I am not a taxonomist or systematist. Nor am I a geneticist. Thus I will almost certainly not do this topic its full justice - but I will give it the old college try.
The taxonomy of the genus Salmo is quite "messy" and likely to see a number of changes in the future. It is nearly impossible to understand the genetics of Brown Trout - but I will make an effort. I often hear anglers talk about "German Brown Trout" or the "Loch Leven strain" but at this point in North America, their genetics are likely a lot more "jumbled" than being true to any particular genetic strain. Anyone that has been trout fishing for years recognizes this; there is a ton of variation in the Brown Trout you catch. This makes Brown Trout in many ways, truly American - a hodgepodge of origins and now more or less unique to "the new world".
First, a bit on the genus Salmo, of which there are are somewhere between 30 and 50 species - depending upon your source (Tougard 2022). And many consider much of the group to be a Salmo trutta species complex, meaning that there are a number of very closely related Salmo species. Quite possibly, only three Salmo species are not part of the Salmo trutta species complex: Atlantic Salmon (S. salar), the only Salmo species native to North America; Adriatic Trout (S. obtusirostris); and Belvica (S. ohridanus) which is a species native to one lake, Lake Ohrid, on the Albania and Macedonia border. Many of these 30 to 50 species are simply called Brown Trout but are given unique Latin names outside of Salmo trutta which is what we recognize as "Brown Trout". So it is not only myself that does not have a great grasp on the genetics and evolution of Salmo species but rather the scientific world that is in the process of figuring it out.
...phylogenetic relationships between evolutionary lineages are poorly resolved, and no phylogeny includes all Salmo species, this history can only be partial at best.
From Tougard 2022 - in other words, our understanding of the genus is less that complete right now.
Brown Trout are distributed in the Atlantic Ocean and Mediterranean drainage. Interestingly enough, in their native range, they suffer some of the same issues as native trout in North America - habitat destruction, climate change, genetic introgression by hatchery stocks and other Salmo species, and the impacts of non-native species - including crazy enough - by Brook Trout in some of their Brown Trout's native range. Brown Trout are quite variable within their native range and often separated into sea trout (S. trutta morpha trutta), a lake morph (S. trutta morpha lacustris), and a river morph (S. trutta morpha fario).
Quite famously, the Brown Trout was first introduced into the United States in Michigan's Baldwin River in 1883. From there - eventually - they were introduced to much of the rest of the United States. The first strain of Brown Trout introduced to Michigan were the "von Behr" strain from Germany (MacCrimmon and Marshall 1968). The eggs came from both streams and lakes in Germany. Soon after, the Loch Leven strain from Scotland's Loch Levin, an impoundment of the River Leven, was introduced to North America. And soon after these introductions and further hatchery growing and stocking of Brown Trout, the genetic identity of these two strains - and probably others brought in from Europe, were lost and the strains intermingled. Robert Behnke, "Dr. Trout", a well known and respected fisheries biologist with the USGS Cooperative Fish and Wildlife Research Unit at Colorado State University, believed all three forms - the morphs described above - had been introduced to North America and referred to them as the "American generic Brown Trout". So while you hear some refer to them as "German Brown Trout", their origins are probably quite a bit more "broadly Northern European".
Brown Trout in Wisconsin date back to 1887, not long after their introduction to Michigan and New York, the first two early adopter states. In the Midwest, Iowa introduced them in 1885 - just two years after Michigan, Wisconsin and Illinois in 1887, and Minnesota a year later (MacCrimmon and Marshall 1968). Brown Trout also moved farther west quite early on - Montana's first Brown Trout were introduced in 1889, Colorado two years before that, and California in 1894/95. Interestingly, Brown Trout were not known to be stocked into Wyoming until 1933 and Idaho was another late adopter, 1915 (MacCrimmon and Marshall 1968). Wisconsin Brown Trout were first of German origin, by way of Michigan. Interestingly, in Canada, the Brown Trout in British Columbia and Saskatchewan have at least a partial Wisconsin origin (MacCrimmon and Marshall 1968) - again, by way of Europe. At this point, the "American generic Brown Trout" was well established - even outside of their United States range.
As important as anything in this discussion is that Brown Trout have evolved in their new landscape in the 140ish years they have been in North America. So our Brown Trout are a function of their origins but also how they have adapted to their environment - including how hatchery strains have contributed and in some places, continue to contribute, to this mixture. Because they are non-native and we generally care less about the genetics of non-native fishes and the fact that Brown Trout genetics are rather "messy", we do not really know a lot about the genetics of North American or specifically Wisconsin Brown Trout. What we do know is that there has been a lot of mixing of European strains and local adaptation (evolution) to North America.
From Wisconsin, we know from Lake Superior streams (Krueger and May 1987), Brown Trout have a population genetic structure based on life history (stream, lake, anadromous) and drainage basin. And, not surprisingly, the drainage basins are less well defined than are European strains due to the more recent "origin" of Lake Michigan Brown Trout (Krueger and May 1987). This is before the "Seeforellen" strain - another German strain - was introduced to the lake in 1991 (WDNR). The Seeforellen Brown Trout have rather revolutionized Brown Trout fishing in the Great Lakes because they grow larger and live longer than other strains that have been stocked in the "big lakes".
John Lyons, retired research biologist at the Wisconsin DNR, wrote about Brown Trout in Wisconsin for WisTrout, reiterating much of what I wrote above. I had a hell of a time finding characteristics of Brown Trout strains until I found John's article. He states that the German "von Behr" fish tended to have more red spots mixed within the black spots which are variable in size. The Scottish Loch Leven fish lacked the red spots and their black spots were fewer and larger. I know from Pennsylvania where I had fished a fair bit, the larger trout seemed to have this Scottish trait. However as Lyons, Behnke, and others note, the genetics of American Brown Trout are quite a jumbled mess and there are unlikely to be pure strains at this point. Even among the "lake run" fish, there seems to be no genetic differentiation between them and the resident trout, much the same as Coaster Brook Trout which are as best we know genetically identical to the stream residents in those same streams. Access to more energy dense foods and an environment without the energetic demands of stream currents seem to be the largest difference. He writes,
It would be fascinating to use modern genetic methods to look at different Wisconsin populations and try to derive their ancestry from the various European forms. A recent study examined Lake Michigan and Lake Superior browns in Michigan and Wisconsin and found evidence of German and Scottish heritage but also some indication of genotypes from Denmark and the French Pyrenees. This finding suggests that the origins of Midwestern browns are more complicated than we thought.
To the best of my knowledge - and after many searches in many different databases - we are no closer to that answer as when John wrote this in 2021. I am pretty confident that the answers would be less than clear, other than there has been a lot of moving of fish around. We are likely to see genetic signatures of German and Scotland as well as those of hatcheries.
And we are likely to see that Brown Trout have evolved to different regions and watersheds in the state. For example, Wisconsin "wild trout stocking program" - a bit of an oxymoron, I know - has been used to establish wild Brook and Brown Trout populations from existing wild populations. Fishes adapted (evolved) to hatcheries often survive poorly in the wild so "wild stocked" fish are grown under minimal human contact from sperm and eggs collected from wild fish, rather than hatchery-reared brood stock. Wild self-sustaining Brown Trout populations have been established in several watersheds throughout the state through this program (Mitro 2004). This has also shown some effects of how Brown Trout have evolved to better fit their Wisconsin environments. Genetic analyses found that Timber Coulee Brown Trout could be stocked anywhere in the state but in northern Wisconsin, wild stocked trout from the Brule and West Branch of the White River performed better in the Waupaca River (Al Niebur, WDNR, unpublished data from Mitro 2004).
There is a ton we do not know about the genetics of Brown Trout - not just here in their non-native range but also in the native range. In many places, Brown Trout are facing declines in populations and of their range which has biologists in their native range - Europe, North Africa, and western Asia - concerned. Expect a good bit of clarity to come in the next few years. For example, Segherloo et al. (2021) recently supported with several lines of genetic evidence that there are many Salmo species within the native range of what has broadly been recognized as the Brown Trout native range. American Brown Trout are quite American - their origins are a mix of a number of different origins - much like the origins of the American people.
Literature Cited and Other Sources of Information
Bernatchez, L. (2001). The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation. Evolution, 55(2), 351-379.
Delling, B., Sabatini, A., Muracciole, S., Tougard, C., & Berrebi, P. (2020). Morphologic and genetic characterisation of Corsican and Sardinian trout with comments on Salmo taxonomy. Knowledge & Management of Aquatic Ecosystems, (421), 21.
Homola, J. J., Samborski, A., Kanefsky, J., & Scribner, K. T. (2019). Genetic estimates of jurisdictional and strain contributions to the northeastern Lake Michigan brown trout sportfishing harvest. Journal of Great Lakes Research, 45(5), 998-1002.
Krueger, C. C., & May, B. (1987). Stock identification of naturalized brown trout in Lake Superior tributaries: differentiation based on allozyme data. Transactions of the American Fisheries Society, 116(6), 785-794.
Mitro, M. G. (2004, September). Stocking trout of wild parentage to restore wild populations: an evaluation of Wisconsin’s wild trout stocking program. In Wild Trout VIII Symposium “Working Together to Ensure the Future of the Wild Trout" (pp. 20-22).
Ninua, L., Tarkhnishvili, D., & Gvazava, E. (2018). Phylogeography and taxonomic status of trout and salmon from the Ponto‐Caspian drainages, with inferences on European brown trout evolution and taxonomy. Ecology and Evolution, 8(5), 2645-2658.
Segherloo, I. H., Freyhof, J., Berrebi, P., Ferchaud, A. L., Geiger, M., Laroche, J., ... & Bernatchez, L. (2021). A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?. Molecular Phylogenetics and Evolution, 162, 107204.
Splendiani, A., Palmas, F., Sabatini, A., & Caputo Barucchi, V. (2019). The name of the trout: considerations on the taxonomic status of the Salmo trutta L., 1758 complex (Osteichthyes: Salmonidae) in Italy. The European Zoological Journal, 86(1), 432-442.
Splendiani, A., Berrebi, P., Tougard, C., Righi, T., Reynaud, N., Fioravanti, T., ... & Caputo Barucchi, V. (2020). The role of the south-western Alps as a unidirectional corridor for Mediterranean brown trout (Salmo trutta complex) lineages. Biological Journal of the Linnean Society, 131(4), 909-926.