Biology subjects

Garroway, C. J.

Publications and source records attributed to Garroway, C. J..

At least 19 recordsLinked to original sources

bioRxiv2025

Exploring contemporary and historic effective population sizes in Atlantic beluga whale populations

Ongoing global environmental changes will require animals to adapt to new conditions, as their necessary resources for survival may shift or decline. Understanding population dynamics in wildlife informs conservation strategies by providing context for genetic diversity and current population abundances. Here, we use whole genome data to reconstruct past demographic trends and estimate contemporary effective population sizes in the beluga whale (Delphinapterus leucas), an Arctic endemic species with significant cultural importance, that is an integral part of the marine ecosystem along the Canadian coast. In line with previous work, we identified six genetic populations: 1) St. Lawrence Estuary, 2) Eastern High Arctic, 3) James Bay, 4) Cumberland Sound, 5) Hudson Bay-Strait Complex and 6) Little and Great Whale Rivers. Demographic history in the deep (up to 1,000,000 years) past revealed all but the Hudson Bay-Strait Complex population declined in effective population sizes following the last glacial period. Within the last several centuries, the Eastern High Arctic and Hudson Bay-Strait Complex populations have shown evidence for an increase in effective population size and have contemporary estimates greater than 2,000. The other four populations have contemporary estimates below 400. The very low effective population size estimates in Cumberland Sound, Little and Great Whale Rivers and James Bay, as well as the high inbreeding in the St. Lawrence Estuary indicate that these populations are in need of protective measures for long-term sustainability. These results have advanced our understanding of the dynamics of beluga genetics across eastern Canada and provide valuable metrics for conservation strategies.

evolutionary biology↗

bioRxiv2024

Urbanization is associated with reduced genetic diversity in marine fish populations

The economic and ecological benefits of living by the ocean have led many coastal settlements to grow into large densely populated cities. Large coastal cities have had considerable environmental effects on marine ecosystems through resource extraction, waste disposal, and use for transportation. Thus, it is important to understand the consequences of urbanization and human activities on evolutionary processes and biodiversity in marine fishes. Using published population genetic datasets for marine fishes amounting to 75,496 individuals sampled from 73 species at 1143 sample sites throughout the worlds oceans, we evaluated how human population density and a composite measure of cumulative human impacts affected genetic diversity and differentiation. We found that genetic diversity was significantly lower in marine fish populations associated with denser human populations regardless of species and locality. The effects of cumulative human impacts on genetic diversity were less prominent, perhaps due to this measure capturing more spatially varying processes. Urbanization in coastal regions has degraded marine biodiversity in a way that erodes adaptive potential for marine fish populations. This highlights the need to mitigate threats from human activities and focus efforts on sustainable urban planning and resource use to conserve marine biodiversity sustaining coastal fisheries and ecosystems.

evolutionary biology↗

bioRxiv2024

Climate change, age acceleration, and the erosion of fitness in polar bears

Climate change is increasingly disrupting evolved life history strategies and reducing population viability in wild species. Using estimates of epigenetic age acceleration, a cellular biomarker of lifetime stress and the expression of age-related phenotypes, we found that polar bears aged approximately one year faster for each degree of warming since the 1960s. Age acceleration was also associated with reproducing early in life, linking this cellular process to well-established life history theory. However, we found evidence for the erosion of fitness as epigenetic aging accelerated and temperatures increased. Finally, using a large pedigree, we found adaptive potential in our study population was approximately zero. Global temperatures will soon reach the levels of warming currently experienced by Arctic species, which could impose widespread physiological costs and limit adaptive capacities worldwide.

ecology↗

bioRxiv2024

Unraveling the genetic legacy of commercial whaling in bowhead whales and narwhals

Commercial whaling decimated many whale populations over several centuries. Bowhead whales (Balaena mysticetus) and narwhal (Monodon monoceros) have similar habitat requirements and are often seen together in the Canadian Arctic. Although their ranges overlap extensively, bowhead whales experienced significantly greater whaling pressure than narwhals. The different harvest histories but similar habitat requirements of these two species provide an opportunity to examine the demographic and genetic consequences of commercial whaling. We whole-genome resequenced Canadian Arctic bowhead whales and narwhals to delineate population structure and reconstruct demographic history. Bowhead whale effective population size sharply declined contemporaneously with the intense commercial whaling period. Narwhals instead exhibited recent growth in effective population size, reflecting limited opportunistic commercial harvest. Although the genetic diversity of bowhead whales and narwhals was similar, bowhead whales had more genetic diversity prior to commercial whaling and will likely continue to experience significant genetic drift in the future. In contrast, narwhals appear to have had long-term low genetic diversity and may not be at imminent risk of the consequences of the erosion of genetic diversity. This work highlights the importance of considering population trajectories in addition to genetic diversity when assessing the genetics of populations for conservation and management purposes.

genomics↗

bioRxiv2023

Climate change introduces threatened killer whale populations and conservation challenges to the Arctic

The Arctic is the fastest-warming region on the planet, and sea ice loss has opened new habitat for sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes, however, we know very little about killer whales in the Arctic. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demography. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic--one population is newly identified as globally distinct. The effective sizes of both populations recently declined, and both are vulnerable to inbreeding and reduced adaptive potential. Furthermore, we present evidence that human-caused mortalities, particularly ongoing harvest, pose an ongoing threat to these populations. The certainty of substantial environmental change in the Arctic complicates conservation and management significantly. Killer whales bring top-down pressure to Arctic food webs, however, they also merit conservation concern. The opening of the Arctic to killer whales exemplifies the magnitude of complex decisions surrounding local peoples, wildlife conservation, and resource management as the effects of climate change are realized.

genomics↗

bioRxiv2023

Migration distance and mating system are not associated with genetic diversity and differentiation among bats (Chiroptera)

Genetic variation is critical for evolutionary responses to environmental change. Links between genetic variation and behavioural or life history traits may reveal how varied strategies influence evolutionary trends in speciation and adaptation. Traits associated with movement typically correlate with population genetic structure and could help predict populations vulnerability to geographic processes such as habitat fragmentation and disease spread. With their wide diversity in behaviours and ecologies, bats provide a useful testing ground for hypotheses about population structure related to species-specific movement patterns. We used a global sample of microsatellite data (n=233 sites from 17 bat species) associated with published studies to examine potential links between genetic variation and migration and mating strategies. The genetic measures we tested were population-specific differentiation, gene diversity, and allelic richness. Using Bayesian models that accounted for phylogenetic distances among species, we identified no correlations between migration or mating strategy and genetic variation. Our results do not support long-standing hypotheses about dispersal-mediated genetic structure, and contrast with prior studies on bat genetic diversity and differentiation. We discuss the need for continued research into the complex association of ecological, biogeographical, and behavioural factors that facilitate gene flow among populations, especially in species with diverse movement patterns.

zoology↗

bioRxiv2023

Differences in the transcriptome response in the gills of sea lamprey acutely exposed to 3-trifluoromethyl-4-nitrophenol (TFM), niclosamide or a TFM:niclosamide mixture

Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America makes use of two pesticides: 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide, which are often co-applied. Sea lamprey appear to be vulnerable to these agents resulting from a lack of detoxification responses with evidence suggesting that lampricide mixtures produce a synergistic effect. However, there is a lack of information pertaining to the physiological responses of sea lamprey to niclosamide and TFM:niclosamide mixtures. Here, we characterized the transcriptomic responses of the sea lamprey to TFM, niclosamide, and a TFM:niclosamide (1.5%) mixture in the gill. Along with a control, larval sea lamprey were exposed to each treatment for 6 h, after which gill tissues were extracted for measuring whole-transcriptome responses using RNA sequencing. Differential gene expression patterns were summarized, which included identifying the broad roles of genes and common expression patterns among the treatments. While niclosamide treatment resulted in no differentially expressed genes, TFM- and mixture-treated fish had several differentially expressed genes that were associated with the cell cycle, DNA damage, metabolism, immune function, and detoxification. However, there was no common differential expression among treatments. For the first time, we characterized the transcriptomic response of sea lamprey to niclosamide and a TFM:niclosamide mixture and identified that these agents impact mRNA transcript abundance of genes associated with the cell cycle and cellular death, and immune function, which are likely mediated through mitochondrial dysregulation. These results may help to inform the production of more targeted and effective lampricides in sea lamprey control efforts.

genomics↗

bioRxiv2023

Microhabitat use of northern and southern flying squirrels in a recent hybrid zone

Secondary contact of closely related species may lead to hybridization if reproductive isolation is incomplete. Selection against hybrids may become reinforced if hybrid fitness is low. This can be evident from the divergence of isolating traits. We examined habitat use of northern (Glaucomys sabrinus (Shaw, 1801)) and southern (Glaucomys volans (Linnaeus, 1758)) flying squirrels in an area of secondary contact in Ontario, Canada. We looked at summer microhabitat use within sites of sympatry and allopatry to test for evidence of reinforcement due to diverging habitat use. We also examined differences in broad-scale habitat features at woodlots to determine predictors of species occurrence across sites. We used 18 years (2002 - 2019) of flying squirrel summer capture data from 6 sites along a north-south transect. Vegetation surveys were conducted at trap locations during summer 2016 to characterize the available microhabitats within sites. Site-level habitat variables were calculated using the collected microhabitat variables. We found microhabitat variables to be weak predictors of trap-level flying squirrel presence and we found no evidence of divergence in microhabitat use over the 18 years. Further, we found latitude, not broad-scale habitat, was the strongest predictor of site-level flying squirrel occurrence. Overall, our findings suggest that microhabitat-based isolation is not being reinforced between flying squirrels; however, hybridization may be limited to areas where climate and habitat is suitable for both species.

ecology↗

bioRxiv2023

Transcriptomic impacts and potential routes of detoxification in a lampricide-tolerant teleost exposed to TFM and niclosamide

Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America often relies on the application of 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide mixtures to kill larval sea lamprey. Selectivity of TFM against lampreys appears to be due to differential detoxification ability in these jawless fishes compared to bony fishes, particularly teleosts. However, the proximate mechanisms of tolerance to the TFM and niclosamide mixture and the mechanisms of niclosamide toxicity on its own are poorly understood, especially among non-target fishes. Here, we used RNA sequencing to identify specific mRNA transcripts and functional processes that responded to niclosamide or a TFM:niclosamide mixture in bluegill (Lepomis macrochirus). Bluegill were exposed to niclosamide or TFM:niclosamide mixture, along with a time-matched control group, and gill and liver tissues were sampled at 6, 12, and 24 h. We summarized the whole-transcriptome patterns through gene ontology (GO) term enrichment and through differential expression of detoxification genes. The niclosamide treatment resulted in an upregulation of several transcripts associated with detoxification (cyp, ugt, sult, gst), which may help explain the relatively high detoxification capacity in bluegill. Conversely, the TFM:niclosamide mixture resulted in an enrichment of processes related to arrested cell cycle and growth, and cell death alongside a diverse detoxification gene response. Detoxification of both lampricides likely involves the use of phase I and II biotransformation genes. Our findings strongly suggest that the unusually high tolerance of bluegill to lampricides is due to these animals having an inherently high capacity and flexible detoxification response to such compounds.

genomics↗

bioRxiv2022

SexFindR: A computational workflow to identify young and old sex chromosomes

Sex chromosomes have evolved frequently across the tree of life, and have been a source of fascination for decades due to their unique evolutionary trajectories. They are hypothesised to be important drivers in a broad spectrum of biological processes and are the focus of a rich body of evolutionary theory. Whole-genome sequencing provides exciting opportunities to test these theories through contrasts between independently evolved sex chromosomes across the full spectrum of their evolutionary lifecycles. However, identifying sex chromosomes, particularly nascent ones, is challenging, often requiring specific combinations of methodologies. This is a major barrier to progress in the field and can result in discrepancies between studies that apply different approaches. Currently, no single pipeline exists to integrate data across these methods in a statistical framework to identify sex chromosomes at all ages and levels of sequence divergence. To address this, we present SexFindR, a comprehensive workflow to improve robustness and transparency in identifying sex-linked sequences. We validate our approach using publicly available data from five species that span the continuum of sex chromosome divergence, from homomorphic sex chromosomes with only a single SNP that determines sex, to heteromorphic sex chromosomes with extensive degeneration. Next, we apply SexFindR to our large-scale population genomics dataset for sea lamprey, a jawless vertebrate whose sex determination system remains a mystery despite decades of research. We decisively show that sea lamprey do not harbour sex-linked sequences in their somatic genome, leaving open the possibility that sex is determined environmentally or within the germline genome.

evolutionary biology↗

bioRxiv2022

Population demography maintains biogeographic boundaries

Global biodiversity is organized into biogeographic regions that comprise distinct biotas. The contemporary factors maintaining differences in species composition between biogeographic regions are poorly understood. Given the evidence that populations with sufficient genetic variation can adapt to fill new habitats, it is surprising that we do not see more homogenization of species assemblages among regions. Theory suggests that the expansion of populations across biogeographic transition zones could be limited by environmental gradients that affect population demography in ways that could limit adaptive capacity, but this has not been empirically explored. Using three independently curated data sets describing continental patterns of mammalian demography and population genetics, we show that populations closer to biogeographic transition zones have lower effective population sizes and genetic diversity, and are more genetically differentiated. These patterns are consistent with reduced adaptive capacity near biogeographic transition zones. The consistency of these patterns across mammalian species suggests they are stable, predictable, and generalizable in their contribution to long-term limits on expansion and homogenization of biodiversity across biogeographic transition zones. Understanding the contemporary processes acting on populations that maintain differences in the composition of regional biotas is crucial for our basic understanding of the current and future organization of global biodiversity. The importance of contemporary, population-level processes on the maintenance of global biogeographic regions suggests that biogeographic boundaries are susceptible to environmental perturbation associated with human-caused global change.

ecology↗

bioRxiv2021

Variation in the transcriptome response and detoxification gene diversity drives pesticide tolerance in fishes

Pesticides are critical for invasive species management, but often have negative effects on non-target native biota. Tolerance to pesticides should have an evolutionary basis, but this is poorly understood. Invasive sea lamprey (Petromyzon marinus) populations in North America have been controlled with a pesticide lethal to them at lower concentrations than native fishes. We addressed how interspecific variation in gene expression and detoxification gene diversity confer differential pesticide sensitivity in two fish species. We exposed sea lamprey and bluegill (Lepomis macrochirus), a tolerant native species, to TFM, a pesticide commonly used in sea lamprey control, and used whole-transcriptome sequencing of gill and liver to characterize the cellular response. Comparatively, bluegill exhibited a larger number of detoxification genes expressed and a larger number of responsive transcripts overall, which likely contributes to greater tolerance to TFM. Understanding the genetic and physiological basis for pesticide tolerance is crucial for managing invasive species.

genomics↗

bioRxiv2021

Determinants of genetic diversity and species richness of North American amphibians

Ecological limits on the population sizes and number of species a region is capable of supporting are thought to simultaneously produce spatial patterns in genetic diversity and species richness. However, we do not know the extent to which resource-based environmental limits jointly determine these patterns of biodiversity in ectotherms because of their low energy requirements compared to endotherms. Here, we adapt a framework for the ways ecological limits may shape genetic diversity and species richness previously tested in mammals for amphibians to determine whether similar processes produce continental patterns of biodiversity across both taxa. Repurposing open, raw microsatellite data from 19 species sampled at 554 sites in North America we found that spatial patterns of genetic diversity run opposite to patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics are poor predictors of genetic diversity. Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in both amphibians and mammals, our results suggest that variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity.

evolutionary biology↗

bioRxiv2020

No Evidence of Toxoplasma Gondii Infection in Urban and Rural Squirrels in Southern Manitoba, Canada

Wildlife in cities can act as reservoirs for parasites that can infect domestic pets and have implications for human health. For example, the Coccidian parasite Toxoplasma gondii can infect all mammalian species, with felids acting as the only definitive hosts. Rodents, such as squirrels, could play an important role in urban infection dynamics of T. gondii, as squirrels occur at higher densities in cities than in natural environments and regularly share their territories with cats. In urban and suburban areas squirrels can encounter infectious oocysts shed in cat feces in contaminated soil or in the food they eat. They are also preyed upon by cats making them a potentially important species for completing the T. gondii life cycle in cities. We hypothesized that due to increased exposure to cats, urban squirrels would be more susceptible to T. gondii infection relative to squirrels in more natural areas. We investigated this using molecular and serological methods on samples collected from American red squirrels (Tamiasciurus hudsonicus), eastern grey squirrels (Sciurus carolinensis), northern flying squirrels (Glaucomys sabrinus), and least chipmunks (Tamias minimus) in and around the city of Winnipeg, Manitoba, Canada. We tested a total of 230 tissue samples from 46 squirrels for T. gondii DNA using quantitative PCR and supplemented these data with analyses of 13 serum samples from grey squirrels (Sciurus carolinensis) testing for T. gondii antibodies by indirect ELISA. We found no evidence of T. gondii infection in any squirrel. This suggests that squirrels may not be important intermediate hosts of T. gondii in cities and do not need to be considered as sources of infection to cats.

pathology↗

bioRxiv2020

Inconsistent effects of urbanization on amphibian genetic diversity

Habitat loss and fragmentation are leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing population sizes in human transformed habitats. With time this can lead to reduced effective population size and genetic diversity which restricts the ability of wildlife to cope with environmental change through genetic adaptation. However, it is not well understood whether these effects are generally applicable across taxa. Here, we repurposed and synthesized raw microsatellite data from online repositories from 19 amphibian species sampled at 554 sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density and the Human Footprint Index, we tested for generalizable effects of human land use on amphibian genetic diversity. We found no consistent relationships for any of our genetic metrics. While we did not detect directional effects for most species, a few generalist species responded positively to urbanization. These results contrast with consistent negative effects of urbanization in mammals and species specific positive and negative effects in birds. In the context of widespread amphibian declines, our results suggest that habitat loss in human transformed habitats is a more immediate concern than declining genetic diversity in populations that persist.

evolutionary biology↗

bioRxiv2020

Evidence for an extreme founding effect in a highly successful invasive species

The adaptive potential of invasive species is thought to decrease during founding events due to reduced genetic diversity, limiting the new populations ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (n = 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (n = 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (n = 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest that A. getulus has undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.

evolutionary biology↗

bioRxiv2020

Common causes drive negative correlations between nuclear genetic and species level biodiversity

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness would also limit population sizes, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and human disturbance explained 78% of variation in genetic diversity and 74% of the variation in species richness. These results suggest we can infer broad-scale patterns of species and genetic diversity using two simple environmental measures of resource availability and ecological opportunity.

evolutionary biology↗

bioRxiv2020

Socioeconomic variation across multiple cities predicts avian life-history strategies

Cities are the planets newest ecosystem and thus provide the opportunity to study community formation directly following major permanent environmental change. The human social and built components of environments can vary widely across different cities, yet it is largely unknown how these features of a city covary with the traits of colonizing species. We constructed a new dataset from open-source data with 44,670 observations of 160 Passerine species observed 1,908 urban areas across the United States. We found that as a citys housing density and median income increased it tended to support more migratory species and species with smaller body sizes and shorter lifespans. This suggests that differential survival and reproduction at the species-level can quickly generate geographical patterns of species trait variation across urban environments similar to those found in natural settings without the need for evolutionary change.

ecology↗