Matt Hale, Ph.D.

 

Broadly, my research interests are at the intersection of evolutionary biology, genomics, genetics, and ecology. To that end I use Next Generation Sequencing (NGS) techniques to answer questions about the evolution and life history of non-model organisms. Most of my research has focused on understanding how genetics plays a role in determining migratory life history in rainbow trout. My lab has used a combination of NGS analysis techniques including QTL, GWAS, RNA-seq, and pooled-seq to identify the genes and molecular pathways associated with this fascinating trait. In addition, my lab has recently been involved in projects looking at the behavioral genetics of life history development in brook trout from Lake Superior and dispersal patterns in Arctic charr from the Canadian Arctic. 

Another key area of my research program focuses on understanding how differences in gene expression between the sexes can cause the expression of different phenotypes. It is well known that males and females differ in lots of different phenotypes, however, how those different phenotypes are determined is less certain. Using RNA-seq techniques in several species of fish, my lab is attempting to identify the genes and molecular pathways altered between the sexes. Interested undergraduate and graduate students are encouraged to email me to enquire about possible positions in my lab. 

• Hale, M. C., Campbell, M. A., and McKinney, G. J. (2021). A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques. G3:Genes, Genomes, Genetics, 11:jkab267.
• Hale, M. C., McLaughlin, R., Wilson, C., Mackereth, R., and Nichols, K. M. (2021). Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis). Comparative Biochemistry and Physiology D- Genomics & Proteomics, 40:100884.
• Blumstein, D. M., Campbell, M. A., Hale, M. C., Sutherland, B. J. G., McKinney, G. J., Stott, W., and Larson, W. A. (2020). Comparative genomic analysis and a novel linkage map for cisco (Coregonus artedi) provide insights into chromosomal evolution and rediploidization across salmonids. G3:Genes, Genomes, Genetics, 10:2863-2878.
• Weinstein, S. Y., Thrower, F. P., Nichols, K. M., and Hale, M. C. (2019). A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One, 14(9).
• Campbell, M. A., Hale, M. C., McKinney, G. J., Nichols, K. M., and Pearse, D. E. (2019). Long-term conservation of ohnologs through partial tetrasomy following whole-genome duplication in Salmonidae. G3: Genes, Genomes, Genetics, 9:2017-2028.
• Claunch, K. C., Bush, M., Evans, C. R., Malmquist, J. A., Hale, M. C., and McGillivray, S. M. (2018). Transcriptional profiling of the clpX mutant in Bacillus anthracis reveals regulatory connection with the lrgAB operon. Microbiology, 164:659-669.
• Hale, M. C., McKinney, G. J., Thrower, F. P., and Nichols, K. M. (2018). Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One, 13(2):e0193009.
• Beal, A. P., Martin, F. D., and Hale, M. C. (2018). Using RNA-seq to determine patterns of sex-bias in gene expression in the brain of the sex-role reversed Gulf Pipefish (Syngnathus scovelli). Marine Genomics, 37:120-127.
• Hale, M. C., McKinney, G. J., Bell, C., and Nichols, K. M. (2017). Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus. G3: Genes, Genomes, Genetics, 6:3821-3830.
• Hale, M. C., McKinney, G. J., Thrower, F. P., and Nichols, K. M. (2016). RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics.

Hale MC, McLaughlin R, Mackereth R, Wilson C, Nichols KM. 2019. Using RNA-seq to characterize gene expression and pathway enrichment associated with behavioral variation in ecotypes of Lake Superior brook trout. American Society of Evolution. Providence, RI.

Weinstein SY**, Hale MC, Thrower FP, Nichols KM. 2018. Should I stay or should I go? Analysing the genetic basis of migration-related traits in rainbow trout (Oncorhynchus mykiss). Coastwide Salmonid Genetics Meeting AFS, Mukilteo, Washington.

Beal AP**, Martin D, Hale MC. 2016. Using RNA-seq to study the sex-role reverse gulf pipefish: Are patterns of sex-bias in gene expression different when we are dealing with Mr. Mom? American Society of Evolution, Austin, Texas.

Smith C*, Bell C*, Hale MC. 2016. Mapping phototransduction genes in the Oncorhynchus mykiss genome. American Society of Evolution, Austin, Texas.

Medders AM*, Hale MC, Jeffries MK. 2016. Male fathead minnow phenotypes: Implications for toxicity testing. South Central Society of Environmental Toxicology and Chemistry Meeting, Fort Worth, TX. 

Awards

University of Waterloo, Canada. 2019-2021. Using next generation sequencing to investigate introgression between dolly varden and Arctic charr from the Canadian Arctic. $11,000.

Grants

The Great Lakes Fisheries Commission. 2015-2017.  Behavioural and genetic diversity amongst ecotypes of Lake Superior brook trout. $53,453. Krista Nichols, Rob McLaughlin, Chris Wilson, Robert Mackereth, and Matt Hale

• Genetics Society of America
• Society of Evolutionary Biology
• Peer reviewer for multiple journals in the fields of genetics, evolution, and genomics.
• Invited guest editor for an upcoming special issue of the jorunal Genes on the genetic basis of migration