Douglas-fir Transcriptome Observatory
The basis of climatic adaptation in Douglas-fir (Pseudotsuga menziesii) - possibly the most ecologically and economically important conifer in western North America - is poorly understood. This limits our ability to predict population changes to climate and offer science-based prescriptions for management. The Transcriptome Observatory merges a large-scale translocation study with expressed gene (transcriptome) sequencing to define seasonal leaf transcriptomes, and differences in gene expression that define trees from different geographic region. Our goal is to identify genes that contribute to climatic sensing and adaptation in Douglas-fir.
Conifer Evolutionary Genomics
We contribute to the Gymnosperm Tree of Life, a collaboration between scientists at 15 universities, state and federal institutions who seek to document the complete evolutionary record of gymnosperms. Our group works with Aaron Liston and Chris Campbell to define chloroplast genomic diversity in members of the pine family (Pinaceae).
Conifer Transcriptome Analysis
The basis of climatic adaptation in conifers is poorly understood, and this limits our ability to predict population changes to climate and offer science-based prescriptions for management. We have initiated transcriptome analyses to define seasonal variation in gene expression for a number of important conifers. The Douglas-fir (Pseudotsuga menziesii) Transcriptome Observatory merges a large-scale translocation study with expressed gene sequencing to define seasonal leaf transcriptomes and differences in gene expression that relate to climatic variation. Similarly, the (Western Forest Transcriptome Survey) is a collaboration to identify climate-responsive genes from diverse forest species.
Mitochondrial DNA sequences are among the most commonly-used molecules for assessing animal biodiversity. Our group has adapted Multiplexed Sequencing-by-Synthesis to enable high-throughput genetic analysis of complete animal mitochondrial genomes. This work is being conducted with the USFS Wildlife Genetics Laboratory , with primary focus on Fisher (Martes pennanti) and other regionally rare carnivores, as well as West-Slope Cutthroat Trout (Oncorhynchus clarkii lewisi) .
Development of DNA tools to aid genetic conservation and restoration in false cypresses
In western North America, Port Orford-cedar and Yellow-cedar both show evidence of decline due to biotic and abiotic stresses. These species have exceptional ecological and economic value, and conservation of genetic resources is a focus of USFS activities. We are developing microsatellite markers for these species using Multiplexed Sequencing-by-Synthesis. Our experience shows this to be an efficient, inexpensive, and rapid way to identify tens of thousands of microsatellite-containing sequences. Microsatellites are being used to define spatial genetic structure and characterize valuable resistant breeding materials in these species.
Restoration Landscape Genetics
We are working to understand how key restoration species respond to climate, with the goal of defining seed transfer guidelines. Efforts to date include Antelope bitterbrush , Big Sagebrush , and a number of grass species.