Marie Clément

Nest site selection and spawning by captive bred Atlantic salmon, Salmo salar, in a natural stream

SynopsisWe examined the physical habitat of nest sites chosen by hatchery Atlantic salmon, Salmo salar, in a recovery program for this extirpated species in Lake Ontario, Canada. We compared the sites used by these captive bred fish to a set of random locations in a wide range of available habitats. Compared to random locations in the stream, the nest sites chosen were lower in the relative abundance of sediment size classes that are detrimental to embryo and juvenile survival. In addition, the process of nest construction by these captive bred fish further reduced the proportions of these detrimental sediments. Although captive breeding may have changed some aspects of the nest site selection and construction behaviour, it has not caused a complete loss or major alteration of the trait and thus does not preclude hatchery fish from restoration or reintroduction programs.

Physical Injuries in Juvenile Atlantic Salmon, Slimy Sculpin, and Blacknose Dace Attributable to Electrofishing

Abstract Juvenile Atlantic salmon Salmo salar captured by electrofishing were X-rayed and dissected to determine rates of electrofishing-induced spinal injuries and hemorrhages. This study showed a low incidence of spinal injuries (11%) in electrofished wild parr captured alive and thereafter sacrificed. A negligible hemorrhage rate (2%) was observed. All of the spinal injuries observed were rated class 1 (minor injury), except for a class 2 injury in one parr. Larger, older wild parr (≥age 2) showed a higher incidence of spinal injuries (17%) than age-1 parr (4%). Parr captured with two or more electrofishing sweeps had a spinal injury rate of 20%, compared with 6% when captured with a single electrofishing sweep. Among the mortalities, 8% of the parr had spinal injuries (class 1 except for one class 3) and 5% had hemorrhages. Spinal injury was observed in 6% of the mortalities of slimy sculpin Cottus cognatus and blacknose dace Rhinichthys atratulus; no hemorrhages were observed in these fish. This stud...

An Evaluation of Mitigation Measures to Reduce Impacts of Peat Harvesting on the Aquatic Habitat of the East Branch Portage River, New Brunswick, Canada

The evaluation of impacts of peat harvesting on riverine ecosystems is essential to the implementation of adequate mitigation measures. The objective of the present study was to determine the potential impacts of peat harvesting on the physical (e.g., flow, suspended sediment concentration (SSC), water temperature) and biological (fish abundance) parameters of the East Branch Portage River, New Brunswick. This study was initiated in 2005 and a before and after study design was used to assess impacts. When the operational activities were initiated (spring 2007), 19 ha of peatland (15% of the total area scheduled for harvesting) was drained. The exploited area was drained through a network of ditches which emptied into a sedimentation pond. Drained water subsequently flowed into a 250 m vegetated buffer zone and discharged into the East Branch Portage River. Drained water did not diffuse throughout the buffer zone as expected. Rather, water tended to concentrate in a natural depression (channel) in the buffer zone, thus connecting the outflow of the sedimentation pond directly to the river. Two main results deserve attention. First, elevated SSC events were recorded in the East Branch Portage River downstream of the confluence of the channel formed in the buffer zone and the river. Periods of elevated SSC could be attributed to poor maintenance of the sedimentation pond. However, elevated SSC events were also recorded after pond maintenance and were concurrent with the timing of ditching activities within the peatland. Secondly, fish abundance was lower in 2007 compared to 2006 (pre-development period). However, potential impacts of peatland development on fish abundance should be interpreted with caution at this stage of the study.

Applications of random forest feature selection for fine‐scale genetic population assignment

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than FST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using FST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

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.

Range-wide parallel climate-associated genomic clines in Atlantic salmon

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences. Here, we investigate genomic consequences of glacial isolation and transAtlantic secondary contact using a 220K single nucleotide polymorphism (SNP) array genotyped in 80 North American and European populations. Throughout North America, we identified large inter-individual variation and discrete linkage blocks within and between chromosomes with known rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population diversity suggesting a derived chromosome fusion polymorphism within North America. Evidence of selection on both regions suggests adaptive variation associated with karyotypes. Our study highlights how Pleistocene glaciations can drive large-scale intraspecific variation in genomic architecture of northern species.

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.

Facilitating local analysis in northern regions: microwave plasma-atomic emission spectrometry for mercury determination in wild Atlantic salmon

ABSTRACT An analytical procedure was developed to quantify mercury concentration in wild Atlantic salmon (Salmo salar) muscle tissue by cold-vapour microwave plasma-atomic emission spectrometry (CV-MP-AES) with microwave-assisted acid digestion. Muscle samples were collected from the Atlantic salmon Food, Social, and Ceremonial fisheries in Lake Melville, Labrador (Canada). Muscle samples were digested with nitric acid and hydrogen peroxide, mercury was stabilised with thiourea, reduced with NaBH4, and quantified by CV-MP-AES. Analysis of fish protein certified reference material (CRM, DORM-3) by CV-MP-AES was used to assess the accuracy and precision of the procedure. CRM recovery averaged 88% with a relative standard deviation of less than 8%. The limits of detection were as low as 0.22 µg∙L−1 in solution which translate to 0.02 µg·g−1. Mercury concentrations in salmon muscle tissue quantified by CV-MP-AES were not significantly different from results obtained by cold vapour-atomic fluorescence spectrometry (CV-AFS) from an accredited laboratory. Our results indicated that the CV-MP-AES procedure is appropriate for the quantification of mercury at background levels (range 0.15–0.29 µg∙g−1 dry weight) in wild fish of Labrador.

Salmonid spawning habitat and remediation: where are we now, where do we go from here?

Concerns regarding the impacts of habitat degradation on salmon populations have resulted in the design and implementation of several remediation programs worldwide. Commonly cited deficiencies of these programs include the small-scale design and vague or undefined objectives. Moreover, the physical processes and biological responses to numerous remediation actions are often inadequately or not monitored at all (Bernhardt et al. 2005). The application of a multidisciplinary approach represents an additional challenge to the elaboration of efficient remediation measures (Benda et al. 2002). To address these issues, the American Fisheries Society (AFS) organized in 2003 an international symposium on salmonid spawning habitat processes and remediation in Quebec City (Canada). This event brought together managers and scientists from diverse disciplines. This resulted in the publication of a volume (edited by Sear & DeVries) in which 16 papers are presented. The main goal of this volume is to provide an overview of the current knowledge and key gaps in the overall understanding of processes governing salmonid spawning habitat in relation to habitat remediation. The authors have, in my opinion, presented a comprehensive coverage of the subject. With the increasing popularity of habitat remediation actions, this volume provides a muchneeded reference source that describes the current concerns related to habitat remediation and provides guidance for future research required to support managerial decisions. These papers, further highlight the importance of an effective dialogue between biologists, geomorphologists, hydrologists, engineers and managers to properly address spawning habitat remediation issues. The introductory paper efficiently sets the tone for the entire volume. As such, it provides a clear, concise and easy-to-understand conceptual framework to summarize the diverse biological and physical parameters influencing salmonid spawning habitat and reproductive success. The 16 contributions are grouped into 3 main sections: 1) biological processes, 2) physical processes and 3) spawning habitat remediation. The complexity of spawning habitat processes and remediation is well identified. This complexity is principally attributable to a series of interactions between and within biological and physical parameters which occur at several temporal and spatial scales. It is apparent from this book that the applied discipline of habitat remediation, while under legislative, political and financial pressures, is wide open for innovative research. Environ Biol Fish (2010) 87:291–293 DOI 10.1007/s10641-010-9589-x