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Workshop on Mathematical Ecology: Modeling Epidemics 

August 10-11, 2022 ⇒ Queen's University, Kingston, Canada 

 

Comparing recent and preindustrial cladoceran assemblages in 35 metal- and smelting-affected lakes near Sudbury (Ontario, Canada)

Brigitte Simmatis, Andrew M Paterson, John P Smol

 

Metal smelting in the Sudbury region of Ontario has persisted for over a century, emitting harmful metals and additional pollutants that have led to the acidification and damage of nearby lakes. Considerable research has evaluated the biological recovery relative to conditions during peak periods of impact; however, pre-impact lake conditions are unavailable without the use of specialized methods and relatively little is known regarding the recovery of lake invertebrates relative to pre-impact conditions. Recent work by Queen’s University Biology alumna Brigitte Simmatis along with John Smol of the Paleoecological Environmental Assessment and Research Laboratory (PEARL) and Andrew Paterson of the Ontario Ministry of the Environment, Conservation and Parks sheds some light.

The study found that many lakes subjected to contamination and acidification from smelting have not seen their invertebrate communities recover to pre-impact conditions. However, modern stressors such as climate change, urbanization, fishery changes, and additional human-driven disturbances were evident in the communities of minimally impacted lakes, suggesting that impacted lakes may never fully recover to pre-impact conditions. Thus, recovery efforts and lake management strategies should adjust conservation goals and expectations for the biological restoration of impacted lakes. Read the article in the Journal of Plankton Research.


Explaining the “greening” of the Arctic with climate change: fungi may help birch become more dominant

Michelle M. McKnight, Paul Grogan, and Virginia K. Walker

To model the impacts of climate change associated warming in Arctic soils, Queen’s University Biology researchers set up greenhouse and fertilizer amendment plots in the low Arctic tundra, 300 km NW of Yellowknife in the North West Territories. After a dozen years of tending the plots, the bacterial and fungal microbial communities of both the surrounding soil and the roots of Arctic birch were characterized using DNA analysis.

DNA sequencing of the green house-warmed plots showed little change in the structure of the soil or the root microbial communities, even though organic decomposers appeared to increase their activity. These increased nutrients seem to be used for growth by the dwarf birch trees and there was little left over for the soil communities. In plots with added  phosphate or phosphate and nitrogen fertilizers, the microbial community did shift since presumably there were plenty of nutrients for both the above ground and below ground communities. Under these circumstances, DNA from bacteria associated with lichens decreased in relative abundance, whereas DNA from plant-associating bacteria and fungi increased. Particularly notable was an overall increase in relative abundance of ectomycorrhizal fungi, which promote plant growth. These changes may indeed foreshadow climate change mediated shits from lichens to a birch shrub dominated landscape, or as popularly termed, the “greening” of the Arctic.. Read the article in Arctic, Antarctic, and Alpine Research.


Current water quality guidelines across North America and Europe do not protect lakes from salinization

Shelley E. Arnott, Danielle A. Greco, Alexandra McClymont et al.

Salinity is increasing in freshwater lakes worldwide, driven by the overuse of road salt, unsustainable agricultural practices, mining operations, and climate change. Increasing salinity is detrimental to biodiversity and overall lake health and a new study suggests that current governmental guidelines are insufficient to protect freshwater organisms. Queen’s University Biology Dr. Shelley E. Arnott, along with graduate students Danielle A. Greco and Alexandra McClymont, and collaborators around the world recently published their findings which illustrate the need for governmental reassessment of current water quality guidelines.

This striking study leveraged the results from an extensive network of experiments conducted across North America and Europe involving freshwater lakes. A collective loss of zooplankton taxa, the pillars of lake food webs and ecosystems, occurred in response to increased salinity even at the lowest water quality guideline thresholds. This loss of zooplankton leads to cascading changes in other components of the food web, resulting in the loss of water clarity and potential declines in fish populations. Overall, this research underscores the need to re-evaluate water quality guidelines in freshwater lakes worldwide to protect lake ecosystems. Likewise, these results show the need for innovative solutions to road de-icing, sustainable agriculture, and mining operations. Read the paper in PNAS.


Similar zooplankton responses to low pH and calcium may impair long-term recovery from acidification

Alexander J. Ross and Shelley E. Arnott

Uncontrolled, pervasive industrial emissions led to the acidification and destruction of biodiversity in North American and European lakes. Zooplankton, the pillars of freshwater ecosystems, are especially vulnerable to the associated pH changes and subsequent calcium depletion plaguing these lakes. New research by Queen’s University Biology professor Dr. Shelley Arnott and former MSc student, Alexander Ross, now with Lakehead University’s Natural Resources Management, investigates the recovery of zooplankton populations in acid-damaged lakes that are experiencing declining calcium using factorial in-lake mesocosms in Killarney Provinical Park.

Despite pH recovery since 1971, lake calcium levels in Killarney Park lakes have decreased over four-fold and lakes continue to have a disproportionately high abundance of small, acid-tolerant species. Mesocosm experiments revealed that the impacts of low calcium concentrations on zooplankton were similar to those of low pH. A subsequent, landscape comparison of mesocosm results with 34 other historically acidified lakes showed parallel changes in zooplankton relative abundance. These results suggest that even though lake pH is recovering, the detrimental effects of declining calcium may prevent biological recovery.

Thousands of lakes are known to have been acidified presenting a major ecological challenge. These new results illustrate the need for improved management and conservation strategies to address the declining calcium levels in lakes stemming from acidification. Altogether, this work presents a step forward towards lake rehabilitation and the development of conservation strategies worldwide. Read the article in Ecological Applications.


Phosphorylation-dependent subfunctionalization of the calcium-dependent protein kinase CPK28

Melissa Bredow, Kyle W. Bender, Alexandra Johnson Dingee, Danalyn R. Holmes, Alysha Thomson, Danielle Ciren, Cailun A. S. Tanney, Katherine E. Dunning, Marco Trujillo, Steven C. Huber, and Jacqueline Monaghan

Plants under stress may divert resources from growth and development to defence, leading to reduced yields for crops. These shifts in allocation are controlled by poorly known and complex signalling pathways involving phosphorylation and are often initiated by an influx of intracellular calcium, the primary currency of plant information processing. Particularly of interest is the initiation of immune response. Fast response to infection enables an effective immune response. But how are plants able to decode calcium signals to initiate an appropriate immune response? Amazing work published last spring by a team of @QueensUBio researchers including NSERC-PDF Dr. Melissa Bredow, NSERC-PGS Katherine Dunning, and Honours thesis students Alexandra Johnson Dingee, Danalyn Holmes, Alysha Thomson, Danielle Ciren, and Cailun Tanney, together with Dr. Jacqueline Monaghan and collaborators Dr. Kyle Bender, Dr. Marco Trujillo, and Dr. Steven Huber, opens the door to new possibilities on the subject.

Calcium-dependent protein kinases (CPKs) are proteins that act as signalling hubs within cells, with individual CPKs tuned to specific calcium concentration sensitivities. CPK28 regulates immune homeostasis and reproductive stage transitions in multiple plant species. The authors found that phosphorylation on a single CPK28 residue, Ser318, initiates a conformational change allowing for CPK28 activity at low calcium concentrations, enabling a quick immune response when required. This phosphorylation and conformational change is required for immune signalling, thus preventing an unintended and energy costly immune response in the absence of pathogens. Intriguingly, Ser318 phosphorylation was not required for CPK28’s additional function in developmental signalling indicating phosphorylation-dependent pathway specificity.

CPK28’s phosphorylation-dependent dual functionality underscores the complexity of plant signalling networks. Further investigation revealed the conserved function of Ser318 phosphorylation in one of the world’s most agriculturally important crops, rice. Furthermore, the authors remarkably found that ablation of Ser318 resulted in enhanced pathogen resistance without reducing growth – a highly sought agricultural trait. Overall, the work outlined in their paper may lead to the development of disease resistant and high yielding crops, contributing to the safeguarding of global food security. Read the article in PNAS.

 

 

 

 

 

 

 

 

 

 


Genome report: a draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

Nikolay Alabi, Yihan Wu, Oliver Bossdorf, Loren H. Rieseberg, Robert I. Colautti

Like many of Ontario’s invasive plants, garlic mustard (Alliaria petiolata) is native to much of Eurasia and was probably introduced for medicinal and culinary purposes. Introduced to North America in the 19th century, the species has rapidly spread across the continent where it can suppress forest regeneration. Garlic mustard and many other invasive plants have been the subject of many ecological studies, but very little is known about the molecular pathways that allow species to become invasive.

To help develop garlic mustard as a model system for invasion genetics, Queen’s Biology researcher’s Nikolay Alabi, Yihan Wu, and Dr. Robert Colautti, together with collaborators at University of Tübingen and the University of British Columbia, have now sequenced and annotated a draft genome for garlic mustard.

The assembled draft genome reads 1.1 Gb in size, one third the size of the human genome, with a total of 64,770 genes! The team found low levels of heterozygosity in the genome which will help researchers around the world find genes associated with ecologically important phenotypes.

With a seedbank and corresponding field data from hundreds of populations across Europe and North America, and a rich ecological literature, a published draft genome will enable future genomic and molecular studies to supplement the growing field of invasion genetics. A more integrated biology of invasive plants can not only improve conservation strategies to manage the impacts of this invasive species, but also provide insights into the genetic basis of plant health and vigour in a changing world. To learn more, read the article in G3: Genes|Genomes|Genetics.

Overhead view of garlic mustard flowers and leaves


THE MORAL DILEMMA OF THE 21ST CENTURY

Lonnie Aarssen

Advances in agriculture and medicine have given us now an overpopulated planet with severely impoverished ecosystem services — and a profound moral dilemma: how can we continue to respond to the still-growing need to feed more mouths and to treat more illness in the coming decades, without continuing to imperil the opportunity for our descendants to enjoy long and healthy lives?

This is the subject of a short video by Lonnie Aarssen, published by Science Animated (Stonehouse, UK, https://sciani.com/).

Click below to watch on Youtube. 

The moral dilemma of the 21st century.jpg

Additional Information:

Aarssen L (2010) Darwinism and meaning. Biological Theory 5: 296 – 311.  https://link.springer.com/article/10.1162/BIOT_a_00060

Aarssen L (2019) Dealing with the absurdity of human existence in the face of converging catastrophes. The Conversation, 1 May, 2019.  https://theconversation.com/dealing-with-the-absurdity-of-human-existence-in-the-face-of-converging-catastrophes-110261

Aarssen L (2020) Meet Homo absurdus — the only creature that refuses to be what it is. Science Animated, 5 Feb 2020.  https://www.youtube.com/watch?app=desktop&v=IY8T_WowpeA&t=0s

Aarssen L (2022, in press) What We Are: The Evolutionary Roots of Our Future. Springer Nature, Cham, Switzerland.

 


Effects of chloride and nutrients on freshwater plankton communities

Danielle A. Greco, Shelley E. Arnott, Isabelle B. Fournier, Brandon S. Schamp

Over seven million tonnes of de-icing salt are dispersed on Canadian roads each winter leading to an increase in lake chloride concentrations that can be toxic to freshwater aquatic life. However, the current Canadian Water Quality Guideline limits for chloride may not sufficiently protect aquatic life against rising lake salinity.

Lake salinity guidelines were developed based on chloride sensitivities of individual species under lab conditions and may not reflect sensitivities under lake conditions. Former Queen’s Biology graduate student Danielle Greco, along with co-supervisors Drs. Shelley Arnott and Brandon Schamp (Algoma University) and collaborator Dr. Isabelle Fournier at Laval University, investigated the effects of salt and nutrient concentrations on the pillar of aquatic life, plankton. By mimicking a natural lake environment using mesocosms, including communities rich in species and from multiple trophic levels, this study provides insight previously not observed during development of guidelines.

Even under relatively low chloride concentrations, zooplankton biomass and abundance significantly decreased. Total community biomass decreased by up to 71% when chloride concentrations reached guideline “safe” limits. This decline included the highly sensitive yet near ubiquitous copepods which were not even included in assessments when guidelines were designed. Zooplankton response to chloride did not differ by nutrient level, despite increased food availability under elevated nutrients. Phytoplankton and protist responses to chloride varied depending on nutrients. Under low nutrients, they increased in abundance, biomass, and richness with chloride. However, under high nutrients, abundance and biomass did not respond to chloride, while their richness decreased.

These results prompt immediate reassessment of Canadian Water Quality Guidelines regarding lake chloride concentrations. Furthermore, this work underscores the need for innovation in road salting practices. Find their article to read more in Limnology and Oceanography Letters.


Experimental tests of selection against heterospecific aggression as a driver of avian colour pattern divergence

Haley L. Kenyon and Paul R. Martin

A healthy ecosystem relies on biodiversity which in turn relies on effective signal divergence to keep closely related, coexisting species distinct. For example, species-specific avian colour patterns allow birds to distinguish potential mates of their own species, maintaining distinct species in nature. Interestingly, closely related sympatric bird species (i.e., species that overlap their ranges) display greater colour pattern divergence than their non-sympatric counterparts. However, the drivers of sympatric avian colour pattern divergence are relatively unknown.

Queen’s Biology graduate student Haley Kenyon (Martin lab) used painted 3D-printed models to investigate aggression as a selective pressure for avian colour pattern divergence. Their lifelike models were used to simulate interactions between chickadee species in the wild to measure competition for territory and females, during breeding seasons, and in competition for access to food, during winter flocking seasons.

This unique study leveraging accessible, 3D-printed, and highly accurately painted bird models found that male black-capped chickadees attacked both sympatric and allopatric species during breeding seasons; however, were equally likely to visit feeders occupied by both sympatric and allopatric species during winter seasons. Inter-species relationships are complex, and these results suggest that colour pattern divergence does not reduce aggression between species. This study simultaneously demonstrates the effectiveness of 3D-printed models for use in simulating measurable species-specific interactions in the wild opening the doors for fascinating future investigations! Find their article in the Journal of Evolutionary Biology.


The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance

Collin L. Juurakko, Melissa Bredow, Takato Nakayama, Hiroyuki Imai, Yukio Kawamura, George C. diCenzo, Matsuo Uemura, and Virginia K. Walker

Freezing damage can be particularly devastating with a single frost event capable of destroying billions of dollars worth of crops. To protect themselves, some plants enhance their freezing tolerance through an intricate process called cold acclimation. The plasma membrane and associated proteins are central to this cold response and maintaining membrane integrity is vital for survival. However, to date, no cold-acclimated plasma membrane proteome has been characterized in a species related to humanity’s most important crops, the cereals.

Current Queen’s Biology graduate student Collin Juurakko and former graduate student Dr. Melissa Bredow led by Dr. George diCenzo and Dr. Virginia Walker together with collaborators at Iwate University in Japan have characterized the first cold-acclimated plasma membrane proteome in a monocot species and uncovered new protein targets to investigate. Crosstalk between stress responses was also mapped and exhaustive, large-scale datasets of all proteins found have been made available to the community for researchers to mine.

It is often said that a plants’ ability to survive freezing is measured by their capacity to protect the plasma membrane. This study has increased our understanding of how crops may respond to cold stress and enhance their freezing tolerance, bringing us one step closer to developing freeze tolerant crops to ensure future food security! To learn more, read the article in G3: Genes|Genomes|Genetics.


Exceptional variation in the appearance of Common Murre eggs reveals their potential as identity signals

Tim R. Birkhead,  Jamie E. Thompson, Amelia R. Cox, and Robert D. Montgomerie

The Common Murre, an avian artisan, crafts wondrously diverse eggs maculated with intricate designs that have enthralled naturalists and collectors for more than two centuries. Every egg is distinct; however, very little is known about the variation in patterning among eggs laid by the same female and the causes of variation in colouration. Former Queen’s Biology graduate student Amelia Cox and our own Dr. Bob Montgomerie investigated and recently published on this topic.

Breeding populations on the rocky coastal cliffs of Skomer Island in Wales were studied for three years, providing some unique insights into the appearance of the Common Murre egg. These birds congregate in dense colonies, laying a single egg that they incubate on the bare rock, without a nest. If the egg is taken by predators or falls off the cliff ledge, females will lay up to two replacements in a season.

Elaborate egg designs are functional as their patterns allow neighbouring eggs, separated by mere centimetres, to be distinguished from one another. Indeed, all eggs laid by an individual female were found to be very similar within and between breeding seasons. The authors also found an absence of distinct appearances between breeding groups and no discernable impact of environmental changes year to year on egg appearance.

This study has laid the foundation for future investigation into the Common Murre egg and provides key insights for researchers of related species. To learn more, read their article in Ornithology.


INVESTIGATING HOLOCENE CLIMATE CHANGE IN BOREAL NORTHEAST ONTARIO

Examining the past is an important tool for predicting the future. This is especially true when trying to predict the effects of global climate change on lakes and other freshwater ecosystems.  Recently, researchers detailed changes in lakes in boreal northeast Ontario associated with changing climate during the Holocene, using paleolimnological methods. The boreal region of northeast Ontario is surprisingly understudied in this context, given its importance as a boundary region between major climate systems.   

Queen’s Biology former PhD student Dr. Cale Gushulak, Professor Dr. Brian Cumming, and Professor Dr. Peter Leavitt (Institute of Environmental Change and Society, University of Regina) used records of pollen, pigments, and diatoms spanning the last ~6000 years to describe trends in phototroph composition associated with middle and late Holocene climate change in two small boreal lakes. They also tested whether within-lake variation in limnological parameters can affect the interpretation of paleolimnological records. 

Gushulak et al. find evidence of regional climate change in northeast Ontario during the middle and late Holocene. They determine that during the middle-Holocene (~6300 to ~4000 years ago), warmer temperatures contributed to eutrophic conditions and lower lake levels, as identified by phototrophic pigment concentrations and diatom assemblages, respectively. Their results for the middle-Holocene contrast with the late-Holocene (after ~4000 years ago), where cooler and wetter climate led to oligotrophication and higher lake levels. The authors also report differential phototrophic responses to climate variation among adjacent basins from the same lake, highlighting the importance of careful study site consideration when making regional climate predictions.  

To learn more, read their article in The Holocene.

Green Lake in northeast Ontario, Canada. 


Demystifying individual heterogeneity

Individual vital rates, such as mortality and birth rates, are important determinants of life-histories and population trends. Models used to analyse population dynamics typically assume that individuals belonging to the same age or stage class have identical vital rates. However, accumulating empirical evidence shows that this assumption rarely holds in natural populations. 

Individual heterogeneity in vital rates can have substantial ecological and evolutionary consequences for populations. For example, it can change predictions of population growth rates, rates of evolution by natural selection, and population persistence, compared to what would be expected in a population of identical individuals. Unfortunately, the existing literature in the field is often hampered by inconsistencies and ambiguities in terminology and definitions. These fundamental differences between frameworks introduce a risk of misunderstandings and unreliable conclusions that often leave studies inaccessible to researchers inside and outside of the field. 

In a recently published paper, Queen’s Biology former MSc student Amy Forsythe, Professor Dr. Troy Day (Dpt. Mathematics and Statistics), and Associate Professor Dr. Bill Nelson synthesize current literature on individual heterogeneity in vital rates and provide a straightforward, conceptual framework for future empirical and theoretical studies. 

Forsythe et al. establish terminology to clarify the meaning of individual heterogeneity and individual stochasticity. Their framework is based on a novel distinction between potential vital rates (the distribution that defines the set of possible vital rates for an individual at a given time) vs. realized vital rates (the vital rate that is actually expressed by an individual). The use of their framework is illustrated in a population projection matrix model, which translates their definitions into precise quantitative terms. They show how their framework and terminology can be applied to common classes of statistical models (such as generalised linear mixed models and capture–mark–recapture analyses) and they draw connections to traditional quantitative genetics models. Overall, their study will aid in understanding how individual heterogeneity in vital rates can impact our broader knowledge of population dynamics. 

To learn more, read their article in Ecology Letters

Figure caption: A conceptual framework for individual heterogeneity in vital rates. 


Cytonuclear discordance in the crowned-sparrows, Golden-crowned (Zonotrichia atricapilla) and White-crowned (Zonotrichia leucophrys

Golden-crowned and white-crowned sparrows have been hypothesized to have undergone rapid, and relatively recent (~50,000 years ago) speciation because they have nearly identical mitochondrial genomes. Nonetheless, the two species display distinct plumages, breeding behaviours, and songs, and appear to be reproductively isolated in their extensive areas of breeding range overlap. 

An alternate hypothesis to explain their similar mitochondrial genomes proposed speciation in the more distant past, but with subsequent hybridization and mitochondrial introgression (where new hybrid individuals mate with individuals from the parental species). Research supporting this hypothesis has previously lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting.

In a recently published paper, former Queen’s Biology postdoctoral fellows Dr. Rebecca Taylor, and Dr. Rute Clemente-Carvalho, former BSc thesis students Ashley Bramwell and Katherine Dares, former PhD Student Dr. Nick Cairns, Associate Professor Dr. Fran Bonier, and Professor Dr. Steve Lougheed investigate opposing hypotheses (rapid speciation hypothesis vs. hybridization hypothesis) regarding golden-crowned and white-crowned sparrow divergence. They investigate speciation and introgression using two different genetic tools, mitochondrial DNA (mtDNA) sequencing and a genome-wide panel of nuclear Single Nucleotide Polymorphisms (SNPs). 

Taylor et al. find that golden-crowned and white-crowned sparrows are deeply divergent in their nuclear DNA, and that the difference seen in the mtDNA is best explained by historical hybridization and mitochondrial introgression (supporting the hybridization hypothesis). They also find evidence that the white-crowned sparrow subspecies comprise two distinct clades. The authors conclude that nuclear sequencing (SNPs), or a combination of mtDNA and SNPs, is a more powerful tool for discovering divergence mechanisms. 

To learn more, read their article in Molecular Phylogenetics and Evolution


Selection for early flowering time in an annual plant (Yellow Rattle, Rhinanthus minor) occurs regardless of an elevational gradient in growing season length 

Plant species that expand their geographic range typically adapt to new, local environmental factors via natural selection, becoming genetically and phenotypically differentiated from their source populations. 

Latitude and elevation are common environmental gradients present in many species’ ranges. Phenological traits, such as flowering time, which rely on temperature and growing season length as biological cues, are predicted to undergo strong selection at either ends of their latitudinal or elevational range.  

Selection on phenological traits should favour early-season emergence and rapid reproduction under shorter growing seasons (higher latitudes and elevations), versus later-season emergence and prolonged reproduction expected under longer growing seasons (lower latitudes and elevation). Few studies have investigated whether selection on phenology acts as expected along growing season gradients in natural habitats. However, previous results from these studies have found that selection consistently favours early flowering regardless of season length. 

In a recently published paper, former Queen’s Biology PhD Student David Ensing, former MSc Student Dylan Sora, and Professor Dr. Christopher Eckert estimate phenotypic selection on naturally occurring and transplanted individuals of the montane annual plant, Rhinanthus minor, across a 1000 m elevational gradient of growing season length in the Canadian Rocky Mountains. They quantify phenotypic selection on five phenological traits over three consecutive generations to test the hypothesis that selection on these traits varies across a gradient of growing season length. They also address common limitations and biases that may contribute to findings of consistent selection on flowering time, which are contrary to general expectations. 

Ensing et al. find that phenotypic selection does not act on most of the phenological traits measured (e.g., time between first flower and first mature fruit). However, selection favours early flowering time across the elevational gradient of growing season length, consistent with previous results. The authors conclude that general expectations of flowering time differentiation based on growing season length may not apply to elevational gradients, in comparison to latitudinal gradients. Determining how selection on phenology differs across elevational gradients can be used as a model for understanding how the force of natural selection might change with anthropogenic effects on the climate. By addressing common sources of bias associated with studies that find selection for early flowering (such as a lack of multiple generations, and missing phenotypic variation), the authors highlight new avenues for further research on the agents and targets of this apparent selection. 

To learn more, read their article in Evolution

Photo by Regan Cross. 


Drivers of freshwater zooplankton communities 

What factors determine the composition and abundance of freshwater communities? We know that smaller scale processes, such as soil or water chemistry, and broader scale processes, such as regional climate, are both important. However, few studies consider how the importance of these processes changes through time to impact the structure of communities.  

In a recent study, former Queen’s Biology PhD student Dr. James Sinclair, Professor Dr. Shelley Arnott, Associate Professor Dr. Bill Nelson, and former BSc thesis student Kaitlyn Brougham compared environmental and spatial drivers of community composition across time using zooplankton from 29 lakes in southern Ontario surveyed over four years.  

Sinclair et al. confirm that some local and regional-scale processes are consistent drivers of zooplankton communities, such as those that exhibit little to no inter-annual variation (like geomorphology). Conversely, other factors varied in their contributions over time, such as lake pH and nutrient concentrations. The researchers’ work demonstrates the importance of considering factors that vary on different scales of both time and space when determining drivers of aquatic invertebrate zooplankton composition. To learn more, read their article in the Journal of Biogeography

Figure caption: A Daphnia pulicaria zooplankton. Photo by K. Brougham. 


A NOVEL ALLELE of THE ARABIDOPSIS THALIANA MACPF PROTEIN CAD1 RESULTS IN DEREGULATED IMMUNE SIGNALING 

Pathogen detection and response are critical components of defense against disease in all organisms. The Membrane Attack Complex/Perforin Family (MACPF) of proteins play an important role in immune responses in eukaryotic cells. There are four MACPF proteins encoded in the genome of the model plant Arabidopsis thaliana. One of these is known as Constitutively Active Defense 1 (CAD1), and although the molecular function of this protein family is unclear, there are some hints that MACPF proteins may be important for cellular and immune homeostasis.

In a recent study, former BSc thesis student Danalyn Holmes, with co-authors Dr. Melissa Bredow, Irina Sementchoukova, Sydney Pascetta, and Kristen Siegel, along with collaborators Dr. Kathrin Thor and Dr. Cyril Zipfel (The Sainsbury Laboratory Norwich), performed a forward-genetic screen that uncovered a novel allele in CAD1 that allowed a thorough genetic investigation into its role in immune signaling. Lead by Queen’s Biology Assistant Professor Dr. Jacqueline Monaghan, this work is an important contribution to our understanding of plant pathogen detection and response. To learn more, read their article in Genetics


ANGLING SEASON CHANGES FOR BASS IN LAKE ONTARIO AND THE ST. LAWRENCE RIVER

Largemouth and smallmouth bass are very popular species for North American anglers, and angling for bass in the Great Lakes region provides economic benefits for many communities. In 2013, a change was implemented regarding the angling season for largemouth and smallmouth bass in Southern Ontario, the start date for the season was advanced by one week, to the third Saturday in June. Concerns were raised on whether this change was appropriate for Lake Ontario and the St. Lawrence River, as these large waterbodies take longer to warm up than other smaller, inland lakes. 

To investigate this potential issue, members of the Queen’s University Freshwater Fisheries Conservation Lab (Principle investigator Dr. Bruce Tufts, Dr. Daniel McCarthy, Serena Wong, Connor Elliott, Sean Bridgeman, Erich Nelson, Eric Taylor, Arthur Bonsall, and Randy Lindenblatt) and collaborator Dr. Mark Ridgeway (Harkness Laboratory of Fisheries Research, Ontario Ministry of Natural Resources) began a three year study to identify the timing of spawning bass in Lake Ontario and the St. Lawrence River. They published their paper, titled ‘Ecology and timing of black bass spawning in Lake Ontario and the St. Lawrence River: Potential interactions with the angling season” in the Journal of Great Lakes Research in 2019.

The authors found that largemouth bass spawning sites warmed more quickly than smallmouth sites. The majority of largemouth bass spawning nests had fry that reached the juvenile stage by the start of the angling season. However, only between 4-13% of the smallmouth nass nests had reached this stage by the same date. Thus, at the time, the current angling season occurred during the peak of the spawning period for smallmouth bass. 

The researchers concluded that smallmouth bass require an additional two weeks for a sufficient number of their fry to reach the juvenile stage. If the angling season remained the same, smallmouth bass spawning nests would have continued to be targeted by anglers who are looking for trophy size bass. Intense angling of the smallmouth bass can leave them vulnerable to their top nest predator in these waterbodies, the invasive round goby. 

The findings produced by Tufts et al. have led to multiple important regulation changes to the angling seasons for largemouth and smallmouth bass. While the opening date for largemouth bass remains the same, the angling season for smallmouth bass will now begin two weeks later on the first Saturday in July, providing this species with ample time to successfully spawn. A better understanding of the timing of bass spawning in these waters also led to the creation of a new “catch and release” season for both bass species. This season takes place before the start of the spawning period for either species and will begin at the start of the new year, and last until May 10th.  These changes, which will come into effect for the first time this year, are a great example of the importance of scientific research for the management of fisheries resources.


ARE CURRENT WATERCRAFT DECONTAMINATION MEASURES EFFECTIVE AGAINST AQUATIC INVASIVE SPECIES? 

Aquatic invasive species pose a major threat to all bodies of water, and the natural diversity that live in these ecosystems. Human activity is an important contributor to the spread of aquatic invasive species, often due to the improper cleaning of equipment/watercrafts that move between bodies of water. 

In a recently published review, Queen's Biology MSc Candidate Shrisha Mohit, Professor Dr. Shelley Arnott, and Dr. Timothy Johnson (Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry) examined studies that evaluated the effectiveness of decontamination measures (rinsing watercrafts with hot water, pressure-washing, and air-drying) for preventing the spread of aquatic invasive species. 

Mohit et al. determined that all three decontamination measures can be effective; however, the effectiveness of the treatment depended on which aquatic invasive species were involved. Regardless of species, washing with hot water was more effective than air-drying, even though most studies test air-drying methods. Although washing with hot water seems to be very effective compared to air-drying, there was still a lot of variation in the test conditions and techniques among the studies assessing these two measures of decontamination. The authors conclude that there is presently no consensus on which decontamination methods and conditions have both the best efficacy against a diversity of species and is also easy for recreational boaters to implement.

To learn more, read their article in Management of Biological Invasions

Figure caption: A group of invasive zebra mussels (Dreissena polymorpha), which are frequently dispersed into waterbodies by attaching to the surface of watercrafts, at Queen’s University Biological Station, Elgin, ON. Photo by S. Mohit. 


THE EFFECTS OF WEATHER ON AVIAN GROWTH AND IMPLICATIONS FOR ADAPTATION TO CLIMATE CHANGE 

Climate change is expected to cause plastic responses and evolutionary change across all taxa. For many bird species, climate change will alter weather patterns (such as temperature, rainfall, and wind), that will likely impact how young birds grow.

In a recent review, Queen's Biology PhD Candidate Drew Sauve, Professor Dr. Vicki Friesen, and Dr. Anne Charmantier (Université de Montpellier, Montpellier, France) sought to characterize how current weather variation affects the growth of birds to predict future changes in nestling growth under climate change. In their review, they concluded that most weather variables can improve and worsen nestling growth, and how weather impacts growth likely depends on the life-history and geographic location of a species. Further, they determined that it is generally unknown how nestling growth might evolve in response to climate change.

Ultimately, understanding how nestlings are affected by weather conditions could help us predict the effects of climate change on future bird populations' stability. To learn more, read their article in Frontiers in Ecology and Evolution

A nestling black-legged kittiwake and one of its parents on Middleton Island, Alaska. Photo by: Hannah Weipert 


SPECIES-SPECIFIC CONSERVATION STRATEGIES TO MINIMIZE GRAY RATSNAKE ROAD MORTALITY 

Worldwide, biodiversity is declining as anthropogenic disturbance increases. A major threat to mammal, reptile, amphibian, and bird survival is road traffic. Many strategies to mitigate the effects of road traffic have been proposed; however, these are typically designed for large mammals, and are not suitable for all affected taxa. 

In a recent study, former Queen’s Biology MSc student Mathew Macpherson, Queen’s Biology Professor Dr. Stephen Lougheed, and collaborators evaluate the effectiveness of different designs and materials used in barrier fencing that act to mitigate gray ratsnake (Pantherophis spiloides) road mortality at the Queen’s University Biological Station. Gray ratsnake is designated a species-at-risk in Canada, with road mortality contributing to their declines.

Macpherson et al. find that fencing material, height, and shape all contribute to variation in ratsnake climbing success. The most effective barrier design was the 100 cm metal mesh fencing with a lip, which prevented the escape of ratsnakes in 93% of trials. The researchers’ work is an excellent example of using behavioural and morphological attributes of at-risk species to determine suitable conservation strategies. To learn more, read their article in Global Ecology and Conservation

This research is co-authored by Jacqueline Litzgus (Laurentian University), and Patrick Weatherhead (University of Illinois at Urbana-Champaign).

A gray ratsnake successfully climbing over one-meter vinyl fencing with a lip. Photo by M. Macpherson.


 

IDENTIFICATION OF UBIQUITINATION SITES ON MEMBRANE-ASSOCIATED PROTEINS IN ARABIDOPSIS 

Protein phosphorylation and ubiquitination are two of the most commonly studied post-translational modifications of proteins in eukaryotes. While previous studies have recorded several ubiquitinated proteins in plants, few ubiquitinated membrane-localized proteins have been identified.

In a recent study, Queen’s Biology Assistant Professor Dr. Jacqueline Monaghan, former Queen’s Biology MSc students Katherine Dunning and Lauren Grubb, and collaborators, describe the large-scale identification of ubiquitination sites on Arabidopsis (Arabidopsis thaliana) proteins associated with or integral to the plasma membrane, including over 100 protein kinases. 

The researchers’ work is an important contribution to plant molecular biology, cataloguing hundreds of in vivoubiquitination sites on plasma membrane proteins. To learn more, read their article in Plant Physiology

This research is co-authored by Paul Derbyshire, Cyril Zipfel, and Frank L.H. Menke (University of East Anglia, Norwich, United Kingdom).

BIK1 (a receptor-like protein kinase) is ubiquitinated on multiple surface-exposed lysines in vivo.


INVESTIGATING TRANSCRIPTIONAL RESPONSES IN PLANT-RHIZOBIA SYMBIOSES

As the global demand for food production rises, a deep understanding of our crops – and their microbiomes – becomes essential. A plant’s microbiome includes a diverse suite of microbial species that are crucial in maintaining plant health through improved plant nutrition and function, pest tolerance, and even responses to changing climate.

Rhizobia-legume symbioses are ecologically and agronomically important. Rhizobia are a group of soil bacteria that fix nitrogen for plants. In nature, the association of rhizobial strains and host plants are highly variable, even within the same species. Because of this, the genetic makeup required for efficient rhizobia-legume associations is still poorly understood.

In a recent study, Queen’s Biology Assistant Professor Dr. George diCenzo and PhD Candidate Rui Huang, with collaborators from the University of Florence (Florence, Italy), used RNA sequencing to determine the RNA transcripts of multiple rhizobial strains in the presence of root secreted compounds produced by three alfalfa varieties. 

Results from this study demonstrated that transcriptional responses of rhizobia associated with alfalfa are influenced by the genotypes of both symbiotic partners and their interaction, suggesting high variability in the genetic determinants involved in phenotypic variation of plant-rhizobium symbiosis. The researchers’ work provides genetic insights into natural rhizobium variation that could potentially improve legume growth in agricultural systems. To learn more, read their article in mSystems, published by the American Society for Microbiology

This research is co-authored by Camilla Fagorzi, Giovanni Bacci, Lisa Cangioli, Alice Checcucci, Margherita Fini, Elena Perrin, Chiara Natali, and Alessio Mengoni.

Rhizobium – legume symbioses. (Left) This photo shows 28-day old alfalfa (Medicago sativa) plants grown in a vermiculite – sand mixture with a nutrient solution lacking nitrogen. The pots on the left contain the rhizobium Sinorhizobium meliloti, whereas the plants on the right did not. The drastic difference in growth provides a nice visual depiction of the value of the symbiosis to the plant. (Top right) A picture of the roots of alfalfa, showing pink nodules, which are the plant organs that house rhizobia. The tips of the nodules appear white, as this region represents a different developmental zone than the pink section of the nodules. (Bottom right) A confocal microscopy image of a nodule containing nitrogen-fixing rhizobia. The image is centered on a single plant cell from the nodule that is packed full of rhizobia (the green, elongated structures).


SEABIRD POPULATION DECLINE FOLLOWING EUROPEAN SETTLEMENT

Seabirds are important indicators of marine ecosystem health, and yet, we often lack long-term population data to inform conservation decisions. With ~70% of the world’s seabird populations in decline since the 1950s, long-term population data become vital to understand the extent of loss. 

The Leach's Storm-petrel (Hydrobates leucorhous) is the most common seabird nesting on islands in the Western Atlantic Ocean. Globally, available surveying data indicate that the storm-petrel populations are vulnerable and have declined by over 30% since the 1980s. Unfortunately, due to a lack of long-term data, it is difficult to establish the true scope of declines. Interestingly, one storm-petrel colony on Grand Colombier Island (~17 km southwest of Newfoundland), was believed to be relatively stable based on the limited available monitoring. 

In a recent study, members of the Paleoecological Environmental Assessment and Research Lab (PEARL, Queen’s University Biology; PhD Candidate Mathew Duda, Professor Dr. John Smol) and collaborators used paleoecological evidence (lake sediments and seabird guano) to reconstruct the last ~5,800 years of storm-petrel population dynamics from Grand Colombier Island, and aimed to investigate if the colony appeared to be stable over longer time periods. 

Duda et al. found that this globally important seabird colony is now only ~16% of its potential carrying capacity, and that the beginning of the decline coincided with nearby European settlement. The researchers’ work provides a unique historical context for present day populations of conservation concern, and contributes to mounting evidence for the historical impacts of humans on marine ecosystems. To learn more, read their article in the Proceedings of the National Academy of Sciences in the United States of America

This research is co-authored by Sylvie Allen-Mahé, Christophe Barbraud, Jules Blais, Amaël Boudreau, Rachel Bryant, Karine Delord, Christopher Grooms, Linda Kimpe, Bruno Letournel, Joeline Lim, Hervé Lormée, Neal Michelutti, Gregory Robertson, Frank Urtizbéréa, and Sabina Wilhelm.

The storm-petrel impacted study pond on Grand Colombier Island. Photo by K Delord.  


FUNCTIONAL SHIFTS OF SOIL MICROBIAL COMMUNITIES CONTRIBUTE TO INVASION SUCCESS 

Invasive plants can have devastating effects on native species and ecosystem processes. Garlic mustard (Alliaria petiolata) is a problematic invader in North American deciduous forests. It produces chemicals that are thought to be allelopathic by disrupting arbuscular mycorrhizal fungi (AMF), which are important symbionts in the microbiomes of competing plants. However, the effect of garlic mustard chemicals on soil pathogens has received little attention, even though accumulating pathogens that are harmful to plant competitors could also explain the success of garlic mustard. 

In a recent study, members of the Colautti lab (former MSc student Katherine Duchesneau, former BSc thesis student Anneke Golemeic, Dr. Rob Colautti), and Dr. Pedro Antunes (Algoma University Biology) use a natural, field setting to examine differences in the soil microbiome and roots of plants found co-occurring with and without garlic mustard 

Contrary to experimental studies, the authors find no changes in diversity or abundance of AMF in plants growing with garlic mustard, indicating that AMF suppression is not critical to the invasion success of garlic mustardInstead, they find changes in microbial pathogen communities and slight increases in the root lesions of plants associated with garlic mustard. Additionally, the authors report changes in microbial communities cycling nitrogen, in line with earlier reports of increased nitrogen in soils from garlic mustard litter.    

Their study is one of the first to investigate garlic mustard invasion in a natural setting and provides new insights into the ecological mechanisms of plant invasion. To learn more, read their article in the Pedobiologia

Plants that grow with garlic mustard do not have altered AMF/EMF communities. However, they do exhibit differences in pathogen communities, increases in root lesions, and increases in microbial communities cycling nitrogen. 


Celebrating Our Women Mentors 

Queen’s Biology thanks our women mentors who are so instrumental to our development as scientists. Women mentors shape our scientific careers. They inspire us to pursue careers in biology, ensure we are confident and comfortable with whatever tasks we take on, foster a positive and supportive environment, help develop our research skills, go above and beyond for their students, and have long-lasting impacts on us. 

Check out our video, where we thank and highlight some of the many women mentors the Queen’s Biology community has had the pleasure of knowing and being mentored by throughout our careers and lives.


DENSE SAMPLING OF BIRD DIVERSITY INCREASES POWER OF COMPARATIVE GENOMICS 

More than 10,000 species of birds are alive today, from the smallest hummingbird to the largest ostrich. Researchers have now captured a broad sampling of genomic information from across the avian tree of life. 

“Dense sampling of bird diversity increases power of comparative genomics”, published this month in Nature, reports on a large collaborative effort that includes members of the Friesen lab (Queen’s University Biology Department): Professor Dr. Vicki Friesen, and former PhD students Dr. Anna Tigano and Dr. Scott Taylor. 

The main findings of this paper include the reporting on the genomes from 363 species of bird (encompassing 92.4% of bird families), 267 of which have been sequenced for the first time. This data has been produced for the Bird 10,000 Genomes (B10K) Project, which aims to sequence the genomes of all extant bird species, and is used to generate a super-phylogeny for the class Aves. 

This collaboration and data collection have created an incredible publicly available genomic resource. Results will facilitate many future studies in evolution, ecology and molecular genetics, from evolutionary relationships among avian families, through the genomic basis of adaptations, to mechanisms of molecular evolution. Results will also aid conservation, for example by clarifying the relationships among species and providing baseline information for population-level sequencing. 

All 10,135 bird species are shown on this phylogeny, purple branches represent the 363 species that now have at least one genomic assembly per sequenced family. 


RANGE-EDGE PLANT POPULATIONS OF HIGH CONSERVATION PRIORITY LACK ADEQUATE HABITAT PROTECTION AND RESEARCH EFFORT 

Southern Canada is home to many plants at the northern limits of their geographic ranges. These species are often rare and at-risk in Canada, though more broadly distributed south of the US border. While the conservation value of these peripheral populations is controversial, the ability of species to move to higher elevations and latitudes may be crucial for responding to climate warming and these peripheral populations may be particularly important for range movements. In a recently published paper, members of Chris Eckert’s lab (Queen’s University; Chris Eckert, Raeya Jackiw) and Anna Hargreaves’ lab (McGill University; Anna Hargreaves, Pascale Caissy, Sandra Klemet-N’Guessan) investigate conservation efforts and risk, as well as the distribution patterns of plants at their northernmost range limit in Canada. They ask if Canadian conservation prioritizes range-edge populations, and if conservation priorities are matched by habitat protection and research effort. 

Caissy et al. find that most federally protected plants in Canada occur only at the northernmost limit of their range, and current habitat protection and research effort is inadequate for these species

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I've spent more time than many will believe [making microscopic observations], but I've done them with joy, and I've taken no notice those who have said why take so much trouble and what good is it?

Antonie van Leeuwenhoek

It's a parts list... If I gave you the parts list for the Boeing 777 and it had 100,000 parts, I don't think you could screw it together and you certainly wouldn't understand why it flew

Eric Lander

What is true for E. coli is also true for the elephant

Jacques Monod

The world becomes full of organisms that have what it takes to become ancestors. That, in a sentence, is Darwinism

Richard Dawkins

Shall we conjecture that one and the same kind of living filaments is and has been the cause of all organic life?

Erasmus Darwin

Nature proceeds little by little from things lifeless to animal life in such a way that it's impossible to determine the line of demarcation

Aristotle

Cells let us walk, talk, think, make love, and realize the bath water is cold

Lorraine Lee Cudmore

In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation. Light will be thrown on the origin of man and his history

Charles Darwin

It is my belief that the basic knowledge that we're providing to the world will have a profound impact on the human condition and the treatments for disease and our view of our place on the biological continuum

J. Craig Venter

Imagine a house coming together spontaneously from all the information contained in the bricks: that is how animal bodies are made

Neil Shubin

A grain in the balance will determine which individual shall live and which shall die - which variety or species shall increase in number, and which shall decrease, or finally become extinct

Charles Darwin

The stuff of life turned out to be not a quivering, glowing, wondrous gel but a contraption of tiny jigs, springs, hinges, rods, sheets, magnets, zippers, and trapdoors, assembled by a data tape whose information is copied, downloaded and scanned

Steven Pinker

We wish to discuss a structure for the salt of deoxyribose nucleic acid. (D.N.A.). This structure has novel features which are of considerable biologic interest

Rosalind Franklin

We are biology. We are reminded of this at the beginning and the end, at birth and at death. In between we do what we can to forget

Mary Roach

The systems approach to biology will be the dominant theme in medicine

Leroy Hood

I've always been interested in animal behavior, and I keep reading about it because it's so surprising all the time - so many things are happening around us that we neglect to look at. Part of the passion I have for biology is based on this wonderment"

Isabella Rossellini

Because all of biology is connected, one can often make a breakthrough with an organism that exaggerates a particular phenomenon, and later explore the generality

Thomas Cech

Nothing in Biology makes sense except in the light of evolution

Theodosius Dobzhansky

Biology is now bigger than physics, as measured by the size of budgets, by the size of the workforce, or by the output of major discoveries; and biology is likely to remain the biggest part of science through the twenty-first century

- Freeman Dyson

Nothing can be more incorrect than the assumption one sometimes meets with, that physics has one method, chemistry another, and biology a third

- Thomas Huxley