Historical and contemporary genetic diversity of Coregonus species from Lake Michigan

Contributing Authors

Amanda Ackiss (USGS, aackiss@usgs.gov), Wendylee Stott (DFO)

Executive Summary

Advancements in molecular biology methods have allowed researchers to analyze genetic variation in extinct or extirpated species where minuscule amounts of cellular material remain. Here for the first time, we have leveraged one of these methods - Genotyping-in-Thousands by sequencing (GT-seq) - to successfully genotype more than a thousand historic samples representing members of the Great Lakes Coregonus artedi species complex from Lake Michigan. Coregonines are important native prey fishes in the Great Lakes and historically supported productive fisheries, however, most of the described diversity from Lake Michigan was lost by the 1970s as a result of invasive species, habitat degradation, and overfishing. Recent changes in the Great Lakes ecosystems, including declines in invasive species such as alewife and smelt, have stimulated strong interest in the restoration of native coregonines. The data generated by this project have enabled comparisons of genetic diversity and differentiation between extinct and extant forms, help clarify questions regarding taxonomic validity, and could guide future restoration efforts to re-establish extirpated diversity. Analysis of GT-seq data for deepwater ciscoes from Lake Michigan showed that many historically recognized taxa exhibited discrete genotypes, including C. nigripinnis, C. reighardi, C. zenithicus, C. hoyi, and C. kiyi. Genomic data also supported the synonymizing of C. zenithicus and C. alpenae (Todd & Smith 1980), whose GT-seq genotypes overlapped. Future, more comprehensive data from whole-genome sequencing could confirm these results with surety. Additionally, comparisons of contemporary ciscoes from Lake Michigan and Superior and historical samples genotyped in this project consistently support shared ancestry of deepwater species across the upper Great Lakes, rather than repeated ecological speciation within lakes which has been hypothesized at the range-wide level (Turgeon & Bernatchez, 2003). Finally, the historic data from this project has supported the discovery of what is believed to be a remnant population of C. reighardi in Lake Superior, which had previously been suggested to be extinct.