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«Ann Marie Reinhold, Robert G. Bramblett, and Alexander V. Zale Montana Cooperative Fishery Research Unit Department of Ecology Montana State ...»

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ANTHROPOGENIC HABITAT CHANGE EFFECTS ON FISH ASSEMBLAGES OF

THE MIDDLE AND LOWER YELLOWSTONE RIVER

Ann Marie Reinhold, Robert G. Bramblett, and Alexander V. Zale

Montana Cooperative Fishery Research Unit

Department of Ecology

Montana State University – Bozeman

Completion Report to:

The United States Army Corps of Engineers

and the Technical Advisory Committee,

Yellowstone River Conservation District Council Montana Fish, Wildlife & Parks University Research Completion Report Series Number 2014-01.2 Disclaimer: not a Montana Fish, Wildlife & Parks product December 2014 ii

TABLE OF CONTENTS

1. INTRODUCTION

References

2. CUMULATIVE EFFECTS OF FLOODPLAIN DIKES AND LINEAR BANK

STABILIZATION ON YELLOWSTONE RIVER SIDE CHANNELS................ 4

Abstract

Introduction

Study Area

Methods

Spatial Analyses

Statistical Analyses

Results

Discussion

Figures

References

3. USE OF SIDE CHANNELS BY A LARGE-RIVER FISH ASSEMBLAGE..... 31 Abstract

Introduction

Study Area

Methods

Sampling Design

Fish Sampling

Physical Habitat

Statistical Analyses

Results

Habitat Use

Assemblage Composition and Structure

Physical Habitat

Discussion

Tables

Figures

References

iii

–  –  –

4. SPATIALLY-DEPENDENT RESPONSES OF A LARGE-RIVER FISH

ASSEMBLAGE TO BANK STABILIZATION AND SIDE CHANNELS........ 67 Abstract

Introduction

Study Area

Methods

Sampling Design

Fish Sampling

Spatial Analyses

Statistical Analyses

Depth and Velocity Profiling

Results

Fish Assemblage

Spatial Scale-dependence

Depths and Velocities in Stabilized and Reference Pools

Discussion

Tables

Figures

References

5. CONCLUSIONS AND MANAGEMENT IMPLICATIONS

APPENDICES

APPENDIX A: CATCH PER UNIT EFFORT OF YELLOWSTONE RIVER

FISH

APPENDIX B: LENGTHS OF YELLOWSTONE RIVER FISH.............. 142

APPENDIX C: CATCH PER UNIT EFFORTS OF SELECT COMMONLY

CAPTURED SPECIES AT REFERENCE AND STABILIZED SITES 153

APPENDIX D: AREAL CHANGES IN FISHERIES HABITAT UNITS

FROM THE 1950s TO 2001

–  –  –

Table 3.1.

Yellowstone River fishes captured in fyke nets during runoff and base flow.

Table 3.2.

Habitat-specific differences in fish assemblages during runoff and base flow in alluvial and bluff river bends (perMANOVA).

Models with Bray-Curtis dissimilarity indices assess proportional assemblage compositions. Models with binary dissimilarity indices assess species composition. The P-values for statistically significant terms at α = 0.05 are bolded.

Table 3.3.

Regression results estimating mean differences between physical habitats of side and main channels during runoff and base flow at bluff and alluvial river bends. The P-values for statistically significant terms at α = 0.05 are bolded.

Table 4.1.

Lower Yellowstone River fishes and their feeding guilds.

Abbreviations are used in Table 4.3 and Figures 4.4-4.6. Fish guilds were adopted from Brown (1971), Scott and Crossman (1973), Simon (1998), and Bramblett et al. (2005).

Table 4.2.

Bray-Curtis perMANOVA results for alluvial and bluff sites.

Bolded spatial scales, P-values, and R2 values indicate that fish assemblage structure varied significantly with the factor indicated in the column heading

–  –  –

Table A.1. Base flow electrofishing catch per unit effort (CPUE) of lower Yellowstone River fish. Fish CPUE is the count of fish captured divided by the duration (in seconds) of each electrofishing pass.

Detailed fish capture methods are presented in Chapter 4. The mean (μ) and standard deviation (σ) of the CPUE of each species were calculated from all electrofishing passes within each river segment.

Scientific names of fish are in Table 4.1.

Table A.2. Base flow fyke catch per unit effort (CPUE) of lower Yellowstone River fish. Fish CPUE is the count of fish captured divided by the duration (in hours) that each net was fishing. Detailed fish capture methods are presented in Chapter 4. The mean (μ) and standard deviation (σ) of the CPUE of each species were calculated from all fyke nets deployed within each river segment. Scientific names of fish are in Table 4.1.

Table A.3. Base flow seine catch per unit effort (CPUE) of lower Yellowstone River fish. Fish CPUE is the count of fish captured divided by the length (in meters) of each seine haul. Detailed fish capture methods are presented in Chapter 4. The mean (μ) and standard deviation (σ) of the CPUE of each species were calculated from all seine hauls within each river segment. Scientific names of fish are in Table 4.1.





Table A.4. Base flow trammel net catch per unit effort (CPUE) of lower Yellowstone River fish. Fish CPUE is the count of fish captured divided by the length (in meters) of each trammel net drift. Detailed fish capture methods are presented in Chapter 4. The mean (μ) and standard deviation (σ) of the CPUE of each species were calculated from all trammel net drifts within each river segment. Scientific names of fish are in Table 4.1.

–  –  –

Table B.1. Lengths of lower Yellowstone River fish captured during base flow with electrofishing. Lengths (in mm) were measured for up to 25 arbitrarily selected individuals of each species captured with each electrofishing pass; all individuals of a species were measured if 25 or fewer individuals of a species were captured. Length refers to total length for all species except sturgeons for which fork length was measured. Detailed fish capture methods are presented in Chapter 4.

The mean (μ) and standard deviation (σ) of fish lengths were calculated from all electrofishing passes within each river segment;

however, a standard deviation was not calculated (*) if only one individual was captured. Dashes (-) denote species that were not captured. Scientific names of fish are in Table 4.1.

Table B.2. Lengths of lower Yellowstone River fish captured during base flow with fyke nets. Lengths (in mm) were measured for up to 25 arbitrarily selected individuals of each species captured with each fyke net deployment; all individuals of a species were measured if 25 or fewer individuals of a species were captured. Length refers to total length for all species except sturgeons for which fork length was measured. Detailed fish capture methods are presented in Chapter 4.

The mean (μ) and standard deviation (σ) of fish lengths were calculated from all fyke net deployments within each river segment;

however, a standard deviation was not calculated (*) if only one individual was captured. Dashes (-) denote species that were not captured. Scientific names of fish are in Table 4.1.

–  –  –

Table B.4. Lengths of lower Yellowstone River fish captured during base flow with trammel nets. Lengths (in mm) were measured for up to 25 arbitrarily selected individuals of each species captured with each trammel net drift; all individuals of a species were measured if 25 or fewer individuals of a species were captured. Length refers to total length for all species except sturgeons for which fork length was measured. Detailed fish capture methods are presented in Chapter 4.

The mean (μ) and standard deviation (σ) of fish lengths were calculated from all trammel net drifts within each river segment;

however, a standard deviation was not calculated (*) if only one individual was captured. Dashes (-) denote species that were not captured. Scientific names of fish are in Table 4.1.

Table B.5. Lengths of lower Yellowstone River fish captured during base flow with otter trawls. Lengths (in mm) were measured for up to 25 arbitrarily selected individuals of each species captured with each trawl deployment; all individuals of a species were measured if 25 or fewer individuals of a species were captured. Length refers to total length for all species except sturgeons for which fork length was measured. Detailed fish capture methods are presented in Chapter 4.

The mean (μ) and standard deviation (σ) of fish lengths were calculated from all trawl deployments within river segments 4 and 5;

however, a standard deviation was not calculated (*) if only one individual was captured. Dashes (-) denote species that were not captured. Scientific names of fish are in Table 4.1.

Table D.1. Fisheries habitat unit categories. Categories adapted from Thatcher (memorandum).

Table D.2. Geomorphic reach type classifications. Adapted from Boyd and Thatcher (2004).

Table D.3. Bank full habitat unit areas by reach in the 1950s. Reaches were delineated by Boyd and Thatcher (2004). Habitat unit areas are reported in km2.

–  –  –

Figure 2.1.

The Yellowstone River, Montana, and its major tributaries.

The study area (darkened) extends from the confluence of the Clarks Fork of the Yellowstone River downstream to the confluence of the Missouri River near the Montana-North Dakota border.

Figure 2.2.

Aerial photographs and polygons depicting digitizations of bank-full side channels and main channels from the 1950s (a, c) and 2001 (b, d).

Figure 2.3.

Illustration of methodology for isolating side-channel loss and gain for the river bend shown in Figure 2.2. (a) Polygons depict all channel transitions from the 1950s to 2001. (b) Polygons depict only side-channel transitions: loss, gain, and migration. (c) Polygons from side-channel migration have been filtered out; only side-channel loss and gain remain.

Figure 2.4.

Illustration of the methodology to remove redundant linear bank stabilization. The linear stabilization structure closest to the river was retained where overlap occurred. Analyses of linear bank stabilization refer to “active bank stabilization.”

Figure 2.5.

Longitudinal trends in side-channel loss (a, c, e, and g) and gain (b, d, f, and h) at four spatial scales.

Figure 2.6.

Longitudinal profiles of dike frequency (a), bank stabilization (b), and side-channel loss (c) and gain (d).

Figure 2.7.

Histograms of side-channel area loss (a) and gain (b) from the 1950s to 2001.

–  –  –

Figure 2.9.

Linear bank stabilization and floodplain dikes isolated side channels and swales of the Yellowstone River, Montana. Presentday (2012) linear stabilization structures bisected side channels, effectively functioning as floodplain dikes near Hysham (a, b). The linear stabilization that arrested channel migration near Miles City (c,

d) was installed prior to the 1950s. Flow direction is from bottom left to top right.

Figure 2.10.

A linear bank stabilization structure failed to arrest active channel migration on the Yellowstone River near Billings, Montana, and became a large roughness element in the main channel. Aerial imagery from 2007 (a) and 2012 (b) depicts extent of channel migration; the linear stabilization structure was installed after the 2007 photograph (a). Circles denote a building that collapsed when the linear stabilization failed during snowmelt runoff in 2011. Arrow styles denote position along the large roughness element (c, d) during autumn 2011. Flow direction is from left to right.

Figure 3.1.

Five study segments of the Yellowstone River sampled during runoff and base flow. Four alluvial river bends were sampled in each river segment. Four bluff bends were sampled in each of the three upstream segments

Figure 3.2.

Yellowstone River hydrographs at Segment 3 for years when fish sampling occurred. Dark grey shading denotes timing of runoff sampling. Light grey shading denotes timing of base flow sampling..........56

–  –  –

Figure 3.4.

Estimated mean multiplicative differences (β) in side-channel versus main-channel catches of fish captured in fyke nets during runoff and base flow in alluvial (a and b) and bluff river bends (c and d). Estimates were generated from negative binomial regressions with offsets for sampling effort. Error bars represent 95% confidence intervals.

Figure 3.5.

Habitat-specific comparisons of numbers of species for runoff and base flow conditions. Bar color indicates whether species were captured in side channels, main channels, or both.

Figure 4.1.

Locations of the five study segments in the Yellowstone River.......108 Figure 4.2.

Longitudinal profiles of main-channel bank-stabilization lengths (a) and side-channel bank lengths (b) in the Yellowstone River study area. Sampling sites are marked by dashed lines along the x-axes. Segment 1 (Billings) included the sites near RKM 600;

Segment 2 (Hysham) included the sites near RKM 440; Segment 3 (Miles City) included the sites near RKM 340; Segment 4 (Glendive) included the sites near RKM 160; and Segment 5 (Sidney) included the sites near RKM 75.

Figure 4.3.

Depiction of the twelve buffered spatial scales around one subsample. Buffers were used to extract bank-stabilization lengths, lengths of side-channel banks, and main-channel border lengths at each spatial scale.

–  –  –

Figure 4.5.



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