Daniel D. Heath's research while affiliated with University of Windsor and other places
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Publications (363)
Background
While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fi...
Environmental variation among isolated populations can drive genetic differentiation by selection, while isolation alone results primarily in genetic drift. Genetic analyses can aid in identifying genetically isolated populations and population structure of a species across its range. Additionally, such analyses can provide indirect evidence of loc...
Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression pattern...
Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three...
The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is no...
Does environmental DNA (eDNA) correlate more closely with numerical abundance (N) or biomass in aquatic organisms? We hypothesize that the answer is ‘neither’: eDNA production likely scales allometrically, reflecting key physiological rates and surface area-to-body mass relationships. Building on individual-level frameworks developed from the Metab...
Relating environmental DNA (eDNA) signal strength to organism abundance requires a fundamental understanding of eDNA production. A number of studies have demonstrated that eDNA production may scale allometrically—that is, larger organisms tend to exhibit lower mass‐specific eDNA production rates, likely due to allometric scaling in key processes re...
Abstract Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high detection sensitivity and relative ease of sample collection. Aquatic eDNA analyses have increased wor...
Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression pattern...
Inland fisheries assessment and management are challenging given the inherent complexity of working in diverse habitats (e.g., rivers, lakes, wetlands) that are dynamic on organisms that are often cryptic and where fishers are often highly mobile. Yet, technoscience is offering new tools that have the potential to reimagine how inland fisheries are...
Background
While many studies have reported that the structure of the gut and skin microbiome is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fi...
Among tropical organisms, heightened habitat specialization, limited natal dispersal, and strong philopatry suggests that many species may experience reduced rates of gene flow. Diverse forms of barriers, including geographic, ecological, and behavioural barriers, further promote genetic divergence among tropical bird populations. Here we extend ou...
Environmental DNA (eDNA) monitoring methods have played a significant role in improving fisheries management decisions. Yet, their impact to date has been rather limited in Canada, where eDNA analyses are only beginning to be used to inform management and conservation decisions, practices, and policies. Studies investigating hurdles to the incorpor...
Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week fo...
Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the...
Thriving freshwater fish populations contribute to people’s economic prosperity and wellbeing. Yet, freshwater fish populations are in critical condition around the globe. Most stressors to freshwater fishes, fisheries, and culture stem from habitat impacts, water-quality issues, and aquatic invasive species. Logistical difficulties of monitoring f...
Relating environmental DNA (eDNA) signal strength to organism abundance requires a fundamental understanding of eDNA production. A number of studies have demonstrated that eDNA production may scale allometrically – that is, larger organisms tend to exhibit lower mass-specific eDNA production rates, likely due to allometric scaling in key processes...
Transcriptomics provides a mechanistic understanding of an organism’s response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcr...
Aquaculture in North America is currently dominated by Atlantic salmon, but there has been an increasing interest in the production of species native to the Pacific coast. Chinook salmon is relatively new to production; therefore, the selection of appropriate stocks is critical. Often genes from wild populations are incorporated into farmed stocks...
Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where was...
Human activity can put non-game fishes at higher risk of extinction due to inappropriate management action. Eastern sand darter (Ammocrypta pellucida), a small benthic fish classified as threatened across much of its northern range, inhabits increasingly fragmented sandy habitats and, as a non-game fish, may be easily overlooked in conservation eff...
Environmental DNA (eDNA) is an emerging technology used for understanding ecosystems, environmental change, and stressors. Cellular and extracellular DNA are collected from environmental samples instead of individual wildlife animals, and as such eDNA comes with associated logistical and ethical benefits. It is increasingly being used, yet to date...
Background
Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian...
A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week...
Although genetic techniques are moving toward collecting massive amounts of genome-wide data through genome-scans, microsatellite markers (µsats) still provide a simple and cost-effective method for key applications such as parentage analyses, pedigree tracking, assessing likelihoods of disease conditions and DNA fingerprinting, among others. Newer...
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly...
Abstract Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies hav...
Animal culture changes over time through processes that include drift, immigration, selection, and innovation. Cultural change has been particularly well-studied for animal vocalizations, especially for the vocalizations of male animals in the temperate zone. Here we examine the cultural change in the vocalizations of tropical Rufous-and-white Wren...
The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether th...
Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropo...
Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-thr...
Adult size, egg size, fecundity, and mass of gonads are affected by trade‐offs between reproductive investment and environmental conditions shaping the evolution of life history traits among populations for widely distributed species. Coho salmon Oncorhynchus kisutch have a large geographic distribution, and different environmental conditions are e...
Elevated temperatures resulting from climate change are expected to disproportionately affect ectotherms given their biological function has a direct link to environmental temperature. Thus, as climate change leads to rapid increases in water temperatures in rivers, aquatic ectotherms, such as fish may be highly impacted. Organisms can respond to t...
Alternative reproductive tactics are widespread in fishes. In Pacific salmon, males either become a competitive hooknose, or a sneaker jack, which is undesirable in aquaculture when overabundant. Juveniles often experience accelerated growth prior to becoming jacks, potentially caused by increased competitiveness. We tested the behaviour of hatcher...
Johansson ML, Lavigne SY, Ramcharan CW, Heath DD, MacIsaac HJ. Detecting a spreading non-indigenous species using multiple methodologies. Lake Reserv Manage. XX:XX–XX.
Non-indigenous species (NIS) are often introduced to novel environments at very low population abundance. Detecting the presence of such an NIS can be very challenging, particularly...
As aquatic invasive species (AIS) proliferate worldwide, a better understanding of their roles in invaded habitats is needed to inform management and introduction prevention strategies and priorities. Metabarcoding of stomach content DNA (scDNA) shows considerable promise in such regard. We thus metabarcoded scDNA from two non-native fish species (...
Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhel...
This special issue features eleven articles presented at the Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS) conference in October 2018. The prominent theme in this special issue is methodological developments to enhance species and community characterization using eDNA, covering tree main scientific trends: validation of eDNA...
Analysis of food webs is important for defining functional components of ecosystems, but dietary data are often difficult to obtain and coarsely characterised. We compared three methods of rainbow trout ( Oncorhynchus mykiss (Walbaum); Salmoniformes: Salmonidae) and prickly sculpin ( Cottus asper Richardson; Scorpaeniformes: Cottidae) gut content a...
Biodiverse habitats are increasingly subject to an intensification of anthropogenic stressors that may severely diminish species richness. Invasive species pose a dominant threat to biodiversity and biosecurity, particularly in biodiversity hotspots like Kruger National Park, South Africa. The invasive silver carp, Hypophthalmichthys molitrix , was...
Improving the ability to detect and quantify rare freshwater fishes in remote locations is of growing conservation concern, as the distributions of many native fishes are contracting to such locations where there are reduced anthropogenic and invasive species pressures. However, conventional sampling methods, e.g., backpack electrofishing and seine...
Background:
Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate whether the same loci were involved in controlling body size and gene expression phenotypes, and to assess whether physiological tran...
The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for str...
Background
Aquatic invasive species (AIS) threaten ecosystems and native species.
Methods
To determine spatial distributions of at‐risk native taxa and AIS in two biologically diverse Laurentian Great Lakes tributaries, we extracted environmental DNA (eDNA) from water samples and used a universal PCR primer set targeting the CO1 gene for metabarco...
The view of maternal effects (non-genetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for st...
Carotenoids are primarily responsible for the characteristic red flesh coloration of salmon. Flesh coloration is an economically and evolutionarily significant trait that varies inter- and intra-specifically, yet the underlying genetic mechanism is unknown. Chinook salmon (Oncorhynchus tshawytscha) represents an ideal system to study carotenoid var...
![Heatmap of qPCR amplification (based on log10 [CT]) using TaqMan®...](publication/336048106/figure/fig1/AS:11431281180095831@1691499067245/Heatmap-of-qPCR-amplification-based-on-log10-CT-using-TaqManR-assays-in-the_Q320.jpg)
![Heatmap of qPCR amplification (based on log10 [CT]) using TaqMan®...](publication/336048106/figure/fig2/AS:11431281180095837@1691499069835/Heatmap-of-qPCR-amplification-based-on-log10-CT-using-TaqManR-assays-to-detect_Q320.jpg)
Improved recreational water monitoring using rapid molecular genetic methods would decrease both public health risks and unnecessary beach closures. Hence, we developed a novel nanofluidic quantitative real‐time PCR (qPCR) in the OpenArray platform to (a) detect and quantify fecal indicator bacteria (FIBs; N = 2), (b) identify contaminant sources (...
The most probable number dilution-culture assay (MPN) is used to enumerate viable phytoplankton in regulatory tests of ballast water treatment systems. However the United States Coast Guard has not yet accepted MPN, in part due to concerns of biased results due to cells being viable but not growing. MPN does not assess the fate of every cell, and t...
Salmon farming is one of Canada's fastest growing industries and contributes to Canada's economy as well as creating jobs in rural areas; however, the industry is challenged by the need to balance production economics against environmental impacts. While Atlantic salmon (Salmo salar) are the most commonly farmed species on the west coast of Canada,...
While outbreeding is a common method used to introduce variation to a broodstock in aquaculture to maintain healthy genetic stocks, little consideration is given to identifying stocks that can experience easy acclimation to captivity. Because the ability of individuals to behaviourally adjust to novel captive conditions influences who will reach br...
In British Columbia, Atlantic salmon (Salmo salar) are the top finfish aquaculture export of the province, although native Chinook salmon (Oncorhynchus tshawytscha) are also farmed locally. Few commercial facilities rear Chinook salmon, limiting the availability and development of their broodstocks, potentially reducing the ability to improve produ...
Aquaculture practices continuously seek to improve efficiency to produce larger fish at lower cost. Selective breeding within brood stocks can result in undesirable effects, promoting hatcheries to use outbreeding to increase or maintain genetic diversity. This practice however, could result in the introduction of wild behavioural phenotypes unable...
Olfaction mediates behaviors necessary for survival and reproduction in fishes. Anthropogenic inputs of contaminants into aquatic environments, specifically copper, are known to disrupt a broad range of olfactory-mediated behaviors and can cause long-lasting damage even at low concentrations that have profound impacts on the biology of aquatic orga...
Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population‐level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from...
Acid mine drainage (AMD) remediation commonly produces byproducts which must be stored or utilized to reduce the risk of further contamination. A mussel shell bioreactor has been implemented at a coal mine in New Zealand, which is an effective remediation option, although an accumulated sludge layer decreased efficiency which was then removed and r...
The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variabl...
The occurrence data based on eDNA metabarcoding analyses in my study focused on AIS and rare and at-risk native species can inform management strategies for both AIS eradication efforts and for conservation of native taxa. AIS appeared to occur mainly in the mid to upper reaches of the Grand River and the lower to mid-reaches in the east channel of...
Despite increased global interest in Chinook salmon aquaculture, little is known of their viral immune defenses. This study describes the establishment and characterization of a continuous cell line derived from Chinook salmon spleen, CHSS, and its use in innate immune studies. Optimal growth was seen at 14-18 °C when grown in Leibovitz's L-15 medi...
The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was suggested based on internal transcribed spacer 1 (ITS1) sequences from samples collected in Svalbard, Norway. Anothe...
A fundamental hypothesis about vocal learning is that young animals learn vocalizations in their natal areas and, following postnatal dispersal, they may introduce new types of vocalizations into their breeding areas. We tested this hypothesis in a tropical bird, the Rufous-and-white Wren (Thryophilus rufalbus), a species in which both sexes produc...
Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics it is commonplace for...
The selection for a single organismal trait like growth in breeding programs of farmed aquaculture species can counterintuitively lead to lowered harvestable biomass. We outbred a domesticated aquaculture stock of Chinook salmon (Oncorhynchus tshawytscha (Walbaum in Artedi, 1792)) with seven wild stocks from British Columbia, Canada. We then examin...
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical suppo...
The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify la...
Non-native species may be introduced either intentionally or unintentionally and their impact can range from benign to highly disruptive. Non-native salmonids were introduced into Lake Ontario, Canada, to provide recreational fishing opportunities; however, the establishment of those species has been proposed as a significant barrier to the reintro...
The gut microbial community in vertebrates plays a role in nutrient digestion and absorption, development of intestine and immune systems, resistance to infection, regulation of bone mass and even host behavior and can thus impact host fitness. Atlantic salmon (Salmo salar) reintroduction efforts into Lake Ontario, Canada, have been unsuccessful, l...
Low levels of heterozygosity can have detrimental effects on life history and growth characteristics of organisms but more subtle effects such as those on trade-offs of expensive tissues and morphological laterality, especially of the brain, have not been explicitly tested. The objective of the current study was to investigate how estimated differe...
Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute...
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designe...
Animals exhibit diverse dispersal strategies, including sex-biased dispersal, a phenomenon common in vertebrates. Dispersal influences the genetic structure of populations as well as geographic variation in phenotypic traits. Patterns of spatial genetic structure and geographic variation may vary between the sexes whenever males and females exhibit...
Post-copulatory sexual selection processes, including sperm competition and cryptic female choice (CFC), can operate based on major histocompatibility (MH) genes. We investigated sperm competition between male alternative reproductive tactics (jack (sneaker) and hooknose (guard)) of Chinook salmon (Oncorhynchus tshawytscha). Using a full factorial...
Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus...
Despite a well-developed theoretical basis for the role of genetic diversity in the colonization process, contemporary investigations of genetic diversity in biological invasions have downplayed its importance. Observed reductions in genetic diversity have been argued to have a limited effect on the success of establishment and impact based on empi...