| I'm not an expert on the subject, but i'll try to give you an educated guess. The small black spots (about 2mm in diameter) that you see on perch and other fish is a disease commonly referred to as blackspot and is caused by a fluke (scientific name Cryptocotyle lingua). Fish are an intermediate host to this fluke and it doesn't cause them any harm (final host is fish-eating birds). I have never seen or heard of it in muskie or pike, so that's probably not it. I haven't seen or heard of the large black spots on your fish either. Muskie can be infected with the disease called lymphosarcoma, and exhibit large red tumors or sores on their body. These sores can heal, leaving a scar. I've never seen a scar that looks like the 1-inch diameter black spots on your fish, but I guess it could be possible.
The only thing that I can come up with is that your fish may have been in the vicinity of an electrofishing event. Electrofishing is a method used in fisheries management to capture fish. If an excessive electrical current was used, it can leave "burn" marks on the fish that resemble the colour of the marks on your fish. Larger fish conduct more electricity than smaller fish because they have a larger surface area, and may explain the black marks. Higher concentrations of dissolved solids in water will increase conductivity and electrical current (amperage), increasing the chance for "burn" marks.
The large abdominal region and skinny body could be an indication of a large amount of intestinal parasites.
I guess I really don't know. Again, I'm not an expert. Just a few things I remember from my college days.
Keep your hooks sharp.
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