contaminant. Governments of the industrialized countries have invested considerable financial and human resources, in order to better understand the biogeochemical behavior and cycling of Hg and its impacts on the health of populations. Indeed, our knowledge of the sources and fate of this pollutant has greatly evolved since these early reports. Numerous protocols, technical documents, epidemiological and clinical studies, detailing precise aspects of the Hg cycle have been published. However, given the complexity of environmental processes leading to the accumulation of Hg in fish tissue, and the relative importance of fish as a protein source among communities, most available literature fails to fully evaluate the level of risk to health (and/or the health benefits related to fish consumption) encountered by fish consumers in their daily lives. This paper summarizes the learning acquired through a wide-scale integrated study of the mercury (Hg) pathways in lake environments of three distinct regions located in Eastern Canada : Lake St. Pierre (LSP), Labrador (Lab), and Abitibi (Ab). This research was accomplished by a multidisciplinary team of researchers assembled under the auspice of the Collaborative Mercury Research Network (COMERN), a major Canadian initiative supported by numerous universities and government agencies throughout the country. The prime focus of the study was to link human exposure to Hg with particular local/regional environmental and socioeconomic characteristics and settings. Two conditions must co-occur to define a situation where higher Hg exposure can be identified for populations/sub-populations/ groups : Frequent fish consumption;Mercury levels of concern in the edible fish resource.

Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America

Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon‐based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine‐learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate‐associated, fine‐scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.

Whole body‐element composition of Atlantic salmon Salmo salar influenced by migration direction and life stage in three distinct populations

Body-element content was measured for three life stages of wild Atlantic salmon Salmo salar from three distinct Newfoundland populations as individuals crossed between freshwater and marine ecosystems. Life stage explained most of the variation in observed body-element concentration whereas river of capture explained very little variation. Element composition of downstream migrating post-spawn adults (i.e. kelts) and juvenile smolts were similar and the composition of these two life stages strongly differed from adults migrating upstream to spawn. Low variation within life stages and across populations suggests that S. salar may exert rheostatic control of their body-element composition. Additionally, observed differences in trace element concentration between adults and other life stages were probably driven by the high carbon concentration in adults because abundant elements, such as carbon, can strongly influence the observed concentrations of less abundant elements. Thus, understanding variation among individuals in trace elements composition requires the measurement of more abundant elements. Changes in element concentration with ontogeny have important consequences the role of fishes in ecosystem nutrient cycling and should receive further attention.