Research
Overview
The Cresko Laboratory studies the genomic basis of evolutionary change using comparative studies of natural populations in the wild and experimental approaches in the laboratory. Our research combines field work, laboratory experiments, and computational approaches to understand how organisms adapt to changing environments.
Major Research Areas
Evolutionary Genomics of Adaptation
We investigate how organisms adapt to new environments at the genomic level. Using the threespine stickleback fish as our primary model system, we study:
- Parallel evolution: How do independent populations evolve similar solutions to environmental challenges?
- Genomic architecture: What is the genetic basis of complex adaptive traits?
- Evolutionary constraints: What factors limit or facilitate evolutionary change?
Our work has revealed fundamental principles about how natural selection shapes genomic variation and produces evolutionary change.
Host-Microbiome Coevolution
Recently, our lab has developed stickleback as a model for studies of how host genetic variation influences associated microbial communities. This research addresses:
- How host genetics shapes microbiome composition
- The role of the microbiome in host adaptation
- Coevolutionary dynamics between hosts and their microbiota
- Environmental influences on host-microbiome interactions
Population Genomics Methods Development
Our laboratory has been at the forefront of developing genomic tools and computational methods for evolutionary biology:
RAD-seq Technology
We developed Restriction site Associated DNA sequencing (RAD-seq), a method that has revolutionized population genomics by enabling cost-effective genome-wide SNP discovery and genotyping in non-model organisms.
Stacks Software Pipeline
We created Stacks, a software pipeline for building loci from short-read sequences. Stacks is now used by thousands of researchers worldwide for: - De novo and reference-based assembly of RAD-seq data - SNP discovery and genotyping - Population genomics analyses - Phylogenomics applications
Syngnathid Fish Evolution
In collaboration with international partners, we study the unique evolutionary innovations of syngnathid fishes (seahorses, pipefishes, and seadragons):
- Male pregnancy and its genomic basis
- Evolution of morphological novelties
- Comparative genomics across the syngnathid phylogeny
- Conservation genomics of threatened species
Climate Change and Evolutionary Responses
We investigate how organisms respond to rapid environmental change, including:
- Thermal adaptation in natural populations
- Ocean acidification effects on marine organisms
- Evolutionary rescue and adaptive potential
- Predicting evolutionary responses to climate change
Current Projects
NSF-Funded Research
Title: “Genomic Architecture of Parallel Evolution”
Duration: 2023-2027
Summary: This project investigates the repeatability of evolution by comparing genomic changes in multiple independently evolved stickleback populations.
NIH-Funded Research
Title: “Host Genetic Control of the Microbiome”
Duration: 2022-2026
Summary: Using experimental evolution and genome-wide association studies to understand how host genetics shapes microbiome composition and function.
Collaborative Projects
- Pacific Northwest Stickleback Survey: Long-term monitoring of stickleback populations across Oregon and Washington
- International Syngnathid Genome Consortium: Sequencing and analyzing genomes across the syngnathid family
- Oregon Climate Assessment: Evaluating evolutionary responses of native species to climate change
Field Sites
Our research takes us to diverse field sites across the Pacific Northwest and beyond:
- Willamette River Basin: Long-term studies of freshwater stickleback populations
- Oregon Coast: Marine-freshwater transitions and adaptation
- Alaska: Extreme latitude adaptations and seasonal responses
- International Sites: Collaborative work in Japan, Iceland, and Scotland
Techniques & Approaches
Our research employs a wide range of modern techniques:
Field Methods - Population sampling and ecological surveys - Environmental monitoring - Behavioral observations - Transplant experiments
Laboratory Methods - Whole genome sequencing - RNA-seq and gene expression analysis - CRISPR genome editing - Experimental evolution - Microbiome profiling (16S and metagenomics)
Computational Approaches - Population genomics analyses - Phylogenomics - Genome-wide association studies (GWAS) - Machine learning applications - Bioinformatics pipeline development
Collaborations
We maintain active collaborations with researchers around the world:
- University of Oregon: Knight Campus for Accelerating Scientific Impact
- Stanford University: Hopkins Marine Station
- University of British Columbia: Biodiversity Research Centre
- Max Planck Institute: Department of Evolutionary Biology
- Uppsala University: Department of Ecology and Genetics
Join Our Research
We welcome inquiries from prospective students and postdocs interested in: - Evolutionary genomics - Host-microbiome interactions - Bioinformatics and computational biology - Field ecology and evolution - Conservation genomics