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The Alliance of Independent Authors - Author Member

colauttilab.bsky.social's user avatar
Don’t get me started…
dpmoriarity.bsky.social's user avatarDaniel P. Moriarity @dpmoriarity.bsky.social2d
"A study of federally funded research projects in the United States estimated that principal investigators spend on average about 45% of their time on administrative activities related to applying for and managing projects rather than conducting active research" www.pnas.org/doi/10.1073/...
 
inneslab.bsky.social's user avatar
Very happy to start the new year with publication of our new work on leaf surface RNA. Plant leaves secrete diverse RNAs that are surprisingly stable on their surfaces. Next question to answer: What do they do? www.pnas.org/doi/epub/10....
Protocol for isolating RNA from the surfaces and apoplastic spaces of plant leaves.
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colauttilab.bsky.social's user avatar
What are some good examples of genetic assimilation in plants?
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jenncoughlan.bsky.social's user avatar
Prepping to teach intro evolution for the first time- what are everyone's favorite misconceptions about evolution? I've got a few: - evolution happens to individuals - evolution happens because it's needed - evolution is hierarchical/directional/has an end point
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drcraigmc.bsky.social's user avatar
We don’t talk enough, or at all, about whether people can actually afford the pathway to becoming a scientist—or staying one. And let’s face it: having wealth makes it much easier, often paving the way for greater success than those without. #science #academia
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colauttilab.bsky.social's user avatar
First ever final exam in 8 years of university teaching. Previously, I moved from lectures with PowerPoint slides to whiteboard notes and self-guided tutorials + assignments. Next, should I do overhead projector with transparencies or go full neon to continue my regression to the 80s?
 
gavan.ca's user avatar
‘Tis the season (or at least evening) to enjoy the Candlelight Christmas concert, performed by the Kingston Symphony and Kingston Choral Society, at the Isabel Bader Centre for the Performing Arts.
The image shows a full orchestra on stage, illuminated by soft lighting with red and green accents. A choir is seated in the upper background, and snowflake-shaped lights are projected onto the back wall. The wooden architecture of the concert hall, including its striking ceiling design, adds to the elegant atmosphere. The audience is seated in rows, watching the performance attentively.
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1pantunes.bsky.social's user avatar
I'm looking forward to give a talk on how we can use invasive species curves and plant traits to increase the capacity to predict plant species' invasions. ontarioinvasiveplants.ca/wp-content/upl…
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ecoinvasions.bsky.social's user avatar
We (the authors) had much discussion and unresolved debate over the terms and the concepts behind them. Hence the caveat: "Even among ourselves, there remains disagreement about how some terms should be defined, reflecting the diversity of opinions within our evolving field" #bioinvasions
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pkpd-babe.bsky.social's user avatar
One of my favorite feeds is ‘Quiet Posters’, a feed of posts from people you follow who don’t post very often. A nice way to make sure I don’t miss things 🤗 bsky.app/profile/did:...
unknown @unknownunknown
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annatigano.bsky.social's user avatar
Do you know of any examples of population structure identified with whole genome data but not with microsats or RADseq-type methods?
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colauttilab.bsky.social's user avatar
We need to talk about the Novel Weapons Hypothesis (NWH) and allelopathy as an evolutionary strategy…
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katelaskowski.bsky.social's user avatar
I'm working on updating my "Data Detectives" class where students read about research misconduct and mistakes. I have lots of examples of misconduct, but am now looking for examples of popular press just going buck wild and over-interpreting scientific results. What are your fav examples??
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cmhmaliani.bsky.social's user avatar
I spent the last five summers sharing the infamous mediterranean heat with 15 species of thistles that flower at that somewhat absurd time of year, seeking to understand (something about) their thermal ecology. Here are the results. I think all my sweat was worth it. biorxiv.org/cgi/content/...
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neddochtermann.bsky.social's user avatar
Since Bluesky has grown just in the last week, I thought I’d repost this to see if there are any other suggestions. Thanks!
neddochtermann.bsky.social's user avatarNed Dochtermann @neddochtermann.bsky.social2m
I'm teaching a graduate course on meta-analyses this coming semester. Question for the bluesky ecology and evolution community: What are some of your favorite meta-analyses that changed your understanding of a topic? Or, just cool questions? Please repost! 🧪 #Evolution #Ecology #Biology
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ipbes.bsky.social's user avatar
Invasive alien species are a threat to #nature, nature’s contributions to people, and good quality of life. Read the @ipbes.bsky.social #InvasiveAlienSpecies Report at: www.ipbes.net/ias 🧪🌍
An infographic detailing facts about the impacts of invasive alien species from the IPBES Invasive Alien Species Report. The infographic also depicts images of various different invasive alien species such as the grey squirrel, alexandrine parakeet and red fox.
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kevinlala.bsky.social's user avatar
I'm very happy to see my article "Genes, Culture and Scientific Racism", coauthored with Marc Feldman, published in Proc Natl Acad Sci USA (see rb.gy/x0e4lw). We explain why people wrongly believe race is a biological classification.
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anibalpauchard.bsky.social's user avatar
I'm new in @bsky.app so I can use this opportunity to advertise the amazing work of over 200 authors in the @ipbes.bsky.social Invasive Alien Species assessment. Please check here all the outputs, including factsheets and the cool IAS learning tool: www.ipbes.net/ias
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itaiyanai.bsky.social's user avatar
Would you prefer to lead a lab alone or together with a science buddy? How interesting would be a research institute where joint labs are the standard?!
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lars-brudvig.bsky.social's user avatar
Starter Packs are great, but they favor well established individuals (understandably so). To help prop up new voices, here is a set of early career ecologists (self defined) who are, or would like to become, active on BlueSky Please reply if you would like to be included! go.bsky.app/Di74bDy
unknown @unknownunknown
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colauttilab.bsky.social's user avatar
mopia.bsky.social's user avatarMaria Gallegos @mopia.bsky.social2m
If you see this, please repost with a favourite photo of the sky that you’ve taken recently
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bossdorf.bsky.social's user avatar
Two amazing jobs at Uni Bern. Assistent professorships in conservation biology and computational ecology. Bern is a wonderful place to live and work in! www.iee.unibe.ch/about_us/job...
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ctrlalttim.bsky.social's user avatar
Everyone is creating starter packs, and it's great! But PLEASE! Let's be very intentional about building diverse, inclusive starter packs. If we're rebuilding a social networks of researchers from scratch, let's do it right. 🧪
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donnag.bsky.social's user avatar
JOB! Assistant Collection Manager, Invertebrate Research & Collections, Canadian Museum of Nature ME-05 - $71,754 to $87,705 per year Permanent full-time position (37.5 hours per week) Work Location: Natural Heritage Campus (NHC) – Gatineau, QC nature.ca/en/join-give...
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martin-nunez.bsky.social's user avatar
If you are an invasion biologist or work on related topics please comment on this post and I will add you to the starter pack! go.bsky.app/WsevAe
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Inflorescence of Lythrum salicaria (purple loosestrife) (© Colautti Lab).

Change is Constant

The Colautti Lab investigates rapid evolution in a changing world

Human activity is causing rapid changes to the earth's ecosystems, benefitting some species with adverse effects on others. We investigate how human activity is changing genes, genomes and phenotypic traits of species in nature, and how this in turn affects the viability of species. Our approach combines cutting-edge advances in genomics and computational biology with experiments in controlled and natural environments. We think knowledge from these experiments can help improve human health and management of ecosystem services threatened by global change.


Main Research Projects

Stress-Constraint Model
A comparison of local adaptation models: the 'Classic Model' (top row) is widely used in theoretical studies of adaptation and range limits. Our 'Stress-Constraint Model' (bottom row) makes subtle but distinct predictions about constraint and adaptation along environmental gradients. Each model can be formulated as a fitness landscape (left column) or fitness reaction norms (right column). (© Colautti Lab)

Will Evolution Save Us?

Evolution can happen very fast in nature, but it has limits.

We are currently researching hard limits to evolutionary change that may be important for understanding how species evolve in response to human activity over the next century. This research grew from our empirical work on the invasive plant Lythrum salicaria (see below), and it's a good example of how basic research on non-model systems can provide new scientific insigth.

Our first paper on this topic is now published and available (Free, Open Access): Effects of species interactions on the potential for evolution at species' range limits

This 10 minute YouTube video summarizes our ongoing work. The video was recorded in June 2021 for the (Virtual) Evolution 2021 conference, held annually by the Society for the Study of Evolution (SSE), Society of Systematic Biologists (SSB) and the American Society of Naturalists (ASN).

SARS-CoV-2 Anatomy
Anatomy of the SARS-CoV-2 virus responsible for the COVID-19 pandemic

COVID-19 & SARS-CoV-2

Our lab's expertise in Data Science and Genomics have been put to use in COVID-19 research, including genome sequencing of SARS-CoV-2 genomes -- the virus responsible for the disease more commonly known as COVID-19. This work is currently ongoing with collaborators from Queen's University and Kingston Health Sciences Centre including Dr. Prameet Sheth, Dr. Calvin Sjaarda and others (see coauthors on papers linked below).

Phlogenomics of early-stage COVID-19 patients in Ontario, Canada

Our first research paper (published in Nature Scientific Reports) describes our sequencing of SARS-CoV-2 genomes using two different technologies, including a 'handheld' nanopore-based sequencer called the MinION by Oxford Nanopore. We analyzed SARS-CoV-2 genomes using evolutionary phylogenetics to identify sources of introduction and spread among the first COVID-19 cases in eastern Ontario. This work shows how portable sequencers and applied evolution can improve the public health response to emerging pandemics.

Fully reproducible code for this project is available on GitHub.

Temporal Dynamics and Evolution of SARS-CoV-2 in Ontario, Canada

Different genetic lineages (i.e. variants) have different mutations that may affect the rate of spread of COVID-19. In this study published in eSphere, we found variable infection rates in different lineages through time. Even in these early stages of the pandemic, variability in infection rates and the growing number of genetic lineages was cause for concern.

Metabolomics and Immune Response

Current projects (unpublished) track the immune response of COVID-19 patients and use chemistry of nasal swabs to identify biochemical changes in COVID-19 patients. These provide insights into the pathology of SARS-CoV-2, potential therapeutic targets, and the need for age-specific booster shots.

tick
Dissected deer tick (Ixodes scapularis) exposing gut microbes and salivary glands (© Colautti Lab)

Ticks & tick-borne diseases

In situ detection, characterization, and risk assessment of tick-borne pathogens

Our 2021 opinion paper makes the case for a transdisciplinary research programme in vector-borne diseases, published in Trends in Parasitology

Rates of Lyme disease and other tick-borne illnesses are rapidly increasing in Canada and the United States. To better address this growing threat to human health, we are taking a multidisciplinary and integrated approach for in situ detection, characterization, and risk management of tick-borne pathogens. The objectives of this project are:

  1. Screen for known pathogens and identify environmental factors affecting disease risk.
  2. Develop and test field protocols and analytical tools for in situ microbiome analysis of tick, human and pet samples. This includes identification of known pathogens including distinct strains of Borrelia (the causative agent of Lyme disease).
  3. Build bioinformatics tools to match microbial DNA sequences between ticks and bite victims to identify candidates for new and emerging pathogens.
  4. Develop new risk assessment tools that, for medical educators, public health officials, and the affected populace, using updated models of risk of tick-borne pathogens.

Media coverage:

2021

Tick Sequencing:
CTV | CTV (website) | National Post | Globe & Mail | CBC Radio Ottawa | Toronto Star | Kingston Whig-Standard

Tick Surveys:
Ottawa Citizen | Global Kingston | CBC Radio CTV Ottawa | CTV Ottawa Website | May 2021 Press Release

2020

Tick Surveys:
Queen's Gazette | CTV | Global | ICI(CBC) Radio-Canada | Ottawa Sun | Whig-Standard | Kingston Herald

tick
Hand-labelled tubes (top) and a variety of use-cases of the open-source baRcodeR package (© Colautti Lab)

Open-source for Open Science

baRcodeR

baRcodeR is a tool for generating unique identifier strings and printable Linear or 2D (QR) barcodes. It improves repeatability of labelling biological samples and facilitates data collection, tracking and curating.

Available for R and on the web

Features:

  1. Graphical interface (R Studio) and command line options : install.packates(baRcodeR) in R
  2. Generate simple ID codes (Ex001, Ex002, Ex003,…)
  3. Generate hierarchical (i.e. nested) ID codes (Pop01-Trt01-01:00, Pop01-Trt01-02:45, Pop01-Trt02-01:00, Pop01-Trt-02-02:45, Pop02-Trt01-01:00,…)
  4. Generate printable PDF files of paired ID codes and QR barcodes
  5. Customize the PDF layout for any type of printable format (e.g, vinyl stickers, waterproof paper)
  6. Generate reproducible code for archival purposes (e.g. in publications or online repositories)
  7. Create CSV files to link unique IDs and sampling hierarchy with downstream data collection workflows.
  8. Integration with the PyTrackDat pipeline to set up a web-based data collection platform: PyTrackDat
baRcodeR links:
2pg Cheat Sheet | Quick-start guide | RStudio GUI instructions
GitHub | CRAN

Overhead view of ~4,000 Lythrum salicaria (purple loosestrife) plants growing in a common garden study at Queen's University Biological Station (QUBS) (© Colautti Lab)

Invasive Species and Evolution:

Rapid evolution facilitates invasion of invasive purple loosestrife

Climate and biotic interactions (e.g. herbivores, pollinators) can dramatically affect survival and reproduction in plants. We are combining genome and transcriptome sequencing with a large field experiment at the Queen’s University Biological Station (QUBS) to understand ecological and genetic factors that promote or constrain rapid adaptation in invasive Lythrum salicaria (purple loosestrife). This research helps to understand the role that evolution plays in the spread of invasive species.

Key references:

Science | PNAS

Media coverage:

CBC | Popular Science | io9

tick
Garlic mustard (Alliaria petiolata) growing in a common garden experiment at the Queen's University Biological Station (QUBS) (© Colautti Lab)

Invasive Species and Evolution:

Null and Neutral Models of Evolution

Rapid evolution of local adaptation may play an important role in the spread of invasive species, however it can be very difficult to detect when evolution has occurred, and how much it has contributed to invasion. We have been carefully reassessing published evidence for evolution to determine the extent to which evolution has contributed to the spread of invasive species.

This 30 minute YouTube video was recorded at the 2023 Invasomics Workshop in Hamilton, New Zealand. It discusses the importance of null models for inferring adaptive evolution during biological invasions and some of the unique challenges for defining null models in these systems.

Collecting seeds from native plants in the Northwest Territories (© Pippa Seccombe-Hett)

P-PLANT Project

Predicting Plant Local Adaptation in the Northwest Territories

A major challenge for resource extraction and industrial development in Northern Canada is lack of access to biological resources for restoring disturbed habitats to near-pristine states.

The P-PLANT project is a collaboration with the Aurora Research Institute in the Northwest Territories. We are applying genomic tools and field studies to characterize population genetic structure in native species used in restoration and reclamation projects. Many of these species can be difficult to distinguish based on morphological characteristics, and the extent to which populations are differentiated and adapted to local conditions is largely unknown. Our research will help restoration projects maintain the integrity of locally adapted populations.


Research Methods

Clockwise from top left: 1. Boechera retrofracta rosette in prototype imaging chamber; 2. Sequence alignment close-up; 3. Transplanting for large growth chamber experiment; 4. Illumina HiSeq Next-Generation DNA Sequencer (© Illumina)
Genetics

Genetics & Bioinformatics

Decoding the Building Blocks of Life

We use high-throughput sequencing, 'big data', and bioinformatics to probe genetic variation underlying ecologically important traits and to understanding the complex relationship between genoype, phenotype, and the environment. Our ultimate goal is to understand how naturally-occurring genetic variants affect survial and reproductive rates (i.e. performance) under a variety of natural environments.

Lythrum salicaria a.k.a. purple loosestrife growing in a common garden study at the Koffler Scientific Reserve (University of Toronto). See Colautti and Barrett (2013)
Ecology

Ecology

Our research begins and ends in the field

Observations of organisms in natural and human-altered environments underpin our research in ecological genomics and evolutionary ecology. To investigate genes in nature we rely on field surveys and experimental manipulations at Queen's University Biological Station (QUBS) and other field sites around the world. These are complemented with the analysis of 'Big Data' characterizing aspects of the natural environment and human activity at regional to global scales.

Fitness surface from Colautti and Barrett (2010)
Evolution

Evolution

The Theoretical Foundation of Modern Biology

From the elegant simplicity of the Price Equation to the profound complexity of living systems, evolutionary theory provides a robust scientific foundation to develop a better understanding of the structure, function and dynamics of living systems.

Eco-Evo-Geno

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