PhD, Biology, University of New Mexico

Research is focused on how fish respond to environmental change, including climate change, non-native species, contaminants, and overfishing. A central aim is to understand what fish can tell us about aquatic ecosystem health and help us key-in on emerging issues.

The Krabbenhoft Lab studies the ecology of fish in a changing world. Research in the Krabbenhoft Lab is focused on how fish respond to environmental change, including climate change, invasive species, contaminants, and fishing pressure. We rely heavily on functional genomics and bioinformatics to test hypotheses related to mechanisms underlying how fish respond to their environment. By focusing on mechanisms, we can better predict outcomes for future scenarios of environmental change.

This research has important management and conservation implications both locally for Great Lakes and more broadly for aquatic ecosystems worldwide. 

Examples of ongoing projects in the Krabbenhoft Lab include:

(1)  The development of RNAseq-based methods for studying the trophic ecology of organisms.  We are exploring how high-throughput DNA sequencing can be used to complement more traditional methods of studying energy flow in ecosystems – such as stomach contents and analysis of stable isotopes from tissue samples. Ultimately, our goal is to more thoroughly integrate evolution and genomics with ecology.

(2)  Studies of sex determination and gene silencing in allopolyploid catostomid fishes. Along with colleagues, we are using restriction-site associated DNA sequencing (RADseq) and long read genome sequencing to understand mechanisms of sex determination in catostomid fishes. For example, what is the relative contribution of environmental versus genetic variation in determining sex in catostomids?  We are also interested in evolutionary processes shaping genome evolution following whole genome duplication in this group of fishes. For example, are patterns of gene silencing random with respect to gene function, or are some types of genes preferentially retained or lost?   

(3)  Genomic mechanisms underlying phenotypic diversity and adaptation in coregonid fishes in the Great Lakes. We are using long read genome sequencing and sequence capture to identify genetic changes driving the extensive morphological and ecological diversity in a species flock in the genus Coregonus.  We are focusing on protein coding regions and non-coding regulatory regions to understand how natural selection and other evolutionary forces shape the genomes of these fishes. Our hypothesis is that genetic variants most strongly associated with phenotypic forms should be related to the functional pathways that give rise to that variation.  In a broad sense, this research aims to help us understand proximate forces that generate and maintain biodiversity.

(4)  Global- and regional-scale studies of climate effects on inland fish and fisheries.  We are also involved in collaborative efforts to understand how climate change is affecting fish and fisheries around the world.  To date, climate change has been shown to affect fish in five general categories: (1) distribution, (2) phenology, (3) demographics, (4) evolution, and (5) assemblage dynamics. We are working to find novel ways to document and understand previous climate effects on fishes and refine our predictions for future responses to ongoing climate change.

(4)  Global- and regional-scale studies of climate effects on inland fish and fisheries.  We are also involved in collaborative efforts to understand how climate change is affecting fish and fisheries around the world.  To date, climate change has been shown to affect fish in five general categories: (1) distribution, (2) phenology, (3) demographics, (4) evolution, and (5) assemblage dynamics. We are working to find novel ways to document and understand previous climate effects on fishes and refine our predictions for future responses to ongoing climate change. The Fish and Climate Change Database is here. 

• Krabbenhoft TJ, Turner TF (2017) Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities. DNA Research. Online Early.
• Myers BJE, Lynch AJ, Bunnell DB, Chu C, Falke JA, Kovach R, Krabbenhoft TJ, Kwak TJ, Paukert CP (2017) *Authors 3-9 listed alphabetically. Global synthesis of the projected and documented climate change effects on inland fishes. Reviews in Fish Biology and Fisheries 27:339-361. Invited contribution for special issue: Impacts of climate change on marine and inland fishes and fisheries.
  
• Lynch AJ, Myers BJE, Chu C, Eby LA, Falke JA, Kovach RP, Krabbenhoft TJ, Kwak TJ, Lyons J, Paukert CP, Whitney JE (Authors 3-9 listed alphabetically) (2016) Climate change effects on North American inland fish populations and assemblages. Fisheries 41:346-361. Invited contribution for special issue on climate change effects on inland fishes. Publication led to briefings to US Congressional panel on climate change effects on inland fish.