Long Term Resource Monitoring Program Research Articles

Habitat Use by Five Turtle Species in the Middle Mississippi River

Abstract Turtles face unique conservation challenges in modern modified river systems. Despite their ecological importance, gaps in knowledge still exist that may hinder their conservation. Turtle by-catch data from the US Army Corps of Engineers' Long-Term Resource Monitoring Program were analyzed for 5 turtle species (false map turtle, Graptemys pseudogeographica; red-eared slider, Trachemys scripta; common snapping turtle, Chelydra serpentina; smooth softshell turtle, Apalone mutica; and spiny softshell turtle, Apalone spinifera) to better understand macrohabitat and mesohabitat use. These species demonstrated differences in habitat use between various macrohabitats, substrata, velocity classes, and depth classes. Common snapping turtles and spiny softshell turtles were captured most often in tributaries, whereas red-eared sliders were captured most often in tributaries and closed side channels. Smooth softshell turtles used open side channels and unstructured main-channel borders most often. False map...

Channel Catfish Habitat Use and Diet in the Middle Mississippi River

Abstract River modifications have had detrimental effects on biota that depend on river systems; therefore, information is needed to understand these effects and direct management efforts. Channel catfish (Ictalurus punctatus) are important recreationally, commercially, and ecologically in the Middle Mississippi River (MMR), but few studies have examined their habitat requirements, and food habits have not been evaluated in the MMR. Information about habitat use and food habits could help direct management efforts for channel catfish. To more thoroughly understand the synergistic relation between channel catfish and the associated habitat, we used data from the United States Army Corps of Engineer’s Long-Term Resource Monitoring Program to evaluate channel catfish use of large-scale river features (i.e., macrohabitats) and more fine scale mesohabitats (i.e., substrate type, depth, and velocity). Stomach contents from channel catfish were identified and quantified to determine the relative importance of sp...

Fish Associations among Un-notched, Notched and L-head Dikes in the Middle Mississippi River

Wing dikes and other anthropogenic modifications have heavily altered riverine ecosystems. Recent efforts to reach a compromise between the needs of the river transportation industry and natural resource conservation include dike modification. Dike notching permits water flow through the landward portion of the dike and has been purported to provide suitable habitat for fish and other river biota while maintaining the navigation channel. L-head dikes are flow-control structures that create calm backwater-like habitats downstream. However, few researchers have examined the actual effects of dike notching on water quality or fish communities. We compared standardized catch per unit effort and overall community structure for 50 fish species among un-notched dikes, notched dikes and L-head dikes in the Middle Mississippi River, sampled as part of the US Geological Survey's Long-Term Resource Monitoring Program. There were no differences in standardized catch per unit effort for 64% of the fishes examined. Five species known to be associated with lotic habitats were most abundant near L-head dikes. Seven species were more abundant at un-notched dikes than notched dikes, while six species were more abundant at notched dikes than un-notched dikes. Non-metric multidimensional scaling suggested differences in overall fish community structure between un-notched and other dike types. Detailed physical habitat studies should be conducted to better understand the effects of dike modification. Copyright © 2015 John Wiley & Sons, Ltd.

A decade of monitoring on Pool 26 of the upper Mississippi River System

We present information gleaned from 10 years of data collected by the water quality component of the Upper Mississippi River Restoration Environmental Management Program’s Long Term Resource Monitoring Program (LTRMP) from Pool 26 of the Upper Mississippi River System (UMRS). The Pool 26 reach of the UMRS includes the confluence with the Illinois River, and the confluence with the Missouri River just downstream of Mel Price Locks and Dam. The surrounding communities in both Illinois and Missouri benefit greatly from the natural resources provided by these rivers. We estimate that annual expenditures are 55 million for fishing and hunting, respectively, in the region surrounding Pool 26 based on license sales and state expenditure data from the U.S. Fish and Wildlife Service. Additionally, there is a commercial fishery active in Pool 26, recreational boating, and the UMRS provides drinking water for many municipalities in this region. Finally, the Upper Mississippi River System is a major transportation system, and Pool 26 receives the greatest amount of barge traffic for any river reach in the UMRS. The LTRMP began collecting data in 1988, but the first years of the program were experimental. Currently followed monitoring protocols for water quality and fish monitoring were adopted in 1993; however, a major flood event in that year prevented full data collection for that year. Data from the LTRMP water quality component demonstrate that Pool 26 is a highly productive river reach. Long-term averages of chorophyll-a, total phosphorous, total nitrogen, and total inorganic solids are comparable to levels in eutrophic to highly eutrophic lakes. The average current velocity in the main channel of the Mississippi River in Pool 26 ranges from 0.364–0.414 m/sec. during the summer and fall. Even during the lowest discharge levels in a year, the reach has a residence time no longer than 2.7 days. Discharge was significantly related to many water quality parameters, including Secchi depth, turbidity, total suspended solids, total nitrogen, nitrate-nitrite, and total phosphorus. We observed a significant linear increase in mean water temperature in the main channel from 1994 to 2004. When these data were analyzed by season, positive linear trends were found during the spring (0.515°C per year) and fall (0.646°C per year). Continued monitoring is necessary to determine if these observations represent short term fluctuations or long-term trends and to detect any related effects on this river reach.

A COMPARISON OF TWO ELECTROFISHING PROGRAMMES USED TO MONITOR FISH ON THE ILLINOIS RIVER, ILLINOIS, USA

ABSTRACTThe Illinois River Biological Station monitors fish communities in the Illinois River using two different electrofishing programmes, one using three‐phase alternating current [AC; The Long Term Illinois Fish Population Monitoring Program or long‐term electrofishing (LTEF)] and the other pulsed direct current [DC; The Long Term Resource Monitoring Program (LTRMP)]. In 2001, we replicated three‐phase AC sampling sites with pulsed‐DC electrofishing gear to test for differences between the two collection methods and programmes. Electrofishing runs at each site were standardized by length and time, with 48 samples collected for each gear. Our objective was to test for differences in fish catch rates using total catch, species richness, fish size ranges, and sample composition and structure. Total catch was significantly greater for LTRMP electrofishing (4368 total fish, mean = 91.0 fish per sample) compared with LTEF electrofishing (1423 total fish, mean = 29.6 fish per sample). Species richness also was significantly greater for LTRMP electrofishing (50 total species, mean = 12.9 species per site) compared with LTEF electrofishing (38 total species, mean = 7.9 species per site). Size ranges of fishes, composed of 100‐mm‐length groups, showed higher total catches for the LTRMP within all length groups. Although our analyses suggest that collections from the LTRMP were significantly greater in most instances, a consistent pattern of species composition between the two programmes was not evident. Our results suggest that caution must be taken when attempting to compare fish community composition and structure information between these programmes. Copyright © 2011 John Wiley & Sons, Ltd.

ARE TWO SYSTEMIC FISH ASSEMBLAGE SAMPLING PROGRAMMES ON THE UPPER MISSISSIPPI RIVER TELLING US THE SAME THING?

ABSTRACTWe applied an Index of Biotic Integrity (IBI) used on Wisconsin/Minnesota waters of the upper Mississippi River (UMR) to compare data from two systemic sampling programmes. Ability to use data from multiple sampling programmes could extend spatial and temporal coverage of river assessment and monitoring efforts. We normalized for effort and tested fish community data collected by the Environmental Monitoring and Assessment Program‐Great Rivers Ecosystems (EMAP‐GRE) 2004–2006 and the Long Term Resource Monitoring Program (LTRMP) 1993–2006. Each programme used daytime electrofishing along main channel borders but with some methodological and design differences. EMAP‐GRE, designed for baseline and, eventually, compliance monitoring, used a probabilistic, continuous design. LTRMP, designed primarily for baseline and trend monitoring, used a stratified random design in five discrete study reaches. Analysis of similarity indicated no significant difference between EMAP‐GRE and LTRMP IBI scores (n = 238; Global R = −0.052; significance level = 0.972). Both datasets distinguished clear differences only between ‘Fair’ and ‘Poor’ condition categories, potentially supporting a ‘pass–fail’ assessment strategy. Thirteen years of LTRMP data demonstrated stable IBI scores through time in four of five reaches sampled. LTRMP and EMAP‐GRE IBI scores correlated along the UMR's upstream to downstream gradient (df [3, 25]; F = 1.61; p = 0.22). A decline in IBI scores from upstream to downstream was consistent with UMR fish community studies and a previous, empirically modelled human disturbance gradient. Comparability between EMAP‐GRE (best upstream to downstream coverage) and LTRMP data (best coverage over time and across the floodplain) supports a next step of developing and testing a systemic, multi‐metric fish index on the UMR that both approaches could inform. Copyright © 2011 John Wiley & Sons, Ltd.

Estimating site occupancy rates for aquatic plants using spatial sub-sampling designs when detection probabilities are less than one

Estimation of site occupancy rates when detection probabilities are <1 is well established in wildlife science. Data from multiple visits to a sample of sites are used to estimate detection probabilities and the proportion of sites occupied by focal species. In this article we describe how site occupancy methods can be applied to estimate occupancy rates of plants and other sessile organisms. We illustrate this approach and the pitfalls of ignoring incomplete detection using spatial data for 2 aquatic vascular plants collected under the Upper Mississippi River's Long Term Resource Monitoring Program (LTRMP). Site occupancy models considered include: a naïve model that ignores incomplete detection, a simple site occupancy model assuming a constant occupancy rate and a constant probability of detection across sites, several models that allow site occupancy rates and probabilities of detection to vary with habitat characteristics, and mixture models that allow for unexplained variation in detection probabilities. We used information theoretic methods to rank competing models and bootstrapping to evaluate the goodness-of-fit of the final models. Results of our analysis confirm that ignoring incomplete detection can result in biased estimates of occupancy rates. Estimates of site occupancy rates for 2 aquatic plant species were 19–36% higher compared to naive estimates that ignored probabilities of detection <1. Simulations indicate that final models have little bias when 50 or more sites are sampled, and little gains in precision could be expected for sample sizes >300. We recommend applying site occupancy methods for monitoring presence of aquatic species.

A mark-recapture population estimate for invasive silver carp (Hypophthalmichthys molitrix) in the La Grange Reach, Illinois River

Invasive silver carp (Hypophthalmichthys molitrix) populations have expanded greatly in the Upper Mississippi River System (UMRS) since their introduction in the early 1970s. We conducted a Chapman-modified, continuous Schnabel mark-recapture population and biomass estimate for silver carp (106–901 mm) in the La Grange reach, Illinois River during 2007–2008. We estimated a total of 328,192 (95% CI 231,226–484,474) silver carp (2,544 per river km 1,792–3,756) comprising 705 (95% CI; 496–1,040) metric tons of biomass (5.5 metric tons per river km 3.8–8.1). Long Term Resource Monitoring Program (LTRMP) data from the La Grange reach showed an exponential increase in silver carp catches since 1998, with an intrinsic rate of increase approaching 84%. In 2008, silver carp comprised about 51% of the total LTRMP annual fish collection. To our knowledge, this large river reach may contain the greatest ambient densities of wild silver carp in the world. Our findings provide a target for reduction efforts and also emphasize the importance of the La Grange reach as a source population for potential expansion of the species to the Laurentian Great Lakes.

Reduced condition factor of two native fish species coincident with invasion of non‐native Asian carps in the Illinois River, U.S.A. Is this evidence for competition and reduced fitness?

Non‐native, Asian carps bighead Hypophthalmichthys nobilis and silver Hypophthalmichthys molitrix have been present in the Illinois River since the early 1990s. The Long‐Term Resource Monitoring Program (LTRMP) has been collecting bighead and silver carps in routine monitoring of the La Grange Reach, Illinois River, since 1995 and 1998, respectively. Despite variable recruitment, Asian carps abundance and biomass have increased since 2000, as evidenced by commercial landings, and Asian carps now dominate the fish community on La Grange Reach. Previous research suggests dietary overlap among bighead and silver carps and two native Illinois River fishes, gizzard shad Dorosoma cepedianum and bigmouth buffalo Ictiobus cyprinellus. Total length and mass data from c. 5000 fishes were used to test for changes in gizzard shad and bigmouth buffalo body condition after Asian carps establishment and investigate potential competitive interactions and changes in fitness. Analyses revealed significant declines in body condition of gizzard shad (−7%) and bigmouth buffalo (−5%) following the Asian carps invasion from 2000 to 2006. Segmented regression analyses showed no significant change in the rate of decline in gizzard shad condition after 2000, whereas the rate of decline in bigmouth buffalo condition increased significantly after 2000. Statistically significant differences in gizzard shad condition after Asian carps establishment (2000–2006) was observed, whereas condition of bigmouth buffalo was significantly lower in all years following Asian carps establishment as compared to 2000. Declines in gizzard shad and bigmouth buffalo condition were significantly correlated with increased commercial harvest of Asian carps and poorly correlated with other abiotic and biotic factors (e.g. temperature, chlorophyll a and discharge) that may influence fish body condition. These results may suggest that Asian carps are influencing native planktivore body condition, and future research should focus on determining whether food is limited in the Illinois River for native planktivores and other fish species.

Midland Smooth Softshell (Apalone mutica) and Spiny Softshell (Apalone spinifera) Turtles in the Middle Mississippi River: Habitat Associations, Population Structure, and Implications for Conservation

By using 6 years of Long Term Resource Monitoring Program (LTRMP) turtle by-catch data collected from the middle Mississippi River, we investigated smooth softshell (Apalone mutica) and spiny softshell (Apalone spinifera) turtle abundance collected from 5 physical habitats: main channel border, wing dikes, tributary, open side channel, and closed side channel. Females comprised 62% and males 38% of the total catch of smooth softshell turtles. For spiny softshell turtles, females comprised 67% and males 33% of the total catch. We observed skewed reproductive age structure and sex ratios among and within both species. Smooth and spiny softshell turtle captures were dominated by reproductive individuals (62% and 87%, respectively). Smooth softshell turtles were most abundant in open side channels and main channel borders, whereas spiny softshell turtles were most abundant in tributaries and closed side channels. Smooth softshell abundance was greatest in deep waters with faster water velocity, whereas spiny softshell abundance was greatest in waters with higher visibility (e.g., Secchi transparency) and slower water velocity.

Spatial patterns of fish communities in the Upper Mississippi River System: assessing fragmentation by low‐head dams

AbstractWe assessed the similarity of fish communities among river reaches to assess community‐level fragmentation by low‐head dams in the Upper Mississippi River System (UMRS). The spatial coverage of standardized electrofishing sampling used in the Long Term Resource Monitoring Program (LTRMP) was extended for three of the six regional trend areas (RTA; pools 4, 13, and the Open River Reach) to include river reaches (outpools) immediately upstream and downstream from the standard RTA from 15 June to 31 October 2000. Additionally, pools 19 and 20 were sampled in September 2000. Cluster analysis and non‐metric multidimensional scaling of community composition and structure data revealed two major groups, upper and lower reaches, and four (for composition) or five (for structure) sub‐groupings of river reaches. In general, all outpools grouped with the nearest RTA for both community composition (no exception) and community structure (one exception). This suggests that fragmentation of fish communities from low‐head dams is minimal. Mantel correlations demonstrated strong inverse association between the similarity of fish communities with the distance between reaches. Habitat variables measured during electrofishing collections were significantly correlated with spatial variation of fish composition and community structure, but provided only marginal improvements to correlations with distance between reaches alone. Furthermore, habitat variability among river reaches also was related to distance between reaches. Determining the extent to which variation of fish communities is related to habitat or demographic processes (e.g. migration, larval drift, source‐sink dynamics) will be challenging for this system. Although low‐head dams on the UMRS may restrict movements for individuals and populations of certain fish species, we found little evidence that these effects have led to substantial, community‐level fragmentation. Copyright © 2006 John Wiley &amp; Sons, Ltd.

PASSIVE FISHING TECHNIQUES: A CAUSE OF TURTLE MORTALITY IN THE MISSISSIPPI RIVER

We investigated variation of incidentally captured turtle mortality in response to environmental factors and passive fishing techniques. We used Long Term Resource Monitoring Program (LTRMP) data collected from 1996 to 2001 in the unimpounded upper Mississippi River (UMR) adjacent to Missouri and Illinois, USA. We used a principle components analysis (PCA) and a stepwise discriminant function analysis to identify factors correlated with mortality of captured turtles. Furthermore, we were interested in what percentage of turtles died from passive fishing techniques and what technique(s) caused the most turtle mortality. The main factors influencing captured turtle mortality were water temperature and depth at net deployment. Fyke nets captured the most turtles and caused the most turtle mortality. Almost 90% of mortalities occurred in offshore aquatic areas (i.e., side channel or tributary). Our results provide information on causes of turtle mortality (as bycatch) in a riverine system and implications for river turtle conservation by suggesting management strategies to reduce turtle bycatch and decrease mortality of captured turtles.

Relationship among Fish Assemblages and Main‐Channel‐Border Physical Habitats in the Unimpounded Upper Mississippi River

Large rivers worldwide have been altered by the construction and maintenance of navigation channels, which include extensive bank revetments, wing dikes, and levees. Using 7 years of Long-Term Resource Monitoring Program (LTRMP) data collected from the unimpounded upper Mississippi River, we investigated assemblages in two main-channel-border physical habitats—those with wing dikes and those without wing dikes. Fishes were captured using daytime electrofishing, mini-fyke netting, large hoop netting, and small hoop netting. Our objectives were to (1) assess associations among fish species richness, physical measurements, and main-channel-border physical habitats using stepwise multiple regression and indicator variables; (2) identify abundant adult and young-of-year (age-0) families in both physical habitats to further investigate assemblage composition; and (3) calculate standardized species richness estimates within each physical habitat for adult and age-0 fishes to provide additional information on community structure. We found species richness was greater at wing dikes for both adult and age-0 fishes when compared with main channel borders. Stepwise multiple regression revealed significant relationships between adult species richness and passive gear deployment (e.g., hoop nets and mini-fyke nets), physical habitat type, and river elevation, as well as interactions between physical habitat and passive gears, and physical habitat and transparency (i.e., Secchi depth). This model explained 56% of the variance in adult species richness. Approximately 15% of the variation in age-0 species richness was explained by the sample period, sample date, transparency, physical habitat, and depth of gear deployment. Long-term impacts of river modifications on fishes have not been well documented in many large river systems and warrant further study. The findings from this study provide baseline ecological information on fish assemblages using main channel borders in the unimpounded upper Mississippi River, information that will aid managers making channel maintenance decisions in large river systems.

Improving Electrofishing Catch Consistency by Standardizing Power

Abstract The electrical output of electrofishing equipment is commonly standardized by using either constant voltage or constant amperage, However, simplified circuit and wave theories of electricity suggest that standardization of power (wattage) available for transfer from water to fish may be critical for effective standardization of electrofishing. Electrofishing with standardized power ensures that constant power is transferable to fish regardless of water conditions. The in situ performance of standardized power output is poorly known. We used data collected by the interagency Long Term Resource Monitoring Program (LTRMP) in the upper Mississippi River system to assess the effectiveness of standardizing power output. The data consisted of 278 electrofishing collections, comprising 9,282 fishes in eight species groups, obtained during 1990 from main channel border, backwater, and tailwater aquatic areas in four reaches of the upper Mississippi River and one reach of the Illinois River. Variation in p...