This story is a partnership between  Grist and Chicago Public Media , a public media company serving the Chicago metropolitan region. In the creeks and rivers of southern Illinois, a school of bigeye shiners darting along the edge of a stream is a sign of healthy water. The freshwater fish, which is on the state’s endangered species list, has managed to survive despite habitat loss driven by decades of construction and industrial farm runoff. But an ongoing dispute between two state agencies over state species protections is testing how the tiny fish will endure.  Last summer, the state’s top wildlife regulators faced resistance from the Illinois Department of Transportation, or IDOT, when trying to protect the shiner. The Illinois Department of Natural Resources, or IDNR, recommended that the transportation agency crews mapping out construction at a site in Union County should first survey the area and find out if the shiner was present.…