The Stahlke Lab investigates the genomes of wild systems, from invasive plants like whitetop, to biocontrol agents like tamarisk beetles, and pests, like gregarious locusts.
We employ genetic and genomic tools and multi-scale analyses over molecules, space, and time to improve our understanding of the genomic context of rapid evolution in systems of management concern, especially in biocontrol, invasive species, and endangered species.
We employ genetic and genomic tools and multi-scale analyses over molecules, space, and time to improve our understanding of the genomic context of rapid evolution in systems of management concern, especially in biocontrol, invasive species, and endangered species.
Rapid evolution of an introduced biocontrol agent, the tamarisk beetle (Diorhabda spp.)
What are the mechanisms and consequences of range expansion and hybridization?
The tamarisk beetle was introduced to the southwest US in the early 2000s to control the invasive shrub, tamarisk (Tamarix spp., aka saltcedar). With collaborators Ellyn Bitume, Eliza Clark and Ruth Hufbauer at Colorado State University, Dan Bean at the Colorado Department of Agriculture, Matt Johnson of EcoPlateau Research, and Zeynep Ozsoy at Colorado Mesa University, we are characterizing genomic and phenotypic evolution among introduced populations.
What are the mechanisms and consequences of range expansion and hybridization?
The tamarisk beetle was introduced to the southwest US in the early 2000s to control the invasive shrub, tamarisk (Tamarix spp., aka saltcedar). With collaborators Ellyn Bitume, Eliza Clark and Ruth Hufbauer at Colorado State University, Dan Bean at the Colorado Department of Agriculture, Matt Johnson of EcoPlateau Research, and Zeynep Ozsoy at Colorado Mesa University, we are characterizing genomic and phenotypic evolution among introduced populations.
Clonality and habitat interactions in Lepidium draba, an invasive plant
Do different community and soil conditions yield greater rates of clonality?
Whitetop (Lepidium draba) may reproduce by seed or vegetatively. To most effectively manage this invasive plant in an integrative framework considering eco-evolutionary implications, we want to understand mechanisms underlying that life history variation. In collaboration with Natalie West and John Gaskin at the Northern Plains Agricultural Research Lab (USDA-ARS) we're assessing the relationship between clonality, population genetic structure, and environmental heterogeneity.
Do different community and soil conditions yield greater rates of clonality?
Whitetop (Lepidium draba) may reproduce by seed or vegetatively. To most effectively manage this invasive plant in an integrative framework considering eco-evolutionary implications, we want to understand mechanisms underlying that life history variation. In collaboration with Natalie West and John Gaskin at the Northern Plains Agricultural Research Lab (USDA-ARS) we're assessing the relationship between clonality, population genetic structure, and environmental heterogeneity.
Genome assemblies of agricultural pests
As a post-doc with the Ag100Pest project, I generated high-quality reference genome assemblies for pest and beneficial arthropods, using an array of sequencing technology. These projects included Schizaphis graminum (pictured), Helicoverpa zea, and others.
With co-lead Jennifer Chang , we built polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies.
As a post-doc with the Ag100Pest project, I generated high-quality reference genome assemblies for pest and beneficial arthropods, using an array of sequencing technology. These projects included Schizaphis graminum (pictured), Helicoverpa zea, and others.
With co-lead Jennifer Chang , we built polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies.
Historical and contemporary selection in the Tasmanian Devil
How do historical patterns of selection compare to the rapid contemporary response we've observed in response to a transmissible cancer?
Tasmanian Devils (Sarcophilus harisii) have shown a rapid evolutionary response to a unique transmissible cancer, devil facial tumor disease (DTFD). In collaboration with Menna Jones and Rodrigo Hamede at the University of Tasmania, Hamish McCallum at Griffith University, and Andrew Storfer at Washington State University, we're seeking to understand adaptation to DFTD and working to predict and manage disease dynamics in face of the disease.
How do historical patterns of selection compare to the rapid contemporary response we've observed in response to a transmissible cancer?
Tasmanian Devils (Sarcophilus harisii) have shown a rapid evolutionary response to a unique transmissible cancer, devil facial tumor disease (DTFD). In collaboration with Menna Jones and Rodrigo Hamede at the University of Tasmania, Hamish McCallum at Griffith University, and Andrew Storfer at Washington State University, we're seeking to understand adaptation to DFTD and working to predict and manage disease dynamics in face of the disease.