Colautti Lab

Research Vision

The Colautti Lab is best known for our research on the evolutionary ecology and ecological genetics of invasive species. More generally, we apply multiple approaches (e.g. field experiments, high-throughput sequencing, theoretical models, meta-analysis) to address fundamental questions in ecology and evolution, which in turn has fed back to suggest new directions for improving conservation, resource management, and human health. Our long-term research vision is to develop an understanding of species distributions and global biodiversity as an outcome of ecological and genetic factors that promote or constrain contemporary evolution in natural populations.

Projects at a glance

Current Research Projects

Study system:Ixodes scapularis

What is the community composition of tick microbiomes and which landscape factors affect tick movement and microbiome composition? Rapid increases in tick populations and tick-borne diseases are well-documented across Canada and the northern United States. Ticks have a complicated ecology involving multiple hosts with distinct movement behavior, habitat preferences, and disease communities. We are using high-resolution population genomics and microbiome metagenomics of deer ticks (Ixodes scapularis) using high-throughput sequencing. Our working hypothesis is that landscape characteristics affect movement of tick hosts (deer, rodents, birds) and tick survival, which in turn could lead to predictable landscape effects on tick population and microbiome genetic structure. Understanding how land use and landscape features affect disease prevalence is of great significance to human health and welfare. This project combines classic population and community ecology with population genetics and metagenomics to understand a phenomenon that is of major interest to human health agencies. Ticks are a good system for understanding how ecosystem structure and function affect human health.

Study system:Alliaria petiolata

Are introduced populations more vigorous, and if so, why? Along with Oliver Bossdorf (Tübingen) and Steve Franks (Fordham), I coordinated a field survey involving 176 participants from 16 countries to make field measurements of Alliaria petiolata at 395 locations. Measurements generally characterized population size and density, age structure, individual fruit and seed production, herbivore damage, pathogen infection, and habitat characteristics. Seeds were collected from nearly 5,000 plants (up to 20 plants per location). Our analysis of the field data reveals that introduced population sizes are almost 10x larger than natives, on average. We have also identified 14 ‘mega-populations’ with one million or more individuals, and these occur exclusively within the introduced range of North America. Our analysis supports the prediction that individual fitness and population performance are higher in the introduced range of A. petiolata. This supports ‘increased vigour’ in introduced field populations at an intercontinental scale, but this effect weakens significantly after controlling for local environmental factors that can cause spatial auto-correlation in life-history and fitness data. Notably, data from our large field survey provides a rare opportunity validate lab and field experiments at an intercontinental scale. Our current research uses genomic tools and field experiments to investigate the genetic and environmental factors affecting variation in population demographic parameters.

How do invasive species affect soil microbial communities and ecosystem function? Does evolution alter ecological impacts over time? The mechanism of invasion by Alliaria petiolata (garlic mustard) into North American deciduous forests is thought to involve suppression of arbuscular mycorrhizal fungi (AMF) that are beneficial to native plants. We are examining effects of A. petiolata on soil microbial communities as one of many possible explanations for its rapid invasion in North America. To do this, we are combining eco-evolutionary models, field manipulations, common garden experiments, a bespoke MCMC Bayesian model of root colonization, and analysis of high-throughput metabarcode sequences of roots and soils (bacterial 16S + fungal ITS gene). We are finding that A. petiolata does not have a strong effect on AMF in the field but does alter nutrient-cycling bacteria. This research shows the importance of field validation and the complexity of plant interactions mediated through soil.

Study system: Lythrum salicaria

Does assortative mating speed up evolution in colonizing species while restricting evolution of established populations? In eastern North America, northern L. salicaria populations have evolved to flower ~45 days earlier at 1/5 the biomass as their southern relatives, within about 50 years. This is surprisingly fast, given (i) high overlap observed for fitness curves and (ii) legacy effects on the genetic structure of populations expected for a perennial plant. We are exploring one possible explanation: that frequent, stepwise colonization increases the rate of adaptive evolution. In contrast, adaptive genotypes may evolve slower in established native populations experiencing changing environments. Future research will manipulate flowering time in field experiments to quantify assortative mating and the response to selection in experiments simulating invading populations and native populations in novel environments. This line of research has important implications for understanding how native vs. invasive species will perform in the Anthropocene.

Are range limits an emergent property of genetic constraints and ecological complexity? We sampled L. salicaria along a latitudinal gradient while targeting populations with high vs. low levels of herbivory from specialist Gallerucella beetles introduced in the 1990s for biological control. Using selection analysis and quantitative genetics, we are testing the hypothesis that biotic and abiotic selection interact to impose non-additive constraints on flowering time, limiting evolution of locally adapted phenotypes. Future research will manipulate these constraints in the field to better understand (i) where, when and why biological control is successful (or not), (ii) the ecological and genetic basis of southern range limits of this species, and (ii) how genetics can inform ecological niche theory.

Can natural history collections be used to estimate rates of phenological change? Despite tens of thousands of human-hours of work spread across six years at field sites spanning over one thousand kilometers, our research on L. salicaria phenology has been limited to a relatively small proportion of its entire introduced range. However, this experimental work has enabled a climatic model of phenology that my lab has applied to test for geographical clines using 3,427 herbarium specimens. We wrote code to extract 62,208 weather records from 6,303 stations surrounding these specimens and used statistical models to standardize phenological stage – an analysis we call: ‘virtual common garden’. Results support a model of repeated parallel evolution. Future work will complement this analysis using high-throughput sequencing to genetically reconstruct colonization history and selection from herbarium samples. This project demonstrates the value of natural history collections for testing large-scale phenotypic changes occurring over decades to centuries.

Other Systems

What is the genomic architecture of adaptation in invading species? How important is standing genetic variation vs de novo mutation for invasion? We use modern genome and transcriptome sequencing to complements our field experiments and theoretical models to address questions of rapid evolution in a way that can’t be addressed with any single method on its own. We have assembled draft genomes for several species, including L. salicaria (N50 = 2.57Mbp) and A. petiolata (N50 = 1.68 Mbp). We are examining genome-wide variation in these species with plans to genetically map ecologically important traits (e.g. phenology in L. salicaria, glucosinolate chemistry in A. petiolata). We are interested in genotyping to test geographical origin and spread of adaptive alleles over time. Using these data, we are investigating which adaptive variants arise de novo and which were introduced from native sources. We are also investigating the role of structural variants in rapid evolution during invasion.

Predicting Plant Local Adaptation in the Northwest Territories (PPLANTs). This is a new project that applies fundamental concepts in plant local adaptation to advise restoration efforts in Arctic and Boreal Forest habitats, in collaboration with Pippa Seccombe-Hett at Aurora College (Northwest Territories, Canada). We are combining de novo genome assembly and genotype-by-sequencing to characterize population genetic structure of local seed collections in an attempt to reconstruct postglacial colonization vs recent gene flow in response to climate warming and human development. Our first grant was recently approved for a preliminary study to sequence collections of two genera (Calamagrostis and Poa). Future work will add up to 40 genera and include field experiments measuring effects of local adaptation on population demographic parameters. This research program will develop genetic models to help manage northern ecosystems that are robust to future climate change and human disturbance.

Past Contributions

NOTE: Reference numbers refer to citations in CV

Ecological Genetics of Range Expansion^[20-22,26]

Overall: This work demonstrates how classic methods can be used to predict range dynamics in a changing world.

1. Populations of an invasive species have rapidly adapted to climate (< 50 years).
2. Local adaptation can evolve in response nonlinear directional selection and genetic constraint, in contrast to conventional models of antagonistic selection on the same set of traits, producing a distinctive reaction norm.
3. The ecological effects of adaptive evolution and genetic constraints are very strong relative to ecological factors (e.g. escaping natural enemies).
4. Data supports the theory that northward range expansion may ultimately be limited by low genetic variation for multivariate phenotypes.

Spatial Autocorrelation and Ecological Inference ^{[5,9,11-12,15,17-18,28]}

Overall: This work has helped to shift research focus away from the dominant assumption that introduced populations are ecologically and genetically homogeneous.

1. It usually isn’t clear whether introduced populations are invasive or non-invasive, nor the biological criteria used for differentiating these categories.
2. Trait differences between native and introduced genotypes in field and common garden experiments are confounded by spatial autocorrelation (e.g. geographic clines).

Macroecology of Invasions^[2-4,6-8,10]

Overall: This research has helped convince ecologists to consider human activity when studying contemporary macroecology.

1. Human activity affects geographical patterns of invasion that may be erroneously attributed to ecological factors (e.g. empty niche, environmental disturbance).
2. Observations about the history of introductions (i.e. propagule pressure) can help to parameterize neutral models for testing ecological hypotheses from biogeographical patterns of invasive species.

Eco-Evolutionary Dynamics in an Era of Global Change^{[23-25,29,32-33]}

Overall: This work contributed theoretical understanding to the genomic basis of local adaptation and evolutionary responses to climate change.

1. QTL mapping identified a flowering time locus exhibiting antagonistic pleiotropy (AP) in a reciprocal transplant experiment of a native plant – that is, the ‘local’ allele increased fitness relative to the ‘foreign’ allele in each environment.
2. AP loci are rarely observed in natural populations, but theory suggests they should be ubiquitous and important for maintaining genetic diversity.
3. The native plant Boechera stricta rapidly evolves earlier flowering, but not fast enough to track the rate of warming temperatures.

Invasion Genetics^{[13,16,19,27,29,31,35]}

Overall: This work helped to define the emerging field of invasion genetics.

1. As a MSc student, I conducted one of the first studies to use hypervariable nuclear DNA markers to reconstruct the short-term (i.e. human-mediated) demographic history of an invasive species, an approach I called ‘invasion genetics.’
2. I co-edited (with Katrina Dlugosch, Spencer Barrett, and Loren Rieseberg) Invasion Genetic. This book expanded on The Genetics of Colonizing Species (1965), which featured some of the most significant contributors to our modern understanding of ecological and evolutionary theory (e.g. Dobzhansky, Harper, Lewontin, Mayr, Stebbins, Waddington, Wilson).