Data from: Environmental DNA metabarcoding for whole community inventories of vertebrates in rivers of the midwestern United States

The application of environmental DNA (eDNA) methods to simultaneously
study vertebrate diversity holds promise to accelerate conservation
efforts, especially in freshwater systems which are among the most
imperiled in the world. Here, using eDNA sampling, we identify patterns of
vertebrate biodiversity across different habitats of the Kankakee River
watershed, one of the most diverse lotic systems in Illinois, USA. Our
eDNA metabarcoding analyses identified 147 different taxa, including 77
fishes, 38 birds, 24 mammals, five amphibians and three reptiles at 11
locations in the watershed, including tributaries and mainstem stretches
upstream and within the Kankakee River State Park protected area. When
compared to seining, eDNA sampling consistently detected more fish
species, including non-native and imperiled species. We also found that
vertebrate communities among the different habitats significantly varied
in taxonomic composition, showing an upstream-downstream shift along the
mainstem river as well as tributary-specific assemblages. Our study
demonstrates the ability of single-marker eDNA metabarcoding to
simultaneously document aquatic and terrestrial communities across large
temperate lotic ecosystems and to monitor diversity patterns across
protected areas.