Biology subjects

Colautti, R. I.

Publications and source records attributed to Colautti, R. I..

11 recordsLinked to original sources

bioRxiv2026

Assortative mating may have facilitated rapid evolution of locally adaptive phenologies during a biological invasion

Assortative mating for a trait under selection can increase the rate of adaptive evolution and limit introgression of detrimental alleles. We therefore hypothesized that assortative mating facilitated the rapid evolution of flowering phenology observed in the self-incompatible perennial Lythrum salicaria (purple loosestrife) as it invaded eastern North America. We characterized flowering schedules of 600 individuals representing 20 populations sampled along a latitudinal gradient of 10 degrees and grown in a common garden at mid-latitude. Consistent with our hypothesis, we found that flowering schedules were less synchronous in the mixed population of the common garden (s = 0.50) relative to the 20 locally adapted populations comprising it (s = 0.56 to 0.86), and flowering synchrony decreased towards higher latitudes of origin. Despite high synchrony, assortment potential ({rho}) by growth and phenology varied by population ({rho} = 0.03 to 0.61), but the predicted negative correlation between s and {rho} was masked by among-individual fitness variation in the common garden. We show how fitness variation and asynchrony associated with locally adapted phenology can reduce the fitness impacts of maladaptive gene flow and accelerate the rate of adaptive evolution during invasion.

evolutionary biology↗

bioRxiv2026

Blocking primer improves detection of tick-borne pathogens in Ixodes scapularis (black-legged ticks) from a Lyme disease hotspot region in eastern Ontario, Canada.

Tick-borne pathogen (TBP) surveillance strategies that rely exclusively on targeted methods like PCR (PCR) or immunoblots do not benefit from strain-level sequence variation. Bacterial 16S rRNA metabarcoding offers more agnostic detection but is constrained in I. scapularis by the dominance of a maternally inherited endosymbiont, Rickettsia buchneri. Here we report the design and evaluation of three R. buchneri-specific blocking primers to suppress endosymbiont amplification during full-length 16S rRNA library preparation. Of these, primer 18F-Rb-C3 reduced R. buchneri relative abundance approximately 32-fold. We applied 18F-Rb-C3 with V4-16S metabarcode sequencing on 67 ticks collected from farm animals in Eastern Ontario and compared Borrelia species detection against qPCR. The V4-16S rRNA metabarcoding identified Borrelia species in 21 samples, whereas qPCR detected Borrelia in 24 samples and 11 samples were detected by both methods. Additionally, metabarcoding detected Anaplasma phagocytophilum in 12 samples, including seven samples coinfected with Borrelia, in the same assay. Variation relevant to strain surveillance was also detected by sequencing, though V4-16S was not sufficient to resolve closely related Borrelia genospecies or A. phagocytophilum variants. These findings demonstrate that blocking primer 18F-Rb-C3 enhances sensitivity of amplicon sequencing to the level of qPCR while also detecting other pathogens and sequence variants in a single assay.

genomics↗

bioRxiv2025

Genome-wide SNP diversity in natural and cultivated populations informs restoration ecology with three Calamagrostis species from the Northwest Territories of Canada

There is growing demand for data-driven frameworks to guide robust plant restoration strategies in response to anthropogenic disturbances. Several seed-sourcing (i.e., provenancing) strategies have been proposed, which balance the use of locally adapted genotypes against mixed genotypes to reduce mutation load or assistant migration to anticipate future climate scenarios. However, taxonomic uncertainty and lack of data characterizing genetic differentiation and gene flow have hindered provenancing strategies for many ecologically important non-model plant species--especially those in remote but vulnerable regions like the boreal forests of northern Canada. To guide provenancing strategies following anthropogenic disturbance in Canadas Northwest Territories, we characterize species-specific markers, population structure, and hybridization among three Calamagrostis species. Double digest RAD sequencing (ddRAD) resulted in 2,951 polymorphic loci across 27 individuals, which we used to design loci for genotyping in thousands by sequencing (GT-seq), a cost-efficient target loci approach resulting in 256 polymorphic loci across 93 individuals from wild C. canadensis, C. stricta ssp. inexpansa and C. purpurascens populations. To help define the scale of local populations for seed sourcing, we characterized geographic variation and population structure among 57 wild collection sites. We also assessed genetic relationships of wild C. canadensis to 69 individuals across eight commercially maintained populations used in restoration projects. We found that GT-seq yields similar genetic differentiation patterns as common neutral molecular marker approaches like ddRAD-seq. Specifically, we resolve morphologically misidentified individuals, identify genetic hybrids, and characterize the scale of genetic isolation-by-distance. Finally, we determined that three cultivar seed sources were genetically similar to southern wild populations, whereas five cultivars aligned with northern wild populations of C. canadensis in the Northwest Territories of Canada. Overall, our results highlight the benefits of cost-effective methods for genome-wide multi-locus genotyping to inform provenancing best-practices and support more effective and sustainable restoration efforts.

genomics↗

bioRxiv2024

Latitudinal clines in floral display associated with adaptive evolution during a biological invasion

PremiseFlowering phenology strongly influences reproductive success in plants. Days to first flower is easy to quantify and widely used to characterize phenology, but reproductive fitness depends on the full schedule of flower production over time. MethodsWe examined floral display traits associated with rapid adaptive evolution and range expansion among thirteen populations of Lythrum salicaria, sampled along a 10-degree latitudinal gradient in eastern North America. We grew these collections in a common garden field experiment at a mid-latitude site and quantified variation in flowering schedule shape using Principal Coordinates Analysis (PCoA) and quantitative metrics analogous to central moments of probability distributions (i.e., mean, variance, skew, and kurtosis). Key ResultsConsistent with earlier evidence for adaptation to shorter growing seasons, we found that populations from higher latitudes had earlier start and mean flowering day, on average, when compared to populations from southern latitudes. Flowering skew increased with latitude whereas kurtosis decreased, consistent with a bet-hedging strategy in biotic environments with more herbivores and greater competition for pollinators. ConclusionsHeritable clines in flowering schedules are consistent with adaptive evolution in response to a predicted shift toward weaker biotic interactions and less variable but more stressful abiotic environments at higher latitudes, potentially contributing to rapid evolution and range expansion of this invasive species.

ecology↗

bioRxiv2023

Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant

O_LIInvading species encounter novel communities of consumers, pathogens, and competitors. Both phenotypic plasticity and rapid evolution can facilitate invasion across these heterogenous communities. However, the rate and extent of adaptive evolution on contemporary timescales can be constrained by adaptive phenotypic plasticity and the genetic architecture of traits under selection. C_LIO_LIWe measured phenotypic plasticity and quantified genetic variation for growth, leaf chlorophyll a (Chl a) and glucosinolates, and lifetime fitness among 23 naturally inbred seed families of Alliaria petiolata (garlic mustard) collected across its invasive range in eastern North America. After growing a self-pollinated generation in a uniform common garden to reduce maternal effects, we reared second-generation plants in a two-year greenhouse and field experiment with naive soil from an uninvaded habitat. We estimated selection gradients and causal factors affecting lifetime fitness when reared alone, with an intraspecific competitor, and under interspecific competition with naive Acer saccharum (sugar maple) saplings. C_LIO_LIWe defined Total Metabolite Production (TMP) as the first principal component of Chl a and glucosinolate concentrations, accounting for 84% of variation in these two traits. TMP was significantly plastic across growing environments (p < 0.001) with limited broad-sense heritability (H2 = 2.91; p = 0.08). Path analysis revealed that plastic phenotypes with higher TMP had an indirect positive effect on A. petiolata fitness via a direct, negative effect on performance of A. saccharum competitors. In contrast, the second principal component defined Relative Glucosinolate Investment (RGI), which was significantly heritable (H2 = 16.91, p < 0.001) with no detectable plasticity across treatments. Variation in RGI among A. petiolata genotypes had a direct, positive effect on A. saccharum performance and an indirect negative effect on A. petiolata fitness. C_LIO_LISynthesis. Adaptive evolution of allelopathy during invasion has been constrained by (i) a lack of heritable genetic variation for allelopathy, (ii) high plasticity for TMP across competition treatments, and (iii) selection for lower RGI under interspecific and intraspecific competition. As an alternative to eco-evolutionary feedbacks, plasticity in TMP may be an overlooked explanation for variable performance of A. petiolata across its introduced range. C_LI

ecology↗

bioRxiv2022

Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada

Ticks in the family Ixodidae are important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from the Borreliella (Borrelia) burgdorferi sensu lato (Bbsl) complex. The blacklegged tick (Ixodes scapularis) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated with I. scapularis in Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adult I. scapularis (N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within a LD hotspot near Kingston, Ontario, Canada. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and a Babesia sp. intracellular parasite. We show that {beta}-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing also differed among dissected tissues only, including a Borrelia from the Bbsl complex, Borrelia miyamotoi, and Anaplasma phagocytophilum. Importantly, we find co-infection of I. scapularis by multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (B. burgdorferi sensu stricto). IMPORTANCEA vector of human health concern, blacklegged ticks, Ixodes scapularis, transmit pathogens that cause tick-borne diseases (TBDs), including Lyme disease (LD). Several hotspots of elevated LD risk have emerged across Canada as I. scapularis expands its range. Focusing on a hotspot in southeastern Ontario, we used high-throughput sequencing on whole ticks and dissected salivary glands and midguts. Compared to whole ticks, analysis of salivary glands and midguts revealed greater {beta}-diversity among microbiomes that are less dominated by Rickettsia endosymbiont bacteria and enriched for pathogenic bacteria including a Bbsl- associated Borrelia, Borrelia miyamotoi, and Anaplasma phagocytophilum. We also find evidence of co-infection of I. scapularis in this region by multiple microbes. Overall, our study highlights the challenges and opportunities associated with the surveillance of the microbiome of I. scapularis for pathogen detection using metabarcoding and metatranscriptome approaches.

microbiology↗

bioRxiv2021

Evidence for continent-wide convergent evolution and stasis throughout 150 years of a biological invasion

The extent to which evolution can rescue a species from extinction, or facilitate range expansion, depends critically on the rate, duration, and geographical extent of the evolutionary response to natural selection. Adaptive evolution can occur quickly, but the duration and geographical extent of contemporary evolution in natural systems remains poorly studied. This is particularly true for species with large geographical ranges and for timescales that lie between long-term field experiments and the fossil record. Here, we introduce the Virtual Common Garden (VCG) to investigate phenotypic evolution in natural history collections while controlling for phenotypic plasticity in response to local growing conditions. Reconstructing 150 years of evolution in Lythrum salicaria (purple loosestrife) as it invaded North America, we analyze phenology measurements of 3,429 herbarium records, reconstruct growing conditions from more than 12 million local temperature records, and validate predictions across three common gardens spanning 10 degrees of latitude. We find that phenology clines have evolved along parallel climatic gradients, repeatedly throughout the range, during the first century of evolution. Thereafter, the rate of microevolution stalls, recapitulating macroevolutionary stasis observed in the fossil record. Our study demonstrates that preserved specimens are a critical resource for investigating limits to evolution in natural populations. Our results show how natural selection and trade-offs measured in field studies predict adaptive divergence observable in herbarium specimens over 15 decades at a continental scale.

evolutionary biology↗

bioRxiv2021

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

The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70 x coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7 % of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99 % of plant BUSCO genes and 98 % of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2 % genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

genomics↗

bioRxiv2020

Functional shifts of soil microbial communities associated with Alliaria petiolata invasion

Soil feedback is thought to be an important contributor to the success of invasive plants. Despite evidence that invasive plants change soil microbial diversity, the functional roles of microbes impacted by invasion are still unclear. This knowledge is a critical component of our understanding of ecological mechanisms of plant invasion. Mounting evidence suggests Alliaria petiolata can suppress arbuscular mycorrhizal fungi (AMF) to disrupt native plant communities in controlled laboratory and greenhouse experiments, though it is less clear if allelochemicals persist under natural field conditions. Alternatively, invasive plants may accumulate pathogens that are more harmful to competitors as predicted by the Enemy of my Enemy Hypothesis (EEH). We examined changes in functional groups of soil bacteria and fungi associated with ten naturally occurring populations of A. petiolata using amplicon sequences (16S and ITS rRNA). To relate soil microbial communities to impacts on co-occurring plants, we measured root infections and AMF colonization. We found no changes in the diversity and abundance of AMF in plants co-occurring with A. petiolata, suggesting that mycorrhizal suppression in the field may not be as critical to the invasion of A. petiolata as implied by more controlled experiments. Instead, we found changes in pathogen community composition and marginal evidence of increase in root lesions of plants growing with A. petiolata, lending support to the EEH. In addition to these impacts on plant health, changes in ectomycorrhiza, and other nutrient cycling microbes may be important forces underlying the invasion of A. petiolata and its impact on ecosystem function.

ecology↗

bioRxiv2020

Chasing the origin of SARS-CoV-2 in Canada's COVID-19 cases: A genomics study

The emergence and global spread of SARS-CoV-2 has had profound social and economic consequences and has shed light on the importance of continued and additional investment in global health and infectious disease surveillance. Identifying changes in viral genomes provides key insights into viral diversity, how viruses spread within populations, and viral strategies for evasion of host immune systems. Here we report twenty-five SARS-CoV-2 genome sequences collected from some of the first COVID-19 cases in eastern Ontario, Canada (March 18-30, 2020). The reported genomes belong to the S-clade (n=2) and G-clade (n=23) of SARS-CoV-2 and contain 45 polymorphic sites including one shared missense and three unique synonymous variants in the gene encoding the spike protein. A phylogenetic analysis enabled the tracing of viral origin and potential transmission into and within Canada. There may be as many as sixteen unique infection events represented in these samples, including at least three that were likely introduced from Europe and seven from the USA. In addition, four separate genomes are each shared by multiple patients, suggesting a common origin or community spread even during this early stage of infection. These results demonstrate how molecular epidemiology and evolutionary phylogenetics can help local health units track origins and vectors of spread for emerging diseases like SARS-CoV-2. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to prevent future pandemics.

microbiology↗

bioRxiv2018

baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science

Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Several flexible, open-source tools developed for the R and Python coding environments aid the reproducibility of data wrangling and analysis in scientific research. In contrast, analogous tools are generally lacking for earlier stages, such as systematic labelling and processing of field samples with hierarchical structure (e.g. time points of individuals from multiple lines or populations) or curating heterogenous data collected by different researchers over several years. Such tools are critical for modern research given trends toward globally distributed collaborators using higher-throughput technologies. As a step toward improving repeatability of methods for the collection of biological samples, and curation of biological data, we introduce the R package baRcodeR and the PyTrackDat pipeline in Python. The baRcodeR package provides tools for generating biologically informative, hierarchical labels with digitally encoded 2D barcodes that can be printed and scanned using low-cost commercial hardware. The PyTrackDat pipeline integrates with baRcodeR output to build a web interface for sample management and tracking along with data collection and curation. We briefly describe the application of principles from baRcodeR and PyTrackDat in three large research projects, which demonstrate their value to (i) help document sampling methods, (ii) facilitate collaboration and (iii) reduce opportunities for human errors and omissions that could otherwise propagate through downstream data analysis to compromise biological inference.

bioinformatics↗