2008 Annual Report. Pallid Sturgeon Population Assessment and Associated Fish Community Monitoring for the Missouri River: Segment 14

Transcription

1 2008 Annual Report Pallid Sturgeon Population Assessment and Associated Fish Community Monitoring for the Missouri River: Segment 14 Prepared for the U.S. Army Corps of Engineers Missouri River Recovery Program By: Patricia Herman, Andrew Plauck, Wyatt Doyle and Tracy Hill U.S. Fish & Wildlife Service Columbia National Fish & Wildlife Conservation Office 101 Park DeVille Drive, Suite A Columbia, MO April 2009

2 EXECUTIVE SUMMARY Over the past five years, the number of hatchery reared and unknown origin (potentially wild) pallid sturgeon that have been captured in Segment 14 has increased. In particular, from 2003 through 2006, the total number of pallid sturgeon captured increased from two in 2003 to four in 2004, 13 in 2005, 9 in 2006, 19 in 2007 and 22 in Of these 69 fish, more than half were confirmed to be from hatchery stockings. The increase in recaptured hatchery-stocked pallid sturgeon indicates some level of survival and success of the stocking program. Of the 22 pallid sturgeon collected in 2008, two were confirmed by genetics to be of wild origin, 16 were positively identified as hatchery origin and gentic results are still pending on four fish. The wild pallid sturgeon were both adults measuring 783 mm and 906 mm. The larger of the wild fish was a reproductive male and was used in 2008 spawning efforts at Blind Pony State Fish Hatchery. Despite having captured adult wild pallid sturgeon in Segment 14 for several years, no newly recruited pallid sturgeon have been captured. Four of the pallid sturgeon captured had only a coded wire tag mark and ranged in size from 776 mm to 831 mm, suggesting that these were 1992 and/or 1997 year classes. A suite of gears were used throughout the year over a wide range of habitat types and temperatures. Eight of the 22 pallid sturgeon were captured with standard stationary set gill nets. With active gears, one pallid sturgeon was captured in an otter trawl and none were caught in trammel nets. Thirteen pallid sturgeon were captured with trotlines. Nine of the 22 pallid sturgeon captures occurred within inside-bend (ISB) macrohabitat, which was the habitat most sampled with all gears. During 2008, 15 pallid sturgeon were captured in channel border (CHNB) mesohabitat. Results from past years show that pallid sturgeon are most often captured in CHNB mesohabitat. The data suggest that pallid and shovelnose sturgeon tend to congregate near confluences of major tributaries to the Missouri River. Concentrated and targeted trotline sampling efforts at the mouth of the Osage River were conducted in high water conditions. These efforts produced high pallid and shovelnose sturgeon catch rates in tributary mouth-large and confluence habitats, however these catch rates may be a reflection of habitat conditions rather than habitat preference. Stocked pallid sturgeon condition factors (Kn) ranged from to Mean pallid sturgeon growth rates ranged from mm/day for the 2004 year class to mm/day for the 2002 year class. Two young-of-year sturgeon were captured in Segment 14 in otter trawls during Since standard sampling began in Segment 14, only two pallid sturgeon have been recaptured for a second time despite dozens being potentially at large within this reach. The only pallid stockings in this reach of the river were 2,445 fish in 1994 and 1,200 in 1997 for a total of 3,632 fish. However, since 2002, 21,035 pallid sturgeon have been stocked at Boonville, MO, which is only 65 miles upstream of Segment 14. At present, there has been a cumulative total of 24,667 fish stocked between Booneville (RM 195) and St. Charles (RM 25). The combined total percentage of stocked fish captured (N = 16) versus proximate availability (N= 24,667) was 0.06%. The ratio of hybrid sturgeon to pallid and shovelnose sturgeon has been a useful tool to monitor the pallid sturgeon population trends and the potential effects of hybridization. The ratio of hybrid sturgeon captured in gill nets relative to shovelnose sturgeon increased from 1 ii

3 hybrid for every 1489 shovelnose in 2007 to 1 hybrid for every 626 shovelnose in The number of pallid sturgeon to hybrid sturgeon had remained relatively constant since 2004 until this year. During 2008, the number of pallids to hybrids increased to four to one. The ratio of pallid sturgeon to shovelnose sturgeon captured in otter trawls increased from one to 333 in 2007 to one in every 176 in No pallid sturgeon were captured in trammel nets and no hybrid sturgeon were captured in trammel nets or otter trawls during These catch rates are likely due to the inability to complete sampling with the full suite of gears during Sturgeon Season 2008 because of high water conditions. Community target fish species are used as a gauge for relative change in the river in the absence of pallid sturgeon information. Young of the year shovelnose sturgeon (YOY) were present but not abundant in 2008 (N = 26). Sturgeon of larger sizes (> 250 mm) were the most abundant large fish represented in the sampling effort (N = 2,310) which suggests that the appropriate gears are being used to detect adult sturgeon, particularly shovelnose. Of the 2,336 shovelnose sturgeon captured, they were represented in the gear as follows: 1,229 in gill nets, 404 in 1-inch trammel nets, 159 in 16-foot otter trawls, none captured in mini-fyke nets and 518 on trotlines. Using standard gears, 58 species were captured throughout the year. Different gears were used to target different fishes in the community. The population assessment project, in turn, is adapting to determine the best methods to ensure efficiency within these gears. Sturgeon chubs, sicklefin chubs and speckled chubs have been captured most often with otter trawls. Sand shiners and Hybognathus spp. have been captured most often with mini-fyke nets. Blue suckers have been captured with gill nets, trammel nets and otter trawls; and the majority of sauger have been captured with gill nets. Since 2005, there has been a notable decline in both abundance and catch rates of all three target chub species in Segment 14. We assume that variations in the populations are directly related to environmental conditions in the river (i.e., water levels, spring rise, etc ) but a true correlation can only be attained over several more years of trend data. In 2006, field crews captured a large number of YOY blue suckers for the first time since project implementation in Despite high spring rises, these YOY blue suckers were not observed again during 2007 or In all, abundances and catch rates of all three target chub species, sand shiners, blue suckers and sauger were at all time lows during In addition, field crews only captured one Hybognathus spp. in Segment 14 during Correspondingly, the catch rate of blue catfish, a non-target native species, has declined every year since Conversely, the catch rate of channel catfish has increased every year since The life history of the pallid sturgeon, as well as shovelnose sturgeon, may be closely linked to these catfish species because of their predaceous nature. It will be important to monitor changes in these native fish populations closely in future years. iii

4 TABLE OF CONTENTS Introduction...1 Study Area...2 Methods...5 Sample site selection and description...6 Sampling gear...7 Data Collection and Analysis...9 Results Pallid sturgeon...13 Shovelnose X Pallid Sturgeon Hybrids...40 Targeted Native River Species Shovelnose sturgeon...41 Sturgeon chub...58 Sicklefin chub...64 Speckled chub...71 Sand shiner...78 Hybognathus spp...85 Blue sucker...91 Sauger...99 Missouri River Fish Community Discussion Acknowledgments References Appendices iv

5 LIST OF TABLES Table 1. Number of bends sampled, mean number of deployments and total number of deployments by macrohabitat for Segment 14 on the Missouri River during Sturgeon Season and Fish Community Season in Table 2. Number of bends sampled, mean number of deployments and total number of deployments by mesohabitat for Segment 14 on the Missouri River during Sturgeon Season and Fish Community Season in Pallid sturgeon Table 3. Pallid sturgeon capture summaries for all gears relative to habitat type and environmental variables on the Missouri River during Means (minimum and maximum) are presented...20 Table 6. Mean fork length, weight, relative condition factor (Kn) and absolute growth rates for all hatchery-reared pallid sturgeon captures by year class at the time of stocking and recapture during 2008 from Segment 14 of the Missouri River. Relative condition factor was calculated using the equation in Keenlyne and Evenson (1993)...25 Table 7. Incremental relative stock density (RSD) for all pallid sturgeon captured with all gear by a length category during 2008 in the Missouri River. Length categories b determined using the methods proposed by Shuman et al. (2006)...26 Table 9. Total number of sub-stock size (0-199 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 10. Total number of sub-stock size (0-199 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 11. Total number of sub-stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 12. Total number of sub-stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 13. Total number of stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during v

6 Table 14. Total number of stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 15. Total number of quality size and greater ( 630 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 16. Total number of quality size and greater ( 630 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Shovelnose sturgeon Table 17. Total number of sub-stock size (0-149 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 18. Total number of sub-stock size (0-149 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 19. Total number of sub-stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 20. Total number of sub-stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 21. Total number of stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in segment 14 of the Missouri River during Table 22. Total number of stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Table 23. Total number of quality size and greater ( 380 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 24. Total number of quality size and greater ( 380 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during vi

7 Table 25. Incremental relative stock density (RSD) and mean relative weight (Wr) by a length category for shovelnose sturgeon in Segment 14 of the Missouri River captured during Sturgeon chub Table 26. Total number of sturgeon chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 27. Total number of sturgeon chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Sicklefin chub Table 28. Total number of sicklefin chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 29. Total number of sicklefin chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Speckled chub Table 30. Total number of speckled chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 31. Total number of speckled chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Sand shiner Table 32. Total number of sand shiners captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 33. Total number of sand shiners captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during vii

8 Hybognathus spp. Table 34. Total number of Hybognathus spp. captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 35. Total number of Hybognathus spp. captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Blue sucker Table 36. Total number of blue suckers captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 37. Total number of blue suckers captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during Sauger Table 38. Total number of saugers captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during Table 39. Total number of saugers captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during viii

9 LIST OF FIGURES Figure 1a. Map of Segment 14 of the Missouri River with major tributaries, common landmarks and historic stocking locations for pallid sturgeon. Segment 14 encompasses the Missouri River from the confluence with the Osage River (River Mile 130.2) to the confluence with the Mississippi River (River Mile 0.0)...12 Figure 1b. Distribution of pallid sturgeon captures by river mile for Segment 14 of the Missouri River during Black bars represent pallid captures during Sturgeon Season and white bars during Fish Community Season. Figure includes pallid captures from standard, non-random and wild sampling efforts Pallid sturgeon Figure 2. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars) and unknown origin (cross-hatched bars) pallid sturgeon using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season Pallid sturgeon of unknown origin are awaiting genetic verification. NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...27 Figure 3. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars) and unknown origin (cross-hatched bars) pallid sturgeon using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season Pallid sturgeon of unknown origin are awaiting genetic verification. NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...28 Figure 5. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars) and unknown origin (cross-hatched bars) pallid sturgeon using 1-inch trammel nets and otter trawls in Segment 14 of the Missouri River during Fish Community Season Pallid sturgeon of unknown origin are awaiting genetic verification...29 Figure 8. Length frequency of pallid sturgeon captured during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Figure 9. Annual capture history of wild (black bars), hatchery reared (white bars) and unknown origin (cross-hatched bars) pallid sturgeon collected in Segment 14 of the Missouri River from 2003 to Figure is designed to compare overall pallid sturgeon captures from year to year and is biased by variable effort among years. Figure includes pallid captures from standard, non-random and wild sampling efforts ix

10 Shovelnose sturgeon Figure 11. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars) and quality and above size ( 380 mm; black bars) shovelnose sturgeon using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...44 Figure 12. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars) and quality and above size ( 380 mm; black bars) shovelnose sturgeon using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...45 Figure 14. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars) and quality and above size ( 380 mm; black bars) shovelnose sturgeon using 1-inch trammel nets and otter trawls in Segment 14 of the Missouri River during Fish Community Season Figure 15. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars) and quality and above size ( 380 mm; black bars) shovelnose sturgeon using mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 17. Length frequency of shovelnose sturgeon from Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Sturgeon chub Figure 18. Mean annual catch per unit effort (+/- 2 SE) of sturgeon chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 19. Mean annual catch per unit effort (+/- 2 SE) of sturgeon chub using otter trawls in Segment 14 of the Missouri River during Fish Community Season Figure 21. Length frequency of sturgeon chub during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during x

11 Sicklefin chub Figure 22. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 23. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using otter trawls in Segment 14 of the Missouri River during Fish Community Season Figure 24. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 25. Length frequency of sicklefin chub during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Speckled chub Figure 26. Mean annual catch per unit effort (+/- 2 SE) of speckled chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 27. Mean annual catch per unit effort (+/- 2 SE) of speckled chub using otter trawls in Segment 14 of the Missouri River during Fish Community Season Figure 28. Mean annual catch per unit effort (+/- 2 SE) of speckled chub using mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 29. Length frequency of speckled chubs during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Sand shiner Figure 30. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 31. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with otter trawls in Segment 14 of the Missouri River during Fish Community Season xi

12 Figure 32. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 33. Length frequency of sand shiner during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Hybognathus spp. Figure 34. Mean annual catch per unit effort (+/- 2 SE) of Hybognathus spp. with otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...86 Figure 36. Mean annual catch per unit effort (+/- 2 SE) of Hybognathus spp. with mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 37. Length frequency of Hybognathus spp. caught during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during Blue sucker Figure 38. Mean annual catch per unit effort (+/- 2 SE) of blue sucker with gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...93 Figure 39. Mean annual catch per unit effort (+/- 2 SE) of blue sucker with 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season...94 Figure 41. Mean annual catch per unit effort (+/- 2 SE) of blue sucker using otter trawls and 1-inch trammel nets in Segment 14 of the Missouri River during Fish Community Season Figure 44. Length frequency of blue suckers during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during xii

13 Sauger Figure 45. Mean annual catch per unit effort (+/- 2 SE) of sauger using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 46. Mean annual catch per unit effort (+/- 2 SE) of sauger using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season Figure 48. Mean annual catch per unit effort (+/- 2 SE) of sauger using otter trawls and 1- inch trammel nets in Segment 14 of the Missouri River during Fish Community Season Figure 49. Mean annual catch per unit effort (+/- 2 SE) of sauger using mini-fyke nets in Segment 14 of the Missouri River during Fish Community Season Figure 51. Length frequency of sauger during Sturgeon Season (fall through spring; black bars) and Fish Community Season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during xiii

14 LIST OF APPENDICES Appendix A. Phylogenetic list of Missouri River fishes with corresponding letter codes used in the long-term pallid sturgeon and associated fish community sampling program Appendix B. Definitions and codes used to classify standard Missouri River habitats in the long term pallid sturgeon and associated fish community sampling program Appendix C. List of standard and wild gears, their corresponding codes in the database, seasons deployed, years used and catch per unit effort units for collection of Missouri River fishes for the long-term pallid sturgeon and associated fish community sampling program Appendix D. Stocking locations and codes for pallid sturgeon by Recovery Priority Management Area in the Missouri River Basin Appendix E. Juvenile and adult pallid sturgeon stocking summary for Segment 14 of the Missouri River (RPMA 4) Appendix F. Total catch, overall mean catch per unit effort and mean CPUE by mesohabitat within a macrohabitat for all species caught during Sturgeon Season and Fish Community Season combined in segment 14 of the Missouri River during Appendix F1. Gill Net: Appendix F2. 1 Inch Trammel Net: Appendix F4. : Appendix F6. Mini-fyke Net: Appendix G. Hatchery names, locations and abbreviations Appendix H. Alphabetic list of Missouri River fishes with total number caught by gear type for Sturgeon Season (fall through spring) and Fish Community Season (summer) during 2008 for Segment 14 of the Missouri River Appendix I. Comprehensive list of bend numbers and locations for Segment 14 of the Missouri River comparing bend selection between years from Appendix J. Ratios of pallid to shovelnose sturgeon, hybrid to shovelnose sturgeon and pallid to hybrid sturgeon, standardized by catch per unit effort for Segment 14 between 2004 and xiv

15 Appendix K. Percentage of shovelnose sturgeon captured in each length group for each gear during Sturgeon Season and Fish Community Season in Segment 14 of the Missouri River during NE = no effort due to hight water condtions in Segment 14 during Sturgeon Season Appendix L. Trotline: overall season and segment summary. Lists total catch and CPUE (fish/hook night) Appendix M. Missouri River discharge at Hermann, MO USGS Gauge from November 2007 through October Graph courtesy of U.S. Geological Survey xv

16 Introduction Pallid sturgeon (Scaphirhynchus albus) have declined throughout the Missouri River since dam construction and inception of the Bank Stabilization and Navigation Project in 1912 (Carlson et al. 1985). Loss of habitat, reduced turbidity, increased velocity, loss of natural flows, reduction in forage, increased hybridization and inadequate reproduction and recruitment are factors contributing to the decline of the pallid sturgeon and other native species (Pflieger and Grace 1987). Since 1996, surveys conducted throughout the Missouri and Mississippi Rivers illustrate an increase in hybridization and continued decline of pallid sturgeon relative abundance (Grady et al. 2001, Doyle and Starostka 2003, Doyle and Starostka 2004). In an independent scientific evaluation of the condition and management of the Missouri River, the National Research Council (2002) concluded that altered flow and habitat conditions associated with current management practices on the Missouri River have resulted in an unhealthy river ecosystem. Similar conclusions presented in the U. S. Fish and Wildlife Service Biological Opinion recommended, in part, that the Army Corps of Engineers (COE) initiate modified flow regimes by 2003 to avoid jeopardizing three listed species (endangered pallid sturgeon and least tern (Sternula antillarum); threatened piping plover (Charadrius melodus) and begin restoring the river s ecological processes. The COE is responsible for monitoring and evaluating biotic responses of the pallid sturgeon to operational and habitat changes on the Missouri River (USFWS 2000). Habitat restoration, higher spring and lower summer flows combined with adaptive management are recommended measures to restore pallid sturgeon populations on the lower Missouri River. Adaptive management is an approach to natural resources management that promotes carefully designed management actions, monitoring and assessment of impacts and application of results and findings to subsequent policy and management strategies. Monitoring sturgeon populations will provide vital information needed to guide restoration of habitat, hydrology and aquatic communities in the lower Missouri River. 1

17 In response to the 2000 Missouri River Biological Opinion, the COE is developing monitoring and restoration projects to avoid jeopardizing pallid sturgeon populations. As part of their Implementation Plan, the COE is working with the U. S. Fish and Wildlife Service (USFWS) and state natural resource agencies to develop and conduct a pallid sturgeon monitoring and assessment program. The objectives of the program are: 1. Document annual results and long-term trends in pallid sturgeon population abundance and geographic distribution throughout the Missouri River System. 2. Document annual results and long-term trends of habitat use of wild pallid sturgeon and hatchery stocked pallid sturgeon by season and life stage. 3. Document population structure and dynamics of pallid sturgeon in the Missouri River System. 4. Evaluate annual results and long-term trends in native target species population abundance and geographic distribution throughout the Missouri River System. 5. Document annual results and long-term trends of habitat usage of the native target species by season and life stage. 6. Document annual results and long-term trends of all non-target species population abundance and geographic distribution throughout the Missouri River System, where sample size is greater than fifty individuals. Study Area Historically, the Missouri River was very wide and shallow, containing meandering channels with many islands and snags (Grady and Milligan 1998). Today, portions of the profoundly altered Missouri River and many of its tributaries are characterized by deep reserviors and narrow, stabilized channels. Alterations to the river were executed by the COE to serve as a navigation channel for barge traffic. High levees and armored banks not only serve to manage the navigation channel but also to protect adjacent farm land. Revetted banks and dikes line the lower potion of the river creating a self-scouring channel. Alterations to the river have come at a price. While management has resulted in power generation, recreational areas and stable farmland, alterations have negatively impacted flow regimes, water quality and habitat heterogeneity (Dieterman and Galat 2004). In Segment 14, the most downstream reach of the Missouri River, water velocities exceed 1.3 m/s in the main channel and drop to zero in pools formed behind dike structures. Depths 2

18 generally range from six meters in the main channel to 12 meters behind dikes, depending on water levels. Turbidities can vary widely from over 1,000 Nephelometric Turbidity Units (NTU) in spring flood events to around 40 NTU in the winter months. Substrates range from silt to fine sand and gravel in the main channel and bordering habitats. Rock revetment dominates the outside bend shore-line; whereas silt and sand banks make up the inside bend shoreline. In low water, sand bars are visible on the insides of bends with water often carving secondary channels behind. Debris is often discharged from upstream tributaries whereby, it is then frequently lodged in sand bars or on dike structures as water levels drop. The Osage River is the largest tributary feeding Segment 14; it enters the Missouri River at the top of the study area (RM 130.2). The Osage River originates in the foothills of the Ozark Mountains and feeds Lake of the Ozarks, a reservoir used to generate hydroelectric power. Because it is a bottom release reservoir, cool and clear water travels the remaining 80 miles (with low sediment inputs) over coarse sand and gravel substrates until its confluence with the Missouri River. Other smaller tributaries, such as the Gasconade River, deliver large silt loads from rain events and can quickly alter water stage height. Catastrophic spring floods are rare, however, levies are occasionally breeched allowing water to flow onto the floodplain. Over the last two decades, the COE has made efforts to diversify habitats by notching dikes, creating pilot channels on the flood plain and by releasing waters to imitate flood events. In recent years, much emphasis has been given to these dike modification projects and many of the existing dikes in this reach of river have been altered. Notches are now deeper and wider, following modifications initialized in 2003 and can divert water allowing for increased erosion or deposition. Dike types vary in design but, in general, outside bends contain L- shaped dikes pointing down stream while dikes on the inside bend are more perpendicular to water flow, projecting straight into the channel and slightly downstream. Subsequent habitats that exist behind modified dikes vary widely and can provide habitat and refuge for fish and other aquatic species. In its current condition, the river vaguely resembles the one explored by Lewis & Clark, though some remnant historical habitats still exist at different water 3

19 stages. These remnant habitats are important biologically and this project aims to define and determine those most used by pallid sturgeon and associated native target species. 4

20 Methods Sampling was conducted in accordance with Standard Operating Procedures established by a panel of representatives from various State and Federal agencies involved with pallid sturgeon recovery on the Missouri River (Drobish 2007). The sampling guidelines were meant to be adaptive and have been modified to ensure sampling efficiency and scientific accuracy. Bag seines were removed from standard sampling in 2006 due to their similarity of results with mini-fyke nets. In addition, 2.5 inch trammel nets were removed from standard sampling in 2007 because they were not significantly improving the capture rate of pallid sturgeon and associated native target species. In 2007, sampling effort was increased to improve statistical power. Prior to 2007, eight subsamples were deployed on each bend. In 2007, active gears were deployed based on bend length, with longer bends receiving more effort than shorter bends. Power analysis revealed that this extra effort had no impact on the ability to detect change over time (Bryan et al. 2009). In 2008, sampling effort was returned to the previous sampling regime of ten subsamples for gill nets and eight subsamples per bend for all other gears. The push trawl (PT) was added as a new gear for Fish Community Season in 2007 and was evaluated as a possible supplement or replacement for mini-fyke nets (MF). Push trawl data from 2007 were analyzed to determine if this would be a suitable supplemental gear to the program or could replace the more labor intensive mini-fyke net. Analyses revealed that neither PT nor MF were suitable for detecting change in fish populations over time. In 2008, it was decided that PT would not be used as a standard gear for this project; however, MF were kept. In 2008, trotlines were implemented for additional sampling. Trotlines have been used on the Mississippi River by commercial fishermen and Missouri Department of Conservation for catching sturgeon for years. Trotlines have also been used as an effective monitoring tool for lake sturgeon in the Great Lakes. The utility of this gear was tested at various flows and 5

21 temperatures, though deployed in a random manner similar to gill nets. An exception to this occurred at the mouth of the Osage River where efforts were concentrated due to historical success of large pallid captures at this location. Sampling Site Selection and Description Segment 14 begins at the confluence of the Osage River (RM 130.2) and ends at the confluence with the Mississippi River (RM 0.0; Figure 1a). Each segment represents a sampling stratum. Segments were divided into bends (defined as the crossing of the thalweg from one bank to the other) and bends were randomly selected from each segment to be sampled as replicates, with a suite of gears. Twelve bends were randomly selected prior to November These twelve bends were each sampled twice, once between 1 November 2007 and 30 June 2008 (referred to as Sturgeon Season) and once between 1 July 2008 and 31 October 2008 (referred to as Fish Community Season). The river was categorized into distinct river components called Mesohabitats which exist within Macrohabitats (Appendix B). Each Mesohabitat was sampled twice within each Macrohabitat. When a diversity of habitats was unavailable, a minimum of eight sub-samples were used to ensure some consistent level of effort per bend. For example, most active gear effort was applied to inside bend channel border habitat because this habitat was available at all water stages in all bends. Samples that occurred outside of the predetermined sampling protocol were given a Wild designation and not included in data analysis. Drobish (2007) described habitats in a hierarchical manner in Drobish (2007; Appendix B). The broadest habitat description (macrohabitat) describes the general location of the sample within a bend (e.g., inside bend, outside bend, etc.). Mesohabitat describes the habitats that occur within the respective macrohabitat (e.g., pool, channel border, etc.). Microhabitat is used to specifically characterize the individual gear deployment as it relates to features within the sample area (e.g., wing dikes, sandbars, etc.). If available, all macro- and mesohabitat combinations were sampled. In Segment 14, sampling was distributed among the following available habitats: 6

22 MACRO CHXO (channel cross over) ISB (inside bend) OSB (outside bend), CONF (confluence- area downstream of a tributary) SCCS or SCCL (side channel connected small or large) SCCN (side channel not connected) TRMS or TRML (small or large tributary mouth) TRIB (tributary) MESO CHNB (channel border- where depth is > 4 ft. to toe of thalweg) POOL (scour hole) ITIP (island tip- associated with SCCS or SCCL where the two water currents meet behind an island BARS (sand bar or shallow water habitat were depth is < 4 ft. meters TLWG (thalweg- main channel between channel borders conveying majority of water) Sampling Gear To avoid fish mortality, gill nets (GN) were only deployed when water temperatures were below 12.8ºC, during Sturgeon Season. Gill nets were anchored upstream with a heavy grappling hook-style anchor and back-anchored with a cement weight tied to a buoy. Gill nets were fished overnight with a minimum soak time of 12 hours and a maximum of 24 hours. Otter trawls (OT or OT16) were pulled downstream with a jet powered stern trawler. Otter trawls were used in both Sturgeon and Fish Community Seasons. Due to safety concerns, trawls were not pulled on outside bend revetment or in the thalweg for safety reasons. Trawls frequently encountered snags but a procedure was used to safely untangle the gear. A GPS enabled sonar, capable of detecting woody debris, was used to detect and avoid many snags in daily operations. One-inch trammel nets were deployed perpendicular to the current from the bow with a 10 meter lead line. Orientation of the net was maintained by pulling the net back to a perpendicular position when necessary. An estimate of sampling distance lost was accounted for. Trammel nets were fished in moderately shallow water and away from eddies which 7

23 could tangle the net. Snags occurred frequently but did not prevent effective sampling. Trammel nets were used in both Sturgeon and Fish Community Seasons. Mini-fyke nets were deployed during Fish Community Season. Mini-fykes (MF) were set on mud bars behind dikes and on sand bars in the main-channel. Steep slopes and shallow sand bars may have affected the efficiency of this gear. In many cases, the gear was set close to the bank behind bars and the lead wing was not fully extended because of the steep slope of the bank or the velocity of the water. In contrast, on shallow sand bars there was not always enough lead to ensure the throat was in the water, especially when water levels were rising or falling. Mini-fykes could only be applied in emergent bar habitat and thus all bends did not receive similar amounts of effort. Trotlines were set similarly to gill nets and in similar habitat types. Lines were deployed with a heavy grappling hook-style anchor upstream and back-anchored with a cement weight tied to a buoy. Hooks on 35 cm tuna leader were attached to the mainline using ganion clips. Twenty to 40 hooks were attached per 61 m of mainline. Type of hook, length of the mainline, number of hooks deployed and retrieved and bait type were recorded. Trotlines were fished overnight with a minimum soak time of 12 hours and a maximum of 24 hours. This gear was given a wild designation. Segment 14 sampling gear dimensions: Otter trawl: 1-inch trammel net: Innovative Nets Systems (Greg Faulkner) custom Skate design, # 9 Sapphire, 1.5 inch (38 mm)stretch mesh, 16ft (4.9 m) wide and 30 inch (0.76 m) boards 125 ft. (38.1 m) X 6 ft. (1.8 m) outer wall X 8 ft. (2.4 m) inner wall; 1-inch (25.4 mm) bar X 8 inch (203 mm) bar panels Mini- Fyke: 2 cab 4 ft. (1.2 m) X 2 ft. (0.6 m), two 2 ft. (0.6 m) hoops, 15 ft. (4.6 m) X 2 ft. (0.6 m) lead, 1/8 th in. (3.2 mm) mesh Gill net: 100 (30.5 m) X 8 ft. (2.4 m) with 25 ft. (7.6 m) repeating 1.5 (38 mm), 2 (51 mm), 3 (76 mm) and 4 (102 mm) inch mesh 8

24 panels, nets were sewn together making a 200 ft. (61 m) net with two series of repeating panels Trotline: 61 m (205 ft) negatively buoyant ground lines (additional lines can be attached up to 905 ft in total length), 3/0 circle hooks attached to 35 cm tuna leader with ganion clips attached to ground line at m intervals, baited with earthworms. Data Collection and Analysis Associated Environmental Data GPS locations, temperature and depth (beginning, mid-point and end for all gears except mini-fykes; where depth is measured at the opening/box) were taken for each sample. Additionally, turbidity and velocity samples were collected randomly from 25% of the mesohabitat types within each macrohabitat. Water column velocity in meters per second (m/s) was measured at bottom, 80% and 20% of the depth. All habitat data were collected when pallid sturgeon were encountered. In an attempt to determine if flow/water velocity can be visually estimated by a trained eye, an additional box was added to the data sheet. The data collector recorded a water velocity value corresponding with a set of categories (0 = could not be estimated, 1 = Eddy, 2 = m/s, 3 = m/s, 4 = m/s, 5 = >0.9 m/s). Species Data and Genetic Verification Length (mm) and weight measurements (g) were collected on all target species and length measurements were collected on a sub-sample of non-target species. A series of additional measurements were taken on pallid sturgeon and their suspected hybrids using Sheehan s index for verification (Sheehan et al. 1999). Sturgeon were deemed hybrid when they were verified to be within the hybrid range (-0.50 to +0.60) on Sheehan s Character Index scale. Passive Integrated Transponder (PIT) tags were implanted under the dorsal fin of pallid sturgeon, hybrids (<0.5) and lake sturgeon. Additionally, fin clips were collected from pallid sturgeon and hybrids to be analyzed for genetic purity and digital images were taken for documentation. All pallid sturgeon that were captured with no evidence of previously being 9

25 tagged, or otherwise could not be positively identified as being of hatchery or wild origin, were deemed unknown until genetic verification. All pallid sturgeon deemed wild have been genetically verified as not being of hatchery origin. Relative Condition Relative condition of recaptured hatchery reared pallid sturgeon was calculated using Kn = (W / W ), where W is weight of the individual and W is the length-specific mean weight predicted by the weight-length equation calculated for that population. Keenlyne and Evenson (1993) provided a weight-length regression [log10 W = log10 L (r2 = )] for pallid sturgeon throughout its range which was used to calculate a relative condition factor. Stock Densities Stock densities were calculated to assess pallid and shovelnose sturgeon population structure. A length frequency index measures changes in fish population structure. Length categories based on the percentage of the largest known pallid sturgeon are as follows (Shuman et al. 2006): sub-stock fork length < 330 mm (20%), stock fork length = mm (20-36%), quality fork length = mm (36-45%), preferred fork length = 840-1,039 mm (45-59%), memorable fork length = 1,040-1,269 mm (59 74%) and trophy fork length > 1,270 mm (>74%). Length categories based on the percentage of the largest known shovelnose sturgeon are as follows (Quist et al. 1998): sub-stock fork length <250 mm (20%), stock fork length = mm (20-36%), quality fork length = mm (36 45%), preferred fork length = mm (45-59%), memorable fork length = mm (59-74%) and trophy fork length > 810 mm (> 74%). Proportional Stock Density (PSD) is the proportion of fish of quality size in a stock. Relative Stock Density (RSD) is the proportion of fish of a size group in a stock. 10

26 Data Analysis A sample target effort for each gear was defined as follows: 300 m drift (TN), 300 m tow (OT) and one overnight set (GN, MF, TL). Due to the large numbers of snags encountered, a minimum effort of 75 m was accepted for OT and TN. Catch per unit of effort (CPUE) was calculated as catch per 100 meters for active gears (OT and TN). Gill net effort was calculated as catch per 100 feet of net set overnight (less than 24 hours). Because the standard gill nets used in Segment 14 were 200 feet long, CPUE was calculated for the net and divided by two. Mini-fyke nets were calculated as catch per overnight set. Samples that occurred outside of the standard gear deployment protocol, habitat effort protocol, or samples that occurred in non-random bends were excluded from CPUE calculations. These data were, however, included in length frequencies, relative condition and population structure calculations. Several figures and tables have been omitted from this report in an effort to maintain consistency between years and segments. For example, if no pallid sturgeon were captured in mini-fyke nets, the figure showing CPUE of mini-fyke nets would be excluded from the pallid sturgeon discussion as well as the list of figures. 11

27 Figure 1a. Map of Segment 14 of the Missouri River with major tributaries, common landmarks and historic stocking locations for pallid sturgeon. Segment 14 encompasses the Missouri River from the confluence with the Osage River (River Mile 130.2) to the confluence with the Mississippi River (River Mile 0.0). 12

28 Results Pallid Sturgeon This section covers the following objectives from the Pallid Sturgeon Monitoring and Assessment Program: Objective 1. Document annual results and long-term trends in pallid sturgeon population abundance and geographic distribution throughout the Missouri River system. Objective 2. Document annual results and long-term trends of habitat usage of wild pallid sturgeon and hatchery stocked pallid sturgeon by season and life stage. Objective 3. Document population structure and dynamics of pallid sturgeon in the Missouri River System. During 2008, biologists from Columbia National Fish and Wildlife Conservation Office (Columbia NFWCO) randomly selected 14 bends during Sturgeon Season (1 November 2007 to 30 June 2008); however, due to multiple extreme and sustained high water events, sampling efforts were unable to be completed (Appendix M). Eleven of the 14 bends were gill netted (total effort = 212 net nights). None of the bends in Segment 14 were trammel netted or trawled during Sturgeon Season. Selected Segment 14 bends were successfully sampled with all gears during Fish Community Season (1 July to 31 October 2008). For Fish Community Season; 14 bends were sampled with 1-inch trammel nets (total effort = 112 deployments; 15,997 m drifted), 14 bends with 16-foot otter trawls (total effort = 114 nets deployed; 23,727 m trawled) and 14 bends with mini-fyke nets (total effort = 107 net nights: Tables 1 and 2). A total of 22 pallid sturgeon were captured during Of those captured, 9 were encountered with standard gear during random sampling, whereas 13 were captured with wild gear during non-random sampling. 13

29 While trotlines were not a standard gear in 2008, they accounted for 59% of the pallid sturgeon captured in Segment 14 (N = 13; Appendix L). This effort included random and non-random bends, however the gear was deployed in a random manner similar to our gill net protocol (8 10 lines with hooks per line). Pallid sturgeon captured with trotlines ranged in length between mm (Figure 8). On average, trotlines captured one pallid sturgeon per every 340 hooks deployed in Segment 14 during 2008 (CPUE = fish per hook per night; Appendix L). Catch rates were highest in TRML macrohabitat and CHNB mesohabitat (CPUE = 0.007; Appendix L). Of the 22 pallid sturgeon that were captured in Segment 14 during 2008, two were wild and 16 were stocked (Figure 9). Four pallid sturgeon are of undetermined origin. Genetic results are still pending on these fish. Only one pallid sturgeon was captured (0.5%, N = 1) in the lower half of the segment (RM 70.0 to 0.0). The majority of pallid sturgeon in Segment 14 (95%; N = 21) were captured in the upper half of the segment (RM to 70; Figure 1b). Eight of the 16 hatchery stocked pallid sturgeon captured during 2008 were positively traced back to a stocking site. Four of the hatchery origin pallid sturgeon were stocked near Boonville, Missouri (BOO, Appendix D), two were stocked at Miami, MO (MIA, Appendix D) and one was stocked near Bellevue, NE (BEL, Appendix D; Table 6). The pallid sturgeon stocked near Bellevue traveled 471 miles downstream before being captured near the mouth of the Osage River at river mile Interestingly, a 1992 pallid sturgeon stocked at Two Rivers Recreational Reach on the Platte River as part of a study in 1998 was captured 527 miles downstream. Three of the pallid sturgeon stocked at Boonville were spawned in 2002, stocked in 2003 and were age 6 at capture. The other pallid sturgeon stocked at Boonville was spawned in 2003 and stocked in 2004, captured at age 4. The pallid sturgeon stocked at Bellevue was spawned in 2003, stocked in 2004 and was age 5 at capture. The two pallid sturgeon stocked at Miami were spawned in 2004, stocked during 2005 and were age 4 at capture. Five of the eight traceable hatchery origin pallid sturgeon were reared at Neosho National Fish Hatchery, two from Gavins Point National Fish Hatchery and the one stocked in 1998 was reared at Blind Pony State Fish Hatchery. 14

30 Condition (Kn), which is a measure of the fish s plumpness, was averaged for all recaptured pallid sturgeon from Segment 14. All fish that leave the hatchery are considered to be in good or robust condition (Kn > 1.0). All pallid sturgeon recaptured had lower condition factors than at time of stocking (Table 6). However, 2002 through 2005 year classes exhibited positive growth rates. Pallid sturgeon captured during Sturgeon Season were in better condition at the time of recapture (Kn = 0.826) than the fish captured later in the year during Fish Community Season (Kn = 0.710; Table 7). When examining only standard random samples, the majority of pallid sturgeon were captured during Sturgeon Season (89%; N = 8) versus Fish Community Season (11%; N = 1). Of the pallid sturgeon that were captured during Sturgeon Season, all (100%; N = 8) were captured in ISB macrohabitat relative to an average of 72% of the total effort being expended in that habitat during Sturgeon Season (Tables 13 and 14). Similarly, the majority of pallid sturgeon (71%; N = 5) were captured in POOL mesohabitat relative to an average of 39% of the total effort in that habitat (Tables 14 and 16). During Fish Community Season, the pallid sturgeon was captured in ISB CHNB habitat relative to 97% of the total effort occurring in both of those habitat types. On average, pallid sturgeon were captured at a mean depth of 6.1 m when considering all gears. Pallid sturgeon were captured at a mean depth of 4.48 m in standard gears. Pallid sturgeon were captured at depths closer to the mean than the extremes (captured between 1.8 and 10.2 m whereas the sample mean was between 0.3 to 11.0 m; Table 3). This trend was similar for bottom velocity where pallid sturgeon were captured at a mean bottom velocity of 0.56 m/s with a sample range of 0.01 to 1.07 m/s. The majority of pallid sturgeon (96%; N = 21) were captured in water temperatures equal to or less than 15.0 ºC. On average, pallid sturgeon were captured at a water temperature of 11.1 ºC ( ºC) with an average sample temperature of 21.3 ºC ( ºC; Table 3). Average turbidity for pallid sturgeon captures was 88 NTU s (19 to 296 NTU s) with a mean turbidity per sample of 59 NTU s (12 296; Table 3). 15

31 The population structure may indicate the influence of recently propagated fish (stock size N = 5) with ten quality size and six preferred size pallid sturgeon being collected in Segment 14 (Table 7). In general, RSD values indicate health of fish populations relative to reproductive potential and age of fish. The continued absence of sub-stock size pallid sturgeon indicates we are either not detecting sub-stock pallid sturgeon with our current gear or fish are not present in Segment 14. Given a truncated Sturgeon Season sampling set, gill nets continue to be the most effective standard gear at capturing pallid sturgeon in Segment 14 (mean overall CPUE = fish per net night). One pallid sturgeon was captured in an otter trawl during Fish Community Season with a mean overall CPUE of fish per meter trawled (Figures 1-5; Appendix F). The CPUE for hatchery reared and wild pallid sturgeon in gill nets increased in 2008 (Figure 2). Catch rates with 1-inch trammel nets were unable to be determined in 2008 (Figure 3). No pallid sturgeon were captured with 1-inch trammel nets in Segment 14 during Fish Community Season (Figure 5). Since 2003, there has been a steady increase in the number of pallid sturgeon captured in Segment 14; in particular, there was considerable increase in the capture of hatchery origin pallid sturgeon (2003 = 1; 2004 = 2; 2005 = 9; 2006 = 7; 2007 = 14, 2008 = 16; Figure 9). Recent findings, not summarized in this report, suggest dispersal from stocking sites increases after the fish has been at large for more than two years (unpublished data, Andrew Plauck). The increase in hatchery fish is likely a result of this dispersal of surviving hatchery fish. 16

32 Table 1. Number of bends sampled, mean number of deployments and total number of deployments by macrohabitat for segment 14 on the Missouri River during sturgeon season and Fish Community Season in N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net Number of Bends Mean deployments BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Macrohabitat a Fall through Spring - Sturgeon Season Gill Net N-E 26 0 N-E N-E N-E N-E 2 0 N-E 1-Inch Trammel Net Summer Fish Community Season N-E 26 0 N-E N-E N-E N-E 1 0 N-E Mini-Fyke Net N-E 26 1 N-E N-E N-E N-E 3 3 N-E N-E 28 0 N-E N-E N-E N-E 2 0 N-E a Habitat abbreviations and definitions presented in Appendix B. 17

33 Table 2. Number of bends sampled, mean number of deployments and total number of deployments by mesohabitat for segment 14 on the Missouri River during sturgeon season and Fish Community Season in N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net Number of bends Mean Mesohabitat a deployments BARS CHNB DTWT ITIP POOL TLWG Fall through Spring Sturgeon Season Gill Net N-E Inch Trammel Net Summer Fish Community Season N-E Mini-Fyke Net N-E N-E a Habitat abbreviations and definitions presented in Appendix B. 18

34 Segment 14 - Pallid Sturgeon Captures by River Mile 10 Pallid Capture Frequency N = River Mile Figure 1b. Distribution of pallid sturgeon captures by river mile for Segment 14 of the Missouri River during Black bars represent pallid captures during Sturgeon Season and white bars during Fish Community season. Figure includes pallid captures from standard sampling, non-random and wild sampling effort. 19

35 Table 3. Pallid sturgeon capture summaries for all gears relative to habitat type and environmental variables on the Missouri River during Means (minimum and maximum) are presented. Habitat definitions and codes presented in Appendix B. N-E indicates the habitat is non-existent in the segment. Habitat Depth Bottom Velocity (m/s) Temperature Turbidity (ntu) Macro- Meso- Effort Catch Effort Catch Effort Catch Effort Catch Total pallids caught BRAD BARS. CHNB. DTWT. ITIP. POOL. TLWG. CHXO BARS 0.7 ( ) 24.3 ( ) 40.2 ( ). CHNB 4.2 ( ) 8.0 ( ) 0.61 ( ) 22.0 ( ) 8.3 ( ) 60.0 ( ) 23.0 ( ) 1 DTWT. ITIP. POOL 4.9 ( ) 5.3 ( ) 0.44 ( ) 0.27 ( ) 11.2 ( ) 11.7 ( ) 107 ( ) 109 ( ) 3 TLWG. CONF BARS 0.4 ( ) 29.6 ( ) 38.0 ( ). CHNB 8.8 ( ) 10.1 ( ) 9.7 ( ) 9.2 ( ) 42.0 ( ) 42.0 ( ) 3 DTWT. ITIP. 20

36 Table 3 (continued). Habitat Depth Bottom Velocity (m/s) Temperature Turbidity (ntu) Macro- Meso- Effort Catch Effort Catch Effort Catch Effort Catch Total pallids caught CONF POOL. TLWG. DEND BARS. CHNB. DTWT. ITIP. POOL. DRNG BARS. CHNB. DTWT. ITIP. POOL. TLWG. ISB BARS 0.7 ( ) 0.14 ( ) 23.5 ( ) 50.2 ( ). CHNB 3.1 ( ) 3.3 ( ) 0.64 ( ) 0.65 ( ) 21.1 ( ) 13.5 ( ) 64.0 ( ) 126 ( ) 7 DTWT. ITIP. POOL 4.9 ( ) 4.4 ( ) 0.47 ( ) 11.2 ( ) 10.1 ( ) 83.6 ( ) 57.0 ( ) 2 21

37 Table 3 (continued). Habitat Depth Bottom Velocity (m/s) Temperature Turbidity (ntu) Macro- Meso- Effort Catch Effort Catch Effort Catch Effort Catch Total pallids caught ISB TLWG. OSB BARS 0.8 ( ) 24.7 ( ) 48.6 ( ). CHNB 5.4 ( ) 12.2 ( ). DTWT. ITIP. POOL 3.7 ( ) 12.1 ( ) 92.0 ( ). TLWG. SCCL BARS 0.7 (0.7.07) 0.10 ( ) 29.0 ( ) 32.0 ( ). CHNB 3.9 ( ) 10.0 ( ). DTWT. ITIP 1.2 ( ) 12.2 ( ) 153 ( ). POOL. TLWG. SCCS BARS 0.5 ( ) 0.03 ( ) 28.9 ( ) 70.0 ( ). 22

38 Table 3(continued). Habitat Depth Bottom Velocity (m/s) Temperature Turbidity (ntu) Macro- Meso- Effort Catch Effort Catch Effort Catch Effort Catch Total fish caught SCCS CHNB. DTWT. ITIP 3.0 ( ) 0.68 ( ) 26.7 ( ) 59.0 ( ). POOL. TLWG. SCN BARS. POOL. CHNB. TLWG. TRIB BARS. POOL. CHNB. ITIP TLWG. ITIP. TRML BARS 0.8 ( ) 25.2 ( ) 46.0 ( ). POOL 9.3 ( ) 9.1 ( ) 11.9 ( ) 11.9 ( ) 120 ( ) 120 ( ) 2 23

39 Table 3 (continued). Habitat Depth Bottom Velocity (m/s) Temperature Turbidity (ntu) Macro- Meso- Effort Catch Effort Catch Effort Catch Effort Catch Total fish caught TRML CHNB 6.8 ( ) 8.0 ( ) 0.02 ( ) 12.7 ( ) 8.7 ( ) 29.0 ( ) 35.0 ( ) 4 TLWG 4.3 ( ) 0.04 ( ) 19.7 ( ) 14.7 ( ). ITIP. TRMS BARS 0.6 ( ) 0.01 ( ) 24.4 ( ) 50.0 ( ). POOL. CHNB. TLWG. ITIP. WILD BARS. POOL. CHNB. TLWG. ITIP. 24

40 Table 6. Mean fork length, weight, relative condition factor (Kn) and absolute growth rates for all hatchery-reared pallid sturgeon captures by year class at the time of stocking and recapture during 2008 from segment 14 of the Missouri River. Relative condition factor was calculated using the equation in Keenlyne and Evenson (1993). Standard error (+/- 2 SE) was calculated where N>1 and is represented on second line of each year. Year class N Length (mm) Stock Data Recapture Data Growth Data Weight (g) K n Length (mm) Weight (g) K n Length (mm/d) Weight (g/d) (48) (49.2) (0.064) (51) (168.6) (0.078) (0.027) (0.081) (30) (28.0) (0.097) (75) (299.5) (0.056) (0.044) (0.053) (7) (8.0) (0.016) (29) (30.0) (0.084) (0.006) (0.001)

41 Table 7. Incremental relative stock density (RSD) a and relative condition factor (Kn) for all pallid sturgeon captured with all gear by a length category during 2008 in the Missouri River. Length categories b determined using the methods proposed by Shuman et al. (2006). Relative condition factor was calculated using the equation in Keenlyne and Evenson (1993). Length Category N RSD K n (+/- 2 SE) Sturgeon Season Sub-stock (0-199 mm) 0. 0 Sub-stock ( mm) 0. 0 Stock (0.033) Quality (0.056) Preferred (0.037) Memorable 0. 0 Trophy 0. 0 Overall K n (0.031) Fish Community Season Sub-stock (0-199 mm) 0. 0 Sub-stock ( mm) 0. 0 Stock Quality 0. 0 Preferred 0. 0 Memorable 0. 0 Trophy 0. 0 Overall K n a RSD = (# of fish of a specified length class / # of fish minimum stock length fish) * 100. b Length categories based on the percentage of the largest known pallid sturgeon: Sub-stock FL < 330 mm (20 %), Stock FL = mm (20 36 %), Quality FL = mm (36 45 %), Preferred FL = mm (45 59 %), Memorable FL = mm (59 74 %), Trophy FL > 1270 mm (>74 %). 26

42 Segment 14 - Pallid Sturgeon / Sturgeon Season 0.06 Gill Net CPUE (fish/net night) CPUE (fish/100 m) Wild-SS-GN Hatchery-SS-GN Unknown-SS-GN Year NE Figure 2. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars), and unknown origin (cross-hatched bars) pallid sturgeon using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season Pallid sturgeon of unknown origin are awaiting genetic verification. NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 27

43 Segment 14 - Pallid Sturgeon / Sturgeon Season Inch Trammel Net CPUE (fish/net night) Year NE Figure 3. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars), and unknown origin (cross-hatched bars) pallid sturgeon using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season Pallid sturgeon of unknown origin are awaiting genetic verification. NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 28

44 Segment 14 - Pallid Sturgeon / Fish Community Season Inch Trammel Net CPUE (fish/100 m) CPUE (fish/100 m) Year Figure 5. Mean annual catch per unit effort (+/- 2 SE) of wild (black bars), hatchery reared (white bars), and unknown origin (cross-hatched bars) pallid sturgeon using 1-inch trammel nets and otter trawls in Segment 14 of the Missouri River during Fish Community season Pallid sturgeon of unknown origin are awaiting genetic verification. 29

45 Table 9. Total number of sub-stock size (0-199 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 30

46 Table 10. Total number of sub-stock size (0-199 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Mesohabitat Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Gill Net Sturgeon Season (Fall through Spring) (58) 0 (1) (39) (2) Fish Community Season (Summer) 1-Inch Trammel Net. 0 (100) Mini-Fyke Net. (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 31

47 Table 11. Total number of sub-stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 32

48 Table 12. Total number of sub-stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Mesohabitat Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Gill Net Sturgeon Season (Fall through Spring) (58) 0 (1) (39) (2) Fish Community Season (Summer) 1-Inch Trammel Net. 0 (100) Mini-Fyke Net. (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 33

49 Table 13. Total number of stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 34

50 Table 14. Total number of stock size ( mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 35

51 Table 15. Total number of quality size and greater ( 630 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 36

52 Table 16. Total number of quality size and greater ( 630 mm) pallid sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 7. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 37

53 Segment 14 - Pallid Sturgeon 5 Standard Samples N = 9 4 Frequency All Samples N = 22 4 Frequency mm Length Group Figure 8. Length frequency of pallid sturgeon captured during Sturgeon Season (fall through spring black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri River during Standard samples include standard gears, random bends and random subsamples. Additionally, all samples include all non-random and wild samples collected during

54 14 - Annual Pallid Sturgeon Capture History 20 Wild; N = 7 Hatchery; N = 49 Unknown ; N = Frequency Year Figure 9. Annual capture history of wild (black bars), hatchery reared (white bars), and unknown origin (cross-hatched bars) pallid sturgeon collected in Segment 14 of the Missouri River from 2003 to Figure is designed to compare overall pallid sturgeon captures from year to year and is biased by variable effort among years. Figure includes all pallid captures including non-random and wild samples. 39

55 Shovelnose X Pallid Sturgeon Hybrids Two suspected hybrid sturgeon were captured in Segment 14 during Genetic species confirmation is still pending on these fish. One of the hybrid sturgeon was captured in CHXO macrohabitat and POOL mesohabitat. The other hybrid was caught in TRML macrohabitat and TLWG mesohabitat. Hybrid sturgeon were captured in shallower water (mean depth = 3.8 m) than pallid sturgeon (mean depth = 6.1 m). Velocities were not recorded at the capture locations of these fish. Ratios of hybrid sturgeon to shovelnose and pallid sturgeon are a useful way to document change from year to year due to the effects of hybridization and availability of true pallid sturgeon for successful spawning. The ratio of hybrid sturgeon captured in gill nets relative to shovelnose sturgeon increased from 1 hybrid for every 1,489 shovelnose in 2007 to 1 hybrid for every 626 shovelnose in 2008 (N = 2 SNPD, 1,229 SNSG). The number of pallid sturgeon to hybrid sturgeon had remained relatively constant since 2004 until this year. In 2008, the number of pallids to hybrids in gill nets increased to 4 to 1 (N = 8 PDSG). The ratio of pallid sturgeon to shovelnose sturgeon captured in otter trawls increased from 1 to 333 in 2007 to 1 in 176 in 2008 (N = 1 PDSG, 174 SNSG) (Appendix J). No pallid sturgeon were captured in trammel nets and no hybrid sturgeon were captured in trammel nets or otter trawls during These catch rates are likely due to an inability to complete sampling with the full suite of gears during Sturgeon Season 2008 because of high water conditions. Ratios are standardized by catch per unit effort. 40

56 Targeted Native River Species This section covers the following objectives from the Pallid Sturgeon Monitoring and Assessment Program: Objective 4. Document annual results and long-term trends in native target species population abundance and geographic distribution throughout the Missouri River system. Objective 5. Document annual results and long-term trends of habitat usage of the target native species by season. Shovelnose Sturgeon A total of 1,812 shovelnose sturgeon were captured in Segment 14 during Nearly 68% of shovelnose were collected during Sturgeon Season (N = 1,229; Tables 17-24). As in past years, no sub-stock sized shovelnose sturgeon mm (young-of-year (YOY)) or sub-stock shovelnose sturgeon mm were captured in gill nets during Stugeon Season in Thirteen stock size (SS) shovelnose sturgeon ( mm) were captured in gill nets. Gill nets were most successful in capturing quality sized (Q) and greater shovelnose (>380 mm) as 1,216 fish were captured (98.9% of total catch; Appendix K). Gill nets were the most effective gear for capturing shovelnose sturgeon with an overall CPUE of 5.64 fish per net night. Overall catch rates exhibited a decline from 2007 (2008 SS CPUE = 0.06, Q = 5.58). Gill netting efforts were incomplete and no trammel net or otter trawl effort was deployed in Segment 14 during Sturgeon Season due to flooding (Figures 11 & 12). Most shovelnose sturgeon were collected in CHXO POOL habitat (CPUE = 9.46) followed by ISB POOL habitat (CPUE = 9.92; Appendix F1). During Fish Community Season, 583 shovelnose sturgeon were captured. As in previous years, otter trawls were the most effective gear at capturing YOY shovelnose sturgeon (100% of YOY catch, N = 2). Few sub-stock mm shovelnose sturgeon were captured in Segment 14 (1% of total catch, N = 24). Three times as many sub-stock mm shovelnose were captured by otter trawls (N=18) as were encountered in 1-inch trammel nets (N = 6). Trammel nets proved to be the most effective gear for capturing shovelnose sturgeon greater than 250 mm. 41

57 Twenty-six SS shovelnose were collected during Fish Community Season with nearly 77% (N = 20) being encountered in drifted trammel nets. Over 91% of the sturgeon captured during Fish Community Season were greater than 380mm (N = 531; Figure 14; Tables 17 24). In drifted trammel nets, 93.2% of the total catch and 84.5% of the total catch of otter trawls were quality sized and greater (Appendix K). No shovelnose sturgeon were captured in mini-fyke nets in 2008 (Figure 15; Tables 17-24). Overall Fish Community Season catch rates of shovelnose sturgeon exhibited an increase from 2007 (Figure 14). Drifted 1-inch trammel nets were the most effective gear for capturing shovelnose sturgeon during Fish Community Season with an overall CPUE of 3.09 fish/100 m. Most sturgeon caught in trammel nets were encountered in CHXO macrohabitat (CPUE = 3.61) followed by ISB macrohabitat (CPUE = 2.96; Appendix F2). All trammel nets were drifted in CHNB mesohabitats. Otter trawls were less effective for capturing shovelnose sturgeon with an overall CPUE of 0.70 fish/100 m. However, this gear may be the most effective standard gear for targeting YOY and sub-stock mm shovelnose (CPUE = and 0.08; respectively). Otter trawls were successful at catching sturgeon in SCCS ITIP habitats (CPUE = 1.14), followed by CHXO CHNB habitat (CPUE = 0.90) and ISB CHNB habitats (CPUE = 0.64; Appendix F4). While trotlines were not a standard gear during 2008, they accounted for 22% of the shovelnose sturgeon captured in Segment 14 (N = 518; Appendix L). This effort included random and nonrandom bends, however the gear was deployed in a random manner similar to our gill net protocol (8 10 lines with hooks per line). Shovelnose sturgeon captured with trotlines ranged in length between mm (Figure 8). On average, trotlines captured one shovelnose sturgeon per every 9 hooks deployed in Segment 14 during 2008 (CPUE = 0.12 fish per hook per night; Appendix L). Shovelnose sturgeon were most often captured in TRML macrohabitat and CHNB mesohabitat (CPUE = 0.23; Appendix L); however, this may not reflect true habitat selection by shovelnose sturgeon. Intensive and concentrated effort was targeted in this specific habitat during spring broodstock efforts coupled with high water conditions. These catch rates may be more a reflection of seasonal habitat conditions (refugia from high flows and debris) rather than habitat preference. 42

58 The size distribution of shovelnose sturgeon in Segment 14 is typical of long-lived species and depicts minor contribution of smaller fish to the population (Figure 17). According to Steffensen and Hamel (2008) and Pflieger (1997), shovelnose sturgeon reach 210 mm in their first year and 315 mm, 409 mm, 485 mm, 541 mm and 600 mm in each of the subsequent years. Based on these length-at-age analyses, the majority of shovelnose sturgeon captured in Segment 14 were greater than age 4 (Figure 17). An additional 524 fish were included in the all samples length frequency histogram but depicted no differences in length frequency distributions from the Standard samples. Length frequency distributions for shovelnose sturgeon were similar to previous years. Based on relative stock densities (RSD), a higher proportion of preferred sized and greater shovelnose sturgeon were captured during the sturgeon season (RSD-P = 66, RSD-M = 17) relative to Fish Community Season (RSD-P = 61, RSD-M = 15; Table 25). Similar to 2007 (Utrup et al. 2008), few sub-stock shovelnose sturgeon were captured in either season (N = 0 Sturgeon Season; N = 26 Fish Community Season). No trophy size shovelnose sturgeon were captured in Segment 14. Relative weight (Wr) of stock sizes showed a general decrease for the larger, more mature fish when compared to the smaller fish (Table 25). 43

59 Segment 14 - Shovelnose Sturgeon / Sturgeon Season CPUE (fish/net night) CPUE (fish/100 m) Gill Net Year NE Figure 11. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars), and quality and above size (> 380 mm; black bars) shovelnose sturgeon using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 44

60 Segment 14 - Shovelnose Sturgeon / Sturgeon Season CPUE (fish/100 m) Inch Trammel Net Year NE Figure 12. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars), and quality and above size (> 380 mm; black bars) shovelnose sturgeon using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 45

61 Segment 14 - Shovelnose Sturgeon / Fish Community Season 5 1-Inch Trammel Net CPUE (fish/100 m) CPUE (fish/100 m) Year Figure 14. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars), and quality and above size (> 380 mm; black bars) shovelnose sturgeon using 1-inch trammel nets and otter trawls in Segment 14 of the Missouri River during Fish Community season

62 Segment 14 - Shovelnose Sturgeon / Fish Community Season 0.25 Mini-Fyke Net CPUE (fish/net night) Year Figure 15. Mean annual catch per unit effort (+/- 2 SE) of sub-stock size (0-149 mm; white bars), sub-stock size ( mm; cross-hatched), stock size ( mm; gray bars), and quality and above size (> 380 mm; black bars) shovelnose sturgeon using mini-fyke nets and bag seines in Segment 14 of the Missouri River during Fish Community season

63 Table 17. Total number of sub-stock size (0-149 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 48

64 Table 18. Total number of sub-stock size (0-149 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 49

65 Table 19. Total number of sub-stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 50

66 Table 20. Total number of sub-stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 51

67 Table 21. Total number of stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 52

68 Table 22. Total number of stock size ( mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 53

69 Table 23. Total number of quality size and greater ( 380 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is nonexistent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 54

70 Table 24. Total number of quality size and greater ( 380 mm) shovelnose sturgeon captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. Size categories described in Table 25. N-E indicates the habitat is nonexistent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 55

71 Segment 14 - Shovelnose Sturgeon 200 Standard Samples N = Frequency All Samples N = 2336 Frequency mm Length Group Figure 17. Length frequency of shovelnose sturgeon during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri Rive during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

72 Table 25. Incremental relative stock density (RSD) a and mean relative weight (Wr) by a length category for shovelnose sturgeon in Segment 14 of the Missouri River captured during Length categories b determined using methods proposed by Quist (1998). Length category N RSD Wr (+/- 2 SE) Sturgeon Season Sub-stock (0-149 mm) 0. 0 Sub-stock ( mm) 0. 0 Stock (4.718) Quality (3.567) Preferred (0.743) Memorable (1.502) Trophy 0. 0 Overall Wr (0.797) Fish Community Season Sub-stock (0-149 mm) 2.. Sub-stock ( mm) (16.55) Stock (83.44) Quality (4.139) Preferred (1.471) Memorable (2.160) Trophy 0. 0 Overall Wr (4.106) a RSD = (# of fish of a specified length class / # of fish minimum stock length fish) * 100. b Length categories based on the percentage of the largest known shovelnose sturgeon: Sub-stock FL < 250 mm (20 %), Stock FL = mm (20 36 %), Quality FL = mm (36 45 %), Preferred FL = mm (45 59 %), Memorable FL = mm (59 74 %), Trophy FL > 810 mm (>74 %). 57

73 Sturgeon Chub A total of 7 sturgeon chubs were captured in Segment 14 (Table 26). All were captured in the otter trawl during Fish Community Season. Though the number of fish encountered has decreased steadily over the past five years, CPUE of sturgeon chub was 0.04 fish per 100 m trawled, similar to the last two years (Figures 18 and 19). The majority of sturgeon chubs were captured in CHXO (71% of the total catch relative to 21% of the total effort; Table 26). All sturgeon chubs were captured in CHNB mesohabitat relative to 97% of the effort during Fish Community Season (Table 27). Length frequency diagrams illustrate size ranges from 35 mm to 80 mm where most sturgeon chubs were in the 35 to 50 mm range. Not enough sturgeon chubs (N < 50) were captured in Segment 14 during 2007 to summarize year-to-year trends or population dynamics. 58

74 Segment 14 - Sturgeon Chub / Sturgeon Season CPUE (fish/100 m) NE Year Figure 18. Mean annual catch per unit effort (+/- 2 SE) of sturgeon chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 59

75 Segment 14 - Sturgeon Chub / Fish Community Season CPUE (fish/100 m) Year Figure 19. Mean annual catch per unit effort (+/- 2 SE) of sturgeon chub using otter trawls in Segment 14 of the Missouri River during Fish Community season

76 Table 26. Total number of sturgeon chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 61

77 Table 27. Total number of sturgeon chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 62

78 Segment 14 - Sturgeon Chub 2.5 Standard Samples N = Frequency All Samples N = Frequency mm Length Group Figure 21. Length frequency of sturgeon chub during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri Rive during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

79 Sicklefin Chub A total of 33 sicklefin chubs were captured in Segment 14 (Table 26). All were captured in the otter trawl during Fish Community Season. There has been a notable decline in the total number of sicklefin chubs captured in Segment 14 since 2004 (N = 1,029 in 2004, N = 355 in 2005, N = 200 in 2006 and N = 98 in 2007). The CPUE of sicklefin chub has also decreased since In 2008, CPUE was 0.18 fish per 100 m trawled, as compared to 0.25 in 2007 and 0.38 in 2006 (Figure 23). The majority of sicklefin chubs were captured in ISB (52% of the total catch relative to 76% of the total effort; Table 28), closely followed by CHXO macrohabitat (48 % of the total catch relative to 21% of the effort). All sicklefin chubs were captured in CHNB mesohabitat relative to 97% of the effort during Fish Community Season (Table 29). Length frequency diagrams illustrate a bimodal distribution of sizes from 40 mm to 100 mm where sturgeon chubs were grouped in the 50 mm range and 95 mm range. Herman et al. (2008a) found YOY sicklefin chubs attain lengths of about 50 mm in their first year of life. The distribution of fish between the sizes of 40 mm and 65 mm suggest the presence of YOY and age-1 sicklefin chubs in the Fish Community samples during The presence of fish smaller than 50 mm suggest that spawning occurred during Fish at 50 mm and slightly larger suggest that spawning occurred in 2007 and there was first year recruitment in 2008 (Figure 25; Utrup et al. 2007). An insufficient number of sturgeon chubs (N < 50) were captured in Segment 14 during 2007 to summarize year-to-year trends or population dynamics. 64

80 Segment 14 - Sicklefin Chub / Sturgeon Season CPUE (fish/100 m) NE Year Figure 22. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 65

81 Segment 14 - Sicklefin Chub / Fish Community Season CPUE (fish/100 m) Year Figure 23. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using otter trawls in Segment 14 of the Missouri River during Fish Community season

82 Segment 14 - Sicklefin Chub / Fish Community Season CPUE (fish/net night) Mini-Fyke Net Year Figure 24. Mean annual catch per unit effort (+/- 2 SE) of sicklefin chub using mini-fyke nets in Segment 14 of the Missouri River during Fish Community season

83 Table 28. Total number of sicklefin chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 68

84 Table 29. Total number of sicklefin chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 69

85 Segment 14 - Sicklefin Chub Standard Samples N = Frequency All Samples N = Frequency mm Length Group Figure 25. Length frequency of sicklefin chub during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri Rive during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

86 Speckled Chub A total of 138 speckled chubs were captured in Segment 14 (Table 30). Most were collected with the otter trawl and only two were captured in mini-fyke nets. All speckled chubs were captured during Fish Community Season. In 2008, the overall otter trawl CPUE of speckled chub exhibited a marked increase from 2007 despite not having otter trawl samples from Sturgeon Season. Otter trawl CPUE was 0.49 fish per 100 m trawled in 2008, as compared to 0.26 in 2007 (Figure 27). The majority of speckled chubs were captured in otter trawls (99% of total catch). Most were found in SCCS macrohabitat (89% of the total catch relative to 2% of the total effort), followed by CHXO (7 % of the total catch relative to 21% of the effort) and ISB macrohabitat (4% of the total catch relative to 76% of the effort). A majority of these speckled chubs were captured in ITIP mesohabitat (89% of the total catch relative to 2% of the total effort) followed only by CHNB mesohabitat (11% of the total catch relative to 97% of the total effort). Only two speckled chubs were captured in mini-fyke nets (CPUE = 0.02 fish per net night; Appendix F6). Both speckled chubs were collected in ISB macrohabitat (41% of total effort) and BARS mesohabitat (99% of total effort) (Tables 30 and 31). Mini-fyke CPUE has decreased consistently since 2004 (2004 = 0.58; 2005 = 0.37; 2006 = 0.18, 2007 = 0.10; Figure 28). Only 42 speckled chubs were included in length frequency analyses. Length frequency diagrams reflect only a subsample of the total number of speckled chubs sampled due to a single subsample recording error. Only 25 lengths of 121 fish were recorded, which is a sub-sampling strategy used in this project for non-target species. Based on length frequencies of this truncated dataset, speckled chubs ranged in size from 10 mm to 75 mm. According to Herman et al. (2008b), YOY speckled chubs in Segment 14 of the Missouri River, on average, attain lengths of about 36 mm in their first year of life. Most speckled chubs measured were smaller than 25 mm suggesting that these were YOY fish. Because speckled chubs are short-lived (seldom living longer than one and a half years; Pflieger 1997), much of the reproduction is accomplished by age 1 fish that subsequently die after spawning. Similar to what was found in 2005, 2006 and 2007; it appears that only a small portion of speckled chubs measured were greater than 40 mm (Figure 29). 71

87 Segment 14 - Speckled Chub / Sturgeon Season CPUE (fish/100 m) NE Year Figure 26. Mean annual catch per unit effort (+/- 2 SE) of speckled chub using otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 72

88 Segment 14 - Speckled Chub / Fish Community Season CPUE (fish/100 m) Year Figure 27. Mean annual catch per unit effort (+/- 2 SE) of speckled chub in Segment 14 of the Missouri River during Fish Community season

89 Segment 14 - Speckled Chub / Fish Community Season CPUE (fish/net night) Mini-Fyke Net Year Figure 28. Mean annual catch per unit effort (+/- 2 SE) of speckled chub using mini-fyke nets in Segment 14 of the Missouri River during Fish Community season

90 Table 30. Total number of speckled chubs captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 75

91 Table 31. Total number of speckled chubs captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 76

92 Segment 14 - Speckled Chub 30 Standard Samples N = Frequency All Samples N = Frequency mm Length Group Figure 29. Length frequency of speckled chub during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri River during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

93 Sand Shiner Only 1 sand shiner was captured in Segment 14 during The total number of sand shiners captured in segment 14 has declined dramatically since 2005 (N = 216 in 2005, N = 57 in 2006 and N = 2 in 2007; Utrup et al. 2007). The sand shiner was captured in a mini-fyke net during Fish Community Season. It was captured in TRML macrohabitat (3% of total effort) and BARS mesohabitat (99% of total effort; Tables 32 and 33). Catch-per-unit-effort has declined considerably for both otter trawl and mini-fyke nets since a record high in 2005 (Figures 30-32). Sturgeon Season otter trawl CPUE has decreased from 0.01 fish per 100 m trawled in 2005 to in 2006 and 0.00 in 2007 and 2008 (Figure 30). Similarly, CPUE for mini-fyke nets has decreased from a high of 1.4 fish per net night in 2005 to 0.43 in 2006 and a low rate of fish per net night in 2008 (Figure 32, Appendix F6). There were not enough sand shiners (N < 50) captured in Segment 14 during 2007 to summarize year-to-year trends or population dynamics. Pflieger (1997) reported that the maximum life span of sand shiners is 3 years and that most do not reach sexual maturity until their second or third year. According to Dattilo et al. (2008a), on average, sand shiners in Segment 14 of the Missouri River reach about 50 mm in length during their first year. The sand shiner captured was 30 mm in length suggesting that it was YOY from 2008 (Figure 33). 78

94 Segment 14 - Sand Shiner / Sturgeon Season CPUE (fish/100 m) NE Year Figure 30. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. 79

95 Segment 14 - Sand Shiner / Fish Community Season CPUE (fish/100 m) Year Figure 31. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with otter trawls in Segment 14 of the Missouri River during Fish Community season

96 Segment 14 - Sand Shiner / Fish Community Season CPUE (fish/net night) Mini-Fyke Net Year Figure 32. Mean annual catch per unit effort (+/- 2 SE) of sand shiner with mini-fyke nets in Segment 14 of the Missouri River during Fish Community season

97 Table 32. Total number of sand shiners captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 82

98 Table 33. Total number of sand shiners captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 83

99 Segment 14 - Sand Shiner 2.0 Standard Samples N = Frequency All Samples N = Frequency mm Length Group Figure 33. Length frequency of sand shiner during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri Rive during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

100 Hybognathus spp. Very few Hybognathus spp. (HBNS, PNMW, SVMW, WSMW; Appendix A) have ever been captured in Segment 14 of the Missouri River. During 2008, field crews only collected one western silvery minnow in Segment 14. It was captured in a mini-fyke net (overall CPUE = fish per net night) in CHXO macrohabitat (24% of total effort) and BARS mesohabitat (99% of total effort; Tables 33 and 34). Since the beginning of standardized sampling in 2003, only 86 Hybognathus spp have ever been captured in Segment 14; 10 in 2003, 4 in 2004, 47 in 2005, 24 in 2006 and 0 in 2007 (Doyle and Starostka 2004, Doyle et al. 2005, Utrup et al. 2006, Utrup et al. 2007). In past years, Fish Community Season has experienced the highest catch rates and mini-fyke nets have been the most successful gear for capturing Hybognathus spp.; however, catch rates in mini-fyke nets have exhibited a general decrease since 2005 (CPUE = 0.12 in 2005, CPUE = 0.01 in 2006 and CPUE = 0.00 in 2007, Figure 36). HBNS were only captured in otter trawls during 2006 (Figure 34). Age keys are not definitive for Hybognathus species in the lower universe of the Missouri River. Based on the length of the fish, it is assumed that this is an age-0 fish. 85

101 Segment 14 - Hybognathus spp. / Sturgeon Season CPUE (fish/100 m) NE Year Figure 34. Mean annual catch per unit effort (+/- 2 SE) of Hybognathus spp. with otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water in Segment 14 during Sturgeon Season. 86

102 Segment 14 - Hybognathus spp. / Fish Community Season CPUE (fish/net night) Mini-Fyke Net Year Figure 36. Mean annual catch per unit effort (+/- 2 SE) of Hybognathus spp. with mini-fyke nets in Segment 14 of the Missouri River during Fish Community season

103 Table 34. Total number of Hybognathus spp. captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 88

104 Table 35. Total number of Hybognathus spp. captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 89

105 Segment 14 - Hybognathus spp. 5 Standard Samples N =1 4 3 Frequency All Samples N =1 4 3 Frequency mm Length Group Figure 37. Length frequency of Hybognathus spp. caught during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri River during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

106 Blue Sucker A total of 55 blue suckers were captured during 2008 in Segment 14. Nearly 15% of the blue suckers were captured in Sturgeon Season (N = 8, Tables 36 & 37). Blue sucker captures in gill nets have declined in Segment 14 since Gill netting efforts were incomplete for Segment 14 during Sturgeon Season due to flooding, which may have affected the catch rates of the gear. Otter trawls and trammel nets have also exhibited an overall decline in blue sucker catch rates since 2004, except 2008 (no effort) (Figures 38 and 39). By default, gill nets were the most successful gear for catching blue sucker during Sturgeon Season with an overall CPUE of 0.04 fish per net night (Appendix F-1). Most blue suckers were captured in ISB macrohabitat (75% total catch relative to 72% of total effort) followed by OSB macrohabitat (13% total catch relative to 2% of total effort) and CHXO macrohabitat (13% total catch relative to 24% of total effort, Table 36). Blue sucker were captured equally in both POOL and CHNB mesohabitat with 39% of total effort and 58% of total effort, respectively. During Fish Community Season, 47 blue suckers were captured (85% of total catch). As in previous years, trammel nets were the most effective gear at capturing blue sucker (60% of catch, N = 33). Since 2003, catch rates of blue sucker in 1-inch trammel nets have been relatively steady, averaging 0.08 fish per 100 m drifted. However, trammel net catch rates in 2008 exhibited a strong increase to 0.24 fish per 100 m drifted (Figure 41). Most blue suckers were collected in ISB macrohabitat (94% total catch relative to 81% of total effort) followed by CHXO macrohabitat (6% of total catch relative to 19% of total effort). All blue suckers captured in trammel nets were from CHNB mesohabitat. Otter trawls were the second most successful gear for capturing blue suckers in Segment 14 during Fish Community Season (N = 14, Table 36). Catch rates of blue suckers have been widely variable with otter trawls since As with trammel nets, a marked increase in catch since 2007 was noted (CPUE = 0.07 fish per 100 m trawled in 2008, CPUE = 0.08 in 2007; Figure 41). To date, blue suckers have not been captured in mini-fyke nets. According to LaBay et al. (2008), blue suckers in Segment 14 of the Missouri River reach a length of about 500 mm in their first year of life. Based on this knowledge, the majority of blue suckers captured in 2008 were older than age-1. This age data may be inaccurate, however, because aging methods for blue suckers produce highly variable results resulting in low reader 91

107 agreement (Steve LaBay, South Dakota Game and Parks, personal communication). Pflieger (1997) noted that blue suckers sexually mature at a size between 500 and 660 mm which is the most common size at capture during the Sturgeon Season. Using both sources of information (Pflieger 1997 and LaBay et al. 2008), we can assume that the majority of blue suckers captured in 2008 (86% of the total catch, N = 50) were older than age-1 and perhaps sexually mature (Figure 44). During 2008, field crews captured eight blue suckers that may have been YOY (< 500 mm), ranging in size from 230 mm to 500 mm. 92

108 Segment 14 - Blue Sucker / Sturgeon Season CPUE (fish/100 m) CPUE (fish/net night) Gill Net NE Year Figure 38. Mean annual catch per unit effort (+/- 2 SE) of blue sucker with gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water in Segment 14 during Sturgeon Season. 93

109 Segment 14 - Blue Sucker / Sturgeon Season CPUE (fish/100 m) Inch Trammel Net NE Year Figure 39. Mean annual catch per unit effort (+/- 2 SE) of blue sucker with 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water in Segment 14 during Sturgeon Season. 94

110 Segment 14 - Blue Sucker / Fish Community Season CPUE (fish/100 m) CPUE (fish/100 m) InchTrammel Net Year Figure 41. Mean annual catch per unit effort (+/- 2 SE) of blue sucker using otter trawls and 1-inch trammel nets in Segment 14 of the Missouri River during Fish Community season

111 Table 36. Total number of blue suckers captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 96

112 Table 37. Total number of blue suckers captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 97

113 Segment 14 - Blue Sucker 8 Standard Samples N =55 6 Frequency All Samples N = 58 6 Frequency mm Length Group Figure 44. Length frequency of blue sucker during Sturgeon Season (fall through spring; black bars) and Fish Community season (summer; white bars) in Segment 14 of the Missouri River during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

114 Sauger A total of 19 sauger were captured in Segment 14. The majority of saugers were captured during sturgeon season (79%; N = 15; Tables 38-39). As previously mentioned, sampling efforts were unfinished in Segment 14 during Sturgeon Season in 2008 due to high water. Though gill netting effort was incomplete, this gear was effective at capturing sauger during Sturgeon Season (CPUE = 0.07 fish per net night; Figures 45 and 46). Catch rates of sauger were notably higher in 2008 than in Overall, catch rates of sauger have steadily declined since 2004, however catch rates in 2008 returned to 2006 levels (CPUE = 0.07). Most saugers were captured in TRML macrohabitat (80% total catch relative to 2% of total effort) followed by CHXO macrohabitat (7% total catch relative to 24% of total effort) and ISB macrohabitat (13% total catch relative to 72% of total effort, Table 36). Saugers were more often captured in TLWG mesohabitat followed by CHNB mesohabitat with 80% and 20% of total effort, respectively (Tables 39 and 40). During Fish Community Season, 4 saugers were captured (21% of total catch). In 2008 Fish Community Season, otter trawls were the most effective gear at capturing sauger (75% of catch, N = 3). Catch rates of sauger have been widely variable with otter trawls since A strong increase in catch compared to 2007 was indicated (CPUE = 0.02 fish per 100 m trawled in 2008, CPUE = in 2007; Figure 48). All saugers captured in otter trawls were from CHXO macrohabitat (relative to 21% of total effort) and CHNB mesohabitat (relative to 97% of total effort). Only one sauger was captured in 1-inch drifted trammel nets during Fish Community Season. Catch rates of sauger in trammel nets have been consistently low since The catch rate was slightly improved from 2007 (CPUE = 0.01 fish per 100 m drifted in 2008, in 2007; Figure 48). The sauger captured in the trammel net was found in CHXO macrohabitat (relative to 19 % of total effort) and CHNB mesohabitat (relative to 100% of total effort). No saugers were captured in mini-fyke nets during 2008 (Figure 49). There were not enough sauger (N < 50) captured in Segment 14 during 2008 to summarize yearto-year trends or population dynamics. Based on age structure described by Pflieger (1997) and Dattilo et al. (2008b), saugers in Segment 14 of the Missouri River reach age-1 at about 200 mm and age-2 at about 280 mm. Given these benchmarks, all saugers captured during 2008 from Segment 14 were older than age-2 (Figure 51). 99

115 Segment 14 - Sauger / Sturgeon Season CPUE (fish/100 m) CPUE (fish/net night) Gill Net NE Year Figure 45. Mean annual catch per unit effort (+/- 2 SE) of sauger using gill nets and otter trawls in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water in Segment 14 during Sturgeon Season. 100

116 Segment 14 - Sauger / Sturgeon Season CPUE (fish/100 m) Inch Trammel Net NE Year Figure 46. Mean annual catch per unit effort (+/- 2 SE) of sauger using 1-inch trammel nets in Segment 14 of the Missouri River during Sturgeon Season NE = no effort due to high water in Segment 14 during Sturgeon Season. 101

117 Segment 14 - Sauger / Fish Community Season CPUE (fish/100 m) CPUE (fish/100 m) Inch Trammel Net Year Figure 48. Mean annual catch per unit effort (+/- 2 SE) of sauger using otter trawls and 1-inch trammel nets in Segment 14 of the Missouri River during Fish Community season

118 Segment 14 - Sauger / Fish Community Season CPUE (fish/net night) Mini-Fyke Net Year Figure 49. Mean annual catch per unit effort (+/- 2 SE) of sauger using mini-fyke nets in Segment 14 of the Missouri River during Fish Community season

119 Table 38. Total number of saugers captured for each gear during each season and the proportion caught within each macrohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Gear 1-Inch Trammel Net N Macrohabitat a BRAD CHXO CONF DEND DRNG ISB OSB SCCL SCCS SCN TRIB TRML TRMS WILD Sturgeon Season (Fall through Spring) Gill Net (24) (72) (2) (1) (2) 0 0 Fish Community Season (Summer) 1-Inch Trammel Net Mini-Fyke Net (19) (81) (24) (1) 0 0 (41) (25) (1) (2) 0 0 (3) (3) (21) (76) 0 0 (2) 0 0 (1) 0 0 a Habitat abbreviations and definitions presented in Appendix B. 104

120 Table 39. Total number of saugers captured for each gear during each season and the proportion caught within each mesohabitat type in Segment 14 of the Missouri River during The percent of total effort for each gear in each habitat is presented on the second line of each gear type. N-E indicates the habitat is non-existent in the segment. Mesohabitat a Gear N BARS CHNB DTWT ITIP POOL TLWG 1-Inch Trammel Net Sturgeon Season (Fall through Spring) Gill Net (58) 0 (1) (39) (2) 1-Inch Trammel Net Mini-Fyke Net Fish Community Season (Summer) (100) (99) (1) (97) 0 (2) 0 (1) a Habitat abbreviations and definitions presented in Appendix B. 105

121 Segment 14 - Sauger 6 Standard Samples N = 19 4 Frequency All Samples N = 19 4 Frequency mm Length Group Figure 51. Length frequency of sauger during Sturgeon Season (fall through spring; black bars and Fish Community season (summer ; white bars) in Segment 14 of the Missouri River during Standard Samples include standard gears, random bends and random subsamples. Additionally, All Samples include all non-random and wild samples collected during

122 Missouri River Fish Community This section covers the following objectives from the Pallid Sturgeon Monitoring and Assessment Program: Objective 6. Document annual results and long-term trends of all non-target species population abundance and geographic distribution throughout the Missouri River system, where sample size is greater than fifty individuals. During 2008, 7,199 total fish were captured in Segment 14 of the Missouri River, 6,551 with standard gear in random bends. Standard gears captured 65 species with shovelnose sturgeon comprising the largest percentage of the total catch (27.8%; N = 1,822), followed by blue catfish (18.4%; N = 1,206) and gizzard shad (10.6%; N = 692). The next abundant species were: emerald shiner (7.4%; N = 486), red shiner (6.7%, N = 439), channel catfish (5.6%, N = 367), unidentified Ictalurus (3.5%, N = 229), unidentified minnow (2.2%, N = 146), speckled chub (2.1%, N = 138), unidentified Lepomis (2.0%, N = 130) and freshwater drum (1.7%, N = 116). Also notable were goldeye (1.1%, N = 73), bluegill (0.9%, N = 60) and blue sucker (0.8%, N = 55). The 9 target species accounted for 31.8% of the total catch with each contributing to the total of target species in the following order of abundance: shovelnose sturgeon (87.3%; N = 1,822), speckled chub (6.6%; N = 138), blue sucker (2.6%; N = 55), sicklefin chub (1.6%; N = 33), sauger (0.9%; N = 19), pallid sturgeon (0.4%; N = 9), sturgeon chub (0.3%; N = 7), sand shiner (0.05%; N = 1) and Hybognathus spp. (0.05%; N = 1). Twenty-three species were captured fewer than five times during the entire sample year (Appendix F). Gill nets captured 25 species and were most effective at capturing shovelnose sturgeon (86.9% of the gill net catch; N = 1229), with an average overall CPUE of 5.6 fish per net night (Appendix F1). Blue catfish (3.0%; N = 43), longnose gar (1.7%; N = 24) and sauger (1.1%; N = 15) were the next most abundant fish species collected in gill nets (mean overall CPUE = 0.91, 0.11 and 0.07 fish per net night, respectively; Appendix F1). Gill nets were only used during Sturgeon Season. It is notable that two paddlefish and two lake sturgeon were also captured in gill nets from Segment 14 during

123 One-inch trammel nets, fished only during Fish Community Season in 2008, captured a total of 11 species with shovelnose sturgeon making up the majority of the catch (76.7%; N = 412; mean overall CPUE = fish per 100 m drifted). Other large bodied fish, such as blue catfish (11.0%; N = 59; mean overall CPUE = 0.42 fish per 100 m drifted) and blue suckers (6.1%; N = 33; mean overall CPUE = 0.24 fish per 100 m drifted), were also captured effectively with 1-inch trammel nets (Appendix F2). Otter trawls, also only used during Fish Community Season, captured 35 species of fish. Blue catfish were captured most frequently (46.7%; N = 1,063; mean overall CPUE = 6.1 fish per 100 m trawled). Channel catfish (11.6%; N = 267; mean overall CPUE = 1.7 fish per 100 m trawled), young-of-year catfish (9.9%; N = 225; mean overall CPUE = 1.5 fish per 100 m trawled) and shovelnose sturgeon (7.6 %; N = 174; mean overall CPUE = 0.7 fish per 100 m trawled). Otter trawls were also the most effective gear for capturing chub species in Segment 14, such as speckled chub (6.0%; N = 136; mean overall CPUE = 0.49 fish per 100 m trawled), sicklefin chub (1.5%; N = 33; mean overall CPUE = 0.18 fish per 100 m trawled) and sturgeon chub (0.3%; N = 7; mean overall CPUE 0.04 fish per 100 m trawled; Appendix F4). Mini-fyke nets captured 41 species of fish in Segment 14 with gizzard shad making up the majority of the total catch (28.7%; N = 634) with emerald shiners, red shiners and unidentified minnows making up 21.5%, 19.2% and 6.6% of the total mini-fyke catch, respectively (Appendix F6). Of the 41 species captured by mini-fyke nets, 18 species were not captured with any other gear type. Only eight Asian carp were captured in Segment 14 in Asian carp are rarely captured at young life stages with our standard gear, however anecdotal information through collections using other gear types from related projects (e.g., push trawl, electrofishing and hoop nets) suggests these species are increasing in abundance throughout the lower Missouri River. Additional sampling gear and improved sampling techniques need to be further investigated to help document the population dynamics of these invasive exotic species. 108

124 Discussion Young-of-year (0-250 mm) or sub-stock size (< 330 mm) pallid sturgeon have never been captured in Segment 14 as part of standard sampling. Of the 22 pallid sturgeon that were captured during 2008, five were stock size and 16 were quality size and above. In addition to the 22 pallid sturgeon, two hybrid sturgeon were also captured during Six hatchery origin and four unmarked (presumed wild) pallid sturgeon were captured near a confluence during Nine of these fish were captured at the mouth of the Osage River, during the middle of April when the Osage and Missouri Rivers are running full. These pallids were potentially using the slack water at the mouth of the Osage River as refuge from the high flows. One of these ten pallids was captured across from the mouth of the Gasconade River on the channel side of a large sandbar that lies between two wing dikes. No pallid sturgeon were captured at the confluence with the Mississippi River, as this area was not part of our standard sampling in However, pallid captures from past years suggests that this confluence is also an important feature in Segment 14 in terms of both wild and hatchery origin pallid sturgeon immigrating and emigrating between the Missouri and Mississippi Rivers. Four quality size and greater pallid sturgeon were captured on the side or tail of channel sandbars and on the channel border along the current seam of inside bends. This corresponds with telemetry data provided by USGS/CERC which illustrates that adult sturgeon move along the current seam as water temperature begins to rise, presumably to migrate upstream to spawn (Aaron Delonay, U.S. Geological Survey, personal communication). Two pallid sturgeon were captured behind rootless dikes. The two largest pallid sturgeon captured were 988 mm and 931 mm. Both were captured at the mouth of the Osage River. Sixteen of the 22 pallid sturgeon detected in Segment 14 were recaptured from hatchery stockings. The recaptured fish ranged in size from 485 mm to 896 mm. In Segment 14, pallid sturgeon were stocked at St. Charles, Washington and Hermann in 1994 and Fish stocked at these sites had coded wire tags as primary marks and dangler tags as secondary marks. While none of the recaptured pallid sturgeon had danglers, many of the larger fish had coded wire tags. Due to the number of years at large and environmental conditions, these fish have most likely shed the dangler tag. Based on the size ranges of pallid sturgeon with coded wire tags captured, 109

125 evidence of survivorship from these stockings is present. Recaptured pallid sturgeon also indicate that fish are dispersing from stocking sites. Four pallid sturgeon were captured from stockings in Segment 13, two fish were from stockings in Segment 10, one fish was from Segment 9 and another fish was from a stocking site 40 miles upstream in the Platte River. Trotlines have proven to be an exceptional gear for catching all sturgeon species. More than half of the pallid sturgeon captured in Segment 14 were caught on trotlines. The major increase in pallid sturgeon captures in 2008 can be attributed to the addition of higher effort with trotlines. The development of this gear in Segment 14 has led to a notable increase in sturgeon captures. Seventeen lake sturgeon, a state endangered fish in Missouri, were captured and 518 shovelnose sturgeon were captured on trotlines in Segment 14 in This gear is being implemented into the standard sampling protocol as an evaluation gear for 2009 and preliminary data suggests 2009 captures will be even greater. A more in-depth evaluation of the trotline captures in lower segments of the Missouri River (Segments 7 14) is currently in progress. This gear is not only effective for capturing target species but also extremely cost effective for use as monitoring tool. It is also notable that trotlines can safely be used at high water stages and flows when other gears cannot be deployed. Previous years catch with standard gears have been fairly consistent but low. The addition of trotlines during fall and spring sampling in 2008 led to a total catch for the year eclipsing the entire sampling period from 2003 to This gear is being implemented into the standard sampling protocol as an evaluation gear for 2009 and preliminary data suggests 2009 captures will be even higher. A more in depth evaluation of the trotline captures in lower segments of the Missouri River (Segments 7 14) is in progress. Notable Trends The most notable trend is the apparent decline in target species in Segment 14. At the very least, there is a decline in both abundance and catch rate for all target species except shovelnose and pallid sturgeon. In many cases, there has been a decline in both abundance and catch rate since Conversely, annual catch of pallid sturgeon has increased since 2003 due to the influence of hatchery stocked fish. At present, there are nearly 80,000 hatchery reared pallid sturgeon 110

126 potentially at large in the lower Missouri River below Gavins Point Dam. The influence of the stocking program will be evident when we compare hatchery versus wild pallid sturgeon abundance through time. Catch rates of shovelnose sturgeon remained relatively stable in 2008 compared to 2007, despite incomplete sampling efforts due to extreme and sustained high water events. However, an overall decline in catch rates of shovelnose sturgeon has been documented since Gill nets showed a decline in catch rates from 2007, though the catch rate is similar to rates experienced in 2004 through Catch rates of 1-inch trammel nets during Fish Community Season illustrated a marked increase from years 2003 and Otter trawls from Fish Community Season also exhibited a modest increase in shovelnose sturgeon catch rates over the two previous years. Otter trawls and trammel nets have been found to be the least biased sampling methods available for detecting trends in shovelnose sturgeon because they are not as influenced from seasonal migrations or winter aggregations. Otter trawls have an advantage, however, because these nets are not biased to larger (>200 mm) fish. Drought conditions from 2003 through 2005 may have played a role in the decline in shovelnose sturgeon catch rates. The last two years have been rather wet for the lower Missouri River, possibly triggering spawning behavior and causing the increase in catch rates during One issue that may be effecting the shovelnose sturgeon population in Segment 14 may be commercial fishing. Commercial harvest of sturgeon in Segment 14 is a legitimate concern. Belly scars (egg checks) from knife probes in shovelnose sturgeon suggest that commercial fishermen may be harvesting more fish than are documented from harvest reports. The differences in catch rates between Segment 13 and 14 suggest that Segment 14, which is closer to the Mississippi River, receives more fishing pressure than other segments of the Missouri River. In the past this was further confounded by the use of many commercial fisherman from the Mississippi River (Tennessee and Arkansas) traveling up the Missouri River in early spring (before seasons open on the Mississippi River) to harvest Missouri River sturgeon roe. Since 2005, however, non-residents are no longer allowed to fish in the lower Missouri River. Because of Segment 14 s proximity to the Mississippi River and the migrational nature of the pallid sturgeon, there is still reason for concern. Anecdotal information from federal law enforcement officers indicate commercial fishermen from other states have already been observed fishing (legally and illegally) in the Mississippi River near the confluence. Over the past several years, 111

127 there have been numerous violations on the Mississippi River where pallid sturgeon have been mistaken for shovelnose and been found in the creels of commercial fishermen. Shovelnose sturgeon numbers will most likely continue to decline in Segment 14, due to the rising prices of caviar. Documentation of egg check scars on two pallid sturgeon in Segment 14, one during 2006 and another during 2007, suggests that uneducated or unscrupulous commercial fishers may harvest pallid sturgeon roe along with the shovelnose sturgeon. Declines in abundance and catch rates were detected for all target species in Segment 14 in Since 2005, there has been a decline of all three target chub species as well as sand shiners in Segment 14. It may be important to look at how environmental conditions in the river could be impacting these species. Few Hybognathus species have been captured in Segment 14 from the inception of the monitoring program. Overall abundance and capture rates of blue suckers have dramatically declined since The capture of young blue suckers (< 200 mm) has always been minimal in Segment 14 and in 2008 field crews were not able to capture any YOY blue suckers. In all, abundances and catch rates of all three target chub species, sand shiners, blue suckers and sauger were at all time lows during Declines in these species may be associated with the dike notching program, started in 2003, which may be inadvertently destroying important pseudo-backwater habitat needed for macroinvertebrate production and rearing habitat. Also, low flows indicated in the BiOp have not occurred as a result of the dike notching program. These flows may be an important component of the life history of these fishes. Channel and blue catfish have been among the most abundant fish captured in Segment 14 since the implementation of the standard sampling program in Trends for these two non-target species may be as important to the health of the Missouri River and pallid sturgeon as the target species discussed in detail within this report. Otter trawls have been the best and most consistent gear for describing the population of both catfish species over time. Despite the decline in target species CPUE over time, channel catfish CPUE with otter trawls in Segment 14 has increased from 0.95 fish per 100 m trawled in 2004 to 1.65 fish in 2008 (Doyle et al. 2005). Catch rates for blue catfish in otter trawls, have also increased from 5.18 fish per 100 m trawled in 2005 to 5.63 fish in 2008 (Doyle et al. 2005). 112

128 The life histories of pallid and shovelnose sturgeon may be dependent on the target species in this study, as well as other native fish, such as catfish. While one year cannot document population trends, fluctuations in populations over time is of great importance. Because of this, changes that are evident within the fish populations of Segment 14 will need to be monitored closely in future years. 113

129 Acknowledgments Special thanks to the staff of the U.S. Fish and Wildlife Service, Columbia National Fish & Wildlife Conservation Office (Columbia NFWCO), especially Cliff Wilson, Courtney Culler, Marie Delatour and Jeremiah Smith for data collection in the field and in the lab, scientific expertise in data interpretation and dedication to the recovery of the federally endangered pallid sturgeon. Many thanks go to Debra Turner, Columbia NFWCO Administrative Technician, for her assistance with our many office issues. Funding for this project is provided by the U. S. Army Corps of Engineers, Omaha District. Appreciation is extended to Yan Hong, Lauren Williamson, Vince Travnichek and the staff at the Missouri Department of Conservation s Chillicothe Office for maintaining the database and providing and summarizing the data for this report. Thanks to Mark Drobish for his flexibility and efforts in facilitating discussion and incorporating changes in the adaptive process of this project. Thanks to Mark Wildhaber for his contributions in project design and his willingness to help in the protocol development process. Craig Paukert has been providing data analyses that are becoming important tools as we continue to refine our sampling efforts. Aaron Delonay of USGS/CERC continues to be an asset to our sampling efforts; providing locations and general information regarding movements and habitat use of this elusive fish. 114

130 References American Fisheries Society (AFS) Common and scientific names of fishes from the United States and Canada. Special Publication 20, American Fisheries Society, Bethesda, Maryland. Bryan, J. L., M. L. Wildhaber, D. Gladish, S. Holan, and M. Ellerseick The power to detect trends in Missouri River fish populations within the Pallid Sturgeon Population Assessment Program. Final report to the Army Corp of Engineers. 419 p. Carlson, D.M., W.L. Pflieger, L. Trial, and P.S. Haverland Distribution, biology and hybridization of Scaphirhynchus albus and S. platorynchus in the Missouri and Mississippi Rivers. Environmental Biology of Fishes 14(1): Dattilo, J.E., R.R. Dirnberger, P.T. Horner, D.J.Niswonger, M.L. Miller, and V.H.Travnichek. 2008a. Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for sand shiner (Notropis stramineus). Missouri Department of Conservation. Chillicothe, MO. Dattilo, J.E., R.R. Dirnberger, P.T. Horner, D.J.Niswonger, M.L. Miller, and V.H.Travnichek. 2008b. Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for sauger (Sander canadensis). Missouri Department of Conservation. Chillicothe, MO. Dieterman, D.J. and D.L. Galat Large-scale factors associated with sicklefin chub distribution in the Missouri and lower Yellowstone Rivers. Transactions of the American Fisheries Society. 133: Doyle, W. and A. Starostka, Annual Report: Lower Missouri River Pallid Sturgeon Monitoring and Population Assessment Project. United States Fish and Wildlife Service Columbia Missouri Fishery Resources Office. Doyle, W. and A. Starostka Annual Report: Lower Missouri River Pallid Sturgeon Monitoring and Population Assessment Project, Segments 13 and 14. United States Fish and Wildlife Service, Columbia Missouri Fishery Resources Office. Doyle, W., N. Frohnauer, C. Lee, A. Plauck, N. Utrup, and T. Hill Pallid sturgeon population assessment project and associated fish community monitoring for the Missouri river: segments 13 and Annual Report. U.S. Fish and Wildlife Service, Columbia, MO. Drobish, M.R. (editor), Missouri River Standard Operating Procedures for Sampling and Data Collection, Volume 1.2. U.S. Army Corps of Engineers, Omaha District, Yankton, SD. Grady, J.M. and J. Milligan Status of selected Cyprinid species at historic lower Missouri River sampling sites. United States Fish and Wildlife Service, Columbia Fisheries Resources Office, Columbia, MO. Grady, J.M., J. Milligan, C. Gemming, D. Herzog, G. Mestle, and R.J. Sheehan Pallid 115

131 and shovelnose sturgeons in the Lower Missouri and Middle Mississippi Rivers. Final Report for MICRA. Herman, P.A., A.T. Plauck, N.J. Utrup, and T.D. Hill. 2008a. Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for sicklefin chub (Macrhybopsis meeki). U.S. Fish and Wildlife Service. Columbia, MO. Herman, P.A., A.T. Plauck, N.J. Utrup, and T.D. Hill. 2008b. Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for speckled chub (Macrhybopsis aestivalis). U.S. Fish and Wildlife Service. Columbia, MO. Keenlyne, K.D. and P.D. Evenson Standard and Relative Weight for the Pallid Sturgeon, Scaphirhynchus albus. Proceedings of the South Dakota Academy of Sciences 2: LaBay, S., J. Kral, and S. Stukel Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for blue sucker (Cycleptus elongates). South Dakota Department of Game, Fish and Parks. Yankton, SD. National Research Council The Missouri River Ecosystem: Exploring the Prospects for Recovery. National Academy Press, Washington, D. C. Pflieger, W.L Revised Edition. The Fishes of Missouri. Missouri Department of Conservation. Jefferson City, MO Pflieger, W.L. and T.B. Grace Changes in the Fish Fauna of the Lower Missouri River, , pp In: Community and Evolutionary Ecology of North American Stream Fishes. W.J. Matthews and D.C. Heins (eds.). Univ. of Okla. Press, Norman. Quist, M.C., C.S. Guy, and P. Braaten Standard weight (Ws) equation and length categories for shovelnose sturgeon. North American Journal of Fisheries Management 18: Sheehan, R.J., R.C. Heidinger, P.S. Wills, M.A. Schmidt, G.A. Conover, and K.L. Hurley Guide to the Pallid Sturgeon Shovelnose Sturgeon Character Index (CI) and Morphometric Character Index (mci). SIUC Fisheries Bulletin No. 14, Southern Illinois University, Carbondale, Illinois. 16pp. Shuman, D.A., D.W. Willis, and S.C. Krentz Application of a length categorizing system for pallid sturgeon (Scaphirhynchus albus). Journal of Freshwater Ecology. 21: Steffensen, K. and M. Hamel Pallid sturgeon population assessment and associated fish community monitoring for the Missouri River. Three year summary age and growth report for shovelnose sturgeon (Scaphirhynchus platorynchus). Nebraska Game and Parks Commission. Lincoln, NE. Utrup, N., W. Doyle, C. Lee, A. Plauck, and T. Hill Pallid sturgeon population 116

132 assessment project and associated fish community monitoring for the Missouri River: Segment Annual Report. U.S. Fish and Wildlife Service. Columbia, MO. Utrup, N., W. Doyle, C. Lee, A. Plauck, and T. Hill Pallid sturgeon population assessment project and associated fish community monitoring for the Missouri River: Segment Annual Report. U.S. Fish and Wildlife Service. Columbia, MO. Utrup, N., W. Doyle, C. Lee, A. Plauck, and T. Hill Pallid sturgeon population assessment project and associated fish community monitoring for the Missouri River: Segment Annual Report. U.S. Fish and Wildlife Service. Columbia, MO. U.S. Fish and Wildlife Service Biological Opinion on the Operation of the Missouri River Main Stem Reservoir System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project and Operation of the Kansas River Reservoir System. Fort Snelling, MN. 117

133 APPENDICES 118

134 Appendix A. Phylogenetic list of Missouri River fishes with corresponding letter codes used in the long-term pallid sturgeon and associated fish community sampling program. The phylogeny follows that used by the American Fisheries Society, Common and Scientific Names of Fishes from the United States and Canada, 5 th edition. Asterisks and bold type denote targeted native Missouri River species. Scientific name Common name Letter Code CLASS CEPHALASPIDOMORPHI-LAMPREYS ORDER PETROMYZONTIFORMES Petromyzontidae lampreys Ichthyomyzon castaneus Chestnut lamprey CNLP Ichthyomyzon fossor Northern brook lamprey NBLP Ichthyomyzon unicuspis Silver lamprey SVLP Ichthyomyzon gagei Southern brook lamprey SBLR Petromyzontidae Unidentified lamprey ULY Petromyzontidae larvae Unidentified larval lamprey LVLP CLASS OSTEICHTHYES BONY FISHES ORDER ACIPENSERIFORMES Ascipenseridae sturgeons Acipenser fulvescens Lake sturgeon LKSG Scaphirhynchus spp. Unidentified Scaphirhynchus USG Scaphirhynchus albus Pallid sturgeon PDSG* Scaphirhynchus platorynchus Shovelnose sturgeon SNSG* S. albus X S. platorynchus Pallid-shovelnose hybrid SNPD Polyodontidae paddlefishes Polyodon spathula Paddlefish PDFH ORDER LEPISOSTEIFORMES Lepisosteidae gars Lepisosteus oculatus Spotted gar STGR Lepisosteus osseus Longnose gar LNGR Lepisosteus platostomus Shortnose gar SNGR ORDER AMMIFORMES Amiidae bowfins Amia calva Bowfin BWFN ORDER OSTEOGLOSSIFORMES Hiodontidae mooneyes Hiodon alosoides Goldeye GDEY Hiodon tergisus Mooneye MNEY ORDER ANGUILLIFORMES Anguillidae freshwater eels Anguilla rostrata American eel AMEL 119

135 Appendix A. (continued). Scientific name Common name Lettter Code ORDER CLUPEIFORMES Clupeidae herrings Alosa alabame Alabama shad ALSD Alosa chrysochloris Skipjack herring SJHR Alosa pseudoharengus Alewife ALWF Dorosoma cepedianum Gizzard shad GZSD Dorosoma petenense Threadfin shad TFSD D. cepedianum X D. petenense Gizzard-threadfin shad hybrid GSTS ORDER CYPRINIFORMES Cyprinidae carps and minnows Campostoma anomalum Central stoneroller CLSR Campostoma oligolepis Largescale stoneroller LSSR Carassus auratus Goldfish GDFH Carassus auratus X Cyprinius carpio Goldfish-Common carp hybrid GFCC Couesis plumbens Lake chub LKCB Ctenopharyngodon idella Grass carp GSCP Cyprinella lutrensis Red shiner RDSN Cyprinella spiloptera Spotfin shiner SFSN Cyprinus carpio Common carp CARP Erimystax x-punctatus Gravel chub GVCB Hybognathus argyritis Western slivery minnow WSMN* Hybognathus hankinsoni Brassy minnow BSMN Hybognathus nuchalis Mississippi silvery minnow SVMW Hybognathus placitus Plains minnow PNMW* Hybognathus spp. Unidentified Hybognathus HBNS* Hypophthalmichthys molitrix Silver carp SVCP Hypophthalmichthys nobilis Bighead carp BHCP Luxilus chrysocephalus Striped shiner SPSN Luxilus cornutus Common shiner CMSN Luxilus zonatus Bleeding shiner BDSN Lythrurus unbratilis Western redfin shiner WRFS Macrhybopsis aestivalis Speckled chub SKCB* Macrhybopsis gelida Sturgeon chub SGCB* Macrhybopsis meeki Sicklefin chub SFCB* Macrhybopsis storeriana Silver chub SVCB M. aestivalis X M. gelida Speckled-Sturgeon chub hybrid SPST M. gelida X M. meeki Sturgeon-Sicklefin chub hybrid SCSC Macrhybopsis spp. Unidentified chub UHY Margariscus margarita Pearl dace PLDC Mylocheilus caurinus Peamouth PEMT Nocomis biguttatus Hornyhead chub HHCB Notemigonus crysoleucas Golden shiner GDSN Notropis atherinoides Emerald shiner ERSN Notropis blennius River shiner RVSN Notropis boops Bigeye shiner BESN Notropis buchanani Ghost shiner GTSN Notropis dorsalis Bigmouth shiner BMSN Notropis greenei Wedgespot shiner WSSN 120

136 Appendix A. (continued). Scientific name Common name Letter Code Cyprinidae carps and minnows Notropis heterolepsis Blacknose shiner BNSN Notropis hudsonius Spottail shiner STSN Notropis nubilus Ozark minnow OZMW Notropis rubellus Rosyface shiner RYSN Notropis shumardi Silverband shiner SBSN Notropis stilbius Silverstripe shiner SSPS Notropis stramineus Sand shiner SNSN* Notropis topeka Topeka shiner TPSN Notropis volucellus Mimic shiner MMSN Notropis wickliffi Channel shiner CNSN Notropis spp. Unidentified shiner UNO Opsopoeodus emiliae Pugnose minnow PNMW Phenacobius mirabilis Suckermouth minnow SMMW Phoxinus eos Northern redbelly dace NRBD Phoxinus erythrogaster Southern redbelly dace SRBD Phoxinus neogaeus Finescale dace FSDC Pimephales notatus Bluntnose minnow BNMW Pimephales promelas Fathead minnow FHMW Pimephales vigilas Bullhead minnow BHMW Platygobio gracilis Flathead chub FHCB P. gracilis X M. meeki Flathead-sicklefin chub hybrid FCSC Rhinichthys atratulus Blacknose dace BNDC Rhinichthys cataractae Longnose dace LNDC Richardsonius balteatus Redside shiner RDSS Scardinius erythrophtalmus Rudd RUDD Semotilus atromaculatus Creek chub CKCB Unidentified Cyprinidae UCY Unidentified Asian Carp UAC Catostomidae - suckers Carpiodes carpio River carpsucker RVCS Carpiodes cyprinus Quillback QLBK Carpiodes velifer Highfin carpsucker HFCS Carpiodes spp. Unidentified Carpiodes UCS Catostomus catostomus Longnose sucker LNSK Catostomus commersoni White sucker WTSK Catostomus platyrhyncus Mountain sucker MTSK Catastomus spp. Unidentified Catastomus spp. UCA Cycleptus elongates Blue sucker BUSK* Hypentelium nigricans Northern hog sucker NHSK Ictiobus bubalus Smallmouth buffalo SMBF Ictiobus cyprinellus Bigmouth buffalo BMBF Ictiobus niger Black buffalo BKBF Ictiobus spp. Unidentified buffalo UBF Minytrema melanops Spotted sucker SPSK Moxostoma anisurum Silver redhorse SVRH Moxostoma carinatum River redhorse RVRH Moxostoma duquesnei Black redhorse BKRH Moxostoma erythrurum Golden redhorse GDRH Moxostoma macrolepidotum Shorthead redhorse SHRH Moxostoma spp. Unidentified redhorse URH 121

137 Appendix A. (continued). Scientific name Common name Letter Code Catostomidae - suckers Unidentified Catostomidae UCT ORDER SILURIFORMES Ictaluridae bullhead catfishes Ameiurus melas Black bullhead BKBH Ameiurus natalis Yellow bullhead YLBH Ameiurusnebulosus Brown bullhead BRBH Ameiurus spp. Unidentified bullhead UBH Ictalurus furcatus Blue catfish BLCF Ictalurus punctatus Channel catfish CNCF I. furcatus X I. punctatus Blue-channel catfish hybrid BCCC Ictalurus spp. Unidentified Ictalurus spp. UCF Noturus exilis Slender madtom SDMT Noturus flavus Stonecat STCT Noturus gyrinus Tadpole madtom TPMT Noturus nocturnes Freckled madtom FKMT Pylodictis olivaris Flathead catfish FHCF ORDER SALMONIFORMES Esocidae - pikes Esox americanus vermiculatus Grass pickerel GSPK Esox lucius Northern pike NTPK Esox masquinongy Muskellunge MSKG E. lucius X E. masquinongy Tiger Muskellunge TGMG Umbridae - mudminnows Umbra limi Central mudminnow MDMN Osmeridae - smelts Osmerus mordax Rainbow smelt RBST Salmonidae - trouts Coregonus artedi Lake herring or cisco CSCO Coregonus clupeaformis Lake whitefish LKWF Oncorhynchus aguabonita Golden trout GDTT Oncorhynchus clarki Cutthroat trout CTTT Oncorhynchus kisutch Coho salmon CHSM Oncorhynchus mykiss Rainbow trout RBTT Oncorhynchus nerka Sockeye salmon SESM Oncorhynchus tshawytscha Chinook salmon CNSM Prosopium cylindraceum Bonniville cisco BVSC Prosopium williamsoni Mountain whitefish MTWF Salmo trutta Brown trout BNTT Salvelinus fontinalis Brook trout BKTT Salvelinus namaycush Lake trout LKTT Thymallus arcticus Arctic grayling AMGL 122

138 Appendix A. (continued). Scientific name Common name Letter Code ORDER PERCOPSIFORMES Percopsidae trout-perches Percopsis omiscomaycus Trout-perch TTPH ORDER GADIFORMES Gadidae - cods Lota lota Burbot BRBT ORDER ATHERINIFORMES Cyprinodontidae - killifishes Fundulus catenatus Northern studfish NTSF Fundulus daphanus Banded killifish BDKF Fundulus notatus Blackstripe topminnow BSTM Fundulus olivaceus Blackspotted topminnow BPTM Fundulus sciadicus Plains topminnow PTMW Fundulus zebrinus Plains killifish PKLF Poeciliidae - livebearers Gambusia affinis Western mosquitofish MQTF Atherinidae - silversides Labidesthes sicculus Brook silverside BKSS ORDER GASTEROSTEIFORMES Gasterosteidae - sticklebacks Culea inconstans Brook stickleback BKSB ORDER SCORPAENIFORMES Cottidae - sculpins Cottus bairdi Mottled sculpin MDSP Cottus carolinae Banded sculpin BDSP ORDER PERCIFORMES Percichthyidae temperate basses Morone Americana White perch WTPH Morone chrysops White bass WTBS Morone mississippiensis Yellow bass YWBS Morone saxatilis Striped bass SDBS M. saxatilis X M. chrysops Striped-white bass hybrid SBWB Centrarchidae - sunfishes Ambloplites rupestris Rock bass RKBS Archoplites interruptus Sacremento perch SOPH Lepomis cyanellus Green sunfish GNSF Lepomis gibbosus Pumpkinseed PNSD Lepomis gulosus Warmouth WRMH Lepomis humilis Orangespotted sunfish OSSF Lepomis macrochirus Bluegill BLGL Lepomis magalotis Longear sunfish LESF Lepomis microlophus Redear sunfish RESF L. cyanellus X L. macrochirus Green sunfish-bluegill hybrid GSBG 123

139 Appendix A. (continued). Scientific name Common name Letter Code Centrarchidae - sunfishes L. cyanellus X L. humilis Green-orangespotted sunfish hybrid GSOS L. macrochirus X L. microlophus Bluegill-redear sunfish hybrid BGRE Lepomis spp. Unidentified Lepomis ULP Micropterus dolomieu Smallmouth bass SMBS Micropterus punctatus Spotted sunfish STBS Micropterus salmoides Largemouth bass LMBS Micropterus spp. Unidentified Micropterus spp. UMC Pomoxis annularis White crappie WTCP Pomoxis nigromaculatus Black crappie BKCP Pomoxis spp. Unidentified crappie UCP P. annularis X P. nigromaculatus White-black crappie hybrid WCBC Centrarchidae Unidentified centrarchid UCN Percidae - perches Ammocrypta asprella Crystal darter CLDR Etheostoma blennioides Greenside darter GSDR Etheostoma caeruleum Rainbow darter RBDR Etheostoma exile Iowa darter IODR Etheostoma flabellare Fantail darter FTDR Etheostoma gracile Slough darter SLDR Etheostoma microperca Least darter LTDR Etheostoma nigrum Johnny darter JYDR Etheostoma punctulatum Stippled darter STPD Etheostoma spectabile Orangethroated darter OTDR Etheostoma tetrazonum Missouri saddled darter MSDR Etheostoma zonale Banded darter BDDR Etheostoma spp. Unidentified Etheostoma spp. UET Perca flavescens Yellow perch YWPH Percina caproides Logperch LGPH Percina cymatotaenia Bluestripe darter BTDR Percina evides Gilt darter GLDR Percina maculate Blackside darter BSDR Percina phoxocephala Slenderhead darter SHDR Percina shumardi River darter RRDR Percina spp. Unidentified Percina spp. UPN Unidentified darter UDR Sander canadense Sauger SGER* Sander vitreus Walleye WLEY S. canadense X S. vitreus Sauger-walley hybrid/saugeye SGWE Sander spp. Unidentified Sander (formerly Stizostedion) spp. UST Unidentified Percidae UPC Sciaenidae - drums Aplodinotus grunniens Freshwater drum FWDM NON-TAXONOMIC CATEGORIES Age-0/Young-of-year fish Lab fish for identification No fish caught Unidentified larval fish Unidentified Net Malfunction (Did Not Fish) YOYF LAB NFSH LVFS UNID NDNF 124

140 Appendix B. Definitions and codes used to classify standard Missouri River habitats in the long-term pallid sturgeon and associated fish community sampling program. Three habitat scales were used in the hierarchical habitat classification system: Macrohabitats, Mesohabitats and Microhabitats. Habitat Scale Definition Code Braided channel Macro An area of the river that contains multiple smaller channels and is lacking a readily identifiable main channel (typically associated with unchannelized sections) BRAD Main channel cross over Macro The inflection point of the thalweg where the thalweg crosses from one concave side of the river to the other concave side of the river, (i.e., transition zone from one-bend to the next bend). The upstream CHXO for a respective bend is the one sampled. CHXO Tributary confluence Macro Area immediately downstream, extending up to one bend in length, from a junction of a large tributary and the main river where this tributary has influence on the physical features of the main river CONF Dendric Macro An area of the river where the river transitions from meandering or braided channel to more of a treelike pattern with multiple channels (typically associated with unchannelized sections) DEND Deranged Macro An area of the river where the river transitions from a series of multiple channels into a meandering or braided channel (typically associated with unchannelized sections) DRNG Main channel inside bend Macro The convex side of a river bend ISB Main channel outside bend Macro The concave side of a river bend OSB Secondary channel-connected large Macro A side channel, open on upstream and downstream ends, with less flow than the main channel, large indicates this habitat can be sampled with trammel nets and trawls based on width and/or depths > 1.2 m SCCL Secondary channel-connected small Macro A side channel, open on upstream and downstream ends, with less flow than the main channel, small indicates this habitat cannot be sampled with trammel nets and trawls based on width and/or on depths < 1.2 m SCCS Secondary channel-non-connected Macro A side channel that is blocked at one end SCN Tributary Macro Any river or stream flowing into the Missouri River TRIB Tributary large mouth Macro Mouth of entering tributary whose mean annual discharge is > 20 m 3 /s and the sample area extends 300 m into the tributary TRML Tributary small mouth Macro Mouth of entering tributary whose mean annual discharge is < 20 m 3 /s, mouth width is > 6 m wide and the sample area extends 300 m into the tributary TRMS 125

141 Appendix B. (continued). Habitat Scale Definition Code Wild Macro All habitats not covered in the previous habitat descriptions WILD Bars Meso Sandbar or shallow bank-line areas with depth < 1.2 m BARS Pools Meso Areas immediately downstream from sandbars, dikes, snags, or other obstructions with a formed scour hole > 1.2 m POOL Channel border Meso Area in the channelized river between the toe and the thalweg, area in the unchannelized river between the toe and the maximum depth CHNB Dam Tailwaters Meso Immediate downstream of a dam DTWT Thalweg Meso Main channel between the channel borders conveying the majority of the flow TLWG Island tip Meso Area immediately downstream of a bar or island where two channels converge with water depths > 1.2 m ITIP 126

142 Appendix C. List of standard and wild gears (type), their corresponding codes in the database, seasons deployed (Fall-Spring, Summer, or all), years used and catch per unit effort units for collection of Missouri River fishes in Segment 14 for the long-term pallid sturgeon and associated fish community sampling program. Long-term monitoring began in 2003 for Segment 14. Gear Code Type Season Years CPUE units Gillnet 4 meshes, small mesh set GN14 Standard Sturgeon upstream Present fish/net night Gillnet 4 meshes, large mesh set GN41 Standard Sturgeon upstream Present fish/net night Gillnet 8 meshes, small mesh set GN18 Standard Sturgeon upstream Present fish/net night Gillnet 8 meshes, large mesh set GN81 Standard Sturgeon upstream Present fish/net night Mini-fyke net MF Standard Fish Comm. Present fish/net night Push Trawl 8 ft 4mm x 4mm POT02 Wild Fish Comm. Present fish/ m trawled Trammel net 1 inch inner mesh TN Standard All Present fish/100 m drift Trot Line Circle hooks* TLC_ Wild Sturgeon Present fish/hook night Trot Line Octopus hooks* TLO_ Wild Sturgeon Present fish/hook night Trot Line O Shaughnessy hooks* TLS_ Wild Sturgeon Present fish/hook night Otter trawl 16 ft head rope OT16 Standard All fish/100 m Present trawled Otter trawl 16 ft SKT 4mm x 4mm Fish fish/100 m OT01 Wild HB2 MOR Comm. Present trawled *Code ends with line length in feet (1 = 105 ft, 2 = 205 ft, 3 = 305 ft, 4 = 405 ft). Hooks are placed between 5 and 10 feet apart. 127

143 Appendix D. Stocking locations and codes by Recovery Priority Management Area (RPMA) in the Missouri River Basin. State(s) RPMA Site Name Code River RM MT 2 Above Intake AIN Yellowstone 70 + MT 2 Intake INT Yellowstone 70.0 MT 2 Sidney SID Yellowstone 31.0 MT 2 Big Sky Bend BSB Yellowstone 17.0 ND 2 Fairview FRV Yellowstone 9.0 MT 2 Milk River MLK Milk 11.5 MT 2 Mouth of Milk MOM Missouri MT 2 Wolf Point WFP Missouri MT 2 Poplar POP Missouri MT 2 Brockton BRK Missouri MT 2 Culbertson CBS Missouri MT 2 Nohly Bridge NOB Missouri ND 2 Confluence CON Missouri SD/NE 3 Sunshine Bottom SUN Missouri SD/NE 3 Verdel Boat Ramp VER Missouri SD/NE 3 Standing Bear Bridge STB Missouri SD/NE 3 Running Water RNW Missouri SD/NE 4 St. Helena STH Missouri SD/NE 4 Mullberry Bend MUL Missouri NE/IA 4 Ponca State Park PSP Missouri NE/IA 4 Sioux City SIO Missouri NE/IA 4 Decatur DCT Missouri NE/IA 4 Boyer Chute BYC Missouri NE/IA 4 Bellevue BEL Missouri NE/IA 4 Rulo RLO Missouri NE/MO/KS 4 Kansas River KSR Missouri NE 4 Platte River PLR Platte 5.0 KS/MO 4 Leavenworth LVW Missouri MO 4 Parkville PKV Missouri MO 4 Kansas City KAC Missouri MO 4 Miami MIA Missouri MO 4 Grand River GDR Missouri MO 4 Boonville BOO Missouri MO 4 Overton OVT Missouri MO 4 Hartsburg HAR Missouri MO 4 Jefferson City JEF Missouri MO 4 Mokane MOK Missouri MO 4 Hermann HER Missouri 97.6 MO 4 Washington WAS Missouri 68.5 MO 4 St. Charles STC Missouri

144 Appendix E. Juvenile and adult pallid sturgeon stocking summary for Segment 14 of the Missouri River (RPMA 4 Interior Highlands Unit) Year Stocking Site Number Stocked Year Class Stock Date Age at Stocking a Primary Mark Secondary Mark 1994 St. Charles /9/1994 Fry Coded Wire Dangler 1994 Washington /9/1994 Coded Wire Dangler 1994 Hermann /9/1994 1yo Coded Wire Dangler 1997 St. Charles /15/1997 Coded Wire Dangler 1997 Washington /16/1997 Fingerling Coded Wire Dangler 1997 Hermann /17/1997 Coded Wire Dangler 2002 Boonville /3/2002 PIT Tag Some Elastomer 2002 Boonville /25/2002 PIT Tag Elastomer 2003 Boonville /26/2003 PIT Tag 2003 Boonville /2/2003 Coded Wire Some Elastomer 2004 Boonville /8/2004 PIT Tag Elastomer 2004 Boonville /30/2004 PIT Tag 2004 Boonville /10/2004 Coded Wire Elastomer 2004 Boonville /8/2004 Coded Wire Elastomer a Age of fish when stocked: Fry, Fingerling, Yearling, 1yo, 2yo, 3yo, etc 129

145 Appendix F Total catch, overall mean catch per unit effort [± 2 SE] and mean CPUE (fish/100 m) by Mesohabitat within a Macrohabitat for all species caught with each gear type during sturgeon season and Fish Community Season for Segment 14 of the Missouri River during Species captured are listed alphabetically and their codes are presented in Appendix A. Asterisks with bold type indicate targeted native Missouri River species and habitat abbreviations are presented in Appendix B. Standard Error was not calculated when N <

146 Appendix F1. Gill Net: overall season and segment summary. Lists CPUE (fish/net night) and 2 standard errors in brackets. Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG BESN BHCP BHMW BKCP BKSS BLCF BLGL BMBF BNMW BUSK* CARP CLSR CMSN CNCF CNLP CNSN ERSN FHCF FHMW [0.098] [0.083] [0.406] [0.047] [0.284] [0] [0] [0.028] [0.083] [0] [0.043] [0.062] [0.5] [0] [0.066] [0.112] [0.071] [0.02] [0] [0] [3.5] [0.043] [0] [0] [0] [0.082] [0] [1.5] [0.016] [0] [0.071] [0] [0.051] [0] [0] 131

147 Appendix F1 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG FWDM GDEY GDRH GNSF GSCP GZSD HBNS* HFCS LGPH LKSG LMBS LNGR MMSN MNEY MQTF NFSH OSSF PDFH PDSG* [0.047] [0] [0] [0] [0.037] [0] [2.5] [0.035] [0] [0] [0.047] [0] [0] [1.5] [0.013] [0] [0] [0.02] [0.037] [0] [0] [0.016] [0] [0] [0.02] [0.037] [0] [0.5] [0.046] [0] [0] [0.059] [0] [0] [2] [0.018] [0] [0.143] [0] [0] [0] [0] [0.054] [0.131] [0.163] [0.065] [0.137] [0] [1] [0.013] [0] [0.071] [0] [0.037] [0] [0] [0.025] [0.083] [0.114] [0.027] [0.051] [0] [0] 132

148 Appendix F1 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG QLBK RDSN RVCS RVRH RVSN SBWB SFCB* SGCB* SGER* SHRH SKCB* SMBF SNGR SNPD SNSG* SNSN* STBS SVCB [0.046] [0] [0] [0.062] [0] [0] [2] [0.037] [0] [0] [0] [0] [0] [2] [0.083] [0.083] [0] [0.027] [0] [0] [2] [0.009] [0] [0] [0] [0.037] [0] [0] [0.033] [0.083] [0] [0.043] [0.093] [0] [0.5] [0.04] [0] [0.071] [0.082] [0] [0] [0] [0.013] [0] [0.071] [0] [0] [0] [0.5] [1.371] [4.005] [4.328] [1.039] [3.627] [3] [4] 133

149 Appendix F1 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG SVCP SVRH UCA UCN UCY UHY UIC ULP UNID UPM USG WLYE WSMW* WTBS WTCP YOYF [0.016] [0] [0.071] [0.027] [0] [0] [0] [0.009] [0] [0] [0.02] [0] [0] [0] [0.009] [0] [0] [0] [0.037] [0] [0] 134

150 Appendix F2. 1 Inch Trammel Net: overall season and segment summary. The CPUE (fish/net night) and 2 standard errors are listed in brackets. Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP CHNB BESN BHCP BHMW BKCP BKSS BLCF BLGL BMBF BNMW BUSK* CARP CLSR CMSN CNCF CNLP CNSN ERSN FHCF FHMW [0.14] [0.203] [0] [0.174] [0] [0] [0] [0.138] [0.106] [0] [0.178] [0] [0] [0] [0.046] [0.118] [0] [0.049] [0] [0] [0] [0.02] [0] [0] [0.026] [0] [0] [0] 135

151 Appendix F2 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG FWDM GDEY GDRH GNSF GSCP GZSD HBNS* HFCS LGPH LKSG LMBS LNGR MMSN MNEY MQTF NFSH OSSF PDFH PDSG* [0.031] [0] [0] [0.041] [0] [0] [0] [0.016] [0] [0] [0.021] [0] [0] [0] [0.015] [0.05] [0] [0.012] [0] [0] [0] 136

152 Appendix F2 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG QLBK RDSN RVCS RVRH RVSN SBWB SFCB* SGCB* SGER* SHRH SKCB* SMBF SNGR SNPD SNSG SNSN STBS SVCB [0.046] [0.171] [0] [0.031] [0] [0] [0] [0.083] [0] [0] [0.109] [0] [0] [0] [0.02] [0.085] [0] [0] [0] [0] [0] [0.029] [0.062] [0] [0.033] [0] [0] [0] [1.47] [2.999] [0] [1.712] [0] [0] [0] 137

153 Appendix F2 (continued). Species Total Catch CHXO ISB OSB SCCL TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG SVCP SVRH UCA UCN UCY UHY UIC ULP UNID UPM USG WLYE WSMW* WTBS WTCP YOYF 138

154 Appendix F4. : overall season and segment summary. Lists CPUE (fish/net night) and 2 standard errors in brackets. Species Total Catch CHXO ISB OSB SCCS TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG BESN BHCP BHMW BKCP BKSS BLCF BLGL BMBF BNMW BUSK* CARP CLSR CMSN CNCF CNLP CNSN ERSN FHCF FHMW [0] [0] [0.085] [0] [0] [0] [0] [0] [0] [1.333] [0.012] [0] [0] [0] [0] [0] [0] [0.667] [0] [2.024] [5.84] [0] [1.933] [0] [0] [5.594] [1.333] [0.298] [0.048] [0] [0] [0] [0] [0] [16.667] [0] [0.012] [0] [0] [0] [0] [0] [0] [0.667] [0.048] [0.1] [0] [0.058] [0] [0] [0] [0] [0.023] [0.071] [0] [0.02] [0] [0] [0] [0] [0] [0] [0.826] [2.119] [0] [0.66] [0] [0] [0.804] [25.333] [0] [0] [0.097] [0] [0] [0.025] [0] [0] [0] [5.333] [0.027] [0.053] [0] [0.033] [0] [0] [0] [0] [0] 139

155 Appendix F4 (continued). Species Total Catch CHXO ISB OSB SCCS TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG FWDM GDEY GDRH GNSF GSCP GZSD HBNS* HFCS LGPH LKSG LMBS LNGR MMSN MNEY MQTF NFSH OSSF PDFH PDSG* [0.742] [1.38] [0] [0.377] [0] [0] [2.692] [20] [0.293] [0.234] [0] [0.087] [0] [0] [1.923] [4.667] [0] [0] [0.006] [0] [0] [0.008] [0] [0] [0] [0] [0.431] [0] [0] [0.1] [0] [0] [0] [18] [0] [0] [0] [0] [0] [0.012] [0] [0] [0.017] [0] [0] [0] [0] [0] [0.014] [0.055] [0] [0] [0] [0] [0] [0] [0] [0] [0.012] [0] [0] [0] [0] [0] [0] [0.667] [0] [0.009] [0] [0] [0.013] [0] [0] [0] [0] 140

156 Appendix F4 (continued). Species Total Catch CHXO ISB OSB SCCS TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG QLBK RDSN RVCS RVRH RVSN SBWB SFCB* SGCB* SGER* SHRH SKCB* SMBF SNGR SNPD SNSG* SNSN* STBS SVCB [0] [0.007] [0] [0] [0.01] [0] [0] [0] [0] [0.033] [0.112] [0] [0.022] [0] [0] [0] [0] [0] [0] [0] [0.134] [0.509] [0] [0.054] [0] [0] [0] [0] [0.072] [0.286] [0] [0.015] [0] [0] [0] [0] [0.02] [0.077] [0] [0] [0] [0] [0] [0] [0] [0.833] [0.288] [0] [0.028] [0] [0] [46.538] [0] [0] [0.02] [0.036] [0] [0.025] [0] [0] [0] [0] [0] [0.195] [0.466] [0] [0.212] [0] [0] [2.273] [0] [0] [0] [0.257] [0.071] [0] [0.034] [0] [0] [0.455] [8] 141

157 Appendix F4 (continued). Species Total Catch CHXO ISB OSB SCCS TRML Overall CPUE CHNB POOL CHNB POOL POOL ITIP TLWG SVCP SVRH UCA UCN UCY UHY UIC ULP UNID UPM USG WLYE WSMW* WTBS WTCP YOYF [0] [0] [0] [0.274] [0] [0] [0] [0] [0] [0] [15.333] [0.024] [0] [0] [0] [0] [0] [0] [1.333] [0.214] [0] [0] [0] [0] [0] [0] [12] [1.85] [7.333] [0] [0.323] [0] [0] [7.098] [2.667] [0.119] [0] [0] [0] [0] [0] [0] [1.333] [0.024] [0] [0] [0] [0] [0] [0] [1.333] [0] [0.011] [0.036] [0] [0.01] [0] [0] [0] [0] [0] [0] [0.027] [0] [0] [0] [0] [0] [0.769] [1.333] [0] [0] 142

158 Appendix F6. Mini-fyke: overall season and segment summary. Lists CPUE (fish/net night) and 2 standard errors in brackets. Species Total Catch CHXO CONF ISB OSB SCCL SCCS TRML TRMS Overall CPUE BARS BARS BARS CHNB BARS BARS BARS BARS BARS BESN BHCP BHMW BKCP BKSS BLCF BLGL BMBF BNMW BUSK* CARP CLSR CMSN CNCF CNLP CNSN ERSN FHCF FHMW [0.137] [0.107] [0.126] [0.176] [0] [1.333] [4] [0.169] [0.231] [0.233] [0.463] [0] [0.667] [2] [0.309] [0.107] [0.047] [0] [0] [9.615] [0] [0.215] [0.729] [0.103] [0.404] [0] [1.333] [1.333] [0.122] [0.077] [0.112] [0] [0] [4] [0] [0.032] [0] [0.047] [0] [0] [0] [0.667] [0.16] [0] [0.233] [0] [0] [4.667] [0] [0.368] [0.924] [0.681] [0.327] [4] [0] [0.667] [0.045] [0] [0.103] [0] [0] [0.667] [0] [2.192] [4.904] [3.185] [1.705] [0] [45.7] [5.033] [0.019] [0] [0.047] [0] [0] [0] [0] [0.019] [0] [0] [0] [0] [0] [0.667] 143

159 Appendix F6(continued). Species Total Catch CHXO CONF ISB OSB SCCL SCCS TRML TRMS Overall CPUE BARS BARS BARS CHNB BARS BARS BARS BARS BARS FWDM GDEY GDRH GNSF GSCP GZSD HBNS HFCS LGPH LKSG LMBS LNGR MMSN MNEY MQTF NFSH OSSF PDFH PDSG* [0.051] [0.128] [0.047] [0.123] [0] [0] [0] [0.019] [0.077] [0] [0] [0] [0] [0] [0.019] [0.077] [0] [0] [0] [0] [0] [3.182] [1.444] [5.665] [8.409] [1] [14.667] [15.275] [0.132] [0.077] [0] [0.519] [0] [0] [0] [0.019] [0] [0] [0.074] [0] [0] [0] [0.049] [0] [0.065] [0.163] [0] [0] [0] [0.109] [0.128] [0.103] [0.234] [0] [0] [0.667] [0.113] [0.295] [0.166] [0.074] [0] [0] [1.333]

160 Appendix F6. (continued). Species Total Catch CHXO CONF ISB OSB SCCL SCCS TRML TRMS Overall CPUE BARS BARS BARS CHNB BARS BARS BARS BARS BARS QLBK RDSN RVCS RVRH RVSN SBWB SFCB* SGCB* SGER* SHRH SKCB* SMBF SNGR SNPD SNSG* SNSN* STBS SVCB SVCP [2.306] [3.316] [1.381] [8.263] [2] [5.333] [1.155] [0.208] [0.077] [0] [0.103] [0] [7.333] [0] [0.019] [0] [0] [0.074] [0] [0] [0] [0.037] [0] [0.093] [0] [0] [0] [0] [0.111] [0.262] [0.153] [0.245] [0] [0.667] [0] [0.019] [0] [0] [0] [0] [0.667] [0] [0.026] [0] [0.047] [0.074] [0] [0] [0] [0.026] [0] [0.047] [0] [0] [0] [0] [0.019] [0] [0] [0] [0] [0.667] [0] 145

161 Appendix F6. (continued). Species Total Catch CHXO CONF ISB OSB SCCL SCCS TRML TRMS Overall CPUE BARS BARS BARS CHNB BARS BARS BARS BARS BARS SVRH UCA UCN UCY UHY UIC ULP UNID UPM USG WLYE WSMW* WTBS WTCP YOYF [0.019] [0] [0.047] [0] [0] [0] [0] [0.037] [0] [0.093] [0] [0] [0] [0] [0.059] [0.077] [0] [0.222] [0] [0] [0] [0.709] [1.815] [1.189] [1.143] [0] [.667] [0.667] [0.92] [3.536] [0.219] [0.981] [0] [0] [7.333] [0.06] [0.144] [0.112] [0] [1] [0] [0] [0.095] [0] [0] [0.375] [0] [0] [0] [0.019] [0.077] [0] [0] [0] [0] [0] [0.173] [0.242] [0.152] [0.074] [8] [0.667] [0] [0.237] [0.568] [0.14] [0.515] [0] [0.667] [4] [0.062] [0] [0] [0.232] [0] [0] [0] 146

162 Appendix G. Hatchery names, locations and abbreviations. Hatchery State Abbreviation Blind Pony State Fish Hatchery MO BLP Neosho National Fish Hatchery MO NEO Gavins Point National Fish Hatchery SD GAV Garrison Dam National Fish Hatchery ND GAR Miles City State Fish Hatchery MT MCH Blue Water State Fish Hatchery MT BLU Bozeman Fish Technology Center MT BFT Fort Peck State Fish Hatchery MT FPH 147

163 Appendix H. Alphabetic list of Missouri River fishes with total catch per unit effort by gear type for Sturgeon Season (fall through spring) and Fish Community Season (summer) during for Segment 14 of the Missouri River. Species codes are located in Appendix A. Asterisks and bold type denote targeted native Missouri River species. Sturgeon Season (Fall through Spring) Fish Community Season (Summer) Species Code Gill Net 1-Inch Trammel Net Push Trawl 1-Inch Trammel Net ALSD ALWF AMEL AMGL BCCC BDDR BDKF BDSN BDSP BESN BHCP BHMW BKBF BKBH BKCP BKRH BKSB BKSS BKTT BLCF BLGL BMBF BMSN BNDC BNMW BNSN BNTT BPTM BRBT Mini-Fyke Net 148

164 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1-Inch Trammel Net Fish Community Season (Summer) Push Trawl 1-Inch Trammel Net BSDR BSMN BSTM BTDR BUSK* BVSC BWFN CARP CHSM CKCB CLDR CLSR CMSN CNCF CNLP CNSM CNSN CSCO CTTT ERSN FCSC FHCB FHCF FHMW FKMT FSDC FTDR FWDM GDEY GDFH Mini-Fyke Net 149

165 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1-Inch Trammel Net Fish Community Season (Summer) Push Trawl 1-Inch Trammel Net GDTT GFCC GLDR GDRH GDSN GN*? GNSF GSBG GSCP GSDR GSOS GSPK GSTS GTSN GVCB GZSD HBNS* HFCS HHCB IODR JYDR LESF LGPH LKCB LKSG LKTT LKWF LMBS LNDC LNGR Mini-Fyke Net 150

166 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1-Inch Trammel Net Fish Community Season (Summer) Push Trawl 1-Inch Trammel Net LSSR LTDR LVLP MDSP MMSN MNEY MQTF MSDR MSKG MTSK MTWF NFSH NHSK NRBD NTPK NTSF OSSF OTDR OZMW PDFH PDSG* PEMT PKLF PLDC PNMW* PNSD PTMW QLBK Mini-Fyke Net 151

167 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1-Inch Trammel Net Fish Community Season (Summer) Push Trawl 1-Inch Trammel Net RBDR RBST RBTT RDSN RDSS RKBS RRDR RUDD RVCS RVRH RVSN RYSN SBLR SBSN SBWB SCSC SDBS SDMT SESM SFCB* SFSN SGCB* SGER* SGWE SHDR SHRH SJHR SKCB* SLDR SMBF Mini-Fyke Net 152

168 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1 Inch Trammel Net Fish Community Season (Summer) Push Trawl 1 Inch Trammel Net SMBS SMMW SNGR SNPD SNSG* SNSN* SPSK SPSN SPST SRBD SSPS STBS STCT STGR STPD STSN SVCB SVCP SVLP SVMW SVRH TFSD TPMT TPSN TTPH UAC UBF UCA UCN UCS Mini-Fyke Net 153

169 Appendix H. (continued). Sturgeon Season (Fall through Spring) Species Code Gill Net 1-Inch Trammel Net Fish Community Season (Summer) Push Trawl 1-Inch Trammel Net UCT UCY UDR UET UHY UIC ULP UNID UPC UPM URH USG UST WLYE WRFS WRMH WSMN* WSSN WTBS WTCP WTPH WTSK YOYF YWBS YWPH Mini-Fyke Net 154

170 Appendix I. Comprehensive list of bend numbers and locations for Segment 14 of the Missouri River comparing bend selection for both Sturgeon Season (ST) and Fish Community Season (FC) between years from Bend Bend River Coordinates* Number Mile Latitude, Longitude , ST ST, FC , FC ST, FC ST, FC , , FC ST, FC ST, FC , ST, FC FC , FC , ST, FC ST, FC , , ST, FC , ST, FC , ST, FC , FC ST, FC , ST , FC , ST FC ST, FC ST, FC , FC ST, FC , ST, FC ST, FC , , FC ST, FC , FC , ST, FC ST, FC , , ST, FC , ST FC , FC ST, FC , ST FC ST, FC , ST, FC , ST ST, FC , ST ST, FC , ST, FC 155

171 Appendix I. (continued). Bend Bend Coordinates* Number River Mile Latitude, Longitude , FC ST, FC , FC ST ST, FC , ST, FC , ST, FC ST, FC , FC ST ST, FC , FC ST , , FC ST, FC , ST, FC , ST, FC ST, FC , ST, FC ST, FC , ST , , ST ST ST, FC , , , ST FC , ST ST, FC , FC ST, FC , ST ST, FC , FC ST, FC , , FC ST, FC , FC , FC ST, FC ST, FC , ST Coordinates represent the upper most point of the bend (i.e., the top of the bend going upstream). 156

172 Appendix J. Ratios of pallid to shovelnose sturgeon, hybrid to shovelnose sturgeon and pallid to hybrid sturgeon, standardized by catch per unit effort for Segment 14 between 2004 and Gill Net 1-inch Trammel Net Pallid: Hybrid: Pallid: Pallid: Hybrid: Pallid: Pallid: Hybrid: Pallid: Shovelnose Shovelnose Hybrid Shovelnose Shovelnose Hybrid Shovelnose Shovelnose Hybrid : : : 2 1 : : : 1 1 : 87 1 : : : : : 2 1 : 673 N/A N/A 1 : : 97 1 : : : : 1 1 : : : 1 N/A N/A N/A : : : 1 1 : : : 1 1 : : : : : : 0.24 N/A N/A N/A 1 : 176 N/A N/A 157

173 Appendix K. Percentage of shovelnose sturgeon captured in each length group for each gear during Sturgeon Season and Fish Community Season in Segment 14 of the Missouri River during NE = no effort due to high water conditions in Segment 14 during Sturgeon Season. Sub-stock Sub-stock Stock Quality Season Gear Type N (0-149mm) ( mm) ( mm) (>380mm) ST 1-inch trammel Net NE Gill Net NE FC 1-inch trammel Net

174 Appendix L. Trotline: overall season and segment summary. Lists total catch and CPUE (fish/hook night). Species Total Catch CHXO CONF ISB OSB SCCL TRML TRML TRML CHNB CHNB CHNB CHNB CHNB CHNB POOL TLWG BLCF CNCF FWDM GDRH LKSG PDSG SMBF SNSG SVCB ULY Total Hooks

175 Appendix M. Missouri River discharge at Hermann, MO USGS Gauge from November 2007 through October Graph courtesy of U.S. Geological Survey. Maximum discharge for sampling 160