HABITAT SELECTION BY JUVENILE SALMONIDS IN A LAKE MICHIGAN TRIBUTARY By Mitchell Thomas Nisbet A THESIS Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Fisheries and Wildlife – Master of Science 2020 HABITAT SELECTION BY JUVENILE SALMONIDS IN A LAKE MICHIGAN ABSTRACT TRIBUTARY By Mitchell Thomas Nisbet Recruitment of potadromous salmonid populations in the Great Lakes is a combination of annual plantings of hatchery reared fish and natural reproduction. Determining the input of smolts and juveniles from natural sources is critical to our understanding of these populations as they are both economically and recreationally important species. I found Bear Creek to be a potentially important contributor of potadromous salmonids to the Lake Michigan basin, producing approximately 15,000 Rainbow Trout smolts, 5,000 Chinook Salmon smolts, and 23,000 Coho Salmon smolts in addition to supporting 43,000 young-of-year Rainbow Trout, 9,200 young-of- year Brook Trout and 21,000 young-of-year Brown Trout. I concluded that while Bear Creek may produce lower numbers of individual species, the total sum of potadromous salmonids produced is roughly equivalent to other similarly sized Lake Michigan tributaries. I also evaluated microhabitat use by young salmonids in Bear Creek using the modified Chesson’s Index. My results showed that young-of-year salmonids tended to select for near shore habitat with finer sediments, in slower moving shallow water that provided both overhead cover and woody debris. This is in contrast to age-1 Rainbow Trout, that selected for more midstream sections of the river with deeper and faster moving currents that still provided overhead cover and woody debris. I also showed that univariate descriptions of habitat preference may not provide an accurate picture of the true habitat utilization of these species. Copyright by MITCHELL THOMAS NISBET 2020 ACKNOWLEDGEMENTS My gratitude goes to the Michigan Department of Natural Resources, the Schrems West Michigan Trout Unlimited Graduate Fellowship, and the Red Cedar Fly Fishers Graduate Fellowship in Fisheries Management who provided funding for this research project. I would also like to thank Dr. Daniel Hayes, Dr. Michael Jones, Dr. Brian Roth, and Mark Tonello for their assistances and guidance on this project. Their knowledge of fisheries management, statistical analysis, and fisheries population dynamics provided me the tools to be successful in completing this project. You all have been instrumental in allowing me to succeed. Additionally, I would like to highlight, James Beaubien, Matt Curry, Jerrod Lepper, Corrine Highley, Darrin Mccullough, Elle Gulloty, Jason Smith, Kelley Smith, Ryan Andrews, Samantha Tank, Joe Nohner, Phillip Ankley, Ben Bejcek, Katie Kierczynski, and Mitchell Konieczny for their assistance in the field and in the laboratory. Countless hours were spent electrofishing in the field, collecting habitat data, hiking miles of river, or entering data. I would have been unable to complete this project without your support and dedication. Finally, I would like to thank my wife Adrienne, and family Tom, Catherine, and Cara, for the financial and emotional support they have given me to help me pursue higher education. Their belief in me has been instrumental in helping me reach my goals and I would not have been able to do it without them. iv TABLE OF CONTENTS LIST OF TABLES ........................................................................................................................ vi LIST OF FIGURES ..................................................................................................................... vii INTRODUCTION .......................................................................................................................... 1 METHODS ..................................................................................................................................... 6 Site Selection ........................................................................................................................ 6 Fish Surveys: Field Methods ................................................................................................ 9 Habitat Selection ................................................................................................................ 10 Selectivity Analysis ............................................................................................................ 13 Population Estimation ........................................................................................................ 14 RESULTS ..................................................................................................................................... 17 Juvenile Salmonid Abundance ........................................................................................... 17 Total Abundance of Juvenile Salmonids in Bear Creek and Tributaries ........................... 22 Habitat Relations to Juvenile Abundance .......................................................................... 22 Habitat Selection ................................................................................................................ 24 DISCUSSION ............................................................................................................................... 42 Relative Contribution of Tributaries ...................................................................................46 Microhabitat Use and Selection ......................................................................................... 47 Future Research .................................................................................................................. 51 APPENDIX. .................................................................................................................................. 54 REFERENCES ..............................................................................................................................65 v LIST OF TABLES Table 1. Catchability estimates used to estimate density of fish in the Bear Creek watershed….15 Table 2. Density (fish/km) in Bear Creek and its tributaries in 2015. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis…………..………………………….19 Table 3. Density (fish/km) in Bear Creek and its tributaries in 2016 Early. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis……...……………………20 Table 4. Density (fish/km) in Bear Creek and its tributaries in 2016 Late. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis……...……………………21 Table 5. Estimation of total fish abundance within the study reach of Bear Creek……………...22 Table 6. Correlation (R) between habitat measures and salmonid density for 2016 Early. Significant values (p-value <0.05) are highlighted in yellow……………………………………23 Table 7. Correlation (R) between habitat measures and salmonid density for 2016 Late. Significant values (p-value <0.05) are highlighted in yellow……………………………………24 Table 8. Proportion of observations of randomly selected points, and points where target fishes occurred along a gradient of substrate size. Particles 1-10, 10-20, and 20-50 mm are classified as gravel, and particles >50 mm are classified as cobble…………………………………………...25 Table 9. Chesson’s selection index for target fishes along a gradient of substrate size. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). Particles 1-10, 10-20, and 20-50 mm are classified as gravel, and particles >50 mm are classified as cobble………………………………………………………………………………26 Table 10. Proportion of observations of randomly selected points, and points where target fishes occurred related to the presence or absence of woody debris and overhead cover……………...27 Table 11. Chesson’s selection index for target fishes with respect to the presence or absence of woody debris and overhead cover. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………28 Table 12. Proportion of observations of randomly selected points, and points where target fishes occurred related to percent distance from the nearest bank……………………………………...29 vi Table 13. Chesson’s selection index for target fishes with respect to distance from the nearest bank. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)…………………………………………………………………...30 Table 14. Proportion of observations of randomly selected points and points where target fishes occurred along a velocity gradient……………………………………………………………….31 Table 15. Chesson’s selection index for target fishes along a velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………………………………………………………………32 Table 16. Proportion of observations of randomly selected points and points where target fishes occurred along a depth gradient………………………………………………………………….33 Table 17. Chesson’s selection index for target fishes along a depth gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………………………………………………………………….34 Table 18. Proportion of observations of randomly selected points that occurred along a velocity and depth gradient. Fish proportion points are located in Appendix Table 5……………………35 Table 19. Chesson’s selection index for trout along a depth and velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………………………………………………………………36 Table 20. Chesson’s selection index for YOY salmon along a depth and velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………………………………………………38 Table 21. Chesson’s selection index for trout along a depth and % distance from nearest bank. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2)……………………………………………………………………………39 Table 22. Young of the year Rainbow Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses……………….44 Table 23. Young of the year Brook Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses……………….44 Table 24. Young of the year Brown Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses……………….44 vii Table 25. Age-1 Rainbow Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses………………………...45 Table 26. Young of the year Coho Salmon density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses………………45 Table 27. Young of the year Chinook Salmon density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses………….45 Table A1. 2016 fish community results came from 2016 Early triple pass shocking results from both main stem and tributary sites. No 2016 Late data was used as only salmonid species were recorded during those passes. *Tiger Trout was captured in 2016 Late surveys………………..55 Table A2. Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites……………………………………………………56 Table A3. Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites……………………………………………………57 Table A4. Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites……………………………………………………58 Table A5. Proportion of observations of fish capture points for trout species across age groupings that occurred along a velocity and depth gradient……………………………………………….59 Table A6. Proportion of observations of fish capture points for salmon species across age groupings that occurred along a velocity and depth gradient…………………………………...61 Table A7. Proportion of observations of fish capture points for trout species across age groupings that occurred along a % distance to nearest bank and depth gradient…………………………...62 Table A8. Proportion of observations of fish capture points for salmon species across age groupings that occurred along a % distance to nearest bank and depth gradient………………..64 viii LIST OF FIGURES Figure 1. Map of sampling sites on the main stem of Bear Creek. Sites are denoted by a yellow circle. The star represents Tippy Dam, a large impoundment on the Manistee River……………7 Figure 2. Map of sampling sites for tributaries of Bear Creek. Sites are denoted by a red circle. The star represents Tippy Dam, a large impoundment on the Manistee River…………………...8 Figure 3. Diagram of hypothetical sampling plan for determining available and used habitat….12 Figure 4: Simplified table of interaction of depth and velocity based of off habitat selection of YOY Rainbow Trout in Bear Creek. The light green shading represents one variable positive selection. The darker green shading represents expected positive selection with two variables, while the oval represents actual positive selection………………………………………………52 ix INTRODUCTION Recruitment of potadromous salmonid populations in the Great Lakes is a combination of annual plantings of hatchery reared fish and natural reproduction. Success of naturally produced smolts is often weakly related to prey populations, and managers must face the challenge of maximizing salmonid production without decimating the forage base. As early as the mid 1980’s researchers recognized that, if natural recruitment continued to increase and stocking levels were maintained, prey fish populations would sharply decrease (Eck and Brown 1985). Natural reproduction is now driving many populations and the high abundance of salmonids has led to declines in prey fish abundance (Claramunt 2009), complicating management of this predator- prey system (Tsehaye et al. 2014). Determining the input of smolts and juveniles from natural sources is critical to our understanding of these populations, particularly so in the face of a declining forage base. Surveys conducted during the 1980s and 1990s (Carl 1982; Keller et al. 1990) in the Great Lakes and their tributaries provided evidence of natural recruitment occurring for migratory salmonids. While these studies were useful in providing some system-specific estimates of natural recruitment, they did not provide a clear picture of the total contribution of natural recruitment lake wide. More recent surveys have been conducted, indicating that natural reproduction levels of salmonids are approximately equal to the additions made through artificial stocking (Hesse 1994; Rutherford 1999; Jonas et al. 2008; Williams 2012), however, there appears to be substantial variation among salmonid species. Large scale oxytetracycline marking efforts have shown that approximately 50% of Chinook Salmon (Oncorhynchus tshawytscha) are being produced through natural reproduction (Williams 2012). Historical observations were that 9% of the total Coho Salmon (Oncorhynchus kisutch) population in the Great Lakes region came 1 from natural reproduction (Patriarche 1980), but no recent estimates have been produced (Jonas et. al 2008). Migratory Rainbow Trout (i.e., Steelhead; Oncorhynchus mykiss) populations have been heavily stocked since the 1980’s. These stocking events shifted the percentage of naturally reproduced Steelhead from approximately 96% down to 17% (Rand et al. 1993; Barton and Scribner 2004) of total recruitment. However, during the late 1990’s, the Manistee River still had catches of naturally produced Steelhead of between 30 and 50% (Rutherford 1999). The Manistee River basin is a well-known source of hatchery reared and naturally reproducing potadromous salmonids to the Great Lakes (Carl 1983). Historically, stocking efforts supplemented natural reproduction, but as stocking efforts have been eliminated on some of the tributaries flowing into the Manistee River (Tonello 2014), the reliance on natural reproduction has increased. The Manistee River Management Plan, Management Action 7 (Rozich 2006), highlights the fact that there are a large number (over 100) of tributaries to the Manistee River, but the data are not up-to-date with regards to information on the levels of natural reproduction of potadromous salmonids. Bear Creek, a National Scenic River and Blue-Ribbon trout stream, has been identified as a potentially important contributor to potadromous salmonid production (Tonello 2014). Bear Creek flows into the Manistee River downstream of Tippy Dam, allowing access by migratory fish species. This unimpeded access allows Bear Creek to support both potadromous and resident salmonid species. The number of salmonids produced in Bear Creek is currently unknown, but surveys conducted in the 1960’s and early 2000’s show relatively large populations of juvenile Steelhead, juvenile Chinook Salmon, juvenile Coho Salmon, as well as resident Brook Trout (Salvelinus fontinalis) and Brown Trout (Salmo trutta) (Tonello 2014). Preliminary habitat surveys were taken in tandem with the early 2000 fish surveys, but only at a single sampling 2 location since 1983, providing evidence that Bear Creek has high quality spawning and rearing habitat (Tonello 2014). With data being collected from a single location, it raises the question of how the available habitat within Bear Creek relates to the total population of salmonids supported in this stream. This leads to the first objective of my research, to quantify the density of juvenile salmonids in tributaries to the Lower Manistee River, with an emphasis on Bear Creek, to estimate total potential production of potadromous smolts. Previous surveys conducted on the Bear Creek system focused on the main stem of the river, but smaller tributaries to Bear Creek are also cold-water streams that provide potential habitat for salmonids. Consequently, the second objective of my research is to determine the extent to which tributaries of Bear Creek contribute to juvenile salmonid production and how that amount compares to the main stem of Bear Creek. Not all habitats provide equal utility to organisms in terms of physical conditions, protection from predators, and access to food. This variation across habitats leads to non-random use of space, or habitat selection. Utility of a habitat can depend on many factors, such as energetic cost, energetic gains through foraging, and risk of predation. Organisms select habitats to fulfill their requirements for individual growth and survival (Hayes et al. 1996). This combination of traits comprises an organism's niche, which varies among species and individuals based on an organism’s genotype and phenotype (Shuter 1990). The habitat requirements of an individual organism can change at various life stages, thus changing the ontogenetic niche of that individual. The habitat requirements of an organism can be grouped as either biotic or abiotic or alternatively classified as consumable or non-consumable (Tilman 1982). Pielou (1974) argues that consumable resources (i.e. prey resources or oxygen) typically function as density dependent factors to determine fish production. Non-consumable resources (i.e. water depth or velocity) 3 function as density independent regulators, as they are not affected by the number of fish present. However, non-consumable resources are closely linked to an area or space where they are present, and as such, the space associated with these conditions functions as a consumable resource within an environment. For example, water depth is a non-consumable resource, but the availability of habitats with the preferred water depth may function in a limiting manner to population growth, thus acting as a density dependent variable. The more closely the consumable and non-consumable resources match the requirements of an organism, the higher the population production will be, as organisms have higher growth and survival (Rosenburg et al. 2000). In general, fish populations depend strongly on the growth and survival of young-of-year individuals, which further depends on habitat conditions present in the environment. As such, understanding habitat selection by young fishes is particularly important to understand environmental factors that could limit their production (Freeman et al. 2001). For example, Lobon-Cervia and Rincon (2004) found that environmental variability, notably discharge, influenced the population dynamics of Brown Trout to a greater extent than density dependent factors. They concluded that the availability of preferred micro-habitats that afford protection from high discharge for juvenile trout was a key factor that determines annual recruitment. There is evidence this also occurs within the Great Lakes basin. Benson (1953), Latta (1965), and Newcomb (1998) linked young of year and mature salmonid populations to groundwater and flow conditions, both environmental factors. More recently, Zorn et al. (2006) stressed the influence of regional and local scale habitat conditions on trout population dynamics. While these studies stress the importance of favorable environmental conditions, Chadwick (1982) provides evidence for migratory salmonids that it is a combination of both favorable environmental conditions and spawning stock size that determines annual recruitment. 4 Despite the importance of habitat conditions for juvenile fishes and the interest in salmonids in the Great Lakes region, there is still a knowledge gap associated with habitat selection by juvenile salmonids living in this region, and particularly when these species occur in sympatry. Fausch (1981) examined how habitat selection changed with the removal of competitive species but his study was limited to Brook Trout and Brown Trout. He determined that increases in juvenile Brown Trout populations led to declines in juvenile Brook Trout populations. In contrast, Kocik et al. (1995) found no significant impacts of introduction of age-0 and age-1 Steelhead on resident Brown Trout populations. Cunjack (1986) contrasted habitat selection between sympatric Brook and Brown Trout, but was only focused on selection during the winter months. He found these species shared similar water velocities throughout the winter months and preferred overhead cover, but varied in the water depth they resided in. McRae et al. (2005) was one of the first studies in the region to focus on young of year habitat selection in trout, rather than population changes as a result of competition. They examined habitat conditions impacting densities of young of year Brook and Brown Trout in the Au Sable River. They found that substrate conditions and the presence of vegetation were the two most important habitat variables for describing young salmonid density. Bellgraph et al. (2006) compared growth rates of age-0 Steelhead and Brook Trout in the Pine River, Michigan, however no link to habitat conditions or competitor density was found to impact their growth rates. The gap in our understanding of detailed habitat selection leads to the third objective of my research: evaluate habitat selection of juvenile salmonids particularly focusing on habitat selection of young of year salmonids living in sympatry. My study is the first of its kind for the region that examines habitat selection where five species of salmonids live in sympatry, and with the focus being on young of year fish. 5 Site Selection METHODS Bear Creek, located in Manistee County, is a cold-water tributary to the Manistee River. Located near the towns of Copemish, Brethern, and Kaleva, the watershed is approximately 140,000 acres (Anonymous 2013). Bear Creek enters the Manistee River downstream of Tippy Dam. There is a lowhead dam located near Coates Highway; the dam does not impede passage of salmonids, allowing them to access most of the Bear Creek watershed (Figure 1 and 2). The headwaters of Bear Creek near the confluences of Third Creek to 9 Mile Road are classified as a “Blue Ribbon Trout Stream” according to the Michigan Department of Natural Resources. After passing Coates Highway, the river flows westward and a 6.5 mile stretch is designated as a “National Scenic River” by the Wild and Scenic Rivers Act (Tonello 2014). Bear Creek is a low gradient system with an average gradient of 1.23 m/km, which is average for the Manistee River watershed (Rozich 1998). The Bear Creek watershed is a combination of agricultural forest (45%), wetland (18%), land (15%), grassland (14%), developed land (6%) and open water (2%), with a majority being private land ownership (Anonymous 2013). This private landownership creates poor public access for much of the river system (Tonello 2014). Bear Creek supports a highly diverse fish community (Appendix Table 1), with salmon and trout being the primary target of anglers (Tonello 2014). 6 Figure 1. Map of sampling sites on the main stem of Bear Creek. Sites are denoted by a yellow circle. The star represents Tippy Dam, a large impoundment on the Manistee River. 7 Figure 2. Map of sampling sites for tributaries of Bear Creek. Sites are denoted by a red circle. The star represents Tippy Dam, a large impoundment on the Manistee River. Sampling sites were distributed widely across the watershed to ensure representation from a variety of habitats along the entire reach of Bear Creek (Figure 1 and 2). Ease of access into the stream had to be considered as there is only one public access site located on 9 Mile 8 Road. The land surrounding Bear Creek is owned by private landowners. Bridge crossings presented an ideal entrance point into the river as they allowed public access and were approximately equally spaced along the river. Permission from private landowners was also granted at sites where bridges did not exist. We sampled from the confluence of First Creek and Second Creek, considered the start of Bear Creek, to Spirit of the Woods, a conservation club located on Coates Highway just before the Manistee National Forest. The sampling area between these two locations equated to approximately 23 miles of river. An additional sampling location was conducted near the confluences of Bear Creek and the Manistee River. Sampling also occurred on the major tributaries to Bear Creek. The major tributaries of Bear Creek were selected from a list generated by the Michigan DNR. Sampling sites on the tributaries occurred at bridge crossings or areas where permission was granted from private landowners. Sampling was conducted at the most downstream location of tributaries where road access was possible. Upstream sampling was also conducted to identify the upstream border to our tributary study area. The cumulative total tributary sampling area was approximately 23 miles of river. Fish Surveys: Field Methods A primary objective of this research was to determine fish density and overall fish species composition within Bear Creek and its tributaries. This objective was addressed by conducting electrofishing surveys. Barge electrofishing surveys were conducted at all mainstream sections and a backpack electrofisher was used in smaller tributaries (sites <5m wide). In 2015, the river was broken into sections based on homogenous geomorphic units, such as runs, riffles, and pools. These sites on average tended to be between 55-60 m in length. In 2016 however, the river was divided into sites with a fixed length of 100 meters in order to encompass greater habitat 9 diversity and for estimating density and habitat selection. Sampling sites were selected based on legal entrance points into the river, as much of the watershed is on private land. GPS locations were recorded at the upstream and downstream edges of the sampling area, as well as total section length using a range finder and section width using a tape measure. Within each sampling area, habitat surveys were conducted to estimate the amount of run, riffle or pool habitat as well as the dominant and secondary substrates. In 2015, triple pass removal sampling was conducted at each main stem site, and a single pass was done at each tributary site. In 2016, triple pass removal surveys were done at each main stem and tributary site. Sampling was conducted using this methodology, twice at each location throughout the summer to account for potential changes in distribution and abundance and to determine growth of young of year salmonid species. The first sampling window occurred during May and June where each site in the main stem and tributary was visited once and all species were measured and recorded. This was repeated in a second sampling window from July to mid-August, but only salmonid species were measured and recorded. Catch of all species was recorded in the multiple pass surveys to better understand the overall fish assemblage within the watershed (Appendix Table 1). All fish were measured for total length to the nearest mm, identified down to species and salmonids were separated as either young of year or non-young of year. True density was estimated using a depletion estimator across all sites and sections allowing for an estimate of the total standing stock, further described in the population estimation section. Habitat Selection The second objective of this research was to evaluate habitat selection by young salmonids. To accomplish this objective, I used a micro level habitat evaluation across multiple 100-meter sections of river throughout the watershed. At each site, a single pass with a barge 10 electroshocking unit was conducted. At each capture location, numbered markers were placed and information on the species of fish and size were transcribed to a data sheet, linking the fish to the capture location. Upon completion of the fish surveys, habitat measurements were taken at each fish capture location. Water depth and velocity, and distance from the bank were measured using a flow meter (SonTek FlowTracker) and fiberglass tape measure respectively. Substrate conditions were determined using a pebble count (n = 5 at each point), where each pebble was measured along its intermediate axis or recorded as clay, silt, or sand based on texture (Wolman 1954). The presence or absence of wood debris and instream overhead cover was determined using visual estimates, these variables were deemed present if they were in the immediate vicinity of a fish capture site. These measurements were taken at each capture site to determine habitat used by salmonids and were also recorded at a random set of points in the river (see Figure 3). Available habitat was characterized using a blended systematic/random sampling design. Every 2 meters along the 100-meter section, a transect was drawn across the river, perpendicular to the flow. A number between one and one hundred was generated using a random number generator to denote the percent width that a random point was dropped to measure available habitat. These random points were used to quantify the amount of available habitat in the river at a site, using the same habitat measurements as at fish capture points. 11 Figure 3. Diagram of hypothetical sampling plan for determining available and used habitat. 12 Selectivity Analysis To evaluate habitat selection by juvenile salmonids the Chesson’s Index (Chesson 1978, 1983) was used to compare habitat types used by salmonids relative to their proportion in the environment to identify habitat selection. Chesson’s (α) is defined as: (cid:1)(cid:2) = (cid:4)(cid:5)(cid:2)(cid:6)(cid:2)(cid:7) (cid:10) (cid:4)(cid:5)(cid:2)(cid:6)(cid:2)(cid:7) ∑(cid:9) Where (cid:1)(cid:2) = selectivity coefficient of habitat type i, (cid:5)(cid:2)= proportion of habitat type i used by the salmonid, (cid:6)(cid:2)=proportion of habitat type i in the environment, and n = number of available habitat types in the environment. Positive selection is indicated when (cid:1)(cid:2)> (1/n), neutral selection when (cid:1)(cid:2)= (1/n), and negative selection when (cid:1)(cid:2)< (1/n). Chesson’s Rescaled Index of Selection (1983) was then calculated to measure selection on a scale of -1 to 1, with -1 representing complete avoidance, 0 representing neutral selection and 1 representing total section for habitat type i. Chesson’s Rescaled Index of Selection ((cid:1)(cid:2) (cid:11)) is defined as: (cid:11) = (cid:1)(cid:2) (cid:10) (cid:13)(cid:14)(cid:15)(cid:9) (cid:16)(cid:10)(cid:15)(cid:17)(cid:18)(cid:13)(cid:14)(cid:19)(cid:9) , (cid:21) = 1, . …,(cid:25) Where (cid:1)(cid:2) (cid:11)=rescaled selectivity coefficient of habitat type i. 13 Population Estimation Triple pass electrofishing was used to estimate catchability of salmonid species, with young of the year (YOY) fish being calculated separately by species, in Bear Creek. Declines in catch (n1, n2, n3) across passes was used to estimate catchability and abundance using the following equation Zippen 1958 as cited in Hayes et al. (2007): where X = 2n1 + n2 and Y = n1 + n2 + n3. (cid:26)(cid:27) = (cid:28) (cid:16)1 (cid:29) (cid:30)(cid:31) (cid:18) and, !(cid:16)(cid:26)(cid:27)(cid:18) = (cid:26)(cid:27)(cid:16)1 (cid:29) (cid:30)(cid:31) (cid:18)(cid:30)(cid:31) (cid:16)1 (cid:29) (cid:30)(cid:31) (cid:18)(cid:17) (cid:29) "#3(cid:16)1 (cid:29) (cid:30)(cid:31)(cid:18)%(cid:17)(cid:30)(cid:31) (cid:15)(cid:9)& Each sampling site was sampled once in May or June 2016 (denoted as Early) and once in July or August 2016 (denoted as Late). In many cases, the total catch of an individual species at a site was too low (e.g., <20) to allow for reliable estimates of catchability and population size. To address this issue, catchability was estimated by pooling catches across sites within a sampling period (Early or Late) and/or by stream type (Mainstem or Tributary). Pooling in this way presumes that catchability was similar within a sampling period and stream type combination. If adequate sample size was still not reached, then catch was pooled across sampling period within stream type. If adequate sample size was still not obtained, catch was pooled across stream type. Pooling of catches was also done in instances where there was not a 14 significant difference between non-pooled catchability estimates using a 95% confidence interval. Using this process, catches were generally pooled by sampling period, within stream type, except for YOY Rainbow Trout where there was a significant difference in catchability across time and a large enough sample size to provide for individual estimates of catchability. Three pass sampling was conducted for all 2015 main stem sites, but was not conducted in 2015 on the tributary sites and thus I could not directly estimate catchability for those sites; I instead applied the 2016 tributary pooled estimate of catchability to single pass catches from 2015 tributary sampling. Table 1 outlines the catchability estimates used for each species and age group. Table 1. Catchability estimates used to estimate density of fish in the Bear Creek watershed. Main Stem Tributaries Species 2015 2016 Early 2016 Late 2015 2016 Early 2016 Late RBT YOY RBT BKT YOY BKT BNT YOY BNT COS CHS 0.20 0.57 0.21 0.70 0.20 0.49 0.43 0.21 0.42 0.45 0.23 0.50 0.25 0.60 0.35 0.25 0.25 0.45 0.23 0.50 0.25 0.60 0.35 0.25 0.29 0.45 0.23 0.50 0.57 0.60 0.50 0.25 0.38 0.45 0.23 0.50 0.57 0.60 0.50 0.25 0.25 0.45 0.23 0.50 0.57 0.60 0.50 0.25 Estimated fish abundance was converted to density expressed both as fish per kilometer and fish per hectare. Measurements of site length and width were taken at each sampling location and used in combination with our site level population estimates to estimate density at across all sites. These were pooled for an average density across all sampling locations and extrapolated out to estimate production within Bear Creek. The estimate for the main stem of Bear Creek is from the most upstream site, down to the furthest downstream site and is approximately 37 total kilometers. The estimate for the tributaries is pooled total distance for each tributary. The 15 downstream point is the confluence of each tributary to Bear Creek and the upstream point of each tributary is the furthest upstream stretch of the river we could access via road crossing and were able to observe salmonids via a brief backpack electrofishing survey. 16 RESULTS Juvenile Salmonid Abundance In 2015 YOY Rainbow Trout were the most abundant species followed closely by YOY Coho Salmon and age-1 Rainbow Trout (Table 2). YOY Brown Trout were the next most abundant, at about 1/3 the density of YOY Rainbow Trout. Brook Trout, Brown Trout, and Chinook Salmon all occurred at similar levels of abundance. YOY Brook Trout were the least common of the salmonid species found in Bear Creek. Age-1 Rainbow Trout were the most widely distrusted being found at 19 of 24 sites. Of the juvenile salmonids, Coho Salmon, were the most widely distributed, being found at 18 of 24 sites (Table 2). YOY Rainbow Trout and Chinook Salmon were also widely distributed being found at 16 sites. YOY Brown Trout and adult Brown Trout were similarly distributed, each being found at 14 sites. YOY Brook Trout and adult Brook Trout were the least distributed being found at 6 and 10 sites of the 24 respectively. The abundance of salmonids caught in triple pass surveys in early 2016 was lower than the previous year (Table 3). Age-1 Rainbow Trout were the most abundant of all salmonids followed by YOY Rainbow Trout. YOY Brown Trout were the next most captured species. Abundance of Brown Trout, Chinook Salmon and Brook Trout and YOY Brook Trout were similar to 2015. Unlike the previous year, Coho Salmon were the least common species caught in Bear Creek in early 2016, whereas it was the second most abundant species found in 2015. Age- 1 Rainbow Trout remained as the most widely distributed species; they were found at 21 of 25 sites. Adult Brown Trout were the second most distributed species at 18 sites, up from 14 in 2015. YOY Rainbow Trout and YOY Brown Trout were found at 15 of the 25 sites. YOY Brook 17 Trout and adult Brook Trout showed a slight increase in distribution and were found at 9 and 12 sites respectively. Chinook and Coho Salmon, which were one of the most widely distributed species in 2015 were only found at 8 and 6 sites respectively. The second sampling period in 2016 differed from the early sampling period in 2016. YOY Rainbow Trout remained the most abundant, with Coho Salmon being the second most abundant, dissimilar to the early 2016 sampling period, but similar to 2015 (Table 4). Age-1 Rainbow Trout were found in lower abundance in the late sampling period compared to the early 2016 sampling period but were third in abundance. YOY Brook Trout were the next most common species followed by YOY Brown Trout and adult Brown Trout. Adult Brook Trout and Chinook Salmon were the least abundant species found in the late sampling period in 2016. YOY Rainbow Trout and age-1 Rainbow Trout were the most widely distributed with each being found at 20 of 25 sites. Coho Salmon and adult Brown Trout were the next most distributed being found at 18 and 17 sites respectively. YOY Brook Trout, adult Brook Trout and YOY Brown Trout were all found at 13 sites. Chinook Salmon had the smallest distribution, with it being at only 7 sites. 18 Table 2. Density (fish/km) in Bear Creek and its tributaries in 2015. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis. RBT YOY Sites 0 (0) Thompsonville 420 (2) Healy Lake 394 (2) Big Bear 703 (3) Leffew 318 (2) 13 Mile 123 (1) Potter 232 (2) 11 Mile 1100 (3) Lahti 1301 (4) 9 Mile 349 (2) Milks 3399 (6) Johnson 1179 (4) Kerry Spirit of the Woods 1161 (3) 3744 (6) River Rd 0 (0) Boswell Podunk 0 (0) 0 (0) Cedar 0 (0) Little Beaver Horseshoe 0 (0) 0 (0) Beaver 0 (0) Lemon 89 (2) Little Bear Dutchman 0 (0) 113 (2) 2nd 3rd - Mean density Sites present 609 16 RBT 37 (7) 619 (28) 57 (8) 676 (29) 26 (6) 16 (4) 96 (11) 799 (31) 537 (26) 211 (16) 59 (8) 250 (17) 85 (10) 0 (0) 0 (0) 0 (0) 253 (9) 0 (0) 717 (15) 4755 (38) 0 (0) 0 (0) 0 (0) 0 (0) - 383 19 BKT YOY BKT 82 (1) 360 (2) 375 (2) 42 (1) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 48 (1) 1667 (5) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) - 197 (36) 468 (55) 263 (41) 375 (49) 0 (0) 0 (0) 65 (21) 41 (16) 36 (15) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 28 (4) 0 (0) 0 (0) 0 (0) 0 (0) 124 (8) 0 (0) 42 (5) 0 (0) - 107 6 68 10 19 BNT YOY BNT 86 (1) 47 (1) 131 (1) 483 (2) 147 (1) 0 (0) 180 (1) 693 (3) 506 (2) 149 (1) 1942 (5) 472 (2) 320 (2) 0 (0) 0 (0) 0 (0) 1306 (40) 243 (17) 1221 (39) 2747 (58) 69 (9) 0 (0) 0 (0) 174 (15) - 175 (9) 315 (12) 107 (7) 25 (3) 28 (4) 0 (0) 87 (6) 138 (8) 407 (14) 0 (0) 126 (8) 0 (0) 0 (0) 0 (0) 0 (0) 46 (9) 326 (24) 0 (0) 742 (36) 1030 (43) 0 (0) 0 (0) 0 (0) 43 (9) - 455 14 150 14 COS 0 (0) 979 (15) 306 (9) 79 (4) 88 (5) 0 (0) 77 (4) 952 (15) 368 (9) 30 (3) 134 (6) 965 (15) 0 (0) 0 (0) 0 (0) 166 (9) 196 (10) 437 (15) 30 (4) 10651 (76) 619 (18) 246 (12) 0 (0) 52 (5) - 682 18 CHS 0 (0) 90 (1) 0 (0) 296 (2) 94 (1) 0 (0) 25 (1) 431 (2) 383 (2) 240 (2) 360 (2) 76 (1) 39 (1) 0 (0) 70 (1) 0 (0) 98 (2) 109 (2) 0 (0) 380 (3) 62 (1) 82 (1) 0 (0) 0 (0) - 118 16 Table 3. Density (fish/km) in Bear Creek and its tributaries in 2016 Early. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis. Sites Thompsonville Healy Lake Big Bear Leffew 13 Mile Potter 11 Mile Lahti 9 Mile Milks Johnson Kerry Spirit of the Woods 394 (9) River Rd Boswell Podunk Cedar Little Beaver Horseshoe Beaver Lemon Little Bear Dutchman 2nd 3rd 18 (2) 0 (0) 0 (0) 0 (0) 0 (0) 2053 (16) 0 (0) 0 (0) 43 (2) 0 (0) 0 (0) 0 (0) RBT YOY RBT 0 (0) 14 (2) 54 (3) 489 (10) 14 (2) 54 (3) 272 (8) 204 (7) 122 (5) 516 (10) 1753 (19) 4647 (31) 315 (10) 4080 (35) 92 (5) 1627 (22) 13 (2) 328 (10) 446 (12) 2191 (26) 577 (13) 394 (11) 1273 (20) 367 (11) 171 (7) 0 (0) 0 (0) 210 (8) 538 (13) 262 (9) 643 (14) 1482 (21) 581 (13) 131 (6) 0 (0) 787 (15) 0 (0) Mean density Sites present 426 15 660 21 BKT YOY 201 (2) 262 (2) 342 (2) 423 (3) 121 (1) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 40 (1) 0 (0) 0 (0) 0 (0) 66 (1) 80 (1) 0 (0) 549 (3) 201 (2) 91 9 BKT 75 (6) 312 (13) 275 (12) 512 (17) 25 (4) 12 (3) 0 (0) 12 (3) 62 (6) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 337 (13) 0 (0) 0 (0) 0 (0) 0 (0) 676 (19) 150 (9) 0 (0) 159 (9) 225 (11) 113 12 20 BNT YOY BNT 57 (1) 57 (1) 0 (0) 246 (2) 38 (1) 454 (3) 605 (4) 246 (2) 208 (2) 1248 (5) 132 (2) 1948 (7) 681 (4) 0 (0) 0 (0) 0 (0) 131 (13) 12 (4) 0 (0) 12 (4) 0 (0) 0 (0) 0 (0) 0 (0) 48 (8) 222 (20) 245 (21) 23 (6) 35 (8) 23 (6) 23 (6) 82 (12) 315 (24) 292 (23) 93 (13) 117 (14) 12 (5) 351 (25) 0 (0) 0 (0) 0 (0) 177 (18) 154 (16) 697 (35) 130 (15) 0 (0) 0 (0) 0 (0) 408 (27) 1654 (54) 245 15 202 18 COS 0 (0) 362 (6) 15 (1) 0 (0) 15 (1) 0 (0) 0 (0) 15 (1) 0 (0) 0 (0) 60 (2) 0 (0) 15 (1) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 19 6 CHS 0 (0) 38 (1) 0 (0) 0 (0) 0 (0) 359 (3) 0 (0) 132 (2) 19 (1) 0 (0) 530 (4) 265 (2) 757 (4) 51 (1) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 38 (1) 88 8 Table 4. Density (fish/km) in Bear Creek and its tributaries in 2016 Late. Main stem sites are ordered from upstream to downstream. Underline denotes the last main stem site; sites below River Rd. are tributary sites. Standard error displayed in parenthesis. Sites Thompsonville Healy Lake Big Bear Leffew 13 Mile Potter 11 Mile Lahti 9 Mile Milks Johnson Kerry Spirit of the Woods 624 (4) River Rd Boswell Podunk Cedar Little Beaver Horseshoe Beaver Lemon Little Bear Dutchman 2nd 3rd 26 (1) 0 (0) 0 (0) 1948 (7) 605 (4) 2365 (7) 1135 (5) 217 (2) 0 (0) 0 (0) 34 (1) 0 (0) RBT YOY RBT 57 (1) 1929 (7) 322 (3) 2800 (8) 1305 (6) 378 (3) 605 (4) 1059 (5) 511 (3) 435 (3) 1967 (7) 2100 (7) 92 (5) 157 (7) 105 (6) 420 (11) 223 (8) 184 (7) 79 (5) 341 (10) 315 (10) 105 (6) 262 (9) 157 (7) 144 (7) 0 (0) 0 (0) 66 (4) 289 (9) 118 (6) 590 (13) 958 (17) 194 (8) 0 (0) 0 (0) 143 (7) 0 (0) BKT YOY BKT 141 (2) 1167 (4) 825 (4) 1046 (4) 40 (1) 0 (0) 0 (0) 20 (1) 0 (0) 0 (0) 40 (1) 0 (0) 0 (0) 0 (0) 0 (0) 20 (1) 0 (0) 0 (0) 40 (1) 20 (1) 165 (2) 282 (2) 0 (0) 110 (1) 443 (3) 112 (8) 137 (9) 137 (9) 187 (10) 50 (5) 0 (0) 12 (3) 12 (3) 25 (4) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 87 (7) 0 (0) 0 (0) 25 (4) 0 (0) 205 (11) 37 (4) 0 (0) 136 (9) 25 (4) Mean density Sites Present 817 20 198 20 174 13 48 13 21 BNT YOY BNT 38 (1) 95 (1) 0 (0) 0 (0) 57 (1) 0 (0) 0 (0) 113 (2) 76 (1) 19 (1) 19 (1) 0 (0) 38 (1) 0 (0) 0 (0) 0 (0) 83 (10) 107 (11) 2685 (57) 380 (22) 0 (0) 0 (0) 0 (0) 22 (5) 285 (19) 105 (14) 199 (19) 12 (5) 70 (11) 70 (11) 12 (5) 82 (12) 199 (19) 269 (22) 47 (9) 47 (9) 0 (0) 315 (24) 0 (0) 0 (0) 0 (0) 187 (18) 105 (14) 315 (24) 58 (10) 0 (0) 0 (0) 0 (0) 234 (20) 795 (37) 161 13 125 17 COS 121 (3) 2141 (14) 60 (2) 1342 (11) 121 (3) 0 (0) 30 (2) 724 (8) 332 (6) 0 (0) 347 (6) 15 (1) 0 (0) 0 (0) 0 (0) 237 (11) 302 (13) 197 (10) 1050 (24) 656 (19) 452 (16) 197 (10) 0 (0) 95 (7) 945 (23) 374 18 CHS 0 (0) 0 (0) 0 (0) 95 (1) 57 (1) 57 (1) 0 (0) 57 (1) 208 (2) 0 (0) 19 (1) 0 (0) 19 (1) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 20 7 Total Abundance of Juvenile Salmonids in Bear Creek and Tributaries Total salmonid production varied amongst sampling periods (Table 5). The sampling period with the largest estimate of salmonids within the Bear Creek watershed was in 2015, followed by the 2016 late sampling period. The 2016 early sampling period estimated the fewest salmonids in the system. The variation in total estimated salmonids in the watershed came from the estimated number of salmonids in the tributaries as the mainstem estimate was consistent (between 74,769- 88,433). The variation in the tributaries was much more pronounced, ranging from 42,648 up to 107,279. Table 5. Estimation of total fish abundance within the study reach of Bear Creek. 2015 Mainstem RBT YOY RBT BKT YOY BKT BNT YOY BNT COS CHS Total Tribs 749 21,190 6,347 717 21,317 8,101 45,888 2,969 2016 Early 2016 Late Mainstem Tribs Mainstem Tribs 22,608 31,390 3,565 3,404 15,654 4,850 1,276 5,687 7,054 15,595 3,152 5,208 680 10,832 0 127 37,328 6,833 8,672 1,784 1,200 3,769 13,832 1,350 21,215 7,931 3,633 1,737 11,986 5,701 13,897 0 38,130 9,169 2,270 3,818 13,633 3,720 10,516 5,374 86,629 107,279 88,433 42,648 74,769 66,100 Habitat Relations to Juvenile Abundance Stream width was the habitat variable most closely related to site-level fish per kilometer density estimates during the early summer sampling period in 2016. YOY Rainbow Trout, YOY Brook Trout, Brook Trout, and Chinook Salmon all had a significant positive correlation with mean width (Table 6). The amount of woody debris at a site was also an important correlate to 22 density; Age-1 Rainbow Trout, YOY Brown Trout, and Coho Salmon all had a significant positive correlation with percent debris. Mean depth and mean velocity were significantly positively correlated with YOY Brook Trout and YOY Brown Trout, respectively. There was no significant correlation between density of any species and percent cover or median particle size. Table 6. Correlation (R) between habitat measures and salmonid density (fish per kilometer) for 2016 Early. Significant values (p-value <0.05) are highlighted in yellow. 2016 Early RBT YOY RBT BKT YOY BKT BNT YOY BNT COS CHS Median Particle 0.28 0.11 0.27 0.23 0.45 0.04 0.14 0.01 Mean Depth 0.09 0.23 0.54 0.42 0.06 0.04 0.01 0.04 Mean Velocity 0.47 0.18 0.14 0.00 0.79 0.10 0.30 0.06 Percent Cover 0.25 0.25 0.26 0.22 0.33 0.34 0.12 0.45 Percent Debris 0.42 0.52 0.47 0.37 0.64 0.16 0.64 0.45 Mean Width 0.55 0.11 0.74 0.64 0.46 0.04 0.17 0.56 Overall, fish density was less closely related to habitat variables during the late summer sampling in 2016, but some similarity was evident. There were no statistically significant correlations between density and median particle, mean velocity, and percent cover across all species and age groupings (Table 7). There was a significant positive correlation between mean depth, mean width and YOY Brook Trout density. Once again there was a positive correlation between Coho Salmon density and percent debris. Similar to the correlation in the early sampling period there was a positive correlation between Brook Trout density and mean width. 23 Table 7. Correlation (R) between habitat measures and salmonid density (fish per kilometer) for 2016 Late. Significant values (p-value <0.05) are highlighted in yellow. 2016 Late RBT YOY RBT BKT YOY BKT BNT YOY BNT COS CHS Median Particle 0.10 0.15 0.21 0.31 0.12 0.14 0.08 0.17 Mean Depth 0.30 0.34 0.38 0.54 0.05 0.09 0.24 0.14 Mean Velocity 0.25 0.01 0.12 0.16 0.33 0.02 0.12 0.07 Percent Cover 0.02 0.19 0.14 0.40 0.39 0.29 0.33 0.33 Percent Debris 0.07 0.07 0.50 0.55 0.46 0.08 0.55 0.06 Mean Width 0.08 0.02 0.57 0.79 0.06 0.00 0.34 0.09 Habitat Selection Microhabitat evaluations for YOY fishes occurred from July to August 2016 at 14 main stem sites, and data from all sites were pooled. Fifty random points were collected at each site, totaling 700 random point measurements. Across all sites, YOY Rainbow Trout were most abundant with a total of 308 individuals that were caught and had their position measured. We additionally caught 70 age-1 Rainbow Trout and evaluated habitat selection for this age group. YOY Brook Trout were next most abundant, with 44 individuals caught. YOY Brown Trout were also commonly caught, with 18 individuals observed. The two remaining salmonid species, Coho Salmon and Chinook Salmon, were caught in much lesser numbers. During our habitat selection surveys, we captured 15 Coho Salmon and 10 YOY Chinook Salmon and our selection indices are impacted by small sample size. Across all sites, sand was the predominant substrate, totaling 40% of the observations (Table 8). Silt was the next most common substrate, with 15% of the observations. Gravel between 10-20 mm and 20-50 mm were the next most observed groups, each with 14% of the 24 observations. All species/age groups were found most often in areas where sand or silt was the predominant substrate. Use of gravel substrates varied among species. YOY Brook Trout, YOY Brown Trout, and YOY Coho Salmon were found at a lower percent of points (23-30%) with gravel substrate than other species (38-52% of points). Clay and cobble substrates were rarely used but were also rare at our random points. Table 8. Proportion of observations of randomly selected points, and points where target fishes occurred along a gradient of substrate size. Particles 1-10, 10-20, and 20-50 mm are classified as gravel, and particles >50 mm are classified as cobble. Particles Random Clay Silt Sand 1-10 mm 10-20 mm 20-50 mm > 50 mm n points 0.03 0.15 0.40 0.10 0.14 0.14 0.04 709 YOY Rainbow Trout 0.02 0.19 0.36 0.11 0.16 0.13 0.04 308 Rainbow Age-1 YOY YOY YOY Coho Salmon YOY Chinook Salmon 0.00 0.10 0.36 0.14 0.18 0.20 0.02 10 0.00 0.28 0.35 0.08 0.07 0.15 0.08 15 Trout 0.05 0.09 0.27 0.17 0.15 0.19 0.10 Brook Trout 0.01 0.23 0.53 0.06 0.09 0.08 0.00 Brown Trout 0.00 0.39 0.37 0.08 0.07 0.10 0.00 70 44 18 Although there were some similarities in species usage of different substrates, each species showed a distinctive pattern of selection (Table 9), with the exception that all species showed negative selection or neutral selection for clay substrates (Table 9). YOY Rainbow Trout showed neutral selection across all substrates (except for clay, referenced above; Table 9). Age-1 Rainbow Trout showed positive selection only towards cobble, and negative selection for silt and sand. YOY Brook Trout exhibited positive selection towards sand and silt substrates with negative selection for cobble, and neutral selection for all other particle sizes. YOY Brown Trout 25 showed positive selection towards silt substrates, with negative selection towards gravel measuring 10-20 mm and cobble, and neutral selection for other substrates. YOY Coho Salmon similarly showed positive selection towards silt substrates and negative selection towards clay and gravel measuring 10-20 mm. They differed, however, with positive selection for cobble. Sample size for YOY Chinook Salmon was very small, but they showed positive selection for gravel, and negative selection for cobble. Table 9. Chesson’s selection index for target fishes along a gradient of substrate size. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). Particles 1-10, 10-20, and 20-50 mm are classified as gravel, and particles >50 mm are classified as cobble. Substrate Clay Silt Sand 1-10 mm 10-20 mm 20-50 mm > 50 mm YOY Rainbow Trout -0.31 0.18 -0.04 0.07 0.08 -0.05 -0.04 Rainbow Age-1 YOY Brook Trout -0.29 0.44 0.34 -0.12 -0.09 -0.18 -0.76 Trout 0.07 -0.42 -0.37 0.17 -0.15 0.00 0.36 YOY Brown Trout -1.00 0.70 0.09 0.01 -0.29 -0.08 -1.00 YOY Coho Salmon YOY Chinook Salmon -1.00 0.38 -0.09 -0.12 -0.41 0.00 0.40 -1.00 -0.14 0.01 0.29 0.21 0.27 -0.31 Across all sites, the presence of woody debris, overhead cover or both was tabulated for all random points and fish capture points (Table 10). Points where both overhead cover and woody debris were absent were the most common combination occurring at 61% of random points. The presence of both occurred 24% of the time. Overhead cover without woody debris 26 occurred 10% of the time, and rarely did we find just woody debris without overhead cover, occurring less than 5% of the time. Across all species, sites where both woody debris and overhead cover were present was the most commonly used habitat. Sites where woody debris and overhead cover were absent were the second most observed habitat type used for all species, except YOY Brook Trout and YOY Coho Salmon. The points where only woody debris was observed was the least observed habitat type for all species, except YOY Coho Salmon. Table 10. Proportion of observations of randomly selected points, and points where target fishes occurred related to the presence or absence of woody debris and overhead cover. Habitat Random Both Cover None Wood n points 0.24 0.10 0.61 0.04 711 YOY Rainbow Trout 0.52 0.14 0.25 0.09 308 Rainbow Age-1 YOY YOY YOY Coho Salmon Trout 0.66 0.06 0.29 0.00 Brook Trout 0.66 0.18 0.09 0.07 Brown Trout 0.44 0.11 0.28 0.17 YOY Chinook Salmon 0.60 0.00 0.40 0.00 10 0.80 0.13 0.00 0.07 15 70 44 18 All species positively selected habitats with both woody debris and overhead cover, except YOY Brown Trout, which had neutral selection (Table 11). All species showed negative selection of habitats that were absent of woody debris or overhead cover, with the exception of YOY Chinook Salmon, which displayed neutral selection. YOY Rainbow Trout and YOY Brown Trout were the only two fishes that exhibited positive selection to habitats with woody debris. No species showed positive selection for habitats containing only overhead cover. 27 Table 11. Chesson’s selection index for target fishes with respect to the presence or absence of woody debris and overhead cover. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). Habitat Both Cover None Wood YOY Rainbow Trout 0.26 -0.07 -0.64 0.23 Rainbow Age-1 YOY Brook Trout Trout YOY Brown Trout YOY Coho Salmon YOY Chinook Salmon 0.78 -0.32 -0.40 -1.00 0.40 0.08 -0.86 0.02 0.01 -0.32 -0.67 0.56 0.55 -0.12 -1.00 0.01 0.84 -1.00 -0.12 -1.00 All random points were grouped into equal bins for percentage distance of total stream width from the nearest bank, each random point bin contained between 8-11% of the total observations as expected (Table 12). In contrast, all species had more than 50% of their total observations close to shore, between 0-20% of stream width. Age-1 Rainbow Trout displayed a bimodal distribution with another cluster of points (36% of observations) between 25-40% of stream width (Table 12). 28 Table 12. Proportion of observations of randomly selected points, and points where target fishes occurred related to percent distance from the nearest bank. Bank Distance % Random 0-5 5-10 10-15 15-20 20-25 25-30 30-35 35-40 40-45 45-50 n points 0.09 0.10 0.10 0.08 0.10 0.11 0.10 0.10 0.11 0.11 714 YOY Rainbow Trout 0.16 0.22 0.18 0.12 0.09 0.04 0.06 0.06 0.02 0.06 308 YOY Chinook Salmon 0.10 0.10 0.10 0.30 0.00 0.10 0.00 0.10 0.10 0.10 10 0.27 0.40 0.20 0.07 0.07 0.00 0.00 0.00 0.00 0.00 15 Rainbow Age-1 YOY YOY YOY Coho Salmon Trout 0.13 0.11 0.13 0.13 0.07 0.16 0.11 0.09 0.06 0.01 Brook Trout 0.14 0.25 0.18 0.09 0.11 0.05 0.09 0.02 0.05 0.02 Brown Trout 0.11 0.11 0.11 0.22 0.22 0.11 0.11 0.00 0.00 0.00 70 44 18 YOY Rainbow Trout had positive selection for areas of the river from 0-20% of stream width and negative selection for locations greater than 25% of the stream width (Table 13). In other words, they selected for areas near stream banks, and avoided mid-channel habitats. Age-1 Rainbow Trout and YOY Chinook Salmon had positive selection only for the 15-20% stream width bin, and negative selection or no selection for other distances from the bank. YOY Brook Trout were similar to YOY Coho Salmon, with positive selection from 0-15% and negative or no selection for locations from 25-50%. YOY Brown Trout had positive selection from 15-25% and negative selection from 35-50%. 29 Table 13. Chesson’s selection index for target fishes with respect to distance from the nearest bank. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). YOY Age-1 YOY YOY YOY Bank Distance % Rainbo w Trout Rainbo w Trout Brook Trout Brown Trout Coho Salmon 0-5 5-10 10-15 15-20 20-25 25-30 30-45 35-40 40-45 45-50 0.29 0.40 0.30 0.21 -0.06 -0.51 -0.29 -0.30 -0.69 -0.35 0.17 0.05 0.13 0.24 -0.19 0.19 0.08 -0.07 -0.36 -0.79 0.20 0.48 0.32 0.05 0.07 -0.44 -0.05 -0.64 -0.45 -0.68 0.07 0.02 0.03 0.51 0.42 -0.01 0.05 -1.00 -1.00 -1.00 0.55 0.70 0.37 -0.13 -0.23 -1.00 -1.00 -1.00 -1.00 -1.00 YOY Chinoo k Salmon 0.01 -0.04 -0.03 0.65 -1.00 -0.07 -1.00 0.00 -0.09 -0.06 Random points had the highest proportion of velocities between 15-30 cm/sec, with 37% of observations (Table 14). The next highest proportion was in slower moving water from 0-15 cm/sec, with 30% of observations. There was a diminishing proportion of observations occurring for river velocity over 30 cm/sec with a max of 87 cm/sec. All species of salmonids with the exception of YOY Chinook Salmon had the highest proportion of velocities used between 0-15 cm/sec. There were fewer observations made in each subsequent bin across all of the species with regards to velocity. YOY Chinook Salmon was the exception, with 50% of observation occurring in the 15-30 cm/sec range, and the next largest proportion in the 0-15 cm/sec range with 30% of observations. 30 Table 14. Proportion of observations of randomly selected points and points where target fishes occurred along a velocity gradient. Velocity Random 0-15 15-30 30-45 45-60 60+ n points 0.30 0.37 0.25 0.05 0.03 705 YOY Rainbow Trout 0.49 0.33 0.13 0.04 0.01 308 Rainbow Age-1 YOY YOY YOY Coho Salmon YOY Chinook Salmon 0.30 0.50 0.20 0.00 0.00 10 0.73 0.20 0.07 0.00 0.00 15 Trout 0.39 0.30 0.21 0.06 0.04 Brook Trout 0.55 0.30 0.16 0.00 0.00 Brown Trout 0.50 0.33 0.11 0.06 0.00 70 44 18 All YOY salmonid species had positive habitat selection for the 0-15 cm/sec bin and negative selection in the fastest moving water (60+cm/sec). All YOY species showed negative or neutral selection for water velocities between 15-60 cm/sec, except YOY Chinook which had positive selection for velocities between 15-30 cm/sec. Age-1 Rainbow Trout were the only species without positive selection for the slowest moving water, and demonstrated positive selection for the highest velocity bin, 60+ cm/sec (Table 15). 31 Table 15. Chesson’s selection index for target fishes along a velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). Velocity YOY Rainbow Trout Rainbow Age-1 YOY Brook Trout Trout YOY Brown Trout YOY Coho Salmon YOY Chinook Salmon 0-15 15-30 30-45 45-60 60+ 0.41 0.02 -0.29 -0.06 -0.30 0.06 -0.21 -0.18 0.00 0.24 0.67 0.14 -0.01 -1.00 -1.00 0.46 0.06 -0.35 0.20 -1.00 0.85 -0.11 -0.47 -1.00 -1.00 0.30 0.50 0.15 -1.00 -1.00 Across all sites, water depth at random points ranged from 0 cm at the shore to a maximum of 129 cm (Table 16). We did not collect data at locations that had water depths in excess of 150 cm, as these points were deemed unsafe to sample. A majority of points (65%) were grouped from 15-60 cm. There were diminishing proportions of observations above 60 cm with fewer observations in subsequent bins. YOY trout species were observed in similar depth conditions with greater than 70% of observations for each species at depths from 15-60 cm. Age-1 Rainbow Trout preferred deeper habitat, where 64% of observations occurred from 45-90 cm. The salmon species displayed variable trends with 73% of Coho Salmon observations occurring from 30-60 cm and 80% of Chinook Salmon observations occurring from 45-75 cm. 32 Table 16. Proportion of observations of randomly selected points and points where target fishes occurred along a depth gradient. Depth (cm) Random 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ n points 0.08 0.20 0.22 0.23 0.15 0.07 0.03 0.01 0.01 709 YOY Rainbow Trout 0.07 0.36 0.28 0.19 0.08 0.02 0.01 0.00 0.00 308 Rainbow Age-1 YOY YOY YOY Coho Salmon YOY Chinook Salmon 0.00 0.10 0.00 0.20 0.60 0.00 0.00 0.10 0.00 10 0.00 0.20 0.40 0.33 0.00 0.07 0.00 0.00 0.00 15 Trout 0.01 0.07 0.10 0.27 0.33 0.14 0.06 0.01 0.00 Brook Trout 0.07 0.39 0.39 0.11 0.05 0.00 0.00 0.00 0.00 Brown Trout 0.17 0.33 0.33 0.17 0.00 0.00 0.00 0.00 0.00 70 44 18 YOY Rainbow Trout, YOY Brook Trout, and YOY Brown showed similar habitat selection with positive selection occurring at depths of 15-45 mm (Table 17). In addition to positive selection at depths from 15-45 mm, YOY Brown Trout showed highest positive selection from 0-15 mm. They all however, exhibited negative selection at any depth greater than 75mm. Age-1 Rainbow Trout selected deeper habitat with positive selection occurring from 60- 90 mm as well as depths of 105-120 mm. They exhibited negative selection from 0-45 mm. Coho Salmon displayed positive habitat selection from 15-60 mm and negative selection over depths of 90 mm. Chinook Salmon, due to small sample size had no discernable trends. 33 Table 17. Chesson’s selection index for target fishes along a depth gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). Depth 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ YOY Rainbow Trout Age-1 YOY Brook Rainbow Trout Trout YOY Brown Trout 0.17 0.57 0.39 0.13 -0.07 -0.52 -0.55 -1.00 -1.00 -0.77 -0.57 -0.47 0.00 0.37 0.27 0.23 0.43 -1.00 0.19 0.64 0.60 -0.10 -0.33 -1.00 -1.00 -1.00 -1.00 0.61 0.51 0.47 0.05 -1.00 -1.00 -1.00 -1.00 -1.00 YOY Coho Salmon -1.00 0.31 0.63 0.51 -1.00 0.25 -1.00 -1.00 -1.00 YOY Chinook Salmon -1.00 -0.70 -1.00 -0.53 0.27 -1.00 -1.00 0.93 -1.00 Salmonids likely select habitat using a combination of two or more variables rather than a single variable. I evaluated usage across two-dimensional habitat characterizations for the combination of water depth and velocity and water depth and distance to bank (Table 18). These combinations of variables were chosen as I felt they represented biologically interpretable habitat features. The highest proportion of points was at depths of 45-60 cm with velocities 15-30 cm/sec. The general trend appears to be that as depth increases; velocity will also increase approximately linearly to a certain point. This trend holds true until 45-60 cm in depth and 30-45 cm/sec in velocity. There are very few points at velocities higher than 45 cm/sec across all depths and few points at depths greater than 90 cm across all velocities. 34 Table 18. Proportion of observations of randomly selected points that occurred along a velocity and depth gradient. Fish proportion points are located in Appendix Table 5. Depth (cm) Random Points 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Velocity (cm/sec) 0-15 15-30 30-45 45-60 60+ 0.06 0.07 0.07 0.05 0.02 0.01 0.01 0.00 0.00 0.01 0.07 0.08 0.10 0.06 0.04 0.01 0.00 0.00 0.01 0.04 0.05 0.06 0.05 0.02 0.01 0.00 0.00 0.00 0.01 0.01 0.02 0.01 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 For YOY Rainbow Trout positive habitat selection occurred at the combination of medium depths, with a max around 60 cm with low velocity, around 0-15 cm/sec (Table 19). Positive habitat selection also occurred at low depths, 0-15 cm, with high velocity, up to 60 cm/sec. The trends displayed in Age-1 Rainbow Trout are similar to those in the YOY Rainbow Trout habitat selection table, but occur at deeper depths with a higher stream velocity (Table 18). Age-1 Rainbow Trout showed positive habitat selection for deeper water, if the velocity is lower, between 60-120 cm for depth and around 0-30 cm/sec for velocity. They also displayed positive selection at medium depths and higher stream velocity when depths were around 30-60 cm and velocities were greater than 45 cm/sec. YOY Brook Trout exhibited different trends in habitat selection where positive selection only occurred for the combination of low depth and low velocity. They positively selected habitats where depths were below 60 cm and velocities were between 0-15 cm/sec. They also selected habitats up to depths of 45 cm and velocities up to 45 cm/sec. YOY Brown Trout displayed similar trends to the YOY Brook Trout where they were more prevalent in habitats of medium depths at low velocities, where depth was below 60 cm 35 and flow was less than 15 cm/sec. There was also positive selection occurring from depths of 15- 45 cm when the velocity was less than 45 cm/sec. Table 19. Chesson’s selection index for trout along a depth and velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). YOY Rainbow Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Velocity (cm/sec) 0-15 -0.19 0.63 0.36 0.46 0.19 -0.14 -1.00 -1.00 -1.00 15-30 0.42 0.36 0.32 -0.19 -0.17 -0.79 -1.00 -1.00 -1.00 30-45 0.39 -0.05 -0.10 -0.29 -0.42 -0.45 -0.07 -1.00 45-60 0.53 0.14 0.32 -0.60 0.10 -1.00 60+ -1.00 -0.25 0.01 0.01 -1.00 Age-1 Rainbow Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-15 -0.67 -0.35 -0.14 -0.09 0.64 0.52 0.14 0.63 -1.00 15-30 -1.00 -0.52 -0.76 -0.26 0.31 -0.25 -0.12 -1.00 -1.00 Velocity 30-45 -1.00 -1.00 -1.00 -0.17 -0.08 0.44 0.40 -1.00 45-60 -1.00 -1.00 -1.00 0.47 -1.00 -1.00 60+ -1.00 -1.00 0.47 0.72 -1.00 36 Table 19 (cont’d) YOY Brook Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-15 0.27 0.79 0.77 0.30 -1.00 -1.00 -1.00 -1.00 -1.00 15-30 0.61 0.49 0.53 0.01 -0.12 -1.00 -1.00 -1.00 -1.00 45-60 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 Velocity 30-45 -1.00 0.61 0.31 -0.13 -0.04 -1.00 -1.00 -1.00 60+ -1.00 -1.00 -1.00 -1.00 -1.00 YOY Brown Trout Velocity (cm/sec) 0-15 15-30 30-45 45-60 Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0.72 0.52 0.64 0.32 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 0.66 0.46 0.04 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 0.48 -1.00 0.25 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 0.84 -1.00 -1.00 -1.00 60+ -1.00 -1.00 -1.00 -1.00 -1.00 YOY Coho Salmon tended to positively select habitat where water had a lower velocity, between 0-15 cm/sec but across a wide range of depths, ranging from 15-90 cm (Table 20). There was sparse positive selection occurring when water velocity was faster, around 15-45 cm/sec, but only at shallow depths, 15-45 cm. There was strong negative selection at the lowest depth, 0-15 cm, across all velocities. While YOY Coho Salmon selected slow moving water 37 across most depths, YOY Chinook Salmon selected slow to medium velocity water (0-45 cm/sec) at a narrow band of depths, from 45-75 cm. Table 20. Chesson’s selection index for YOY salmon along a depth and velocity gradient. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). YOY Coho Salmon Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Velocity (cm/sec) 45-60 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 0-15 -1.00 0.57 0.76 0.84 -1.00 0.87 -1.00 -1.00 -1.00 15-30 -1.00 -1.00 0.52 0.11 -1.00 -1.00 -1.00 -1.00 -1.00 30-45 -1.00 0.53 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 60+ -1.00 -1.00 -1.00 -1.00 -1.00 YOY Chinook Salmon Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Velocity (cm/sec) 45-60 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 0-15 -1.00 -1.00 -1.00 0.55 0.92 -1.00 -1.00 -1.00 -1.00 15-30 -1.00 -1.00 -1.00 0.31 0.83 -1.00 -1.00 -1.00 -1.00 30-45 -1.00 0.67 -1.00 -1.00 0.56 -1.00 -1.00 -1.00 60+ -1.00 -1.00 -1.00 -1.00 -1.00 38 I also looked at the two-variable combination of depth and distance from the nearest bank as I believe this may play a role in selection (Table 21). YOY Rainbow Trout showed positive selection for low to medium depths (15-60 cm) when nearer to the bank (0-20%). For shallow depths (0-30 cm) YOY Rainbow Trout show positive selection for a wide range of locations across the river (0-40%). Age-1 Rainbow Trout showed an approximately linear trend with relationship to depth and river location. Starting with positive selection at medium depth (45-75 cm) and near shore (0-10%) there was an increase in depth with distance from the bank. YOY Brook and YOY Brown Trout showed very similar trends in terms of depth and stream positioning. They both displayed positive selection at lower depths (15-45 cm) across a variety of positions in the steam channel (0-40%). Table 21. Chesson’s selection index for trout along a depth and % distance from nearest bank. Entries highlighted in mauve indicate negative selection (i.e., <= -0.2), uncolored entries indicate neutral selection (i.e., > -0.2 and < 0.2), and entries highlighted in green indicate positive selection (i.e., >= 0.2). YOY Rainbow Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-10 -0.04 0.58 0.50 0.59 0.50 0.23 -1.00 -1.00 -1.00 Distance (% to Nearest Bank) 10-20 20-30 30-40 40-50 0.03 0.56 0.59 0.35 -0.09 -0.44 -1.00 -1.00 -1.00 0.54 0.19 -0.20 -0.21 -0.18 -0.35 -0.12 -1.00 -1.00 0.37 0.27 -0.10 -0.38 -0.10 -0.59 -0.31 -1.00 -1.00 0.03 -0.14 0.06 -0.42 -0.71 -1.00 -1.00 -1.00 -1.00 39 Table 21 (cont’d) Age-1 Rainbow Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-10 -0.57 -0.24 -0.07 0.47 0.73 -1.00 -1.00 -1.00 -1.00 Distance (% to Nearest Bank) 10-20 20-30 30-40 40-50 -1.00 -0.50 -0.49 0.39 0.44 0.58 0.42 -1.00 -1.00 -1.00 -1.00 -0.61 -0.07 0.64 0.19 0.42 -1.00 -1.00 -1.00 -0.41 -0.25 -0.11 0.10 0.53 -1.00 0.67 -1.00 -1.00 -1.00 -1.00 -1.00 -0.33 -0.32 0.47 -1.00 -1.00 YOY Brook Trout Depth 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Distance (% to Nearest Bank) 0-10 0.51 0.69 0.79 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 10-20 -1.00 0.78 0.59 0.51 -1.00 -1.00 -1.00 -1.00 -1.00 20-30 -1.00 0.60 0.46 -0.13 -1.00 -1.00 -1.00 -1.00 -1.00 30-40 -1.00 0.20 0.54 -1.00 0.18 -1.00 -1.00 -1.00 -1.00 40-50 -1.00 -1.00 0.08 -0.07 -0.06 -1.00 -1.00 -1.00 -1.00 40 Table 21 (cont’d) YOY Brown Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-10 0.65 0.54 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 Distance (% to Nearest Bank) 10-20 30-40 -1.00 0.75 0.77 0.46 0.81 -1.00 -1.00 0.38 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 20-30 -1.00 0.49 0.73 0.56 -1.00 -1.00 -1.00 -1.00 -1.00 40-50 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 41 DISCUSSION The first two objectives of my research centered on the related questions of how many juvenile salmonids are produced in the Bear Creek system, and what are the relative contributions of main stem versus tributary habitat. The total standing stock of juvenile salmonids in the 74 km of stream sampled was approximately 106,000 to 178,000 fish. Of these, 52% were YOY and age 1 Rainbow Trout, approximately 21% were Coho Salmon, 16% were YOY Brown Trout and the remaining 11% were split between YOY Brook Trout and Chinook Salmon. Although there was substantial spatial and seasonal variation in density of these species, the final estimates of total production were quite consistent, likely due to the number of sites sampled and their broad spatial coverage across the watershed. My estimates for total standing stock of juvenile Rainbow Trout are similar to, but somewhat higher, than for the Betsie River, a similar sized tributary to Lake Michigan. The Betsie River is approximately 50 miles long with an average width of 60 feet, compared to Bear Creek which is approximately 27 miles long and has an average width of 42 feet. In 1993-1996, average YOY and age-1 Rainbow Trout abundance was approximately 20,000 and 10,000 fish respectively for the Betsie River (Newcomb and Coon 1997), whereas I observed 43,000 and 30,000 fish in these age groups for Bear Creek. These totals are relatively small, however, compared to total production estimated for much larger tributaries to Lake Michigan such as the Muskegon River (Albrecht 2014) which produced a minimal estimate of 224,000 or the Little Manistee River (Seelbach 1993) which had standing stocks in the 200,000 to 300,000 range. Although these estimates were derived by various methods and across different time periods, they indicate that, relative to its size, Bear Creek contributes as a source population of Rainbow Trout for Lake Michigan. 42 Total standing stock for juvenile migratory Chinook and Coho Salmon was lower in Bear Creek than other tributaries to the Manistee River. Bear Creek produced approximately 23,000 juvenile Coho Salmon and 5,000 Chinook Salmon annually during my study period. In comparison, in 1983 Pine Creek, another tributary of the Manistee River produced approximately 50,000 Coho Salmon (Carl 1983), with an approximate density of 4,800 fish/hectare. This was higher than densities found in Bear Creek, which had a maximum site density of 3,400 fish/hectare for Coho Salmon. While standing stock was not directly estimated for Chinook Salmon, the density of Chinook Salmon in Bear Creek was lower (122 fish/hectare) when compared to other large Lake Michigan systems estimated by Carl (1983),which included naturalized and hatchery fish, such as the Muskegon (116,000 fish/hectare), Manistee (30,000 fish/hectare), and the Pere Marquette (20,000 fish/hectare). Estimates of species-specific density of salmonids in Bear Creek tended to be similar to or lower than estimates for other cold-water Great Lakes tributaries (Table 22-27). It should be recognized, however, that the published estimates of density likely do not represent a random sample of tributaries, but often come from locations that are a priori considered important contributors of salmonine production. Further, published estimates tend not to include sites where density is zero. Factors contributing to lower density of salmonid populations within Bear Creek are difficult to ascertain. When comparing the density of salmonids in Bear Creek to other historical densities described in the literature across the Great Lakes, factors beyond habitat conditions and system size should be considered. Most systems within the Great Lakes do not offer the diversity of salmonid species that are present in Bear Creek, and this diversity may lead to lower numbers of individual species, but higher production in aggregate. 43 Table 22. Young of the year Rainbow Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Union Little Garlic Bothwell Huron Chinks Little Huron Bigelow Anna Pine Bigelow Muskegon Platte Bear Creek (MS) Bear Creek (Tribs) Species YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout YOY Rainbow Trout Citation Density (ha) Stauffer 25,550 Stauffer 18,000 Alexander 17,667 Miller 8,600 Stauffer 7,500 Stauffer 6,400 Godby 6,340 Stauffer 4,300 Carl 2,900 Carl 2,650 Godby 2,427 Taube 1,533 10 – 2,656 (562) Nisbet 44 – 7,590 (2,971) Nisbet Table 23. Young of the year Brook Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Au Sable Chinks Little Huron Anna Bear Creek (MS) Bear Creek (Tribs) Species YOY Brook Trout YOY Brook Trout YOY Brook Trout YOY Brook Trout YOY Brook Trout YOY Brook Trout Density (ha) 1029 951 623 393 14 – 894 (352) 38 – 1,000 (295) Citation Zorn Stauffer Stauffer Stauffer Nisbet Nisbet Table 24. Young of the year Brown Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Anna Au Sable Bear Creek (MS) Bear Creek (Tribs) Species YOY Brown Trout YOY Brown Trout YOY Brown Trout YOY Brown Trout Citation Density (ha) Stauffer 393 Zorn 87 9 – 1,114 (228) Nisbet 22 – 8,618 (1,101) Nisbet 44 Table 25. Age-1 Rainbow Trout density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Huron Bothwell Union Little Garlic Little Huron Anna Bigelow Pine Chinks Platte Bear Creek (MS) Bear Creek (Tribs) Species Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Rainbow Trout Citation Density (ha) Miller 8,600 Alexander 1,867 Stauffer 1,600 Stauffer 1,500 Stauffer 1,400 Stauffer 900 Carl 783 Carl 771 Stauffer 500 Taube 300 10 - 2,941(423) Nisbet 261 – 2,827 (1,112) Nisbet Table 26. Young of the year Coho Salmon density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Chinks Pine Union Anna Little Garlic Platte Little Huron Bear Creek (MS) Bear Creek (Tribs) Species Coho Salmon Coho Salmon Coho Salmon Coho Salmon Coho Salmon Coho Salmon Coho Salmon Coho Salmon Coho Salmon Density (ha) Citation 7,600 Stauffer 4,778 Carl 3,200 Stauffer 3,000 Stauffer 1,500 Stauffer 900 Taube 600 Stauffer 9- 1,543 (274) Nisbet 205 – 3,368 (1,135) Nisbet Table 27. Young of the year Chinook Salmon density (fish/hectare) in Great Lakes tributaries. The range of site densities is presented for Bear Creek with the mean in parentheses. Location Muskegon Manistee Pere Marquette White Platte Jordan Crystal Bear Creek (MS) Bear Creek (Tribs) Species Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Chinook Salmon Density (ha) 116,422 30,080 20,030 7,050 5,566 1,440 750 12 – 326 (122) 69 Citation Carl Carl Carl Carl Carl Carl Carl Nisbet Nisbet 45 Relative Contribution of Tributaries The overall contribution of tributaries to total standing stock in the Bear Creek watershed varied seasonally and by species, but the overall contribution ranged from about 25 to 50%. The tributaries comprised only 23% of the total sampling area, and as such, were more productive than the mainstem on a per area basis. More specifically, the standing stock of salmonids in the main stem of Bear Creek averaged 2,250 fish/km and 1,446 fish/ha whereas density in the tributaries averaged 1,945 fish/km, but was 4,862 fish/ha. One idea explaining this is the importance of edge habitat near the bank, it is often shallow and lower in velocity compared to the main channel of the river. From my habitat selection data, we can see that many YOY salmonid species select for edge habitat. With the tributaries being smaller in width than the main stem, much of the habitat they provide is shallow and lower velocity, leading to a high- density system. Beyond their contribution apparent in Tables 22-27, tributaries also appear to provide important seasonal habitat that may augment the productivity of the system as a whole. There are no dams on the section of Bear Creek under study, and as such, fish are able to migrate within the system. Of particular interest is the potential movement of YOY Brown Trout. In the initial sampling of 2016, 328 YOY Brown Trout were caught, with 313 (95%) captured in the main stem of Bear Creek. Of those 313, 223 (71%) were captured downstream of the 9 Mile Road crossing. This crossing is located near the confluences of two tributaries to Bear Creek (Beaver Creek and Horseshoe Creek). In the second sampling period I captured 311 YOY Brown Trout with 287 (92%) captured in the tributaries. Only 3% of the YOY Brown Trout captured were located downstream of 9 Mile Road. Further 90% of the fish located in the tributaries were located in Beaver and Horseshoe Creek. While we did not track or clip fish in this study, this 46 suggests that many of these YOY Brown Trout originated in the main stem of Bear Creek and then migrated upstream into either Beaver Creek or Horseshoe Creek. For all species combined, 26% were located in tributaries early in 2016 (Table X), but nearly 50% were in tributaries in the later sampling period, highlighting the seasonal importance of these habitats. Although small tributaries make substantial contributions to the production of salmonids in the Bear Creek system, most of the management effort and protection is focused on the mainstem. For example, the mainstem of Bear Creek is covered by National Scenic River and Blue-Ribbon Trout Stream designation, whereas the small tributaries feeding into Bear Creek do not receive the protection afforded by these designations. Such a focus on larger stream sections is not uncommon, as management agencies often prioritize larger systems where stakeholders exert higher fishing pressure and recreational use as smaller tributaries can be difficult to access. This is the case for Bear Creek where access to the smaller tributaries is limited as the majority are located entirely on private property. Despite the challenges posed by working on these smaller tributaries, there clearly would be value in protecting the habitat they provide and maintaining connectivity with downstream reaches (Junge 2013) Microhabitat Use and Selection Thomas and Taylor (1990) identified and outlined three study designs for evaluating habitat selection that can be implemented regardless of sampling protocol. In Design I, variables are measured at the population level for the entire study area and individual organisms are not identified. Fisheries habitat studies utilize this design when nets are set to identify used habitat and broad scale habitat features are identified for available habitat. In Design II, individual organisms are identified to quantify used or unused habitat resources, whereas available 47 resources are measured at the population level. Diet studies involving fish often employ this design where gut contents of individuals are collected and random samples of available food items are collected from the study area. This was practical for this study as microhabitat information was collected on a per fish basis, while available resources were identified at a population level. Design III once again identifies individual organisms, but resource units used are sampled or censused for each organism. Radio telemetry studies can be conducted using this design where an individual fish is tagged and available habitat around the fish is randomly sampled to identify available and used habitat. Ultimately Design II was the most appropriate design for this project, where available habitat resources were collected at the population level, while used resources were collected for individual fish. This allowed the opportunity to identify habitat selection using the Chesson’s Index (Chesson 1983), commonly used in diet studies, but rarely if ever used for habitat selection. It is understood that within selection there is a process of determination that organisms employ. Selection is done in a hierarchical way, beginning with the home range of the organism within a broader geographic landscape. The broader geographic landscape for this study is the Bear Creek watershed. It consists of the main stem, Bear Creek, and multiple tributaries that fish potentially move between. The home range of individual fish often encompasses several micro habitat types which can be broken into general use habitats that are then further divided into features where elements of the features are chosen (Manly et al 2002). These elements are what we identify with our microhabitat surveys and can be combined to describe the preferred habitat for a fish species or age class. Adult spawning salmonids utilize both the main stem and tributaries of Bear Creek for egg deposition (Tonello 2014), so juveniles are born across the entirety of Bear Creek. YOY 48 salmonids are not restricted to the section of the river they are born into but begin habitat selection early in their life cycle. We sub-divided the river into the headwaters, middle reaches, and lower reaches. These areas of the river differ in width, water temperature, and other key variables and the salmonids in Bear Creek show varied distributions between these areas, for example are Brook Trout more concentrated in the headwaters. This varied distribution demonstrates large scale habitat selection. Habitat selection at the microhabitat level is the selection of individual habitat features and this occurred within each site. By analyzing used and available habitat variables, such as depth, velocity, substrate, available covers, and the presence of woody debris, I incorporated each variable’s selection index to form a broader picture of habitat selection for each species with the focus on YOY salmonids. Coho and Chinook Salmon were omitted from analysis due to low sample size and the Chesson’s Index struggled to accurately portray selection, when multiple habitat variables were zero, as sample size was small. Habitat selection by YOY and Age-1 Rainbow Trout in Bear Creek was broadly similar to that observed in the literature. I observed age-1 Rainbow Trout to show a preference for larger substrate (>50mm), and for areas of the river that provide a combination of overhead cover and woody debris. In contrast to YOY Rainbow Trout they preferred higher velocity (60+ cm/sec) sections of the river, as well as mid to high range depths (60-120 cm). In comparison, Gatz et al. (1987) found that YOY Rainbow Trout in Appalachian streams selected for somewhat faster water velocity (15-29 cm/s) than in Bear Creek (0-15 cm/s), but both populations selected for similar water depths (30-45 cm) and had little selection preference toward a particular substrate. Appalachian YOY Rainbow Trout selected areas near vegetation, while Bear Creek YOY Rainbow had positive selection towards areas of the stream that provided overhead cover and woody debris. In Newfoundland streams, Cunjack and Green (1983) also found that age-1 49 Rainbow Trout showed a strong preference for higher water velocities, but preferred open water positions. YOY Brook Trout habitat selection in Bear Creek was similar to that described by other authors. I found that YOY Brook Trout show positive selection for fine substrates (silt and sand), and for areas of the river that provide a combination of overhead cover and woody debris. Three studies conducted in Pennsylvania streams found similar results, with minor differences (Johnson 2008, Johnson 2011, and Magoulick 1997). Similar to Bear Creek, close association to cover was found in all three systems, but YOY Brook Trout were found on substrates that were slightly larger (Averaged between 4.9 – 5.5 cm). Bear Creek YOY Brook Trout demonstrated positive selection for areas of the river with depths between 15-45 cm and velocities 0-15 cm/s. This tended is similar to the Pennsylvania systems (Johnson 2008, Johnson 2011, and Magoulick 1997) which had average velocities and depths within the range of selected depths and velocities for Bear Creek. In the study of Newfoundland streams, Cunjack and Green (1983) found that Brook Trout preferred relatively low velocity areas as I observed and had a strong preference for cover. Habitat selection by YOY Brown Trout in Bear Creek was highly similar to habitat selection described in the literature. In Bear Creek YOY Brown Trout had a preference for silt substrates which different in comparison to Gatz (1987) who studied YOY Brown Trout in the presence of YOY Rainbow Trout in Appalachian streams. In Appalachian streams, YOY Brown Trout selected for sandy substrates. They were however similar for other habitat variables, both selected for low velocity water (0-15 cm/sec) and had depth preferences that were overlapping (30-45 cm). Gatz et al. (1987) also looked at proximity to vegetation and how exposed to sunlight the YOY Brown Trout were. He found they selected areas of the stream that were 50 shaded and near vegetation. In Bear Creek we looked at similar variables, YOY Brown Trout selected areas that were near woody debris (downed log, root wads, etc.), which often provide shade from sunlight. One issue with habitat selection is the fish are only able to demonstrate positive selection for areas of habitat that is available to them. If a habitat type was not observed in one of our surveys, the fish are unable to demonstrate positive selection for that type. It may be more preferential than the habitat conditions displayed in this study, but we are unable to account for that preference (i.e. extreme depths or velocities). Considering habitat selection as a multi-variable variable process provides a deeper and more accurate understanding of how fish select habitat. To illustrate this concept, I will discuss how viewing the process as a sequence of single habitat variable selection can be an oversimplification. For instance, YOY Rainbow Trout showed positive selection for depths of 15-45 cm and for water velocities between 0-15 cm/sec as illustrated in Figure 24. As such, one would predict that YOY Rainbow Trout would show positive habitat selection for points in the stream that are 15-45 cm deep and have a water velocity of 0-15 cm/sec. The actual pattern of selection when both variables are considered simultaneously is represented by the oval in Figure 24, where fish show positive selection for shallower points when velocity is high, and for somewhat deeper points when velocity is low. This pattern indicates that fish make habitat choices based on the interaction between habitat variables. While this concept is useful, and I recommend pursuing this in greater depth, a practical limitation is that the density of data points diminishes as more variables are included in a simultaneous analysis. 51 Figure 4: Simplified table of interaction of depth and velocity based of off habitat selection of YOY Rainbow Trout in Bear Creek. The light green shading represents one variable positive selection. The darker green shading represents expected positive selection with two variables, while the oval represents actual positive selection. Depth (cm) Future Research 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105- 120 120+ 0-15 Velocity (cm/sec) 15-30 30-45 45-60 60+ Continuation of this project with the focus of expanding the microhabitat work done could prove beneficial to understanding fisheries habitat selection. For Bear Creek, the microhabitat surveys could be expanded to the tributaries to further explain the importance of how juvenile salmonids use small tributaries within a watershed. Increasing the number of surveys within Bear Creek would increase the sample size of both random and fish capture points to build a large combination of variables for further multi-variable analysis. Conducting the microhabitat surveys in other systems expands the scope of this research to see if the results present in Bear Creek are system specific or rather a trend for salmonids in the Great Lakes region. These surveys would ideally be conducted throughout the year to capture multiple life history stages and to see how habitat selection changes seasonally. The work already conducted 52 focused on juveniles, but the process can be used for non-juveniles and is not salmonid specific. The research done on Bear Creek will help direct management of the system into the future. 53 APPENDIX 54 Table A1: 2016 fish community results came from 2016 Early triple pass shocking results from both main stem and tributary sites. No 2016 Late data was used as only salmonid species were recorded during those passes. *Tiger Trout was captured in 2016 Late surveys Fish Rainbow Trout Sculpin Rainbow Trout YOY Blacknose Dace Brown Trout Brown Trout YOY Brook Trout Common Mudminnow Johnny Darter White Sucker Creek Chub Chinook Salmon Brook Trout YOY Round Goby Coho Salmon Burbot River Chub Stickleback Rock Bass Northern Redbelly Dace Common Shiner Hornyhead Chub Pearl Dace Bluegill Golden Redhorse Logperch Northern Pike Grass Pickerel Longnose Dace Shorthead Redhorse Alewife Largemouth Bass Yellow Perch Tiger Trout* Count Percent 1234 807 775 525 365 330 200 0.23 0.15 0.14 0.10 0.07 0.06 0.04 189 168 150 143 115 96 49 32 31 30 25 20 15 10 10 6 5 5 5 5 2 2 2 1 1 1 1 0.04 0.03 0.03 0.03 0.02 0.02 0.01 0.01 0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 55 Table A2: Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites. Site Thompsonville Healy Lake Big Bear Leffew 13 Mile Potter 11 Mile Lahti 9 Mile Milks Johnson Kerry Spirit of the Woods River Rd Boswell Podunk Cedar Little Beaver Horseshoe Beaver Lemon Little Bear Dutchman 2nd 3rd Mean Width (m) 2015 21.05 2016 20.89 31.141 42 30.5 34.731 28.15 24.1353 47.40 38.1843 34.50 40.6451 39.392 49.85 41.50 52.531 53.25 37.888 44.60 38.8431 47.80 50.6019 41.65 54.6451 7.3 10 7.15 15.35 39.55 46.1829 43.45 42.0529 7.75 7.10 17.85 11.90 11.70 13.00 31.00 20.20 17.60 17.65 N/A 10.25 17.25 31.55 24.15 18.05 17.95 12.5 Width N Substrate 2016 D90 D50 D10 N 1 0.01 255 1 0.01 255 4 0.01 255 3 0 255 1 0.01 255 1 0.01 255 1 0.01 255 15 0.01 255 1 0.01 255 1 255 9 0.01 255 8 0 240 1 0.01 255 5 27 30 37 12 16 25 41 37 275 30 29 47 50 50 50 50 50 50 50 50 50 50 50 50 20 50 50 1 1 0.01 255 Width S.E. 2016 0.4507 0.7641 0.9032 0.8439 1.3708 1.0365 0.8075 1.4008 0.8911 1.3446 1.1904 1.146 0.5206 0.5827 56 Table A3: Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites. Depth N Velocity Velocity Velocity Site Thompsonville Healy Lake Big Bear Leffew 13 Mile Potter 11 Mile Lahti 9 Mile Milks Johnson Kerry Spirit of the Woods River Rd Boswell Podunk Cedar Little Beaver Horseshoe Beaver Lemon Little Bear Dutchman 2nd 3rd Depth S.E. 2016 0.0757 0.1094 0.0729 0.0841 0.073 0.1118 0.1007 0.08 1.055 0.1554 0.1114 0.0992 0.0902 0.1147 Mean Depth 2016 0.9804 1.5118 1.1735 1.0784 1.5982 1.3216 1.6314 1.068 1.982 1.8775 1.5906 1.3449 1.6402 2.148 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 2016 50 50 50 50 50 50 50 50 49 50 50 46 50 50 57 2016 0.6816 0.6629 0.6306 0.9457 0.6757 0.6518 0.8365 0.7078 0.7394 1.013 0.6437 0.9983 S.E. 2016 0.0546 0.0603 0.06 0.0845 0.0448 0.0605 0.0893 0.0983 0.0726 0.1396 0.0743 0.0785 0.8996 0.7541 0.0602 0.0492 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N 2016 50 50 48 50 50 49 50 50 49 49 50 46 50 50 Table A4: Site level details in Bear Creek and its tributaries in 2015 and 2016, main stem sites are ordered from upstream to downstream. River Rd is underlined to denote the last main stem site; sites below River Rd. are tributary sites. Site Thompsonville Healy Lake Temp Mean 2016 62.51 Temp S.E. Temp N 2016 0.06 2016 6156 Big Bear Leffew 13 Mile Potter 11 Mile Lahti 9 Mile Milks Johnson Kerry Spirit of the Woods 64.16 0.04 0.07 6155 6153 River Rd Boswell Podunk Cedar Little Beaver Horseshoe Beaver Lemon Little Bear Dutchman 2nd 3rd 70.74 59.89 0.06 6161 53.18 0.03 6143 58 Table A5. Proportion of observations of fish capture points for trout species across age groupings that occurred along a velocity and depth gradient. Velocity (cm/sec) YOY Rainbow Trout 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-15 0.03 0.21 0.11 0.10 0.03 0.01 0.00 0.00 0.00 15-30 30-45 45-60 0.02 0.11 0.11 0.05 0.03 0.00 0.00 0.00 0.00 0.02 0.03 0.03 0.03 0.02 0.01 0.01 0.00 0.00 0.00 0.01 0.02 0.00 0.01 0.00 0.00 0.00 0.00 60+ 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Depth (cm) Velocity (cm/sec) Age-1 Rainbow Trout Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-15 0.01 0.04 0.07 0.06 0.13 0.04 0.01 0.01 0.00 15-30 0.00 0.03 0.01 0.07 0.14 0.03 0.01 0.00 0.00 30-45 0.00 0.00 0.00 0.06 0.06 0.07 0.03 0.00 0.00 45-60 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.00 0.00 60+ 0.00 0.00 0.01 0.03 0.00 0.00 0.00 0.00 0.00 59 Velocity (cm/sec) 30-45 0.00 0.07 0.05 0.02 0.02 0.00 0.00 0.00 0.00 45-60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Velocity (cm/sec) 30-45 0.00 0.06 0.00 0.06 0.00 0.00 0.00 0.00 0.00 45-60 0.00 0.00 0.06 0.00 0.00 0.00 0.00 0.00 0.00 60+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Table A5 (cont’d) YOY Brook Trout 0-15 15-30 30-45 45-60 Depth (cm) 60-75 75-90 90-105 105-120 120+ YOY Brown Trout 0-15 15-30 30-45 45-60 Depth (cm) 60-75 75-90 90-105 105-120 120+ 0-15 0.05 0.23 0.23 0.05 0.00 0.00 0.00 0.00 0.00 0-15 0.17 0.11 0.17 0.06 0.00 0.00 0.00 0.00 0.00 15-30 0.02 0.09 0.11 0.05 0.02 0.00 0.00 0.00 0.00 15-30 0.00 0.17 0.11 0.06 0.00 0.00 0.00 0.00 0.00 60 Table A6. Proportion of observations of fish capture points for salmon species across age groupings that occurred along a velocity and depth gradient. Velocity (cm/sec) YOY Coho Salmon 0-15 15-30 30-45 45-60 Depth (cm) 60-75 75-90 90-105 105-120 120+ 0-15 0.00 0.13 0.27 0.27 0.00 0.07 0.00 0.00 0.00 15-30 0.00 0.00 0.13 0.07 0.00 0.00 0.00 0.00 0.00 30-45 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 45-60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Velocity (cm/sec) YOY Chinook Salmon Depth (cm) 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-15 0.00 0.00 0.00 0.10 0.20 0.00 0.00 0.00 0.00 15-30 0.00 0.00 0.00 0.10 0.30 0.00 0.00 0.10 0.00 30-45 0.00 0.10 0.00 0.00 0.10 0.00 0.00 0.00 0.00 45-60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 60+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 61 Table A7: Proportion of observations of fish capture points for trout species across age groupings that occurred along a % distance to nearest bank and depth gradient. Depth (cm) Depth (cm) Distance (% to Nearest Bank) YOY Rainbow Trout 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-10 10-20 20-30 30-40 40-50 0.03 0.17 0.09 0.05 0.03 0.00 0.00 0.00 0.00 0.01 0.10 0.10 0.07 0.01 0.00 0.00 0.00 0.00 0.01 0.04 0.03 0.03 0.01 0.01 0.00 0.00 0.00 0.01 0.04 0.03 0.02 0.02 0.00 0.00 0.00 0.00 0.01 0.02 0.03 0.02 0.01 0.00 0.00 0.00 0.00 Distance (% to Nearest Bank) Age-1 Rainbow Trout 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 0-10 10-20 20-30 30-40 40-50 0.01 0.04 0.04 0.06 0.09 0.00 0.00 0.00 0.00 0.00 0.01 0.01 0.11 0.06 0.04 0.01 0.00 0.00 0.00 0.00 0.01 0.06 0.11 0.03 0.01 0.00 0.00 0.00 0.01 0.03 0.04 0.04 0.06 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.03 0.01 0.03 0.00 0.00 62 Table A7 (cont’d) Depth (cm) Depth (cm) YOY Brook Trout 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Distance (% to Nearest Bank) 0-10 10-20 20-30 30-40 40-50 0.07 0.16 0.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.07 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.07 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.07 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.02 0.02 0.00 0.00 0.00 0.00 Distance (% to Nearest Bank) 0-10 10-20 20-30 30-40 40-50 0.11 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.06 0.17 0.06 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.17 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 YOY Brown Trout 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ 63 Table A8: Proportion of observations of fish capture points for salmon species across age groupings that occurred along a % distance to nearest bank and depth gradient. Depth (cm) Depth (cm) YOY Coho Salmon 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Distance (% to Nearest Bank) 0-10 10-20 20-30 30-40 40-50 0.00 0.13 0.33 0.20 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.07 0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 YOY Chinook Salmon 0-15 15-30 30-45 45-60 60-75 75-90 90-105 105-120 120+ Distance (% to Nearest Bank) 0-10 10-20 20-30 30-40 40-50 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.00 0.10 0.00 0.00 0.10 0.00 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.30 0.00 0.00 0.00 0.00 64 REFERENCES 65 REFERENCES Albrecht, N.C. 2014. Evaluation of natural steelhead recruitment in the Muskegon River, Michigan. Masters Thesis, Grand Valley State University, Allendale, MI. Alexander, D.R. and H.R. MacCrimmon. 1974. 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