Freeland, Joanna

Climate change is a major conservation concern, especially for many cold-adapted species. The rate of warming due to climate change will likely outpace adaptive responses, and many populations will likely need to rely on phenotypic plasticity to cope with environmental warming. It is currently unclear whether plasticity in physiological responses to warming will be sufficient to offset the negative consequences of chronic environmental warming in ectotherms. I studied within-generation and transgenerational plasticity in two cold-adapted species of fishes, lake trout (Salvelinus namaycush) and brook trout (S. fontinalis), following temperature acclimation. Adults of both species were acclimated to either cold or warm temperatures and offspring were generated using a fully factorial breeding design, whereby the family thermal histories included crosses made within each temperature treatment and bidirectional crosses between temperatures. Offspring families were subdivided into two groups and acclimated to either warm or cold temperatures, so that offspring thermal experience matched or mismatched that of one or both parents. Offspring metabolic rate and critical thermal maximum during an acute thermal challenge were measured for both species. Limited transgenerational plasticity was detected in both species, but had a lesser effect than within-generationacclimation. In brook trout, the paternal contribution was greater than the maternal contribution. In lake trout, a mismatch in thermal acclimation, where the offspring were cold-acclimated but the parents warm-acclimated, resulted in elevated offspring metabolic rate without a corresponding increase in growth, suggesting that a mismatch in temperatures across generations could be detrimental to offspring. Using RNA-sequencing, transgenerational plasticity was linked to differential gene expression in the liver of lake trout offspring, in that genes were differentially expressed depending on the parental acclimation temperatures. Within-generation warm acclimation had the greatest effect on gene expression profile of offspring, with more genes differentially expressed under conditions of within-generation warm acclimation compared with transgenerational warm acclimation. Although it has been suggested that transgenerational plasticity may help to buffer the impact of warming due to climate change, my work implies that transgenerational plasticity, like within-generation plasticity, will be insufficient for these two species of cold-adapted salmonids to cope with climate change.

Author Keywords: Brook trout, Climate change, Lake trout, Phenotypic plasticity, Thermal tolerance, Transgenerational plasticity

Muskrat populations are declining across North America. In recent decades, hybrid cattail Typha x glauca has been invading wetlands in North America. This invasion is degrading wetland habitat, leading to reduced interspersion of water and vegetation. Muskrats are wetland-obligates and their populations are positively linked to marsh interspersion. Therefore, muskrat populations may be declining due to the invasion of T. x glauca and subsequent reduction in interspersion. To test this hypothesis, I first sampled marshes across south-central Ontario, comparing muskrat densities with the relative frequency of T. x glauca and the degree of interspersion. Second, I measured intensity of use by muskrats in a large wetland along a gradient of interspersion. My findings suggest that reduced interspersion may be contributing to muskrat population declines, but it is unclear to what degree T. x glauca is responsible. Further research is needed to understand the effects of wetland invasions on muskrat populations.

Author Keywords: invasive species, Ondatra zibethicus, Southern Ontario, Typha x glauca, wetlands, wildlife conservation

Advanced generation/backcrossed (non-F1) hybrids can be challenging to identify when their traits are similar to those of parental taxa, F1 hybrids, or both. This is particularly evident in the North American hybrid zone involving Typha latifolia, T. angustifolia, F1 T. × glauca and non-F1 hybrids. Cattails are challenging to differentiate based on gross morphological characteristics. Microscopic characteristics in female inflorescences have not been previously studied to differentiate parental taxa from non-F1 hybrids. To investigate whether researchers can use microscopic floret and bracteole characteristics for taxonomic identification, I compared pistillate flower length, bracteole length and width, and bracteole colour among taxa. I found that floret and bracteole characteristics can be useful for identifying T. latifolia but cannot accurately differentiate T. angustifolia and F1 T. × glauca from non-F1 hybrids. Further, a flowering bias can lead to the underestimation of the frequency of T. latifolia when using floral characters to examine the relative abundance of cattail taxa.

Author Keywords: advanced-generation hybrids, backcrossed hybrids, invasive species, morphology, species identification, Typha spp.

Wetlands are highly susceptible to the invasion of invasive species. The invasive hybrid cattail (Typha × glauca) is prevalent in the southeastern Prairie Pothole Region (PPR) wetlands. However, concerns arise about its recent proliferation in the northwestern PPR without maternal T. angustifolia. To determine taxonomic distribution, I used species-specific PCR-RFLP and microsatellite markers for genotyping 245 samples from 50 northwest PPR sites. I found 75% T. latifolia, 7% T. angustifolia, 16% T. × glauca, and 2% backcrossed or advanced-generation hybrids. F1 T. × glauca has expanded in western PPR without its mother species, and the low occurrence of later-generation hybrids indicates their recent range expansion. Additionally, T. angustifolia offspring make fewer hybrids, which suggests that reproductive barriers may limit hybridization between parental species. This study highlights the vulnerability of prairies to cryptic invasions by Typha hybrids, and early detection of invasive species is a critical factor in wetland management success.

The diversification of mammals has been shaped by climatic fluctuations and geological changes over millions of years. Among them, shrews (Soricidae) stand out as one of the most diverse mammalian lineages. Shrews are found on most continents and have evolved remarkable adaptations at the species and population levels. Although evolutionary studies of shrews have been limited by a lack of genomic resources, this work aimed to address this gap by developing such resources and using various omics approaches to explore adaptation and divergence in shrews, with a particular focus on an isolated population on Bon Portage Island (BPI), Nova Scotia, Canada. BPI shrews exhibit distinctive foraging habits and possess a unique allele for a dietary enzyme, which may represent an adaptation to their specialized diet. My research involved assembling and annotating de novo genomes from three shrew species. In Chapter 2 I conducted a comparative genomic analysis of 20 mammals (including four shrew species) to identify lineage-specific adaptations including accelerated regions, gene family expansions, and positively selected genes. I found shrew-specific variants in genes associated with the nervous, metabolic, and auditory systems, which may underlie some of their unique traits. In Chapter 3, I examined morphological and epigenetic divergence between mainland and island populations of masked shrews (Sorex cinereus), including BPI. Island shrews exhibited smaller body sizes and signs of accelerated biological aging, marked by DNA methylation differences enriched in developmental and digestive pathways. Chapter 4 focused on analyzing genome-wide SNP data to identify regions of differentiation, alongside RNA-seq data to perform a differential gene expression analysis between BPI shrews and other populations. The results from both analyses revealed patterns of differentiation in genes associated with fatty acid metabolism and metabolic regulation that are likely linked to their specialized, largely marine-based diet. Additionally, I reconstructed the demographic history of Nova Scotia masked shrew populations, revealing that the divergence of the BPI population appears to coincide with rising sea levels following the last glacial maximum. These findings shed light on mechanisms of adaptation and divergence, illustrating how ecological pressures, geographic isolation, and dietary specialization shape genomic, epigenomic, and transcriptomic landscapes.

Author Keywords: comparative genomics, epigenetics, genome assembly, island syndrome, population genomics, transcriptomics

Climate change is a major conservation concern, especially for many cold-adapted species. The rate of warming due to climate change will likely outpace adaptive responses, and many populations will likely need to rely on phenotypic plasticity to cope with environmental warming. It is currently unclear whether plasticity in physiological responses to warming will be sufficient to offset the negative consequences of chronic environmental warming in ectotherms. I studied within-generation and transgenerational plasticity in two cold-adapted species of fishes, lake trout (Salvelinus namaycush) and brook trout (S. fontinalis), following temperature acclimation. Adults of both species were acclimated to either cold or warm temperatures and offspring were generated using a fully factorial breeding design, whereby the family thermal histories included crosses made within each temperature treatment and bidirectional crosses between temperatures. Offspring families were subdivided into two groups and acclimated to either warm or cold temperatures, so that offspring thermal experience matched or mismatched that of one or both parents. Offspring metabolic rate and critical thermal maximum during an acute thermal challenge were measured for both species. Limited transgenerational plasticity was detected in both species, but had a lesser effect than within-generationacclimation. In brook trout, the paternal contribution was greater than the maternal contribution. In lake trout, a mismatch in thermal acclimation, where the offspring were cold-acclimated but the parents warm-acclimated, resulted in elevated offspring metabolic rate without a corresponding increase in growth, suggesting that a mismatch in temperatures across generations could be detrimental to offspring. Using RNA-sequencing, transgenerational plasticity was linked to differential gene expression in the liver of lake trout offspring, in that genes were differentially expressed depending on the parental acclimation temperatures. Within-generation warm acclimation had the greatest effect on gene expression profile of offspring, with more genes differentially expressed under conditions of within-generation warm acclimation compared with transgenerational warm acclimation. Although it has been suggested that transgenerational plasticity may help to buffer the impact of warming due to climate change, my work implies that transgenerational plasticity, like within-generation plasticity, will be insufficient for these two species of cold-adapted salmonids to cope with climate change.

Author Keywords: Brook trout, Climate change, Lake trout, Phenotypic plasticity, Thermal tolerance, Transgenerational plasticity

Muskrat populations are declining across North America. In recent decades, hybrid cattail Typha x glauca has been invading wetlands in North America. This invasion is degrading wetland habitat, leading to reduced interspersion of water and vegetation. Muskrats are wetland-obligates and their populations are positively linked to marsh interspersion. Therefore, muskrat populations may be declining due to the invasion of T. x glauca and subsequent reduction in interspersion. To test this hypothesis, I first sampled marshes across south-central Ontario, comparing muskrat densities with the relative frequency of T. x glauca and the degree of interspersion. Second, I measured intensity of use by muskrats in a large wetland along a gradient of interspersion. My findings suggest that reduced interspersion may be contributing to muskrat population declines, but it is unclear to what degree T. x glauca is responsible. Further research is needed to understand the effects of wetland invasions on muskrat populations.

Author Keywords: invasive species, Ondatra zibethicus, Southern Ontario, Typha x glauca, wetlands, wildlife conservation

Advanced generation/backcrossed (non-F1) hybrids can be challenging to identify when their traits are similar to those of parental taxa, F1 hybrids, or both. This is particularly evident in the North American hybrid zone involving Typha latifolia, T. angustifolia, F1 T. × glauca and non-F1 hybrids. Cattails are challenging to differentiate based on gross morphological characteristics. Microscopic characteristics in female inflorescences have not been previously studied to differentiate parental taxa from non-F1 hybrids. To investigate whether researchers can use microscopic floret and bracteole characteristics for taxonomic identification, I compared pistillate flower length, bracteole length and width, and bracteole colour among taxa. I found that floret and bracteole characteristics can be useful for identifying T. latifolia but cannot accurately differentiate T. angustifolia and F1 T. × glauca from non-F1 hybrids. Further, a flowering bias can lead to the underestimation of the frequency of T. latifolia when using floral characters to examine the relative abundance of cattail taxa.

Author Keywords: advanced-generation hybrids, backcrossed hybrids, invasive species, morphology, species identification, Typha spp.

Wetlands are highly susceptible to the invasion of invasive species. The invasive hybrid cattail (Typha × glauca) is prevalent in the southeastern Prairie Pothole Region (PPR) wetlands. However, concerns arise about its recent proliferation in the northwestern PPR without maternal T. angustifolia. To determine taxonomic distribution, I used species-specific PCR-RFLP and microsatellite markers for genotyping 245 samples from 50 northwest PPR sites. I found 75% T. latifolia, 7% T. angustifolia, 16% T. × glauca, and 2% backcrossed or advanced-generation hybrids. F1 T. × glauca has expanded in western PPR without its mother species, and the low occurrence of later-generation hybrids indicates their recent range expansion. Additionally, T. angustifolia offspring make fewer hybrids, which suggests that reproductive barriers may limit hybridization between parental species. This study highlights the vulnerability of prairies to cryptic invasions by Typha hybrids, and early detection of invasive species is a critical factor in wetland management success.

Similar to other shorebird trends around the world, the Piping Plover population (Charadrius melodus circumcinctus) is projected to decline if concerted conservation efforts are relaxed. To date, there is insufficient understanding of the connection between habitat type, prey abundance, and chick behaviour of the Piping Plover breeding population in Ontario. The aim of my thesis was to gain knowledge about prey abundance at recent and historic breeding locations, understanding how habitat influences prey abundance and chick behaviour across the Piping Plover breeding range in Ontario's Great Lakes. The objective of my first study was to understand prey abundance across the breeding region Great Lakes of Ontario from 2018-2019, including occupied and unoccupied sites, and to quantify variation among habitats and periods of reproduction. To evaluate resources, I sampled 17 locations to compare prey abundance using invertebrate traps (n= 3,507). Sampling took place over the reproductive periods of nest initiation, post-hatch, and fledging and in four habitat types of shoreline, wrack, berm, and back dune. Occupied breeding sites had higher prey abundances, and different assemblages of invertebrate prey than unoccupied sites. Additionally, breeding sites had higher prey abundance during nest initiation and supported higher amounts of prey in shoreline and wrack habitat. The objective of my second study was to understand how habitat types influence chick behaviour. To evaluate behaviour-habitat trends, instantaneous chick observations were recorded at the four nest sites from the post-hatch to fledging stages. In total there were 23 fledged chicks that we observed across the two years. Chicks in this study spent 60.9% of their time foraging, 11.9% of the time displaying alert behaviour, 21.4% of their time resting or being brooded, and 5.9% of their time preening. Chicks spent a large proportion of time foraging in the shoreline, resting in the back dune, and alert in berm habitat. The frequency of these alert, defensive behaviours differed among sites, with Sauble Beach chicks spending more time in defensive behaviours compared to other sites. I concluded that in both nesting and brood-rearing periods, habitat is selected non-randomly by adult and young Piping Plovers to maximize access to invertebrate prey for growth and survival. Access by chicks to the most productive habitats should be considered in local management decisions.

Author Keywords: chick behaviour, endangered, Great Lakes Region, habitat, Piping Plovers, prey abundance