FISH ASSEMBLAGES AT ENGINEERED AND NATURAL CHANNEL STRUCTURES IN THE LOWER MISSOURI RIVER: IMPLICATIONS FOR MODIFIED DIKE STRUCTURES † J. T. SCHLOESSER, a,b C. P. PAUKERT, a,c * W. J. DOYLE, d T. D. HILL, d K. D. STEFFENSEN e and V. H. TRAVNICHEK f a Kansas Cooperative Fish and Wildlife Research Unit, Division of Biology, Kansas State University, Manhattan, Kansas, USA b U.S. Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, Ashland, Wisconsin, USA c U.S. Geological Survey, Missouri Cooperative Fish and Wildlife Research Unit, 302 Anheuser-Busch Natural Resources Building, Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, Missouri, USA d U.S. Fish and Wildlife Service, Columbia Fish and Wildlife Conservation Office, Columbia, Missouri, USA e Nebraska Game and Parks Commission, Lincoln, Nebraska, USA f Missouri Department of Conservation, St Joseph, Missouri, USA ABSTRACT Large rivers throughout the world have been modified by using dike structures to divert water flows to deepwater habitats to maintain navi- gation channels. These modifications have been implicated in the decline in habitat diversity and native fishes. However, dike structures have been modified in the Missouri River USA to increase habitat diversity to aid in the recovery of native fishes. We compared species occupancy and fish community composition at natural sandbars and at notched and un-notched rock dikes along the lower Missouri River to determine if notching dikes increases species diversity or occupancy of native fishes. Fish were collected using gill nets, trammel nets, otter trawls, and mini fyke nets throughout the lower 1212 river km of the Missouri River USA from 2003 to 2006. Few differences in species richness and diversity were evident among engineered dike structures and natural sandbars. Notching a dike structure had no effect on proportional abun- dance of fluvial dependents, fluvial specialists, and macrohabitat generalists. Occupancy at notched dikes increased for two species but did not differ for 17 other species (81%). Our results suggest that dike structures may provide suitable habitats for fluvial species compared with channel sand bars, but dike notching did not increase abundance or occupancy of most Missouri River fishes. Published in 2011 by John Wiley & Sons, Ltd. key words: Missouri River; dike; notching; fish community; riverine fishes Received 17 May 2010; Revised 12 June 2011; Accepted 29 June 2011 INTRODUCTION Large rivers throughout the world have been modified for anthropogenic uses that have resulted in loss of habitat for native fishes (Sparks, 1995; Poff et al., 1997; Aarts et al., 2004). The Missouri River has undergone substantial modi- fications since the mid 1900s, which has reduced turbidity, sediment transport, flow variability, and main channel habi- tat complexity (Hesse and Mestl, 1993; Galat et al., 2005). A primary modification is river control structures (e.g. rock dike structures and revetments) in the channelized Missouri River that direct current towards the thalweg to maintain a 2.7-m-deep channel for barge traffic. Substantial declines in several native fish populations in the lower Missouri River were attributed to these river modifications (Pflieger and Grace, 1987; Galat et al., 2005). For example, declines in the populations of the federally endangered pallid sturgeon (Scaphirhynchus albus), shovelnose sturgeon (Scaphirhynchus platorynchus), bigmouth buffalo (Ictiobus cyprinellus), plains minnow (Hybognathus placitus), west- ern silvery minnow (Hybognathus argyritis), sicklefin chub (Macrhybopsis meeki), and sturgeon chub (Macrhybopsis gelida) were associated with habitat modifications (Pflieger and Grace, 1987; Barko et al., 2004a; Galat et al., 2005). Fishes that decreased in abundance were those with specia- lized feeding requirements, adapted to turbid waters, or spe- cies common in low-velocity backwaters (Pflieger and Grace, 1987). River modifications have altered natural habi- tats that may shift the fish assemblage towards more habitat generalists and fewer fluvial specialists (species that need flowing water for most of their life; Kinsolving and Bain, 1993; Barko et al., 2004b; Pegg and McClelland, 2004) and negatively affect native species (Pflieger and Grace, 1987; Gehrke et al., 1995; Galat et al., 2005). Many natural habitats (e.g. sand bars and islands) of the lower Missouri River have been eliminated because of chan- nel modifications (Pflieger and Grace, 1987; Galat et al., *Correspondence to: C. P. Paukert, U.S. Geological Survey, Missouri Cooperative Fish and Wildlife Research Unit Research Unit, 302 Anheuser-Busch Natural Resources Building, Department of Fisheries and Wildlife Science, University of Missouri, Columbia, Missouri 65211, USA. E-mail: paukertc@missouri.edu † This article is a US Government work and is in the public domain in the USA. RIVER RESEARCH AND APPLICATIONS River Res. Applic. (2011) Published online in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/rra.1578 Published in 2011 by John Wiley & Sons, Ltd.