Fish DNA in Ozark streams reveals region’s complex geologic history

Researchers collected water samples from six rivers and streams in the Missouri Ozarks to detect the presence of fish species through their environmental DNA (eDNA). Environmental DNA refers to genetic material shed by organisms into their surroundings, such as skin cells or waste, which can be detected in water samples without needing to physically observe or capture the species. The team identified several species considered at risk in Missouri, including the lake sturgeon, crystal darter, and Alabama shad. Notably, they also found DNA from a cave-dwelling fish, the Salem Plateau cavefish, in a surface water sample from an underground spring, a discovery that would have been impossible using traditional methods like netting or visual surveys.

The researchers expected to detect DNA from the bleeding shiner (Luxilus zonatus), a common fish in Ozark streams, in every sample. However, they found that bleeding shiner DNA was absent in some streams. After verifying their sampling methods and testing for errors, they discovered a pattern: streams with bleeding shiner DNA all drained to the southern Ozarks, while those without it drained to the northern Ozarks. This revealed a north-south divide in the region’s drainage systems, where streams flow in opposite directions and connect to different river systems. The absence of bleeding shiner DNA in northern streams suggested a potential difference in the fish populations between the two regions.

Further investigation showed that northern and southern populations of bleeding shiners, though visually identical, had distinct genetic histories. Hundreds of thousands of years ago, northern populations interbred with another shiner species, leaving behind a genetic signature unique to those drainages. This ancient hybridization event, which occurred during the Pleistocene epoch (from about 2.5 million to 12,000 years ago), left traces in the DNA of modern northern bleeding shiners. The researchers initially overlooked this genetic difference because the fish appeared the same. By analyzing the eDNA data more closely, they identified an unknown DNA sequence that corresponded to the northern populations, revealing the hidden genetic diversity within the species.

The Ozarks’ river systems were shaped by glacial advances during the Pleistocene epoch, which altered drainage patterns and connections between streams. Northern Ozark drainages, flowing into the Missouri and Mississippi rivers, were directly influenced by these glacial movements, which reshaped the landscape and changed water flow directions. In contrast, southern Ozark drainages, such as those of the St. Francis, Black, White, and Spring rivers, remained relatively isolated from these disruptive events. This isolation led to the evolution of more endemic species—species found only in specific locations—and genetically unique populations, such as the Black River walleye and various minnows, sunfishes, and darters.