Current and On-going Research at rare

Researcher Andrew MacDougall and students look over rare’s Blair Flats.     Photo courtesy of Peter Kelly.

At rare, we welcome researchers in a multitude of disciplines and are always looking for new and exciting research opportunities. We view rare as an opportunity to examine restoration and agricultural initiatives and to study the structure and functioning of a natural environment within an expanding urban area. Due to our goal of keeping over 900 acres intact and in perpetuity, we can uniquely offer stability to projects that extend over the long term. Individuals interested in conducting research at rare are encouraged to contact our Research Department to discuss their research ideas and needs. All researchers must file an Application to Conduct Research prior to initiating their project.

Below are the current and ongoing research projects taking place at rare. Click on any to be taken to the respective summary:

The origins and evolutionary history of feral apples in southern Ontario
University of Guelph, Department of Integrative Biology
Dane Cronin, M.Sc. Candidate. Supervisor: Dr. Brian Husband

Summary: Domesticated species can escape cultivation and establish feral populations in natural or semi-natural habitats. Non-native Malus domestica (domestic apple) is known to form feral populations in southern Ontario. At rare, there is a feral M. domestica population growing side by side with its native relative Malus coronaria, a crabapple species uncommonly found in the Carolinian Forest region. Hybridization is possible between the two species and has been shown to contribute to feral establishment in other domesticated species. Leaf samples from both species will be taken from rare and be used to amplify sections of the genome known as microsatellites (SSRs). These SSRs will be used to assess the extent of hybridization occurring between the species. The aim of this research is to genetically quantify the extent of hybridization occurring between M. domestica and M. coronaria and determine if it is key to feral population establishment.

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Understanding the decline of native bumble bee (Bombus spp.) pollinators in Canada using citizen science data
York University, Faculty of Environmental Studies
Victoria MacPhail, PhD Candidate. Supervisor: Dr. Sheila Colla

Summary: Pollinators are very important ecologically and economically but some are in decline.  Habitat loss, pesticide use and climate change may have contributed to the declines, but many hypotheses have not been tested for rare species in Canada due to lack of data.  BumbleBeeWatch.org (BBW) is a program where volunteers upload bumble bee photos to a website and work through an identification key to determine a species name, which experts verify.  Although many records have been submitted, this data has not been analyzed or compared to that collected by experts.  By using a database of expert-confirmed observations, data from BBW, and targeted field surveys, I will attempt to answer questions including: 1. Does BBW show increased distribution and abundance of bumble bees as compared to expert data? 2. Is habitat loss and/or land use changes driving the decline of bumble bees in Canada?  3. How can BBW data allow for increased conservation status assessments and effect conservation actions?  4. What is the diversity of bumble bees at high quality habitats like the rare property?  My work will fill knowledge gaps, improve conservation status assessments, recommend recovery actions and influence policy for actions related to bumble bees.

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Reducing noise pollution through ecosystem restoration
University of Waterloo, School of Environment, Resources, and Sustainability
Jonas Hamberg, PhD Candidate. Supervisor: Dr. Stephen Murphy

Summary: Noise is an increasingly important pollutant in the developed world, causing stress, high blood-pressure and lowered quality of life in humans and reducing habitat and diversity of wildlife. Natural areas are often relatively quiet because of the sound-dampening properties of vegetation and distance from human development. Fragmentation and disturbance of natural areas make it more difficult to find relative quiet, both for humans and for animals that communicate and avoid threats by sound. While noise-reduction and attenuation are considered ecosystem services, there is very little research quantifying the ability of restored ecosystems to reduce noise. This research will look at how restored tallgrass prairie and forest can be used to reduce and attenuate noise. Environmental noise will both be measured passively over time, and by playing back recorded noise at set frequencies and decibel level, measuring its reduction over a distance using a decibel meter. Noise pollution reduction is an important ecosystem service that can be added to the arguments for ecosystem restoration. It may also inform what type of restoration, conservation and enhancements are needed near sources of noise, for both human and animal wellbeing.

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Soil carbon storage in managed agricultural lands of southern Ontario
University of Guelph, Department of Integrative Biology
Annalisa Mazzorato, M.Sc. Candidate. Supervisor: Dr. Andrew MacDougall

Summary: Recent environmental and societal impacts from rising atmospheric carbon levels have motivated the exploration of various interdisciplinary studies with the goal to mitigate problems related to climate change. These rising emissions have been attributed to an increase in direct and indirect human activities such as land use change, expansion and intensification and increased fossil fuel use. Prairie grasslands cover approximately 20% of the Earth and are currently a rare and critical landscape in Canada and are highly influenced by management practices. Interestingly, these prairie grasslands have high biodiversity advantages yet are also renowned for their ability to store carbon and are increasingly the targets of marginal land “carbon farming” initiatives. Previous research on these critical landscapes in Canada have shown that grasslands have a large carbon reservoir when compared to other landscapes. The potential for the use of restored prairie grasslands in agricultural marginal lands for the purpose of long-term carbon sequestration has yet to be extensively examined even though grasslands contain approximately 12% of the global organic matter.

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iNaturalist: How citizen scientists use a smart phone app
University of Waterloo, Department of Anthropology
Stuart Anderson, M.Sc. Candidate. Supervisor: Dr. Goetz Hoeppe

Summary: This project is designed to analyze how scientists, both expert and citizen, make their choices when it comes to the media they use to collect data in the field. At the centre of this study is the smartphone application, iNaturalist, which is used to collect and add information to a database of various species living within an area. Whether or not a scientist chooses to use iNaturalist may affect the end result, and this project aims to explore how and why an individual may choose to use, or not to use, iNaturalist to collect taxonomic data. All media have affordances that make them a better choice for a particular user and part of this project’s aim is to determine what benefits and disadvantages iNaturalist has compared to other forms of media. The BioBlitz at the rare Charitable Research Reserve is an excellent opportunity to observe and participate in an event that uses this medium as a new tool for gathering biodiversity information. While scientists and students are following the plants and animals, I will be following the people to determine what choices are being made and how they come to their decisions.

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Establishing risk maps of emerging infectious diseases for at-risk amphibians in Ontario
Trent University, Department of Biology
Amanda Bennett, Post-doctorate Fellow. Supervisor: Dr. Dennis Murray

Summary: Ranavirus and chytrid have been identified as emerging infectious diseases, and have caused severe declines in amphibian populations worldwide. We are sampling adult and larval amphibians across Ontario to look for the presence and severity of disease in areas of overlap with species-at-risk habitat. Specifically, we’re looking at Ranavirus and chytrid fungus and their distribution in Ontario.

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Rural and urban coyote dietary compositions: insights from DNA analysis
University of Guelph, Department of Integrative Biology
Sarah Yoshida, undergraduate student. Supervisor: Dr. Robert Hanner

Summary: Over the past ten years, the polymerase chain reaction (PCR), has become a common method for conducting dietary analyses of predator scat. This approach enables researchers to gain a more precise insight into diet breadth and predation patterns than traditional morphological identification of animal remains. It may also help researchers detect subtle predation patterns that may not have previously been detectable using morphological techniques. PCR has been used to analyze the scats of many large mammalian predators including many closely related Canid species. However, this technique has not been used to conduct diet analyses in coyotes (Canis latrans) or used to compare diets between populations. By using PCR to perform diet analyses on different coyote populations, researchers can more accurately demonstrate how resource use within species differs spatially and temporally. In this study, we will be assessing how small mammal diversity in coyote diets differs between rural and urban coyote populations in southern Ontario.

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Effects of agricultural intensification on juvenile survival and dispersal in the Savannah Sparrow
York University, Department of Biology
Heidi van Vliet, M.Sc. Candidate. Supervisor: Dr. Bridget Stutchbury

Summary: Grassland birds have been in decline in North America for several decades. Habitat loss and degradation through agricultural intensification is one of the primary causes of these declines. This research will compare the breeding success and survival of juvenile Savannah Sparrows (Passerculus sandwichensis), a declining grassland species, between agricultural and non-agricultural land. I will be testing the hypothesis that agricultural intensification negatively effects breeding success and nestling body condition, and, subsequently juvenile survival. Little is known about the direct effects that agriculture has on the breeding success of grassland songbirds, and there is a large gap in the literature focusing on juvenile survival, dispersal, and migration. In my study, I will be utilizing a new technology for tracking songbirds, the Motus Wildlife Tracking System, to monitor juvenile birds once they leave the nest and their parent’s territory. This radio telemetry array extensively covers southern Ontario, where my proposed research will take place and will allow me to track the juvenile birds to understand their survival, dispersal, and the onset of the fall migration. Understanding all aspects of a bird’s life, and what stages of their life are more sensitive, is critical to the conservation of declining migratory songbirds.

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The significance of synanthropic stress physiology for sylvatic disease dynamics in Sciurus carolinensis
University of Guelph, Department of Integrative Biology
Mason Stothart, M.Sc. Candidate. Supervisor: Dr. Amy Newman

Summary: One of the primary mechanisms hypothesized to facilitate the invasion of nascent niches created by urbanization is synanthropic modification of a species’ stress response. In vertebrates, stress physiology plays an important role in regulating everything from homeostasis and immunity, to ‘fight or flight’ behavioural responses. The closer human-association implicit in synurban adaptive modification of an organism’s stress response, would not only increase incidences of human-wildlife conflict, but also zoonotic disease risk. Further exacerbating this risk is the connection between stress and immune physiology, since changes in the former could compromise the latter, thereby increasing pathogen prevalence on the urban environment. While the importance of understanding these processes is emphasized in the literature, little is known about synurban stress physiology, and even less about its interaction with disease transmission. Using a combination of field, lab, and citizen science techniques, I propose to characterize longitudinal synanthropic patterns in stress/immune physiology, and disease ecology in urban and exurban populations of eastern grey squirrels (Sciurus carolinensis).

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Management of giant hogweed using chemical and manual control options with a focus on seed viability after regeneration
University of Guelph, Department of Plant Agriculture
Meghan Grgruic, M.Sc. Candidate. Supervisor: Dr. François Tardif

Summary: As a human facilitated introduced species, giant hogweed poses a threat to habitat diversity and ecosystem health. As an invasive species, giant hogweed is thought to reduce diversity among native plant communities where its colonies have established. This is especially true when monocultures become established within populations due to the high quantity of seeds produced per plant. Its large leaf area has the potential to shade smaller plants, as well as increase riverbank erosion when the senescence of vegetation creates bare ground in the fall and winter. This erosion can have a number of consequences, including the threat to fish and other organisms, from both changes to their habitat and possible addition of chemical substrates. With these negative influences giant hogweed has on communities it’s invaded, safe and effective management is important. Giant hogweed’s proximity to water makes control without chemicals necessary but challenging due to its persistence and regenerative abilities. This research will investigate different manual control treatments and how they affect the ability hogweed has to produce viable seed through regeneration.

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From field to forest: monitoring the distribution of the invasive fruit fly pest, D. suzukii, in a non-agricultural setting
Wilfrid Laurier University, Department of Biology
Yvonne Young, M.Sc. Candidate. Supervisor: Dr. Tristan Long

Summary:  Drosophila suzukii, commonly referred to as the spotted-wing drosophila, is an invasive vinegar fly of Asian origin that attacks ripening or ripe, sound fruit.  Clearly a significant pest to the soft-fruit industry, it is possible this species may also significantly utilize naturalized plants of wild North America.  In fact,  in Ontario, berries of Rhamnus cathartica (buckthorn) have been confirmed to be infested by this species.  The impact this species has upon natural ecosystems, however, remains far from known.  Here, I propose a research project that will provide a baseline understanding of how D. suzukii is distributed among old forest interiors, forest edges and flood plains using traps and collections of fruit.  Additionally, previously non-identified host plant species attacked by this insect will be catalogued.  Understanding how D. suzukii distributes itself among different landscapes and which plant species are attacked will be an important first step in designing better management strategies (e.g. knowing where to focus efforts for best impact) and will provide direction for future studies looking at ecosystem changes brought about by this invasive species (e.g. knowing which habitat types D. suzukii is attacking).

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Community assessment of invasive earthworms in restored Southern Ontario tallgrass prairie
University of Waterloo, School of Environment, Resources, and Sustainability
Heather Cray, Ph.D. Candidate. Supervisor: Dr. Stephen Murphy

Summary: Since only 1-3% of tallgrass prairie habitat remains in North America, dedicated citizens, scientists, and government officials are working to restore prairie in southern Ontario. Most of these restorations are done by either hand-broadcasting or drilling-in seeds on ex-agricultural land. While there is increasing evidence that invasive earthworms are important ecosystem engineers, surprisingly little is known about their effect on invaded habitat. Despite knowing that exotic earthworms are spreading across Ontario and that they both eat and bury seeds, key information about the presence, community structure, and population density of these seed predators is lacking. This project will address this knowledge gap at rare by assessing the earthworm population in the restored tallgrass prairie at the rare Charitable Research Reserve. The results of this work will inform future prairie restoration by adding another piece to the complex food web of establishing habitats and will deepen our understanding of factors related to earthworm invasion.

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Spatio-temporal and population-level variation in avian immune-genes and parasite communities
Western University, Department of Biology
Leanne Grieves, Ph.D. Candidate. Supervisor: Dr. Beth MacDougall-Shackleton

Summary: Blood-borne parasites are found on nearly every continent and infect approximately 70% of bird species worldwide. Given their ability to infect multiple species and the anticipated range expansions of parasites associated with climate change, understanding host-parasite interactions is increasingly important. The major histocompatibility complex (MHC) is a diverse gene family that plays a crucial role in the immune response to pathogens. MHC genotypes may affect the ability of populations to persevere under changing parasite pressures. I will study three song sparrow populations in Ontario, including sparrows at the rare Charitable Research Reserve. Using next-generation sequencing, microscopy, and song analysis software, I will explore whether 1) MHC genotypes are correlated with parasites, 2) different breeding populations show differences in parasite load (intensity of infection) and diversity (number of lineages), 3) parasite communities differ throughout the breeding season, and 4) increased parasite load decreases song performance. Understanding population differences in how birds cope with parasitic infections and the correlations between infection and fitness may inform future management decisions in songbirds.

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Vibrational signals: sexual selection and species boundaries in Phymata
Royal Ontario Museum, Department of Natural History
Dr. David Puzalan

Summary: Despite a long and successful tradition of studying animal signaling and communication, only recently have biologists been able to uncover a form of communication that is ubiquitous and remarkably diverse among invertebrates: vibrational signaling. In the ambush bug Phymata americana, an insect native to old fields in Southern Ontario, vibrational communication has been observed but not officially described, let alone understood in terms of its adaptive function. David’s goal is to identify how these signals might be employed during courtship and its potential role for maintaining reproductive isolation between P. americana and a related species, P. pennsylvanica. The initial phase of the work simply requires the collection and identification of the species present at rare. Analysis of vibrational signals in these insects is possible due to the advent of technological tools allowing the capture of substrate-borne vibrations (i.e. laser vibrometry) and some preliminary work suggests stereotyped signals are generated by both sexes during courtship. Formal analyses incorporating aspects of vibrational communication are required to determine whether these signals are targets of directional selection as predicted by several models of sexual selection invoking mate choice.

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Assessing the consequences of gene flow between cultivated apples (Malus x domestica) and their wild relatives
University of Guelph, Department of Integrative Biology
Paul Kron, Research Associate. Supervisor: Dr. Brian Husband

Summary: Closely related species can sometimes reproduce to produce hybrid organisms. Two such species are the domestic apple and the wild crabapple. Paul is studying the complex genetic interactions between these two species. This involves several components. What is the genetic variability within the wild crabapple? What is the fate of hybrids in the natural environment; i.e. do they survive and reproduce? Over 25 saplings from each of five genetically different apple strains were grown from seeds collected on rare property (three crabapple variants plus two hybrids with the domestic apple) and planted in the alvar complex. The fate of these individuals is being monitored over a ten-year period. The genetic variation of pollen and seed from mature trees of both species will also be determined. This will provide insight into the nature of the reproductive pathways that occur among these two species that lead to the production of fruits and seed. This research will provide important information on the potential impacts of introducing genetically-modified organisms (organisms intentionally modified by humans) into the landscape.

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Long-term restoration of tallgrass prairie
University of Guelph, Department of Integrative Biology
Dr. Andrew MacDougall

Summary: Tallgrass prairie formerly occupied 80,000 to 100,000 hectares in southwestern Ontario but less than 5% of that remains. Andrew plans to convert an agricultural field on rare property (most recently used to grow soybeans) into a native tallgrass prairie. There are several main goals of this research. The first is to determine the factors that ensure success in prairie restoration especially the ability of tallgrass prairies to resist invasion from non-target species; particularly exotic agronomic grasses. The second objective is to determine the factors that influence the pattern of distribution of plant species in a tallgrass prairie; i.e. are these factors environmental or non-environmental? The third objective is to restore a tallgrass prairie research site that will eventually look like a tallgrass prairie rather than a checkerboard pattern of research plots that will require constant maintenance. This sampling design will help address the research questions but will also restore the function of this ecosystem for creatures such as birds, insects and small mammals. The research project consists of a five-year building phase followed by a longer-term monitoring and manipulation phase.

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Influence of riparian and hyporheic zones on stream hydrology and nutrient biogeochemistry
University of Waterloo, Department of Earth and Environmental Sciences
Philippe Van Cappellen

Summary:Traditionally, management of water resources has focused on surface water bodies (streams, lakes, reservoirs, wetlands, etc.) or on groundwater as if they were separate entities. As the use of land and water resources intensifies, the hydraulic connection between surface water and groundwater has become recognized as a crucial element in water management. This research will monitor the spatial distributions of nutrient elements (C, N, P, Si, K and S) and key biogeochemical redox indicators (in particular, iron) in the riparian and hyphoreic zones of a small, groundwater-fed stream on the rare Charitable Research Reserve over the course of one year. The spatio-temporal patterns will be used to unravel the key biogeochemical transformations affecting nutrient speciation and fluxes within the riparian and hyporheic filter zones, and establish their response to seasonal variations in stream hydrology, soil temperature and biological activity.

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A constructive approach to maintaining nesting habitat for Barn Swallows in Ontario 
Bird Studies Canada
Kristyn Richardson

Summary: Barn swallows nest almost exclusively on human-made structures such as barns, sheds, bridges and culverts and are the most widely distributed of all swallows. As such, many people would be shocked to learn that the Ontario populations has declined by 66% since 1970. Despite how frequently humans overlap with these swallows (part of a group of birds collectively called aerial insectivores because of their habit of eating flying insects while flying high in the air) we know relatively little about them. While the causes of these declines are unknown, here in Ontario educations in the amount of available nesting habitat as well as human-caused disturbance are two potential reasons. The results of the artificial nesting structure project on the rare property, as well as the complimentary social cues research, will be used to determine what breeding habitat characteristics are most important for Barn Swallows in Ontario and inform Best Management Practices for the conservation of this species.

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Exploring toxicity responses and bioaccumulation in the Hyalella azteca species complex
University of Waterloo, Department of Biology,
Jessica Leung, Ph.D. Candidate. Supervisors: Dr. Jonathan Witt and Dr. George Dixon

Summary: Hyalella azteca is not just a single species, but several distinct species erroneously grouped together due to morphological similarities. For my project, I hope to collect different species that belong to the H. azteca complex to monitor their different nutritional needs. In addition, I hope to expose them to metals to see whether differences in mortality and bioaccumulation exists within the H. azteca complex.

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Distribution and function of soil Thaumarchaeota
University of Waterloo, Department of Biology,
Xinda Lu, Ph.D. Candidate. Supervisor: Dr. Josh Neufeld

Summary: Nitrogen is a key element controlling terrestrial productivity. Nitrification, mediated by microorganisms, converts reduced (ammonia) to oxidized (nitrite and nitrate) forms of nitrogen. Nitrification has profound influences on the environment, for example, by contributing greenhouse gasses (nitrous oxide) and leaching fertilizer nitrogen (nitrate). Although nitrification has been studied for over a century, it is only recently that ammonia-oxidizing archaea (AOA) were discovered in addition to their counterparts, ammonia-oxidizing bacteria (AOB), which were formerly regarded as the sole contributors to nitrification. Since their discovery, questions regarding the ecology, physiology, and metabolism of AOA are still not well answered. This project will combine molecular methods, microcosm incubations, and bioinformatics to study the biogeography and activity of soil AOA in an effort to better understand AOA distributions and function. As main part of this project, soil samples will be collected at rare Charitable Research Reserve, and microcosm incubation will be set up under different conditions (temperature and substrate form). Short-term and long-term soil incubation aim at elucidating the influence of temperature and different forms of nitrogen (organic/inorganic) on AOA activity, adding more evidence to the niche seperation of soil AOA.

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DNA Barcoding Aquatic and Soil Mites of the rare Charitable Research Reserve
Centre for Biodiversity Genomics, University of Guelph, Department of Integrative Biology,
Monica Young, Ph.D. Candidate. Supervisor: Dr. Paul Hebert

Summary: Mites are one of the most abundant and diverse groups of arthropods, and inhabit a vast array of ecological niches including aquatic and terrestrial habitats. However, mites are rarely targeted for detailed biodiversity surveys because of taxonomic barriers.  The status of many species is uncertain due to synonymies, morphotypes which are distinct species, and sexual dimorphisms.  These factors inhibit detailed assessments of the fauna, such as estimating species diversity and distribution patterns in space or time. However, the use of DNA barcoding can alleviate such barriers by providing a transparent, consistent method for delineating species, and serve as a window into the patterns of molecular evolution that underlie species diversity.  Evaluating mite diversity with the use of DNA barcoding at the rare Charitable Research Reserve will provide a comprehensive assessment of the mite diversity in aquatic and terrestrial (soil) habitats in the reserve. Moreover, the survey may provide insights into several taxonomic issues common in acarology, such as cryptic species and synonymies related to life stage or sexual dimorphism.

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rare Charitable Research Reserve
1679 Blair Road
Cambridge, ON N3H 4R8
(519) 650-9336
Charitable Registration:
#8776 15914 RR0001