Fall 2021 Seminars


December 10, 2021

Dr. Pierre Legendre, Universite de Montreal POSTER


Temporal beta diversity: identify sites where species communities have changed in exceptional ways


Aim This paper presents the statistical bases for temporal beta diversity analysis, a method to study the changes in community composition through time from repeated surveys at several sites. Surveys of that type are presently done by ecologists around the world. A Temporal Beta-diversity Index (TBI) is computed for each site, measuring the change in species composition between the first (T1) and second surveys (T2). TBI indices can be decomposed into losses and gains; they can also be tested for significance, allowing one to identify the sites that have changed in composition in exceptional ways. This method will be of value to identify exceptional sites in space-time surveys carried out to study anthropogenic impacts, including climate change.
Innovation The null hypothesis of the TBI test is that a species assemblage is not exceptionally different between T1 and T2, compared to assemblages that could have been observed at this site at T1 and T2 under H0. Tests of significance of coefficients in a dissimilarity matrix are usually not possible because the values in the matrix are interrelated. Here, however, the dissimilarity between T1 and T2 for a site is computed with different data from the dissimilarities used for the T1–T2 comparison at other sites. It is thus possible to compute a valid test of significance in that case. In addition, the paper shows how TBI dissimilarities can be decomposed into loss and gain components (of species, or abundances-per-species) and how a B-C plot can be produced from these components, which informs users about the processes of biodiversity losses and gains through time found in space-time survey data.
Applications An application of the method to the Barro Colorado Forest Dynamics plot (BCI, Panama) will be presented in detail, comparing the 1985 and 2015 surveys. Applications of the method to other ecological communities will be mentioned, including a study of paleo-ecological data. This method is applicable worldwide to all types of communities, marine and terrestrial. R software is available implementing the method.
Brice, M.-H., K. Cazelles, P. Legendre & M.-J. Fortin. 2019. Disturbances amplify tree community responses to climate change in the temperate-boreal ecotone. Global Ecology & Biogeography 28:1668–1681.
Kuczynski, L., P. Legendre & G. Grenouillet. 2018. Concomitant impacts of climate change, fragmentation and non-native species have led to reorganization of fish communities since the 1980s. Global Ecology and Biogeography 17: 213–222.
Legendre, P. 2019. A temporal beta-diversity index to identify sites that have changed in exceptional ways in space-time surveys. Ecology and Evolution 9: 3500–3514. https://doi.org/10.1002/ece3.498
Legendre, P. & R. Condit. 2019. Spatial and temporal analysis of beta diversity in the Barro Colorado Island forest dynamics plot, Panama. Forest Ecosystems 6: 1–11.  https://doi.org/10.1186/s40663-019-0164-4
Legendre, P., & B. Salvat. 2015. Thirty-year recovery of mollusc communities after nuclear experimentations on Fangataufa atoll (Tuamotu, French Polynesia). Proceedings of the Royal Society B 282: 20150750.
Winegardner, A. K., P. Legendre, B. E. Beisner & I. Gregory-Eaves. 2017. Diatom diversity patterns over the past ~ 150 years across the conterminous United States: identifying mechanisms behind beta diversity. Global Ecology and Biogeography 26: 1303–1315.


December 3, 2021

Dr. Katie Plaisance, University of Waterloo POSTER  RECORDING

The Science of Team Science: How to Foster Productive Collaboration in Interdisciplinary Science Teams


Interdisciplinary approaches to scientific research are on the rise. This is in part because many of the complex problems we face as a society – and the research questions scientists ask – cannot be addressed by one discipline alone. Universities and funding agencies are encouraging researchers to work across disciplinary boundaries and heavily incentivizing such approaches. However, the common barriers to interdisciplinary collaboration are not always well understood, especially amongst those engaging in such collaborations. In this talk, I will discuss some of the challenges that scientists (and other researchers) face when collaborating with others outside their field. Being aware of these challenges is a crucial first step in managing them. I then go on to discuss strategies for proactively addressing these challenges and highlight resources scientists can use to support their collaborative efforts.  



November 26, 2021

Dr. Marian Schubert, Norwegian University of Life Sciences

Evolution of temperate adaptations in grasses: Insights from molecular and macro-evolutionary studies POSTER. RECORDING


The grass family (Poaceae) is one of the largest and most successful plant families, both economically and ecologically. It contains staple crops such as wheat, rice, and maize and covers a wide geographic and climatic range. Grasses are diverse in areas that regularly experience cold and freezing as well as high seasonality. To meet the challenges of such environments, temperate grasses have evolved a rich arsenal of strategies to cope with stresses imposed by cold and short growing seasons. To better understand the molecular basis of these complex, adaptive mechanisms and how they evolved in the different grass lineages is the main aim of my research. I will sum up findings of different projects to show how we combine physiological, omic and phylogenetic comparative data to elucidate the evolutionary history of temperate adaptions in grasses.


November 19, 2021

Dr. Satoru Miura, University of California San Francisco

Why the world stands still when we move our eyes - Mechanistic insights from mouse visual


Sensory stimuli are often evoked by the animal’s own actions. In both vertebrates and invertebrates, nervous systems distinguish these self-generated stimuli from stimuli evoked by changes in the environment. How this distinction is achieved has been the subject of much investigation, especially in the context of saccades. Saccades are rapid eye movements performed by many animals across phyla, and they induce a quick motion of the visual scene on the retina. Behavioral studies show that this saccade-induced motion on the retina is distinguished by the subjects from motion that occurs in the environment. However, how the two types of motion are differentially processed by the visual systems is not fully understood. To address this issue, we recorded saccade responses in the primary visual cortex (V1) of awake mice and discovered that neurons in V1 are tuned to the direction of saccades, both in freely moving and head-fixed conditions. Given that many neurons in V1 are tuned to the direction of visual motion on the retina, could the directionally tuned saccade responses simply be visual responses? Contrary to this notion, we demonstrate that saccades and motion in the environment evoke distinct patterns of activity in V1, even when the resulting visual stimuli on the retina are identical. Indeed, for many directionally-tuned neurons, the preferred direction for motion in the environment differs from that for saccades. We show that this is because during saccades, neurons in V1 linearly integrate the visual input with a strong, non-visual input arriving from the pulvinar nucleus of the thalamus. This non-visual input can be observed under the complete lack of vision and encodes the direction of saccades. The input both precedes and outlasts saccades by tens of milliseconds, suggesting it may originate, at least partially, from the oculomotor command. Silencing the pulvinar prevented the non-visual input from reaching V1, such that the pattern of the evoked response in V1 was now similar regardless of whether the motion on the retina was generated by saccades or by changes in the environment. Thus, the pulvinar ensures differential responses in V1 to self-generated motion and external motion. The integration of sensory inputs with other inputs encoding postural states may be a general mechanism that allows the animal to interpret sensory information in the context of its own actions.

Host: Prof. Baohua Liu

November 12, 2021

Dr. Otso Ovaskainen, University of Helsinki

Joint species distribution modelling: how to make more out of community data? RECORDING

A central aim of community ecology is to understand the processes that determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we have developed Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. HMSC belongs to the class of joint species distribution models, and it makes it possible to derive simultaneously species- and community level inference from data on species occurrences, environmental covariates, species traits, and phylogenetic relationships. HMSC applies to a wide variety of study designs, including hierarchical data, spatial data, temporal data, and spatio-temporal data. We describe the general HMSC framework and its relationships to other methods for analysing community data, demonstrate the R-package Hmsc by applying it to a case study on Finnish birds, and conclude by discussing the strengths and development needs of this methodological framework.

Host: Prof. Helene Wagner


November 5, 2021

Dr. David Baltrus, University of Arizona

Developing Phage Derived Bacteriocins as Strain Specific Antimicrobials



Since interactions between microbes can determine assembly dynamics within microbiomes, outcomes of these interactions have the potential to directly shape functional outputs of microbial communities. A deeper understanding of the molecules that drive these interactions may therefore enable fine scale manipulation of microbiomes in both clinical and agricultural settings. The Baltrus lab has previously characterized a suite of antimicrobial molecules (tailocins) produced by strains of Pseudomonas but derived from prophage, in which phage tails can be used as weapons to target and lyse specific closely related strains. We show that the host range of these molecules can be far wider than canonically thought but also that resistant mutations by some strains can actually sensitize these strains to killing by divergent tailocins (a phenomenon termed "collateral sensitivity"). Taken together, by understanding the molecular language of how amino acid divergence changes host range and by categorizing the genetic basis of collateral sensitivity, we hope to develop programmable antibiotics that can bind to and eliminate target cells while anticipating and countering resistance as it evolves.

Host: Dr. Marcus Dillon

October 29, 2021

Dr. Kari Segraves, Syracuse University

The evolutionary ecology of species interaction RECORDING

Species interactions play an important role in structuring communities and creating new species. Although these linkages have long been appreciated, understanding the myriad ways in which species interactions contribute to evolutionary change and, ultimately, diversification remain relatively unexplored. In this seminar, I will discuss two ongoing projects. First, I will address how the speciation process itself can affect the ecology of species interactions that span the mutualism-antagonism continuum. In the second half of the talk, I will present results on how the community context of multispecies mutualisms affects the ability of mutualists to ameliorate the negative effects of cheaters. Together, the results underscore the intertwined nature of species interactions, diversification, and community structure.
Dr. Kari Segraves received her Ph.D. from Vanderbilt University, and then was a NSF Interdisciplinary Informatics Postdoc at the University of Idaho before she moved to Syracuse University in 2005 where she is now a Professor of Biology. She is broadly interested in the role of species interactions in shaping biodiversity and uses a combination of field and laboratory experiments on model and non-model systems to test how species interactions influence the ecology and evolution of species and communities. She works with organisms across three kingdoms at both micro and macroevolutionary scales.

HOST: Prof. Marc Johnson


October 22, 2021

Dr. Matt Smear, University of Oregon

Neural correlates of time and place in the olfactory bulb of freely-moving mice RECORDING

Odors provide useful navigational and episodic information, but however numerous the odorant receptor genes in an animal’s genome, there is no receptor for time or place. To optimally orient by olfactory information, brains must incorporate odor-driven activity into representations of self-movement and -location. While a feedforward model might predict that such multimodal integration would be implemented in “high-level” areas, recent studies in other sensory modalities demonstrate that motor- and location-related signals are common in primary sensory areas. Motivated by these findings, and given the strong reciprocal connection between olfactory system and hippocampus, we hypothesized that the olfactory bulb might also encode navigational information. To test this hypothesis, we captured the sniffing and movement of mice while recording spiking activity in their olfactory bulb, in the absence of experimenter-applied stimuli or tasks. As previously reported, we found that many units fired preferentially at characteristic times after inhalation. In addition, many units fired preferentially at characteristic sniff frequencies, particularly during free movement, often in correspondence with the rhythmic states of sniffing. In addition to these time-selective signals, we also found that many olfactory bulb neurons are place-selective during free movement. To test whether this position-selective activity carries usable information about the mouse’s location, we decoded position from ensembles of simultaneously recorded units. We could decode the mouse’s position with above-chance accuracy in all sessions. Thus, even during spontaneous behavior and ambient stimuli, information about time and place can be read out from the activity of the olfactory bulb. A mouse needs to know where and when it encountered different smells: olfactory information must be contextualized and incorporated into cognitive maps of environment and self. Our results suggest that this contextualization process begins as soon as olfactory information enters the brain.


My research focuses on how neural mechanisms coordinate sensing with moving — how do animals sample the environment in order to acquire the information they require to survive? This broad question encompasses a snake flicking its tongue, a primate moving its eyes, or a rodent following its nose. I study the last of these because mice are particularly amenable for studying neural circuits. I am a neuroscientist, born in Saskatchewan, raised in Maryland. I attended Duke and UCSF for school and I did postdocs at Cold Spring Harbor and Janelia Farm. I have been at University of Oregon since 2014.

Host: Dr. Arbora Resulaj


October 8, 2021

Dr. Maitreya Dunham - Department of Genome Sciences at University of Washington

Taking yeast experimental evolution out of the lab and into classrooms and breweries. RECORDING

Host: Dr. Alex Nguyen Ba

Microbial experimental evolution has allowed for real time explorations of many important topics in evolution. Now paired with cheap and easy whole genome sequencing, we have been able to explore the genetics of adaptation at a level of molecular detail never before possible. I will talk about two projects where we've been able to apply the approaches and tools we developed to study evolution of yeast cultures in the lab, but now in classroom and industry settings. First, we have simplified our methods to allow high school students to perform experimental evolution as part of a teaching lab, with results contributing to a multi-school research project on how yeast evolve antifungal resistance. Second, we have taken advantage of a natural experiment happening in breweries, where yeast is "repitched" from one fermenter to the next. Using deep sequencing, we found chromosome rearrangements and copy number variants that repeatedly attained high frequency over yeast reuse, even across multiple breweries. We infer that these mutations are beneficial in the brewery environment and affect traits including osmolarity tolerance, flavor, and flocculation. We are hoping to build on these success stories to find new opportunities to study evolution in real time in non-lab environments.
Dr. Maitreya Dunham' research uses high-throughput experimental evolution to understand and exploit evolutionary processes in natural or biotechnological settings. She has set up chemostats to study laboratory and wild microbes in the lab, and exploits next-generation sequencing and advanced bioinformatics pipelines to decipher their genome evolution. She is extremely fun to talk to even for things outside the lab, for example she is involved in multiple breweries around Seattle as she brews her own and grows her own hops. For more information on her research and publications, visit her webpage (https://dunham.gs.washington.edu/home.shtml).


October 1, 2021

Dr. Cassidy D'Aloia, University of New Brunswick

Genetic approaches to uncovering marine connectivity RECORDING

Host: Dr. Bailey McMeans

Over 70% of marine species disperse as tiny larvae that develop in ocean currents. Determining where those larvae go—and how they get there—has been a major challenge in marine ecology. Genetic relatedness analyses that identify first-order kin, such as parents and their offspring or full siblings, have become a popular tool for documenting marine larval dispersal events. But these analyses come with their own drawbacks. Mainly, these studies are spatially and temporally constrained due to their sampling intensity, rendering them ill-suited for detecting long-distance dispersal and/or temporal fluctuations in connectivity patterns. In this talk, I’ll present recent work that integrates multiple genetic approaches to detecting larval dispersal across spatial and temporal scales. We assess the benefits and shortcomings of our own genetic relatedness studies. Collectively, we find evidence of consistently limited dispersal in a coral reef fish, despite the fact that individuals develop and feed offshore in pelagic waters for nearly a month. These results pave the way for new integrative lines of research that explore the behavioral and oceanographic mechanisms driving these dispersal patterns.
I am a molecular ecologist and marine field biologist who grew up in landlocked upstate NY. My interest in EEB and marine science was first sparked while studying as an undergraduate at Middlebury College and the Universidad Austral de Chile. After that, I spent five years (often underwater!) studying coral reef fishes in Belize during my PhD. I completed postdocs at Woods Hole Oceanographic Institution and the University of Toronto before moving to the University of New Brunswick as an Assistant Professor. In January 2022 I am joining the UTM Department of Biology.
Website: https://www.cassidydaloia.com/


September 24, 2021

Dr. Susan Gasser, Director of ISREC - Swiss Institute for Experimental Cancer Research

How heterochromatin preserves genome stability and tissue identity in worms. Recording


Development of an organism is governed by a carefully orchestrated program of gene regulation, controlled on the level of both chromatin and DNA sequence. Histone modifications are the primary drivers of chromatin structure, which shape the epigenetic information of any cell. Methylation of lysine 9 of histone H3 (H3K9me) characterizes the transcriptionally silent heterochromatin in organisms from yeast to man. It ensures genome stability by silencing repeats (1)  and it silences some genes as cells differentiate (2). In multicellular animals the aberrant gain or loss of heterochromatin and its segregation at the nuclear envelope has been correlated with a loss of tissue integrity, aging and cancer (e.g., 2,3,4).  Nonetheless, how H3K9me restricts expression remains unknown. Here we show in C. elegans that loss of H3K9me results in the limited depression of genes which in some tissues and/or embryos carry H3K9 methylation. We find that the pattern of gene derepression by loss of H3K9me is distinct in embryos and in terminally differentiated cells (5). During organismal development, we find that H3K9me is lost from genes that must be expressed, and is gained on genes that were expressed in prior developmental stages. Active H3K9me maintenance by MET-2/SETDB1 is necessary to ensure silencing, even in post mitotic cells. Despite the fact that H3K9me generally restricts chromatin accessibility at promoters and enhancers, as measured by ATAC-seq, we find that changes in accessibility do not necessarily correlate with gene derepression. Rather, the binding of a specific subset of TFs is controlled in differentiated tissues by H3K9me.  This substantiates the long-standing hypothesis that heterochromatin controls gene expression. Although derepression can be independent of stable chromatin opening, expression reflects the ability of TFs to access gene promoters (5).
  1. Zeller, P. et al. Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability. Nat Genet 48, 1385-1395, doi:10.1038/ng.3672 (2016).
  2. Nicetto, D. et al. H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Science 363, 294-297, doi:10.1126/science.aau0583 (2019).
  3. Chen, M. W. et al. H3K9 histone methyltransferase G9a promotes lung cancer invasion and metastasis by silencing the cell adhesion molecule Ep-CAM. Cancer Res 70, 7830-7840, doi:10.1158/0008-5472.CAN-10-0833 (2010).
  4. Harr, J.C., et al. Loss of an H3K9me-anchor rescues laminopathy-linked changes in nuclear organization and muscle function in an EDMD model. Genes & Dev. 34, 560 - 579. doi: 10.1101/gad.332213.119. (2020).
  5. Methot, S.P., Padeken, J., et al., H3K9me selectively blocks transcription factor activity to ensure differentiated tissue integrity.  In final revision, Nat Cell Biol(2021).

September 17, 2021

Dr. Santiago Claramunt, Associate Curator of Birds, Department of Natural History, Royal Ontario Museum & Assistant Professor, Department of Ecology and Evolutionary Biology, University of Toronto

“Integrative approaches to the study of bird diversification” RECORDING

Phylogenetic approaches are revolutionizing the study of macroevolution but inferences about diversification require accurate time-scaled phylogenies and attention to the fundamental causal processes. Here I show how we can make progress in both fronts using bids as an example. I show new approaches for the calibration of molecular clocks and how new avian time-trees reveal a striking correlation between global temperatures and diversification rates. Then, I show how dispersal ability can be estimated from wing shape and explore the relationship between dispersal ability and diversification rates. These new approaches have great potential for further our understanding of the process of diversification.
I was born and raised in Uruguay, where I became interested in science and nature, and obtained a BSc in Biology. I moved to the USA for doctoral studies at Louisiana State University, followed by a postdoctoral position at the American Museum of Natural History in New York. After teaching biogeography and evolutionary biology for two years in Peru, I moved to Toronto where I am Associate Curator of Birds at the Royal Ontario Museum and Assistant Professor—Status Only—at the Department of Ecology and Evolutionary Biology of the University of Toronto.


September 10, 2021

James Santangelo, PhD Student (Robert Ness & Marc Johnson Supervisors)

Parallel adaptation to the world’s urban jungles

Urbanization dramatically transforms environments in ways that alter the evolution of life. We examined whether global urbanization drives convergent environmental change and parallel evolution by sampling 110,019 white clover plants from 6,169 populations in 160 cities spanning diverse climates. Plants were assayed for hydrogen cyanide—a Mendelian antiherbivore defence that also affects tolerance to abiotic stressors. Urban environments were consistently hotter, less vegetated, and had more impervious surfaces than nonurban areas, which were associated with the evolution of phenotypic clines in 47% of cities throughout the world. Sequencing 520 genomes from 26 cities revealed that parallel clines were best explained by adaptive evolution, and environmental analyses showed that variation in HCN clines was explained by multiple interacting environmental factors. Our results demonstrate that ongoing urban environmental change is leading to parallel evolution globally.

Dr. Jimena Leyria, PostDoctoral Fellow (Angela Lange Supervisor)

A bite, a blood cocktail, and successful reproduction: control of egg-laying in a major vector of Chagas Disease


In the blood-sucking Rhodnius prolixus, a vector of Chagas disease, the nutrients incorporated by a blood meal have a high epidemiological impact since in adult mated females, each meal results in a bout of egg laying, and thereby the production of hundreds of offspring. In insects, insulin-like peptide (ILP) signalling along with the target of rapamycin (ToR) are involved in detecting and interpreting nutrient levels. By means of RNA-Sequencing we have examined how a blood meal influences mRNA expression of the ILP/ToR signalling pathway in key tissues involved in reproduction (fat body and ovaries). Although there is an up-regulation of the genes involved in ILP/ToR signalling in unfed insects, western blot analysis reveals that this signalling is only activated after a blood meal, i.e. phosphorylation of proteins. Immunofluorescence and RNA interference (RNAi) studies suggest that during the unfed condition, FoxO signalling may be responsible for the up-regulation of transcripts involved in the ILP/ToR signalling cascade. Moreover, exogenous insulin stimulates protein phosphorylation in the fat body and ovaries from unfed insects, suggesting that those females are in a sensitized state and respond to food by rapidly activating ILP signalling. Also, by RNAi and ex vivo assays we show that ILP/ToR pathway is involved in juvenile hormone (JH) synthesis and release, a hormone that coordinates the synthesis of yolk protein precursors by the fat body, which in turn influences the numbers of eggs laid per female. Our study reveals a network of regulatory pathways implicated in reproductive performance. These analyses serve as a starting point for new investigations that increase the chances of developing novel strategies for vector population control by translational research, with less impact on the environment and more specificity for a particular organism.
Date Speaker Title Host
Sep 10, 2021
James Santangelo
PhD Student
Parallel adaptation to the world’s urban jungles. POSTER
Sep 10, 2021
Dr. Jimena Leyria
Postdoctoral Fellow
A bite, a blood cocktail, and successful reproduction: control of egg-laying in a major vector of Chagas Disease. POSTER
Sep 17, 2021
Dr. Santiago Claramunt,
Royal Ontario Museum
Integrative approaches to the study of bird diversification. POSTER. RECORDING
Dr. Sanja Hinic-Frlog
Sep 24, 2021
Dr. Susan Gasser,
ISREC – Swiss Institute for Experimental Cancer Research
How heterochromatin preserves genome stability and tissue identity in worms. POSTER. RECORDING
Dr. Mark Currie
Oct 1, 2021
Dr. Cassidy D'Aloia
Genetic approaches to uncovering marine connectivity. POSTER. RECORDING
Dr. Bailey McMeans
Oct 8, 2021
Dr. Maitreya Dunham,
University of Washington
Taking yeast experimental evolution out of the lab and into classrooms and breweries. POSTER. RECORDING
Dr. Alex Nguyen Ba
Oct 22, 2021
Dr. Matt Smear,
University of Oregon
Neural correlates of time and place in the olfactory bulb of freely-moving mice


Dr. Arbora Resulaj
Oct 29, 2021
Dr. Kari Segraves,
Syracuse University
The evolutionary ecology of species interactions. POSTER. RECORDING
Dr. Marc Johnson
Nov 5, 2021
Dr. David Baltrus,
University of Arizona
Developing Phage Derived Bacteriocins as Strain Specific Antimicrobials


Dr. Marcus Dillon
Nov 12, 2021
Dr. Otso Ovaskainen
University of Helsinki
Joint species distribution modelling: how to make more out of community data? POSTER. RECORDING
Dr. Helene Wagner
Nov 19, 2021
Dr. Satoru Miura,
University of California San Francisco
Why the world stands still when we move our eyes - Mechanistic insights from mouse visual. POSTER. RECORDING
Dr. Baohua Liu
Nov 26, 2021
Dr. Marian Schubert,
Norwegian University of Life Sciences
Evolution of temperate adaptations in grasses: Insights from molecular and macro-evolutionary studies. POSTER. RECORDING
Dr. Katharina Braeutigam
Dec 3, 2021
Dr. Katie Plaisance,
University of Waterloo
The Science of Team Science: How to Foster Productive Collaboration in Interdisciplinary Science Teams POSTER
Grad Students
Dec 10, 2021
Dr. Pierre Legendre,
Universite de Montreal
Temporal beta diversity: identify sites where species communities have changed in exceptional ways
Grad Students