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colautti lab main page colautti lab menu home people research resources ecology evolution genetics colautti lab for a changing world people research resources learn more pre order 2nd edition may 2025 r crash course for biologists 1st ed an introduction to r for bioinformatics and biostatistics paperback b w hardcover colour kindle download free pre order spring summer 2025 r stats crash course for biologists an introduction to common statistical models in r for bioinformatics and biostatistics coming soon 2025 2026 r machine learning crash course for biologists an introduction to machine learning in r for bioinformatics and biostatistics invasion genetics the baker and stebbins legacy wiley amazon ca amazon com 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 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 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 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 screen for known pathogens and identify environmental factors affecting disease risk 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 build bioinformatics tools to match microbial dna sequences between ticks and bite victims to identify candidates for new and emerging pathogens 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 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 graphical interface r studio and command line options install packates barcoder in r generate simple id codes ex001 ex002 ex003 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 generate printable pdf files of paired id codes and qr barcodes customize the pdf layout for any type of printable format e g vinyl stickers waterproof paper generate reproducible code for archival purposes e g in publications or online repositories create csv files to link unique ids and sampling hierarchy with downstream data collection workflows 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 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 p redicting p lant l ocal a daptation in the n orthwest t erritories 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 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 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 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 follow google scholar email what next join us contact us back to top content robert i colautti template html5 up