Effects of exposure to culture in fishes: the existence of common morphological responses among species, and their impact on the interaction between escapee and wild Atlantic cod (Gadus morhua)

A major concern regarding the impact of aquaculture is the alteration or reduction of the fitness of wild stocks through interbreeding with escapees. Cultured fishes develop morphologies and behaviours different than those of their wild counterparts, and the spawning success and fitness of cultured fish is frequently lower. However, successful interbreeding between wild and cultured fish is well documented and can lead to negative consequences for the wild population. In this thesis I examined how culture affects the phenotypes of fishes, and how these differences in phenotype in turn relate to reproductive success and offspring early growth and survival. I found that cultured Atlantic cod (Gadus morhua) had relatively smaller fins, heads, eyes, and jaws, but greater condition factor and body depth than wild cod from the same ancestral population. This suite of morphological differences is often referred to as the “cultured phenotype”, and while commonly asserted to exist I was the first to formally test for it using a meta-analysis and a vote-counting analysis. These analyses confirmed that aspects of a general “cultured phenotype” exist. To evaluate the influence of morphology and behaviour on male spawning success, I studied the reproductive interactions of individual cultured and wild male cod in the presence of a cultured female. Despite phenotypic differences, the spawning success of cultured males did not differ from that of wild males. Finally, because the introgression of genetically differentiated escapees into wild populations can lead to fitness declines, I tested the effect of hybridization between two genetically distinct populations of cod. I found no evidence that the pure strain and F1 hybrids differed in their relative fitness, or of differential response to temperature. Finding equal reproductive success of cultured and wild male cod, at least in my experimental conditions, and no differences in early life history fitness between F1 hybrids and non-hybrids suggests that the potential for introgression may be higher than has been predicted by previous studies

Application of Omics Tools in Designing and Monitoring Marine Protected Areas for a Sustainable Blue Economy

FUNDING This work was supported by funding provided to the Marine Conservation Targets Program with Fisheries and Oceans Canada. ACKNOWLEDGMENTS The authors thank Geneviève Faille (DFO Québec) and Kristen Westfall (DFO Pacific) for their helpful review of this article. We also thank the two reviewers for their helpful comments in improving the drafts of this manuscript.Peer reviewedPublisher PD

Temporal dynamics of genetic clines of invasive European green crab (Carcinus maenas) in eastern North America

Evolutionary Applications published by John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Fisheries and Oceans Canada. Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We evaluated current clinal structure by quantifying the distribution of lineages and fine-scale hybridization patterns across the eastern North American range (25 locations, ~39 to 49°N) using informative single nucleotide polymorphisms (SNPs; n = 96). In addition, temporal changes in the genetic clines were evaluated using mitochondrial DNA and microsatellite loci (n = 9–11) over a 15-year period (2000–2015). Clinal structure was consistent with prior work demonstrating the existence of both northern and southern lineages with a hybrid zone occurring between southern New Brunswick (NB) and southern NS. Extensive later generation hybrids were detected in this region and in southeastern Newfoundland. Temporal genetic analysis confirmed the southward progression of clines over time; however, the rate of this progression was slower than predicted by forecasting models, and current clines for all marker types deviated significantly from these predictions. Our results suggest that neutral and selective processes contribute to cline dynamics, and ultimately, highlight how selection, hybridization, and dispersal can collectively influence invasion success

Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Abstract Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at‐risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed “designatable units”; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to “big data” is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non‐model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in‐depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit

Development and evaluation of SNP panels for the detection of hybridization between wild and escaped Atlantic salmon (Salmo salar) in the West Atlantic

Hybridization between wild and escaped cultured Atlantic salmon (Salmo salar) can threaten the stability and persistence of locally adapted wild populations. Here we describe the development and validation of a genomic-based approach to quantify recent hybridization between escapee and wild salmon in the Western Atlantic. Based on genome-wide single nucleotide polymorphism (SNP) scans of wild and cultured salmon, collectively diagnostic panels were created for Newfoundland and the Canadian Maritimes. These panels were capable of both discriminating hybrids from non-hybrids, and of correctly assigning individuals to hybrid class (i.e. pure wild, pure farm, F1, F2 and backcrosses) with a high degree of accuracy (Newfoundland 96 SNPs >90%, Maritimes 720 SNPs >80%). These genomic panels permit the assessment of the impacts of past and future farmed salmon escape events on wild populations, and can inform the protection and conservation of wild Atlantic salmon genetic integrity in the western Atlantic.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Predicting the impacts of escaped farmed Atlantic Salmon on wild salmon populations

The escape of Atlantic Salmon (Salmo salar) from aquaculture facilities can result in both negative genetic and ecological interactions with wild populations, yet the ability to predict the associated risk to wild populations has remained elusive. Here we assess the potential of a spatiotemporal database of aquaculture facility locations, production estimates and escape events to predict the distribution of escaped farmed salmon and genetic impacts on wild populations in the Northwest Atlantic. Industry production data, reported escape events, and in-river detections of escaped farmed salmon were collected from across the Northwest Atlantic. Genetic estimates of impact were obtained using single nucleotide polymorphisms (95 loci) representing aquaculture and wild salmon throughout the region (30 populations, 3048 individuals). Both the number of escaped farmed salmon detected at counting facilities and the magnitude of genetic impacts were positively correlated with a cumulative spatial measure of aquaculture production. Our results suggest that the risk of escapees and genetic introgression from wild-farmed salmon interactions can be assessed using information on farm production characteristics. This represents a first step in predicting the impact of existing cage-based farms on wild Atlantic salmon.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

FinalMicrosat_Renamed_Genepop_ForSim_S1R1_NH

NewHybrids file of simulated individuals for power analyses using microsatellite dat

green_crab_RAD_Filtered

Genepop file of RAD-seq derived loci after filtering for missing data and individuals with low coverage

Simulated_RAD_Data_ForNewHybrids

Simulated Pure 1, Pure 2, F1, F2, and BC1 and BC2 individuals using the top 200 high Fst low linkage disequilibrium loci for testing power of the SNP panel