Browsing by Author "Rogers, Sean M."
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Item Open Access Assessing Temperature Tolerance in Ninespine Stickleback (Pungitius pungitius) in Response to Climate Change(2018-07-13) Tufts, Teresa; Rogers, Sean M.; Yeaman, Sam; Vamosi, Jana C.; Murray, Maribeth S.Temperature is the most important environmental factor influencing fish abundance and distribution but, as temperatures rise globally, the consequences for fishes remains largely unknown. I used populations of ninespine stickleback (Pungitius pungitius) from the northern and southern parts of their range in a common environment to characterize thermal traits in association with varying temperatures. Cold tolerance differed between populations but heat tolerance did not. Furthermore, juveniles demonstrated less tolerance for temperature extremes. When incubated at elevated temperatures, populations exhibited higher plasticity in cold tolerance compared to heat tolerance. Plasticity in heat tolerance was associated with a number of trade-offs. The data suggest that cold tolerance is locally adapted and phenotypically plastic while heat tolerance is conserved and phenotypically restricted in this species. My thesis highlights the need for the inclusion of various life stages, time scales, and biotic interactions in climate change research to better predict its impacts on fishes.Item Open Access Demographic Variation Among Unexploited Alpine Brook Trout (Salvelinus fontinalis) Populations and Responses to Experimental Fisheries(2020-09-22) Glaser, Dylan M.; Post, John Robert; Fraser, Dylan J.; Ciborowski, Jan J. H.; Fox, Jeremy W.; Rogers, Sean M.Primary demographic attributes such as somatic growth, mortality, size- and age-at-maturity, fecundity, and recruitment drive the structure of fish populations, and these processes are also influenced by density-dependent and -independent processes. Here I study multiple populations of unexploited (i.e. assumed equilibria), lentic Brook Trout to describe variation in population structure. Studying unexploited populations gives fisheries managers and scientists an understanding of the intrinsic variation in systems absent from harvest pressure. First, I identify how much primary demographic attributes vary among populations, then attempt to attribute the observed variation to a suite of nested models containing terms for ecosystem productivity (total phosphorus concentration), climate (growing degree days or GDD), and density (fish biomass per hectare) in 9 lakes. I found that (1) populations varied substantially in somatic growth parameters (two-fold), natural mortality (three-fold), age-at-maturity (three-fold), length-at-maturity (two-fold) and recruitment (three-fold), (2) growth early in life was negatively correlated with density (r = -0.58), but maximum length was positively correlated with GDD (r = 0.61), and (3) spawning stock density was negatively correlated with recruitment (r = -0.57), but positively correlated with GDD (r = 0.55). I then experimentally harvested these previously unexploited populations with size selective gillnets by removing 30-70 % of the largest individuals from 5 of the 9 populations over 2 consecutive years. I tested the compensatory response to harvest with a BACI analysis, where I looked to see if absolute growth rate, size- and age-at-maturity, reproductive investment, and recruitment compensate for fisheries harvest. I found (1) strong evidence of recruitment compensation, (2) that overall (i.e. site-wide) stock-recruitment relationship was strongly density dependent and over-compensatory (i.e. a humped, Ricker type relationship), (3) positive but nonsignificant compensation in growth and age-at-maturity, and (4) no change in reproductive investment, but noted that populations may compensate for reproductive capacity in other ways (e.g. a combination of increased somatic growth and younger age-at-maturity). Comparing observed variation in unexploited populations’ demography with environmental variables helps fisheries managers and scientists understand intrinsic variability, and drivers of said variability; further exploiting these populations in an experimental fishery shows the initial mechanisms behind compensation. Examining both unexploited and responses to fisheries will help fisheries managers and scientists understand which populations can have their density reduced (via setting appropriate harvest rates), set realistic targets to recover populations, and increase understanding of the mechanisms that structure populations.Item Open Access Ecological consequences of genetically-based thermal traits in fishes(2019-05-13) Smith Wuitchik, Sara Jayne; Rogers, Sean M.; Barrett, Rowan D. H.; Syme, Douglas A.; Vijayan, Mathilakath M.Unprecedented contemporary rates of environmental change risk irreversible loss of biodiversity and ecosystem functioning in aquatic systems, with population persistence dependent on resiliency in thermal physiology and thermoregulation. The association between thermal physiology and behavioural traits can predict population persistence, range shifts, and evolution in the face of contemporary climate change, but the mechanisms underlying these relationships are unknown. In this thesis, I characterize the impact of abiotic environmental factors on population distributions, assess the relationship between thermal tolerance and preference traits, characterize the genetic architecture of these thermal traits, and use these empirical data to construct a mechanistic species distribution model for a genetically similar cluster in a marine environment. I found that temperature and water volume are significant drivers of age- and size-class distributions within a wild marine population of Oligocottus maculosus. I also found that population and generation significantly impacted various thermal tolerance traits, and that there were significant correlations between physiological and behavioural thermal traits in Gasterosteus aculeatus across generations and populations. I also show that the thermal tolerance limits of freshwater populations of G. aculeatus are closer to observed thermal extremes in their natural environments than their marine counterparts. Using phenotypically-divergent populations of G. aculeatus, I identified four significant quantitative trait loci (QTL) that were associated with thermal tolerance traits and that many of these traits co-localized to the same two QTL. Using these genetically-based thermal traits, I predicted a conservative but northward shift in the geographic range of the marine populations of G. aculeatus. Collectively, these data demonstrate that the inclusion of both physiological and behavioural data will be important in forming more robust predictions regarding species’ responses to climate change, with an emphasis on temperature-associated behaviours when considering predictions regarding population persistence. By integrating multiple responses to climate change and facilitating collaboration across fields, we can begin to produce more accurate and robust predictions concerning the fate of populations, communities, and ecosystems under contemporary climate change.Item Open Access Ecology and Genetics of Phenotypic Integration and the Role for Adaptation in Threespine Stickleback(2019-07-09) Barry, Tegan Nicole; Rogers, Sean M.; Jamniczky, Heather A.; Theodor, Jessica M.; Vamosi, Steven M.Determining the underlying causes for the links between form, function, and the environment, and how these correlations relate to adaptation to novel environments represent integral problems in evolutionary biology. While investigations have been conducted on adaptive divergence involving single, isolated traits, adaptation is multifaceted, requiring the examination of complex, multidimensional phenotypes. In this thesis, I evaluated the hypothesis that phenotypic covariation and phenotypic integration are linked to genetic covariation and facilitate adaptation to novel environments. Phenotypic variation and covariation, along with genetic differentiation between multiple wild stickleback subpopulations and laboratory reared groups were described using three dimensional geometric morphometric data from stickleback skeletal structures as well as genomic information from high density Single Nucleotide Polymorphisms (SNPs; sensu Pool-Seq). I evaluated whether divergence in putatively adaptive traits was higher than expected under expectations for neutral evolution via PST-FST comparisons of phenotypic covariation and contrasted patterns of genetic and phenotypic variation. I determined the genetic basis of phenotypic integration using a controlled common garden experiment and investigated the genetic architecture of integrated skeletal structures through Quantitative Trait Locus (QTL) analysis carried out on linkage maps that I generated from SNPs characterized by double restriction digest reduced representation sequencing (ddRAD-Seq). Finally, I evaluated whether this genetic architecture was being maintained by selection in wild populations by testing the hypothesis that molecular divergence was higher than expected at genetic regions associated with phenotypic traits. I found the amount of phenotypic variation and strength of integration varies across the stickleback skeleton as well as among marine populations and that directional selection is acting on phenotypic integration in all observed populations. I determined that phenotypic integration across the skeleton is controlled by genetic factors, though there is a strong effect of environment on trophic traits. Finally, I characterized 33 significant QTL linked to integrated skeletal traits, finding 2702 SNP outliers within the identified QTL under selection between marine and freshwater environments. Collectively, my thesis highlights integration as an essential component of adaptive divergence and as one of the potential driving forces for the rapid adaptation of populations to novel environments.Item Open Access Ecology of Adaptive Peak Shifts in Alaskan Threespine Stickleback (Gasterosteus aculeatus)(2015-12-04) Vanderzwan, Stevi Lee; Rogers, Sean M.; Vamosi, Steven M.; Jamniczky, Heather A.; Theodor, Jessica M.Divergent natural selection is a major cause of phenotypic differentiation among populations exploiting different environments, but information on the ecological factors contributing to peak shift is largely missing from natural populations. Threespine stickleback (Gasterosteus aculeatus) is an emerging vertebrate model for studying phenotype-environment associations, as ancestral marine populations have adapted independently to postglacial freshwater environments. I characterized antipredator, foraging, and body shape phenotypes of 800+ fish from 16 ecologically diverse sites on the Alaska Peninsula. Gill rakers, antipredator traits, and body shape significantly associated with lake ecology, whereas foraging traits and body shape were influenced by geography. Stickleback from lakes ecologically similar to the ancestral state were more phenotypically similar to marine-influenced populations than fish from ecologically divergent habitats (i.e., small lakes). My study elucidates mechanisms associated with adaptive evolution and is one of relatively few that links ecological features of the adaptive landscape with phenotypic evolution in multiple populations.Item Open Access The genetic basis of convergent evolution among three species of fishes(2019-10-31) Reeve, James; Yeaman, Sam; Rogers, Sean M.; De Koning, A. P. JasonThe genetic basis of convergent evolution can be identified by comparing changes in allele frequencies across multiple species under the same environmental conditions. Patterns of elevated genetic divergence among populations or reduced genetic diversity within populations that are shared among species are often inferred as the product of convergent local adaptation. However, there are several other evolutionary processes that can produce similar patterns, making it hard to infer if these genetic patterns are caused by local adaptation. This study attempted to identify genetic candidates for convergent evolution by comparing pooled whole-genome data among three species of fish. Due to unexpectedly high genetic divergence among populations the ninespine stickleback (Pungitius pungitius) had to be removed from the analysis. Meaning the genetic patterns of local adaptation could only be compared between the two remaining species of fish. No candidates of convergent evolution were identified between the threespine stickleback (Gasterosteus aculeatus) and tubesnout (Aulorhynchus flavidus), indicating that either these species are responding to the same environmental pressure with different genetic changes, or that some unidentified aspect of the environment is leading to divergent patterns of local adaptation. Overall, this study demonstrates some of the potential problems with using genome scans that can make it difficult to identify the genetic basis of convergent evolution.Item Open Access Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)(Wiley, 2015-02-09) Mee, Jonathan A.; Bernatchez, Louis; Reist, Jim D.; Rogers, Sean M.; Taylor, Eric B.The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.Item Open Access Investigating the genetic basis of ivermectin resistance in Haemonchus contortus(2018-04-30) Rezansoff, Andrew Mischa; Gilleard, John Stuart; Hansen, David; Rogers, Sean M.; Mains, Paul E.; Wasmuth, James D.; Geary, Tim C.Parasitic nematodes have a major impact on human and animal health and their control is threatened by the emergence of resistance to the anthelmintic drugs on which control depends. Although resistance to ivermectin is widespread in many livestock parasites, the genetic mechanisms remain elusive. In this thesis, a number of approaches are undertaken to investigate the genetics of ivermectin resistance in Haemonchus contortus, an important parasitic nematode research model. A transcriptomic comparison of the susceptible MHco3(ISE) and two ivermectin resistant strains, MHco4(WRS) and MHco10(CAVR), was undertaken to investigate if differences in gene expression revealed insights into ivermectin resistance mechanisms. Although this approach did not reveal clear ivermectin resistance gene candidates, the results have some important implications for RNAseq analysis in genetically diverse organisms. First, extremely high levels of genetic diversity in H. contortus had a major impact on RNAseq analysis and needed to be accounted for reliable identification of differentially expressed genes. Second, there were a remarkably large number of genes differentially expressed between the three H. contortus strains. In a novel genetic crossing approach, two independent serially backcrossed H. contortus populations were utilized in which ivermectin resistance loci had been introgressed into the MHco3(ISE) genome. Markers for six leading candidate ivermectin resistance genes from the literature were examined and none were found to show evidence of introgression in the backcross populations. A seventh marker, Hcms8a20 showed clear evidence of introgression and was later confirmed by collaborators using a whole genome sequencing approach to show its location in a 11.2 Mb introgressed region. A set of 25 in vivo or in vitro phenotyped ivermectin resistant H. contortus field populations were then used to investigate evidence of selection on the Hcms8a20 marker and four other loci distributed across the 11.2 Mb introgressed region. A deep amplicon sequencing approach revealed that, of the loci tested, only Hcms8a20 showed consistent evidence of purifying selection in the ivermectin resistant field populations. Overall, the results provide strong evidence that a major ivermectin resistance locus is located within a few megabases of the Hcms8a20 locus in many different ivermectin resistant H. contortus field populations.Item Open Access Molecular investigation of stalk formation and growth rates in Didymosphenia geminata(2018-04-02) Larsen, Krista Maria; Jackson, Leland J.; Rogers, Sean M.; Vamosi, Jana C.Didymosphenia geminata, a freshwater diatom, can produce thick benthic mats of stalk material. The cause of excess stalk formation is proposed to be low soluble reactive phosphorus (SRP) concentrations or a mat-forming genetic variant. Molecular studies on D. geminata are few, partly due to the lack of a reliable DNA extraction technique for the diatom, but have the ability to elucidate the drivers of mat formation. Specifically, comparison of gene expression between mat and non-mat-forming sites using reference genomes, may reveal underlying mechanisms behind growth and stalk formation. The objectives of this study were to: 1) identify gene products, expressed only at a mat or non-mat-forming site in Alberta (AB), involved in cell division or stalk formation from the reference genomes of P. tricornutum, T. pseudonana and C. crescentus; 2) compare SRP and growth rate, using frequency of dividing cells (FDC), between a mat-forming and non-mat-forming site; 3) compare FDC between multiple mat-forming sites in AB and British Columbia (BC); and 4) compare the quantity and quality of DNA obtained from mat-forming D. geminata using various preservation buffers, storage temperatures and extraction methods, including organic extraction, the Qiagen DNeasy® Plant Mini Kit, and a version of the kit procedure modified for D. geminata. Sixty-six putative gene products from the reference genomes were expressed only in the mat-forming sample, while 172 were expressed only in the non-mat-forming sample. FDC and SRP were higher at the non-mat-forming site, with no significant difference between FDC in AB and BC. Collectively, these results support previous findings that D. geminata forms excess stalk material under low SRP and increases cell division under higher SRP. However, an anomalous observation of mat formation at a site with 0.00986 mg/L SRP indicates stalk formation may be influenced by additional factors. In addition, the results of this study indicate that DNA extracted from samples stored in 95% EtOH at -80°C, using the modified kit method, had the best combination of quantity and quality.Item Open Access Phylogeography and local adaptation in prickly sculpin, Cottus asper(2013-12-23) Dennenmoser, Stefan; Vamosi, Steven M.; Rogers, Sean M.This thesis examined historical and contemporary effects on genetic population structuring of prickly sculpin (Cottus asper) in British Columbia, Canada. A phylogeographic study was conducted, which disproved the traditional view that prickly sculpin survived the Last Glacial Maximum in only southern coastal and inland refugia, favoring allopatric divergence and giving rise to coastal and inland “prickling” phenotypes, which vary in the degree to which spine-like scales cover the body of the fish. Instead, analyses of mitochondrial DNA and microsatellite markers suggest parallel evolution of highly prickled inland populations, which presumably have evolved independently across three glacial lineages, originating from highly differentiated ancestral coastal populations. Postglacial colonization from coastal towards inland regions and associated founder effects resulted in decreased genetic diversities, which was also evident in a subsequent study on conservation genetics of a recently discovered peripheral population in the Peace River in Alberta. While no divergent “conservation designation unit” was detected in the Peace River, a for freshswater sculpins unusual high genetic connectivity over large geographic scales was found, which could reflect high dispersal capacities of an extended, planktonic larval stage that might have been at least partially retained from an amphidromous life cycle of the putative ancestral coastal populations. While such assumptions on life history characteristics of inland populations remain speculative, the divergence between coastal, amphidromous and inland, purely freshwater life cycles is young (< 14,000 years), and may be in an early, incomplete stage of a life history transition. To better understand life history transitions from amphidromous to freshwater life cycles in C. asper, a population genetics study was conducted in the Lower Fraser River system, which identified sympatric life history ecotypes represented by amphidromous sculpins in the river main channel, and genetically differentiated freshwater sculpins in the river tributaries. These results indicate that that isolation-by-environment to discrete freshwater habitats could play a role for the early stage of amphidromy-freshwater transitions, which may be further favored by the presence of large tributary streams and lakes allowing for large effective population sizes.Item Open Access The Landscape Genetic Patterns of Culaea inconstans(2013-05-01) Kremer, Cory S.; Rogers, Sean M.; Vamosi, Steven M.Landscape genetics is a new field that investigates the consequences of landscape features on population genetic patterns. The small lakes of Alberta, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique system where populations are highly fragmented and isolated from one another. These lakes are prone to winterkills hypothesized to precipitate frequent bottleneck events in brook stickleback populations. As predicted, brook stickleback populations exhibited a high degree of population structure, and were hierarchically structured by small scale watersheds. AIC analyses of the role of spatial features found support for basin characteristics in driving patterns of genetic diversity, which was also consistent with the detection of recent bottlenecks in at least five of the sampled lakes. These results suggest that brook stickleback population genetic patterns are primarily controlled by processes that accelerate genetic drift, reinforcing the importance of connectivity in the maintenance of genetic diversity in fragmented landscapes.