The CSEE Excellence in Doctoral Research Award Symposium showcases excellent Ph.D. student research in ecology and evolution from society members. The 2022 awardees will present an overview of their thesis research in this annual celebration of outstanding student achievement.
Winners: Allison Binley, Carleton University James Santangelo, University of Toronto Tia Harrison, University of Toronto Ariel Greiner, University of Toronto Mason Stothart, University of Calgary
Global urban environmental change drives adaptation in white clover
Presenting Author: James S. Santangelo, Department of Ecology & Evolutionary Biology, University of Toronto
Co-Author: Rob. W. Ness: Department of Biology, University of Toronto Mississauga; Marc T. J. Johnson: Department of Biology, University of Toronto Mississauga
+284 other authors from the Global Urban Evolution Project (email addresses and affiliations not shown)
Approximately 55% of the world’s human population currently lives in cities, a figure that continues to increase annually. Because cities are constructed to suit the needs of humans, urban environments around the world are predicted to be more like one another than to their own surrounding non-urban habitat, which may drive parallel evolutionary responses to urbanization. In my thesis, I tested these predictions and leveraged large-scale, replicated urban environments to examine the extent of parallel evolution in the production of hydrogen cyanide (HCN)—an ecologically important antiherbivore defense that also affects tolerance to abiotic stressors (e.g., drought, frost)— in natural populations of white clover (Trifolium repens). Using observational, experimental, theoretical, and genomic approaches, I have shown that urbanization drives repeated reductions in the frequency of HCN in 16 eastern North American cities. I later expanded this work across the globe and showed that urban habitats around the world have converged to similar environmental features: cities are warmer, less vegetated, and contain more impervious surfaces than surrounding non-urban habitats. These convergent urban environments have driven changes in the frequency of HCN in urban populations (i.e., urban-rural HCN clines) in 47% of the 160 cities sampled. While previous work of mine suggested that clines could be driven by random evolutionary processes, whole genome sequencing of 2,074 plants from 26 cities has confirmed that clines are adaptive. Indeed, variation in the strength of clines could be predicted by urban-rural changes in the strength of drought and herbivory, factors also known to influence HCN frequencies at continental scales. My work has contributed to long-standing questions in evolutionary biology regarding the extent of parallelism in nature and provides fundamental insight into the drivers of evolution in one of the planet’s fastest growing and most environmentally destructive forms of land use-change: urbanization.
Selection and transmission of the feral hindgut fermenter microbiome
Presenting Author: Mason R. Stothart, Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB,
Co-Author: Philip D. McLoughlin, Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada; Alastair J. Wilson, Centre for Ecology and Conservation, University of Exeter, Penryn, UK; Jocelyn Poissant, Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
Animal-associated microbiomes are now recognized to partly define the ecological niche of their host, by helping to shape organismal responses to environmental and homeostatic challenges. However, despite theorization, we lack empirical estimates for the fitness consequences of microbiome variation in the wild, and have yet to fully test the mechanisms that govern the intergenerational transmission of microbiota under ecologically realistic conditions. Using over a decade of survey data and 7 years of archived fecal samples from a long-term individual-based ecological study of Sable Island feral horses (>2700 samples spanning 904 individuals), I used a shallow shotgun metagenomic sequencing approach to: 1) characterize intrinsic and extrinsic determinants of microbiome community structure and functional potential, 2) estimate selection acting on the host through its microbiome, and 3) estimate the heritability and transmissibility of fitness related microbiome features using quantitative genetic animal models. Surprisingly, non-bacterial microbiota had among the most deleterious effects on host survival and reproductive success. Conversely, cellulolytic bacteria and functional traits which contribute to the removal of waste products generally correlated with host survival and reproductive success. However, different mechanisms appear to structure the inter-generational transmission of bacterial versus non-bacterial microbiota between hosts. In size and longitudinal detail this is one of the world's largest microbiome studies of a free-living non-human host population. These results represent some of the first quantitative demonstrations of selection acting on the host-microbiome relationship, and provide the first heritability estimates for fitness-component related microbiome features.
Variation in mutualism: across invaded ranges, latitude, and genomes
Presenting Author: Tia Harrison, Ecology and Evolutionary Biology, University of Toronto Co-Author: Zoe Parshuram, Ecology and Evolutionary Biology, University of Toronto; Anna Simonsen, Department of Biological Sciences, Florida International University; Megan Frederickson, Ecology and Evolutionary Biology, University of Toronto; John Stinchcombe, Ecology and Evolutionary Biology, University of Toronto
Leguminous plants have specific adaptations called root nodules to receive fixed nitrogen from bacteria called rhizobia but they also interact with a wide variety of other soil microbiota at the same time. An important question in ecology and evolution is if host specificity of plant microbiomes shape plant geographic ranges or vice versa. I analyzed published data and 16S rRNA rhizobia sequences that associate with 156 legume species spanning the legume phylogeny and globe to determine if specificity on rhizobia impacts a legume’s invasive ability. I found that generalist legumes (having many rhizobia partners) occur in more introduced ranges than specialists (having one or few partners) suggesting that specialist legumes have difficulty finding compatible rhizobia outside their native range. However, research has shown that nodules can contain diverse communities of bacteria including non-rhizobia microbes that cannot form nodules or fix nitrogen. Therefore, I investigated how the total nodule community varies across geographic space. I sampled Chamaecrista nictitans root nodules from 33 populations ranging from temperate to tropical locations. I uncovered a latitudinal diversity gradient in the non-rhizobia portion of the nodule community but not the rhizobia community. I tested the effects of three non-rhizobia strains on plant growth and found that these bacteria are commensals – species that benefit from associating with a host but are neutral for host fitness. My results suggest that in tropical nitrogen rich soils, plants associate with a higher diversity of non-rhizobia strains because there is less of a need for fixed nitrogen. Most work on mutualism focuses on ecological and evolutionary consequences for the host plant in the interaction and thus there is a need for more research from the microbe’s perspective. It is unclear whether microbes in mutualism experience rapid evolution compared to free-living strains. Molecular resources for bacteria are growing and sequencing technology is improving which allows us to quantify rates of evolution at the molecular level in an increasing number of species. Therefore, I calculated rates of molecular evolution in 22 sequenced bacteria species from NCBI that included 11 mutualistic rhizobia species and 11 closely related free-living bacteria species to determine if mutualism increases or slows rates of molecular evolution. I found that when there is a loss of mutualism with plants in the bacteria phylogeny, the free-living species experience higher rates of molecular evolution genome wide suggesting that rapid evolution is required to adapt to a free-living stage.
Consequences of Multiple Stability and Connectivity in Coral Reef Ecosystems
Presenting Author: Ariel Greiner, University of Toronto, PhD Candidate (ariel.greiner@mail.utoronto.ca) Co-Author: Emily Darling, Marine Program, Wildlife Conservation Society and Ecology and Evolutionary Biology, University of Toronto; Marco Andrello, Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS; Yashika Nand, Wildlife Conservation Society Fiji; Sangeeta Mangubhai, Talanoa Consulting Fiji; Stacy Jupiter, Wildlife Conservation Society Melanesia; Marie-Josée Fortin, Ecology and Evolutionary Biology, University of Toronto; Martin Krkošek, Ecology and Evolutionary Biology, University of Toronto
Background/Question/
Methods: Coral reefs are interconnected by larvae (coral, etc.) dispersing passively along ocean currents, creating networks. The topology of these networks will likely change because anthropogenic stressors are destroying coral habitat and altering coral communities, shifting reefs from the coral-dominated to the unfavourable macroalgal-dominated stable state. However, it is unclear whether these connectivity changes could themselves propagate or contain shifts to the unfavourable state. My doctoral research fills this gap by investigating how reef connectivity and multi-stability combine to affect coral persistence with the goal of informing conservation decisions. First, I explored how plausible scenarios of climate-change-induced loss followed by re-seeding could change global coral dispersal networks. Then, I used a mathematical model to determine how traditional coral-macroalgal bistability is affected by the addition of a second explicit reef. And lastly, I am working with the Wildlife Conservation Society (WCS) Fiji to develop a Fijian reef model to elucidate the interplay between connectivity and multi-stability in larger networks for the first time and posit effective management intervention strategies.
Results/
Conclusions: First, I found that depending on the scenario of loss modelled, vastly different global reef networks could result–though unfortunately, full natural re-seeding was not possible. Secondly, through the use of a mathematical model of two connected reefs, I showed that when coral and macroalgal dispersal is included explicitly, coral reefs may exhibit a novel mixed coral-macroalgal stable state and demonstrate that high and low-grazing reefs are bistable (the coral-dominated and macroalgal-dominated states are both stable) if they are connected by high dispersal to a low or high-grazing reef (respectively). This is in contrast to the traditional perception from single reef models that there are only two possible stable states (coral-dominated or macroalgal-dominated) and that high-grazing reefs only have a coral-dominated stable state and low-grazing reefs only have a macroalgal-dominated stable state, but aligns with empirical observations. Lastly, preliminary results from my research with WCS Fiji show that low levels of grazing and connectivity among Fijian reefs is driving them to low coral levels which could be mitigated by increasing grazer levels. Overall, my thesis emphasises the importance of connectivity to coral reef management by showing that natural larval dispersal is (1) not sufficient to restore coral habitat and (2) is sometimes beneficial to maintaining coral-dominance. Furthermore, my research increases our general understanding of multi-stable ecosystems responses to connectivity changes and pioneers novel methods for improving reef management.
From Better Monitoring to Better Decisions: Improving Conservation using Community Science Data
Presenting Author: Allison Binley, Carleton University; Joseph R. Bennett, Department of Biology, Carleton University Co-Author:Richard Schuster, Nature Conservancy of Canada; Amanda D. Rodewald, Cornell Lab of Ornithology, Cornell University); Frank A. La Sorte, Cornell Lab of Ornithology, Cornell University; Daniel Fink, Cornell Lab of Ornithology, Cornell University; Benjamin Zuckerberg, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison; Scott Wilson, Wildlife Research Division, Environment and Climate Change Canada; Adam C. Smith, Canadian Wildlife Service, Environment and Climate Change Canada, National Wildlife Research Centre; Orin Robinson, Cornell Lab of Ornithology, Cornell University;Tom Auer, Cornell Lab of Ornithology, Cornell University; Alison Johnston, Cornell Lab of Ornithology, Cornell University; Viviana Ruiz-Gutierrez, Cornell Lab of Ornithology, Cornell University; Gregory Golet, The Nature Conservancy; Mark Reynolds, The Nature Conservancy; Jeffrey Hanson, Department of Biology, Carleton University
Understanding and abating threats to biodiversity requires extensive data collection, and yet doing so is logistically challenging and depletes funds that could otherwise be spent on action. Fortunately, we have already accrued vast quantities of data on biodiversity collected by amateurs and professionals alike. My research aims to put these data to work, demonstrating how they can help compensate for monitoring biases, fill knowledge gaps, and improve conservation decision making, all while reducing the cost to do so. Data collected through an opportunistic community science dataset can be used to model population trends under similar frameworks to professional monitoring schemes, while accounting for the additional noise and variability present in such datasets. Since these data are often collected at much broader spatial scales than conventional monitoring programs, it can help us to better understand how species respond to anthropogenic pressures differently across time and space. Basing conservation decisions on community science data can also help redistribute resources from monitoring to action, with ultimately better outcomes for biodiversity. Although large noisy datasets present many analytical challenges, my research shows that using them can directly improve our capacity to make informed decisions and ultimately lead to more effective and efficient conservation. Conservation science is a crisis discipline, and we must bring all possible tools to bear before species are lost for good.
