Browsing by Author "Pavey, Scott A."
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Item An Assessment of Inner Bay of Fundy Atlantic Salmon (Salmo salar) Spawning Success in Fundy National Park(University of New Brunswick, 2023-04) Nason, Jack S. J.; Samways, Kurt M.; Pavey, Scott A.Atlantic salmon (Salmo salar) have declined precipitously throughout most of their North American range. As a result, many strategies have been implemented to try and restore Atlantic salmon (Salmo salar). One such restoration strategy, implemented by the Fundy Salmon Recovery project, involves the collection of endangered inner Bay of Fundy salmon smolts from their natal rivers to be reared at the world’s first marine conservation farm to maturity. This strategy includes both an open net ocean pen and freshwater hatchery components. Upon maturity, these salmon are returned to their natal rivers as adults. This release may be done by hand, by carrying the sexually mature salmon to the water or by carefully lowering them into pools using a helicopter, so they can naturally spawn. In my study, I aim to determine whether these differences in rearing and release strategies led to significant changes in offspring production in the adults of two Fundy National Park rivers. Single nucleotide polymorphisms (SNPs) at 185 loci were used to match parents with the next year’s offspring using Colony, a parentage analysis software. Using a fixed effects linear model, I found that there was no significant effect on offspring production caused by release strategy in both rivers. On the Point Wolfe River, rearing strategy was found to have a significant effect on offspring production – with marine-reared adults out-performing freshwater reared adults. This suggests that the marine-rearing strategy, implemented by the Fundy Salmon Recovery project can outperform, in some cases the more traditional freshwater rearing strategy in terms of releasing high-fitness adult Atlantic salmon.Item Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean(Nature Research, 2021-10-20) Andrews, Adam J.; Puncher, Gregory N.; Bernal‑Casasola, Darío; Di Natale, Antonio; Massari, Francesco; Onar, Vedat; Toker, Nezir Yaşar; Hanke, Alex; Pavey, Scott A.; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Cilli, Elisabetta; Morales‑Muñiz, Arturo; Mantovani, Barbara; Tinti, Fausto; Cariani, AlessiaAtlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.Item Changes in gene expression and physiology following heat stress in migratory fishes(University of New Brunswick, 2023-07) Penny, Faith; Pavey, Scott A.As ectothermic animals, the effects of temperature are evident across nearly all levels of fish biology, from behaviour through to gene expression. Wide-ranging, migratory fishes are generally well adapted to changing environmental temperatures, yet the mechanisms underlying this tolerance to change may vary among or even within species. The Striped Bass (Morone saxatilis), which are the focus of recreational and commercial fisheries, is one such wide-ranging fish species that has a wide temperature tolerance. However, the underlying mechanisms are poorly described. Sturgeons are another group of migratory fishes, with economic importance and a wide temperature range, that also represent an ancient fish lineage and with an interestingly muted cortisol stress response, which is uncommon in fishes. The objective of my thesis was to delineate the physiological and transcriptomic responses of these migratory, non-model fish species to temperature increase. The first chapter assessed the physiological changes in Striped Bass exposed to both chronic and acute temperature increases. This study revealed that Striped Bass have an impressive ability to withstand high temperatures (both acutely and chronically), with little change in hematology. Building from the first chapter, I then characterize changes in gene expression in Striped Bass muscle tissue after temperature change. These transcriptomic analyses suggest that a diverse suite of heat shock proteins (HSPs) likely play a major role in the Striped Bass’ tolerance to warm waters, following both acute and chronic exposure. In the last data chapter, I explore both the physiological and gene expression changes in the muscle tissues of two Sturgeon species (Shortnose and Atlantic Sturgeon; Acipenser brevirostrum and A. oxyrinchus, respectively) after acute temperature change. I found that the two Sturgeon species have a markedly different response to acute temperature change; Atlantic Sturgeon undergo many transcriptomic changes with little cortisol increase and Shortnose Sturgeon do the opposite (higher cortisol; few changes in gene expression). Together, these data highlight the variable nature of how fishes cope with changing temperatures (e.g., marked HSP response in Striped Bass vs. nearly none in Sturgeon) and broaden our understanding of the processes underpinning the response to an important environmental variable.Item Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock(Elsevier, 2019-08-29) Puncher, Gregory Neils; Rowe, Sherrylynn; Rose, George A.; Leblanc, Nathalie M.; Parent, Geneviève J.; Wang, Yanjun; Pavey, Scott A.Following stock collapse and over twenty years of moratoria, the state of Canada’s Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative of a panmictic population. Several outlier SNPs were found to be associated with ecologically relevant physical characteristics (visual pigments, fin development, response to hypoxia, and various metabolic processes), which may be indicative of different ecological niches.Item Considering Fish as Recipients of Ecosystem Services Provides a Framework to Formally Link Baseline, Development, and Post-operational Monitoring Programs and Improve Aquatic Impact Assessments for Large Scale Developments(Springer, 2022-05-21) Brown, Carolyn J. M.; Curry, R. Allen; Gray, Michelle A.; Lento, Jennifer; MacLatchy, Deborah L.; Monk, Wendy A.; Pavey, Scott A.; St-Hilaire, André; Wegscheider, Bernhard; Munkittrick, Kelly R.In most countries, major development projects must satisfy an Environmental Impact Assessment (EIA) process that considers positive and negative aspects to determine if it meets environmental standards and appropriately mitigates or offsets negative impacts on the values being considered. The benefits of before-after-control-impact monitoring designs have been widely known for more than 30 years, but most development assessments fail to effectively link pre- and post-development monitoring in a meaningful way. Fish are a common component of EIA evaluation for both socioeconomic and scientific reasons. The Ecosystem Services (ES) concept was developed to describe the ecosystem attributes that benefit humans, and it offers the opportunity to develop a framework for EIA that is centred around the needs of and benefits from fish. Focusing an environmental monitoring framework on the critical needs of fish could serve to better align risk, development, and monitoring assessment processes. We define the ES that fish provide in the context of two common ES frameworks. To allow for linkages between environmental assessment and the ES concept, we describe critical ecosystem functions from a fish perspective to highlight potential monitoring targets that relate to fish abundance, diversity, health, and habitat. Finally, we suggest how this framing of a monitoring process can be used to better align aquatic monitoring programs across pre-development, development, and post-operational monitoring programs.Item First evidence of White-footed Deer Mouse (Peromyscus leucopus) on mainland New Brunswick, Canada(Ottawa Field-Naturalists’ Club, 2022-01-21) Huynh, Howard M.; McAlpine, Donald F.; Pavey, Scott A.White-footed Deer Mouse (Peromyscus leucopus) and the closely related, and more northerly ranging, Deer Mouse (Peromyscus maniculatus) broadly overlap in distribution and are often difficult to distinguish from each other. Based on molecular genetic data (cytochrome b gene), we report two new distribution records for P. leucopus for New Brunswick, Canada, the first mainland localities for this species in the province. Previous sampling of Peromyscus in New Brunswick may have overlooked the presence of P. leucopus, possibly because the specimens collected were all assumed to be P. maniculatus. However, current detection in New Brunswick may be part of a broader recent northward range expansion documented to be underway in P. leucopus. Although our use of a single mitochondrial gene to identify P. leucopus does not eliminate the possibility that the New Brunswick specimens are of hybrid origin, our results support the presence of P. leuco-pus in New Brunswick and suggest more detailed analyses will be required to determine the nature of any genetic interaction between P. leucopus and P. maniculatus in the province. Recognition of morphologically cryptic Peromyscus in southern New Brunswick also emphasizes the need to incorporate comprehensive methods to ensure the correct identification of speci-mens of this genus in Maritime Canada. We also note the potential implications of this discovery with respect to the incidence of Lyme disease in New Brunswick.Item Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River(Wiley Open Access, 2020-07-14) LeBlanc, Nathalie M.; Gahagan, Benjamin I.; Andrews, Samuel N.; Avery, Trevor S.; Puncher, Gregory N.; Reading, Benjamin J.; Buhariwalla, Colin F.; Curry, R. Allen; Whiteley, Andrew R.; Pavey, Scott A.Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.Item Interannual variation in spawning success of striped bass (Morone saxatilis) in the Saint John River, New Brunswick(Wiley, 2019-11-08) Andrews, Samuel N.; Linnansaari, Tommi; Leblanc, Nathalie; Pavey, Scott A.; Curry, R. AllenBarriers such as dams have been cited as a serious threat to striped bass survival, especially when they affect or impede migration and access to spawning grounds. On the Saint John River, New Brunswick, the installation of the large Mactaquac Dam in the immediate vicinity of a historic striped bass spawning location was suspected to have caused the arrest of striped bass reproduction and the collapse of the native striped bass population. In 2014, juvenile striped bass of confirmed Saint John River origin were documented in the river for the first time since 1979. In the current study, we examined juveniles from 6 years of sampling to determine corresponding years of successful recruitment. We also tracked adult striped bass matching the ancestry of native Saint John River juveniles to determine the timing and location of spawning. Over 5 years, we observed an annual upstream migration by adult striped bass to historic spawning areas near Fredericton, identified a dominant year class of Saint John River origin juveniles reproduced in 2013, and linked the apparent successful production of year classes to definable discharge conditions, that is, extended periods of sustained flow >36 hr downstream from the Mactaquac Dam. The results of this study suggest important first management actions towards recovering and sustaining the re-discovered striped bass population in the Saint John River, New Brunswick.Item Mercury bioaccumulation in aquatic biota along a salinity gradient in the Saint John River estuary(Elsevier, 2018-06-13) Reinhart, Bethany L.; Kidd, Karen A.; Curry, R. Allen; O'Driscoll, Nelson J.; Pavey, Scott A.Although estuaries are critical habitats for many aquatic species, the spatial trends of toxic methylmercury (MeHg) in biota from fresh to marine waters are poorly understood. Our objective was to determine if MeHg concentrations in biota changed along a salinity gradient in an estuary. Fourspine Stickleback (Apeltes quadracus), invertebrates (snails, amphipods, and chironomids), sediments, and water were collected from ten sites along the Saint John River estuary, New Brunswick, Canada in 2015 and 2016, with salinities ranging from 0.06 to 6.96. Total mercury (proxy for MeHg) was measured in whole fish and MeHg was measured in a subset of fish, pooled invertebrates, sediments, and water. Stable sulfur (δ34S), carbon (δ13C), and nitrogen (δ15N) isotope values were measured to assess energy sources (S, C) and relative trophic level (N). There were increases in biotic δ13C and δ34S from fresh to more saline sites and these measures were correlated with salinity. Though aqueous MeHg was higher at the freshwater than more saline sites, only chironomid MeHg increased significantly with salinity. In the Saint John River estuary, there was little evidence that MeHg and its associated risks increased along a salinity gradient.Item Spatial Heterogeneity of eDNA Transport Improves Stream Assessment of Threatened Salmon Presence, Abundance, and Location(Frontiers Media, 2021-04-08) Wood, Zachary T.; Lacoursière-Roussel, Anaïs; LeBlanc, Francis; Trudel, Marc; Kinnison, Michael T.; McBrine, Colton Garry; Pavey, Scott A.; Gagné, NellieThe integration of environmental DNA (eDNA) within management strategies for lotic organisms requires translating eDNA detection and quantification data into inferences of the locations and abundances of target species. Understanding how eDNA is distributed in space and time within the complex environments of rivers and streams is a major factor in achieving this translation. Here we study bidimensional eDNA signals in streams to predict the position and abundance of Atlantic salmon (Salmo salar) juveniles. We use data from sentinel cages with a range of abundances (3–63 juveniles) that were deployed in three coastal streams in New Brunswick, Canada. We evaluate the spatial patterns of eDNA dispersal and determine the effect of discharge on the dilution rate of eDNA. Our results show that eDNA exhibits predictable plume dynamics downstream from sources, with eDNA being initially concentrated and transported in the midstream, but eventually accumulating in stream margins with time and distance. From these findings we developed a fish detection and distribution prediction model based on the eDNA ratio in midstream versus bankside sites for a variety of fish distribution scenarios. Finally, we advise that sampling midstream at every 400 m is sufficient to detect a single fish at low velocity, but sampling efforts need to be increased at higher water velocity (every 100 m in the systems surveyed in this study). Studying salmon eDNA spatio-temporal patterns in lotic environments is essential to developing strong quantitative population assessment models that successfully leverage eDNA as a tool to protect salmon populations.Item The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates(Wiley Open Access, 2020-12-29) Kroetsch, Shawn A.; Kidd, Karen A.; Monk, Wendy A.; Culp, Joseph M.; Compson, Zacchaeus G.; Pavey, Scott A.Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.Item The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome(Public Library of Science, 2020-10-29) Christensen, Kris A.; Rondeau, Eric B.; Minkley, David R.; Sakhrani, Dionne; Biagi, Carlo A.; Flores, Anne-Marie; Withler, Ruth E.; Pavey, Scott A.; Beacham, Terry D.; Godin, Theresa; Taylor, Eric B.; Russello, Michael A.; Devlin, Robert H.; Koop, Ben F.Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.Item Transborder Gene Flow between Canada and the USA and Fine-Scale Population Structure of Atlantic Cod in the Broader Gulf of Maine Region(Wiley, 2021-03-23) Puncher, Gregory Neils; Wang, Yanjun; Martin, Ryan; DeCelles, Gregory; Cadrin, Steven X.; Zemeckis, Douglas; Rowe, Sherrylynn; Leblanc, Nathalie M.; Parent, Genevieve J.; Pavey, Scott A.Fishery managers have struggled for decades to rebuild stocks of Atlantic Cod Gadus morhua in the northwestern Atlantic Ocean, and the resolution of current fine-scale population structure will surely help those efforts. Using double digest restriction-site associated DNA sequencing, we analyzed 248 adult and 215 juvenile Atlantic Cod collected from areas bordering the Canada–USA boundary in 2017–2018. Chromosomal inversions from linkage group (LG) 2 and LG 7 contribute the largest amount of variance to the data set. A southwesterly decrease in the proportion of LG 1 inversion haplotypes may indicate gene flow from areas north of 45°N. Samples from both the northern Gulf of Maine and Bay of Fundy were genetically distinct from all other samples, suggesting that local spawning groups may still be active. Genetic similarities between Atlantic Cod from Browns Bank and eastern Georges Bank indicate that transborder gene flow is ongoing. These results will help to better define the stocks in order to guide the implementation of management strategies in the USA and Canada, which should consider rebuilding exhausted and genetically isolated populations.