Great Lakes Fishery Commission

Updated 2025-03-20 14:22:50

Lake Huron -> 11.0 Genetic Diversity -> Genetic Diversity

11.1.1. Number of species examined and geographic scope of sampling

Fourteen studies of genetic structure were published during the reporting period. There were nine fish species (seven native and two invasive) and three mussel species studied (Table 1). Most (11) of the studies examined diversity across all or some portion of the species range and included a few (less than 10) sites on Lake Huron (Figures 1 and 2). The geographic coverage of the lake varied, but was usually limited in scope. The limited sample range in some studies was usually a reflection of the species range or the goals of the specific study. Nine studies reported genetic differences among one or more of the sample sites. Coregonine species exhibited the most structure, but they were the most widely sampled group of species.

As part of a Great Lakes wide study of cisco (Coregonus artedi) samples from northern Lake Huron were analyzed using microsatellite DNA loci (Stott et al. 2022). Collections from eight sites were classified into five different genetic groups, indicating that significant population structure exists among remaining cisco populations in Lake Huron (Figure 3). More within-lake diversity was observed in Lake Huron than in other lakes where multiple collections were taken (lakes Superior and Ontario).

Single nucleotide polymorphisms were used to analyze lake whitefish (Coregonus clupeaformis) from 22 sites in North America including nine sites throughout Lake Huron (Graham et al. 2020; 2022). Drainage explained most of the observed population structure and diversity estimates were similar across most sites. Collections from Lake Huron had relatively high estimates of heterozygosity when compared to other collections, but this might be because Lake Huron samples represented the most geographically diverse and largest sample sets. Similar to past work using microsatellite DNA loci, modest population structure was observed among collections from Lake Huron. Sites in northwestern Lake Huron were distinct from those in the eastern and western main basin (Figure 4).

Within lake structure was also observed in round whitefish (Prosopium cylindraceum) using single nucleotide polymorphisms, microsatellite DNA loci, and mitochondrial DNA sequence data (Morgan et al. 2018). Glacial origins accounted for most of the observed diversity among collections, followed by watershed and basin. The microsatellite DNA data could not detect differences between fish from Lake Michigan and Lake Huron, but when genomic markers were analyzed it was possible to distinguish between Lake Huron and Lake Michigan and additional within-lake structure was identified. Samples from northern Georgian Bay were distinct from sites in southern Georgian Bay and the main basin (Figure 4).

Most of the current range, including three sites in tributaries of Lake Huron, of redside dace (Clinostomus elongatus) was sampled and genetic variation assessed using microsatellite DNA loci and mitochondrial DNA sequence data (Serrao et al. 2018). Regional structure corresponding to glacial origins was identified using both types of markers and significant structuring was observed among all sites sampled on Lake Huron including a unique mitochondrial DNA haplotype observed only in samples from Two Tree R. Sites in northern Lake Huron grouped with samples from the Upper Mississippi River and sites from Georgian Bay and the southern main basin grouped with samples from the Ohio River. Lower than average heterozygosity was observed at all Lake Huron sites, although all Great Lakes sites reported low levels of heterozygosity. COSEWIC lists redside dace as endangered (COSEWIC 2007) and these data suggest there could be at least three Distinct Population Segments or Designated Units and with two represented by samples from Lake Huron.

Grass pickerel (Esox americanus vermiculatus) (Lujan et al. 2022) were collected from across most of the widespread range of this species which is listed as special concern under SARA (COSEWIC 2014). The authors identified a site in Georgian Bay (Figure 1) that represents a unique genetic population that is distinct from all others and may warrant extra protection.

Lake chub sucker (Erimyzon sucetta) (Hauser et al. 2019) sampled from one tributary of Lake Huron (Ausable River) were analyzed using mitochondrial DNA sequence variation. When compared to collections from Lake St. Clair and Lake Ontario, Lake Huron samples had the largest number of haplotypes despite low overall diversity across all sites. Low observed genetic diversity and limited population structure is likely the result of the shared glacial origins of fish.

Genomic resource development for walleye (Sander vitreus) for mixed stock analysis and kinship identification used walleye from two sites in Lake Huron (Euclide et al. 2022). Low levels of differentiation among Lake Huron, Lake St. Clair, and western Lake Erie collections were observed, consistent with past analyses.

In addition to fish species, analysis of native mussel species identified genetic populations in Lake Huron (Figure 2). Mathias et al. (2018) analyzed mapleleaf mussels (Quadrula quadrula) from the Great Lakes and Mississippi River drainage using mitochondrial DNA sequence and microsatellite DNA loci data. The mapleleaf mussel is considered threatened in Canada in the Great Lakes-St. Lawrence River Designated Unit (COSEWIC 2006). Samples collected from five Lake Huron tributaries were distinct from samples collected in other Great Lakes (lakes Michigan and Erie) and moderately distinct from each other (Figure 5). Genetic diversity was lowest among Great Lakes collections, likely a reflection of their recent colonization history rather than a genetic bottleneck.

Similarly, snuffbox mussel (Epioblasma triquetra) population structure identified using microsatellite DNA locus data was associated with sample drainage and there was some sub-structure observed among samples from Lake Huron (one site in a tributary to the lake), Lake St. Clair, and Lake Erie sample collections (Beaver et al. 2019). There was little evidence of inbreeding or substantial loss of diversity among Great Lakes samples.

In a study of introgression between the freshwater mussels Lampsilis siliquoidea and L. radiata, diversity and population structure of L. siliquoidea was analyzed using samples from four tributaries of Lake Huron as well as samples from the possible hybrid zone in the lower Great Lakes (Porto-Hannes et al. 2021). Microsatellite DNA loci and mitochondrial DNA sequence data were used. Samples from Lake Huron were distinct from the other Great Lakes. No within lake structure was observed, but specific tests were not performed to determine the number of populations within a lake.

As non-native species become established, genetic analysis can provide insight into how they are spreading in the Great Lakes and if they have enough standing variation to persist and evolve in a new environment. Several invasive species in Lake Huron have been analyzed using genetics (Figure 6). Two studies of round goby (Neogobius melanostomus) have examined its population structure and diversity in the Great Lakes using samples from different portions of the lake. Johansson et al. (2018) used microsatellite DNA loci model dispersal routes in Ontario waters and included six sites from Lake Huron (Figure 4). Three genetic signatures corresponded to samples from western and eastern Lake Erie and Lake Huron. Samples from Midland and Port Severn in Georgian Bay were distinct from other sites in Lake Huron, possibly reflecting their different origins. Round goby may have migrated to Lake Huron from Lake St. Clair/Lake Erie or been transported via bait bucket transfer, possibly along the Trent-Severn Waterway. Invasion patterns of round goby were also analyzed using genomic markers (Sard et al. 2019). Round goby from Michigan’s Lower Peninsula, including three Lake Huron tributaries, appear to have come from two main sources, Lake St. Clair and Lake Michigan. All three sites studied in Lake Huron were genetically distinct and all appeared to have round goby from different sources. Round goby in the Au Sable R. came from the main basin of Lake Huron, Lake St. Clair and a third unidentified source, the Flint R. was colonized mainly by goby from Lake Huron which were possibly transported by anglers, and the Cheboygan R. was colonized by round goby from Lake Huron.

Eurasian ruffe (Gymnocephalus cernua) sampled from western Lake Huron and all other sites on the Great Lakes had the same mitochondrial DNA haplotype (Stepien et al. 2018). Based on microsatellite DNA loci the Lake Huron sample was distinct from other Great Lakes populations. All Great Lakes collections of Eurasian ruffe had lower diversity estimates (based on observed heterozygosity and allelic richness) and effective population sizes as compared to native populations, suggesting that the invasion originated from a single source.  This lower level of standing genetic diversity, if not supplemented by new invasions, may limit the longer term persistence of Eurasian ruff in the Great Lakes.

Tables and Figures

Table 1. Summary of species surveyed for genetic diversity and population structure on Lake Huron during the reporting period. The number of sites sampled and genetic populations reported on Lake Huron is listed. Note that most of the studies included other sites on other Great Lakes and other sites in North America and Europe.

Figure 1. Locations of native fish species collected for genetic analysis in Lake Huron taken from studies published 2018-2022.

Figure 2. Locations of native mussel species collected for genetic analysis in Lake Huron taken from studies published 2018-2022.

Figure 3. Genetic populations identified among cisco, Coregonus artedi, collected from Lake Huron (Stott et al. 2022). Points drawn with the same colour belong to the same genetic group.

Figure 4. Locations of genetic populations identified in studies of genetic diversity with three or more sites on Lake Huron. Different symbols correspond to species and sites colored the same way belong to the same population. Sources of data: Graham et al. 2020, 2022; Morgan et al. 2018.

Figure 5. Genetic populations identified among mapleleaf mussels, Quadrula quadrula, collected from Lake Huron (Mathias et al. 2018). Points drawn with the same colour belong to the same genetic group.

Figure 6. Locations of non-native fish species collected for genetic analysis in Lake Huron.