Krabbenhoft publishes study on variants in rhodopsin gene that impact fish vision

Trevor Krabbenhoft, PhD.

Trevor Krabbenhoft, PhD

The journal Genome Biology and Evolution has published a study on restoring fish to North America's Great Lakes, led by Trevor Krabbenhoft, who observes, “Knowledge of a species’ adaptations can help us restore them in environments that are better suited to their biology.” Read the article by Charlotte Hsu.  Related post on WBFO NPR.

Research News

This Great Lakes fish may have evolved to see like its ocean ancestors did

Illustration of a kiyi.

Artist's illustration of Coregonus kiyi. Credit: Illustration © Joseph R. Tomelleri

By CHARLOTTE HSU

Published January 25, 2021

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Trevor Krabbenhoft.
“Evolution is often thought of as a one-way process, at least over deep time, but in this example, over 175 million years, we have this reversal back to a much earlier ancestral state. ”
Trevor Krabbenhoft, assistant professor
Department of Biological Sciences

In the dark waters of Lake Superior, a fish species adapted to regain a genetic trait that may have helped its ancient ancestors see in the ocean, a study finds.

The research focuses on kiyis, which inhabit Lake Superior at depths of about 80 to over 200 meters deep. These fish, known to scientists as “Coregonus kiyi,” belong to a group of closely related salmonids known as ciscoes.

In contrast to three other Lake Superior ciscoes that dwell and feed in shallower regions of water, the kiyis are far more likely to carry a version of the rhodopsin gene that probably improves vision in dim “blue-shifted” waters, the study concludes. Every one of 21 kiyis the team examined from this deep-water population carried only this variant of the gene.

The adaptation appears to mark a return to an ancient state: Some 175 million years ago, the kiyis’ ocean-dwelling forebears likely harbored the same genetic variant, according to a reconstruction of the species’ evolutionary history.

Then, as ancestral fish populations moved from blue-shifted marine waters into shallower, “red-shifted” streams and lakes, a form of rhodopsin that’s beneficial in those habitats became more common, scientists say. Finally, the kiyis, reaching the deep waters of Lake Superior, adapted again to the “blue-shifted” color of the waters they now inhabit.

The study was published online Nov. 28 in the journal Genome Biology and Evolution. The project, funded by the Great Lakes Fishery Commission, was a collaboration among researchers at UB and the U.S. Geological Survey’s Great Lakes Science Center.

“Evolution is often thought of as a one-way process, at least over deep time, but in this example, over 175 million years, we have this reversal back to a much earlier ancestral state,” says Trevor Krabbenhoft, assistant professor of biological sciences, College of Arts and Sciences, and a faculty member in the UB RENEW Institute. Krabbenhoft led the research with first author Katherine Eaton.

“Fishery biologists are trying to restore native fish populations in the Great Lakes, so it’s important to understand the adaptations that species have,” says Eaton, a PhD student at Auburn University who completed the study at UB as an undergraduate in biological sciences. “Knowledge of a species’ adaptations can help us restore them in environments that are better suited to their biology.”

Restoring fish in the Great Lakes

It’s unclear whether the kiyis’ ancestors completely lost the blue-shifted gene variant before re-evolving it, or if the variant simply became less frequent in this fish lineage before re-emerging to become more prolific again.

Either way, today, “There is a really clear distinction between the deep-water and shallow-water species,” Eaton says.

Whereas all of the kiyis studied had the blue-shifted form of rhodopsin, the shallower water ciscoes sampled — Coregonus artedi, Coregonus hoyi and Coregonus zenithicus — primarily had the version of the gene that may be helpful in red-shifted waters.

Eaton notes that the same blue-shifted variant of rhodopsin is present in a number of other fish that live in the sea or deep lake water. This repeated “parallel” evolution can indicate that an adaptation has an important function: in this case, probably helping fish see in different environments, she says.

These insights are important because light in the Great Lakes is changing, Krabbenhoft says. For example, invasive zebra and quagga mussels, which filter organic matter from lakes, are increasing the clarity of the water in places.

The knowledge is also valuable as scientists look to restore native fish populations. In addition to the rhodopsin research, Krabbenhoft is co-author of a study examining the genetics, morphology and ecology of ciscoes more broadly. That work, also funded by the Great Lakes Fishery Commission, was led by Moisés Bernal, now assistant professor of biological sciences at Auburn. The study results were posted on Dec. 16 to the preprint server bioRxiv, and have not yet been published in a peer-reviewed journal.

“Collectively, these projects have implications for restoring the native biodiversity in the Great Lakes toward a healthy ecosystem,” Krabbenhoft says. “Ciscoes were once much more abundant and diverse across the five Great Lakes, but some species went extinct due to overfishing, sea lamprey invasion and pollution. Our data are informing restoration strategies as these fish are being re-established in places where they were lost or highly reduced in number, such as in Lake Ontario.”

“Ciscoes were once the dominant native prey species in the Great Lakes, supporting top predators such as lake trout and walleye. They remain an important component of the tribal, commercial and recreational fisheries, which are valued at more than $7 billion annually,” says Bill Taylor, commissioner for the Great Lakes Fishery Commission and a University Distinguished Professor in Global Fisheries Systems at Michigan State University. “Research to better understand their biology and morphology is critical to designing successful restoration efforts in the future.”

Authors of the rhodopsin paper are Krabbenhoft; Eaton; Bernal, who completed the work as a UB postdoctoral researcher in biological sciences; Nathan Backenstose, a UB PhD student in biological sciences; and Daniel Yule, a research fisheries biologist at the Lake Superior Biological Station, part of the U.S. Geological Survey Great Lakes Science Center. Eaton’s research was supported by the Philip G. Miles Undergraduate Research Fellowships in the UB Department of Biological Sciences, and the UB Honors College.

Faculty Profile

Trevor J. Krabbenhoft

PhD

Trevor J. Krabbenhoft.

Trevor J. Krabbenhoft

PhD

Trevor J. Krabbenhoft

PhD

Research Interests

Fish evolution and ecology; genome evolution; climate change.

Contact Information

H533 Hochstetter Hall

H540 Krabbenhoft Lab

Buffalo NY, 14260

Phone: (716) 645-4934

tkrabben@buffalo.edu

Education

PhD, Biology, University of New Mexico

Office Hours

tba

Research Summary

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

Selected Publications

  • 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.