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Projects:

Evolutionary physiology of diapause


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Phenology and thermal physiology


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Physiological & functional genomics




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Functional and comparative genomics of diapause and life history timing

As genomic methodology become less expensive and more widely available, it is becoming increasingly feasible to ask genomic/functional genomic questions in traditionally non-model organisms. Our group has developed EST libraries for the flesh fly, Sarcophaga crassipalpis, and the apple maggot fly, Rhagoletis pomonella, the former a physiological model for the regulation of diapause and the latter an evolutionary model for speciation via shifts in diapause timing. These libraries provide an excellent resource for development of functional genomic tools, and I have been able to leverage the data in comparative analysis of coding sequence divergence across taxa and across speciating host races of R. pomonella.


DnComparison

Non-synonymous substitutions between S. crassipalpis and D. melanogaster across Gene Ontology (functional) categories.
Modified from Hahn, Ragland, et al. BMC Genomics 10 234. doi:10.1186/1471-2164-10-234

We are using custom microarrays designed from the EST libraries to study the regulation of diapause in S. crassipalpis and the regulation of diapause termination in R. pomonella, a critical determinate of asynchronous reproductive isolation between the host races. Gene expression data are now available for a variety of organisms and phenotypes through GEO, and I have also been able to leverage our expression data in comparative analyses that initially suggest that alternate dormant developmental pathways are evolutionarily labile and not particularly constrained along phylogenetic lines.


lifecycle

Distance-based clustering of arrays measuring differential expression between diapause and non-diapause (S. crassipalpis [Sarc] and D. melanogaster [Dros]) or between daur and non-daur (C. elegans [Elegans]). Note the basal polytomy.

My most recent experiments apply microarray analysis of gene expression along a respirometric trajectory of diapause termination that allows us to precisely identify key developmental transitions (see here). The eventual goal is to integrate genome-wide association studies with comparative transcriptomics to identify the key genes and pathways facilitating the rapid evolutionary divergence of speciating populations in the wild.