1.
Adaptive evolution across multi-scale biological
systems: finding a bridge between molecular evolution
and multi¬species dynamics.
Fundamental questions
surrounding adaptive evolution across multi-scale
systems have resisted investigation because they lie
on the boundary between fields. The traditional
approach to adaptive molecular evolution is rooted in
population genetic theory, and while essential, its
scope is limited by its highly reductive view of the
adaptive landscapes. A complete understanding of
adaptive landscapes will require us to consider (i)
the effect of multi-scale dynamics (e.g., epistasis
and multi-species interactions), (ii) a more
de-centralized mapping of genotype and phenotype, and
(iii) multiple fields of biology. The long-term
objective of this project is to develop theory and
methods appropriate for understanding adaptive
dynamics of genes across multi-scale biological
systems. The research is comprised of three research
arms (RAs) related to fitness landscapes influenced by
inter-species interactions. In RA-1 we are
using a novel combination of (i) Markov models for
within-species gene dynamics and (ii) agent-based
simulation for between-species organism dynamics to
model and explore multi-scale adaptive evolution of
microbial genes that participate in multi-species
metabolic networks. In RA-2 we are
developing and testing a novel class a novel class of
phenotype-genotype models for the inference of
adaptive evolution. The models take as input
high-level properties of complex systems and
lower-level codon sequence data. In RA-3 are
using the new inference models to investigate a
adaptive dynamics across scales of complexity (genes
<--> community <--> environment).
Funding: NSERC Discovery Grant
2. Testing “It’s the song, not
the singer(s)”: microbiomes to Gaia.
“It’s the song, not the singer” (ITSNTS) theory was
developed to legitimize and supplant claims that we and
our microbiomes (“holobionts”) – or complex communities
more generally (maximally, the biosphere) – are units of
selection (“Darwinian individuals”). ITSNTS holds that
it is the processes implemented, not the implementing
taxa (individually or collectively) that are the
relevant units, evolving through differential
persistence and recruitment of implementing taxa, not
differential reproduction (Proc Natl Acad Sci USA 115:
4006-14). ITSNTS engages and challenges traditional
philosophical concerns about individuality, function,
causation, emergence and hierarchy, is increasingly
relevant biomedically (as in the new discipline of
“microbiomics”), and should provide a much-needed and
novel theoretical underpinning for evolutionary biology
and ecology. In this project we are working to (1)
develop the theory of ITSNTS around complex causation in
interacting hierarchies and how these might be
represented and explored philosophically and through
simulation, (2) determine the importance of lateral gene
transfer in microbial community adaptation, asking
whether (sometimes) genes are better thought of as
belonging to processes, not organisms, and (3) deploy a
novel combination of Markov processes within-species and
agent-based simulation between-species to model a
complex network of causal interactions with feedback
between levels of organization (genes, species,
community and ecosystem). We will then explore what
kinds of systems can cause genes (lowest level) to adapt
to persistent top-level structures (e.g., emergent
community individuality) thereby decoupling (to some
extent) top-level from species-level dynamics.
Funding: New Frontiers
in Research Fund - Exploration
EG research group:
https://www.evolutionarygaia.org/
3. ATRAP - Algal Blooms,
Treatment, Risk Assessment, Prediction and
Prevention through Genomics
Cyanobacteria (aka blue-green algae)
occur naturally at low levels in water bodies and are
normally not a cause for concern. But given enough
warmth (e.g., exacerbated by climate change), light, and
nutrients (e.g., from agricultural or municipal
releases) some cyanobacteria bloom in aquatic ecosystems
– and frequently produce and release cyanotoxins.
Cyanotoxins can cause illness or mortality in humans and
animals, and necessitate alternate water sources for
domestic, agricultural, industrial and recreational use.
Even skin contact must be prevented, thus forbidding
showers and swimming. The occurrence of such harmful
cyanobacterial blooms (HCBs) has major economic impacts
(yearly estimates of $825M in USA and $330M in
Australia) and poses a health threat to humans,
livestock, fish and wildlife. A growing number of
drinking water treatment facilities – including those
fed by the Great Lakes, the water source for 8.5 million
Canadians – are now considered at risk and must install
costly treatment barriers to remove cyanobacteria and
their toxins. HCBs occur annually in lakes and rivers
across Canada (with 80 confirmed lakes in Quebec in
2014). Driven by the need of municipalities and water
quality authorities for accurate HCB diagnostics and
treatments, we will develop a chemical- genomic
diagnostic toolkit to assess the risk of toxicity in
water sources and to guide prevention and treatment
strategies (Deliverable 1) and best treatment practices
to prevent toxin breakthrough in drinking water and
ensure safe disposal of toxic sludge (Deliverable 2). In
the longer term, this project aims to protect water
bodies as an essential resource for drinking water and
faunal habitats and propose some preventive measures
(Deliverable 3).
Funding: Large-scale Applied Research
Competition, Natural Resources and the Environment:
Sector Challenges - Genomic Solutions