Final Project Report_301819G032

Great Lakes Fish and Wildlife Restoration Act
Final Report
Project Title: Evaluation of lake trout spawning reef suitability in Illinois waters of Lake
Michigan
Project Sponsor: United States Fish and Wildlife Service
FWS Agreement Number: 301819G032
Principal Investigator(s): Sergiusz Czesny and Scudder Mackey
Report Author(s): Rebecca Redman, Scudder Mackey, Sergiusz Czesny, and Diane Greer
Date Submitted: January 31, 2012
Study Objectives:
Historically, lake trout Salvelinus namaycush was the dominant top predator in Lake Michigan
and throughout the Great Lakes (Wells and McLain 1972; Eshenroder and Burnham-Curtis
1999). It was extirpated from Lake Michigan by the mid-1950s, due to a combination of
commercial overfishing and sea lamprey Petromyzon marinus predation (Coble et al. 1990;
Hansen 1999). With the advent of sea lamprey control, efforts to restore lake trout to Lake
Michigan began in 1965, when stocking first took place (Holey et al. 1995). Because of its role
as a native predator, management for sustainable, naturally reproducing lake trout stocks is a
critical goal of the Great Lakes Fishery Commission (Eshenroder et al. 1995). Fish Community
Objectives call for self-sustaining populations of lake trout that comprise 20 – 25% of the entire
salmonine community, based on harvest (Eshenroder et al. 1995). However, efforts to develop a
self-sustaining population of lake trout in Lake Michigan have been largely unsuccessful.
Spawning aggregations of stocked lake trout are well documented (Holey et al. 1995; Marsden
and Janssen 1997), fertilized eggs have been frequently found (Marsden and Chotkowski 2001;
Fitzsimons et al. 2003; Marsden 1994), fry have been observed (Marsden and Chotkowski 2001),
but only rarely has evidence of naturally produced lake trout been found (Holey et al. 1995).
Although a significant amount of research on lake trout spawning aggregations and habitat
suitability in Lake Michigan has concentrated on the northern third of the lake (Dawson et al.
1997; Bronte et al. 2003; Fitzsimons et al. 2003), lake trout also congregate and spawn farther
south in Lake Michigan, especially at offshore reefs. In Illinois waters, both Julian’s reef and
Waukegan reef were productive commercial fishing sites during fall (Collinson et al. 1979).
More recently, gill net assessment data indicated that the number of adult spawners at Julian’s
reef and Waukegan reef is similar to that found at the mid-lake reefs where eggs and fry have
recently been found (Dale Hanson, personal communication, 2011). However, no detailed maps
of Julian’s and Waukegan reefs exist and there is a lack of recent information on lake trout egg
deposition rates at these sites. The only previous mapping of Waukegan reef was the

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hydrographic map compiled from 1946 USACE soundings. In addition, the current Lake
Michigan GIS database lacks adequate information regarding habitat characteristics of the entire
southwest portion of Lake Michigan.
In order to address these research needs, we established the following objectives for this project:
1) Develop high resolution bathymetric and substrate maps for Julian’s and Waukegan reefs
using geo-referenced sonar readings, sidescan sonar, and underwater video to update the Lake
Michigan GIS.
2) Identify suitable spawning habitat for lake trout at Julian’s and Waukegan reefs using the
collected bathymetric and substrate data. Utilize this information to determine egg deposition
sampling sites by September 2009.
3) Measure lake trout egg deposition with egg traps deployed during the 2009 and 2010
spawning seasons to empirically evaluate the suitability of spawning habitat as determined by
bathymetry and substrate collection in objective 2.
Description of Tasks:
Task 1: Sidescan sonar surveys
Sidescan sonar provided images of acoustic reflectivity created by backscatter from surficial
features and objects at the sediment-water interface. Reflected acoustic energy (backscatter) is
received and processed by the tool in order to provide a continuous acoustic image or “map” of
the bottom.
During 2009, sidescan sonar data were collected from two bedrock reefs off the Illinois Lake
Michigan shoreline, Waukegan and Julian’s reefs. A L3-Klein System 3000 dual-frequency
towfish and L3-Klein SonarProTM
software were used to collect the sidescan sonar data (Figure
1). A Trimble DSM 212H real-time differential GPS (DGPS) receiver operating at 1 Hz provided
navigational data that is automatically integrated into the sidescan sonar data by the SonarProTM
software. Positional accuracies are typically less than one meter. The software generates
navigation waypoints and overlays that are displayed and integrated with MapTech digital
electronic charts. Survey lines were plotted in advance of each survey and were used to generate
waypoints for vessel navigation.
Initially, sidescan sonar data were collected along reconnaissance lines spaced approximately
500 m apart based, in part, on the location of prior reef surveys and fish sampling data over both
Waukegan and Julian’s reefs. The reconnaissance data were collected at a range setting of 150 m
(width of sonar beam to each side of the towfish) resulting in a swath width (total width of lake
bottom surveyed) of 300 m for each survey line. Based on the preliminary results from the
reconnaissance surveys, a more detailed survey grid was established over each reef. Parallel
survey lines were spaced at 112 m to facilitate mosaicking of the higher resolution sidescan
sonar data (75 m range, 150 m swath width). The more detailed sidescan sonar data were then
processed using Chesapeake Technologies SonarWizMapTM
mosaicking software to remove the

3
water column and generate georeferenced sidescan sonar mosaics.
Figure 1. (a) L3-Klein sidescan sonar towfish with light-weight tow cable used for
reconnaissance mapping over Waukegan and Julian’s reefs. (b) Electrically driven hydrographic
winch, armored coaxial cable, and digital cable counter used to deploy L3-Klein towfish during
more extensive surveys over Waukegan and Julian’s reefs. Equipment was deployed from the
INHS R/V SCULPIN.
Waukegan Reef
The Illinois Department of Natural Resources (IDNR) has sampled several locations over the
Waukegan reef for lake trout, and hypothesized that portions of this reef may contain substrate
suitable for lake trout spawning due to large catches of spawning-stage lake trout in the fall.
Virtually no detailed bathymetric data or historic substrate sampling/mapping data are available
for Waukegan reef, so the lake trout spawning habitat potential was unknown for this reef
complex. In the spring of 2009, a reconnaissance sidescan sonar survey was conducted over the
reef; the location of survey lines was based on historical gill net sampling locations provided by
the IDNR (Figures 2 and 3). During this survey, multiple new (unknown) bedrock areas were
discovered south of the area originally associated with Waukegan reef. These bedrock areas are
smaller and more discrete (patchy distribution) than the broad bedrock areas associated with
Waukegan reef to the north. Based on the discovery of these previously unknown bedrock areas,
the survey area was extended to include Waukegan South and a more detailed sidescan survey
was performed during the summer of 2009 at Waukegan and Waukegan South, (collectively
referred to as the Waukegan reef complex). Figures 2 and 3 illustrate the location of sidescan
sonar survey lines and IDNR gill net sites over the Waukegan reef complex. More detailed
information about the sidescan sonar surveys conducted over the Waukegan reef complex is
summarized in Table 1.

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Julian’s Reef
Julian’s reef was selected because prior IDNR surveys have documented spawning lake trout and
the presence of lake trout eggs on substrates at Julian’s reef. In the spring of 2009, a
reconnaissance sidescan sonar survey was conducted over the reef and a more detailed survey
was performed during the summer of 2009 (Figures 2 and 3). The location of sidescan survey
lines was based on historical gill net sampling locations provided by the IDNR and bathymetric
data collected in the 1970’s and 1980’s by the Illinois State Geological Survey and IDNR. More
detailed information about the sidescan sonar surveys conducted over Julian’s reef is
summarized in Table 1. In total, 191 line km (96 line nm) of sidescan sonar data were collected
at Julian’s and Waukegan reef during 2009, which covered an area greater than 17 km2
of
potential lakebed habitat.

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Figure 2. Location map showing survey areas over Waukegan and Julian’s reefs in southwestern
Lake Michigan.

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Figure 3. Sidescan sonar coverage and underwater video drift transects (green lines) at the
Waukegan reef complex (left panel) and Julian’s reef (right panel); the areas delineated by white
lines are where bedrock and/or coarse cobble-boulder substrates were mapped on the lakebed.
Table 1. Summary of sidescan sonar survey data collected at the Waukegan reef complex and
Julian’s reef during this study.
Reef Line km (nm) Area (km2
)
Range
(m)
Swath
width (m)
Waukegan 20.9 (11.3) Recon 150 300
Waukegan 40.4 (21.8) 5.00 75 150
Waukegan South 43.3 (23.4) 5.01 75 150
Waukegan Total 104.6 (56.5) 10.01
Julian’s 23.5 (5.7) Recon 150 300
Julian’s 62.4 (33.7) 7.23 75 150
Julian’s Total 85.9 (39.4) 7.23

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Task 2: Underwater video surveys
Underwater video provide highly-detailed images of the lake bottom which can be used to
validate substrate composition and provide information on environmental characteristics such as
presence of fine-grained sediments and encrustation by invasive mussels. We used drift transects
to collect underwater video data at all study sites. Underwater video data were collected along
ten drift transects at the Waukegan reef complex (Figure 3); the length of these transects
averaged 588 m and a total of 5.88 line km (3.17 line nm) of underwater video data were
collected (Table 2). Seven drift transects averaging 241 m in length were conducted at Julian’s
reef (Figure 3), which totaled 1.68 line km (0.91 line nm) of underwater video data (Table 2).
Table 2. Summary of underwater video data collected within the survey areas for the Waukegan
reef complex and Julian’s reef during this study.
Year Reef
No. of
Transects
Mean Length
of Transects (m)
Total
Line km
Total
Line nm
2009 Waukegan 6 560 3.36 1.81
2009 Waukegan South 4 630 2.52 1.36
Waukegan Total 10 588 5.88 3.17
2010 Julian’s 7 241 1.68 0.91
The underwater video data confirmed the presence of bedrock (Figure 4a) as well as coarse
cobble-boulder substrate with characteristics suitable for use as lake trout spawning habitat on
both reefs (Figure 4b). The underwater video also revealed that virtually all of the coarse cobble-
boulder substrate on both reefs is colonized by lithophyllic, invasive Dreissena spp. and
Cladophora spp., a blue-green filamentous algae (Figures 4 and 5). Cladophora spp. was
observed in water depths up to 40 m on Julian’s reef.
a. Massive bedrock surfaces at Julian’s reef. b. Boulder-cobble near a lake trout egg trap site on
Waukegan reef.
Figure 4. Images of lake bottom captured from underwater video data collected at Julian’s reef
and the Waukegan reef complex.

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Figure 5. Extensive coverage of Dreissenids and Cladophora at Julian’s reef.
Task 3: Spawning habitat analysis
Digital sidescan sonar data were processed and geo-referenced using Chesapeake Technologies
SonarWizMapTM
mosaicking software to produce sidescan sonar mosaics at each of the survey
sites. The resulting mosaics were examined and areas exhibiting similar backscatter
characteristics were identified on the sidescan sonar mosaics and the waterfall displays.
Substrates were then classified based on backscatter characteristics indicative of texture (i.e.
grain size), composition, hardness, and observable surface features or structure (e.g., fractures in
bedrock or sedimentary structures, such as ripples or dunes in sand). Areas with similar
backscatter characteristics (i.e., substrate types) were grouped into polygons that were then
digitized from the geo-referenced sidescan mosaics and incorporated into a GIS database. Prior
work in Lake Michigan and comparable work in Lake Erie has shown that the acoustic response
over similar substrate types is reasonably consistent between sites (Meadows et al. 2005).
Moreover, ongoing work in the eastern basin of Lake Erie has demonstrated that it is possible to
distinguish and map areas of increased or reduced habitat heterogeneity and/or potential lake
trout spawning habitat (e.g. Biberhofer et al. 2010).
Based on similar work done in the eastern basin of Lake Erie (Biberhofer et al. 2010), two
separate geodatabases were created for each survey site, one for substrate type and one for
habitat structure. The approach used here is based on the concept that substrate provides
information on the type and composition of lakebed materials, and that habitat structure provides
information on the physical characteristics (or structure) at the lakebed-water interface, which is
separate from but linked to substrate. It is the combination of substrate and habitat structure that
is the primary factor that determines biological usage as habitat. Potential habitats were
identified and mapped based on the integration of substrate and habitat structure polygons. Once
potential habitats were identified and delineated within the GIS, an ESRI script was used to
generate minimum bounding regions, which were then used to calculate the length and width of
potential habitat areas (polygons) found within each survey area (see MBR; Frye 2008). Results
of these analyses are presented below.

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Waukegan Reef
Initial interpretation of the sidescan sonar data showed extensive sand areas and thin sands
resting on smooth bedrock surfaces with intermittent exposures of massive and/or fractured
bedrock exhibiting moderate relief. More detailed analysis within the survey area at Waukegan
reef showed that predominate substrate classes were sand (49%), massive bedrock (43%) and to
a lesser extent exposed fractured bedrock (5%; Figure 5). Areas interpreted as sand exhibit a
rough acoustic (rippled) texture that may be covered locally by scattered dreissenid shell debris
and a thin veneer of flocculent mud and/or pseudofeces. The Waukegan reef survey area also
contains a complex pattern of boulder-cobble piles, fractured bedrock debris, and boulder-cobble
lag deposits, (<3%; Table 3 and Figure 5). Potential lake trout spawning habitat areas found at
Waukegan reef include boulder-cobble piles (average area 625 m2
), and fractured bedrock debris
(1749 m2
; Table 4); collectively these substrates totaled to 31,363 m2
. Analysis of individual
substrate polygons revealed that potential habitat areas suitable for spawning were typically less
than 80 m in length and 60 m in width (Figure 6).
Table 3. Summary of habitat and substrate assessments using sidescan sonar within the survey
area for Waukegan reef (northern portion). An asterisk is used to identify substrates determined
to be potential lake trout habitat.
Substrate Area (m2
) Percent Area
Scarp (linear feature) 665(m)
Boulder-cobble bedrock* 15625 0.31
Fractured bedrock debris* 15738 0.31
Boulder cobble lag 116646 2.30
Fractured bedrock 261506 5.15
Massive bedrock 2163778 42.62
Sand 2503348 49.31

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Figure 5. Substrate and habitat interpretations from sidescan surveys for Waukegan reef
(northern portion) located within Illinois waters of Lake Michigan. Potential lake trout spawning
habitat is outlined in yellow and the centroid of the egg trap site targeted during the 2009 and
2010 lake trout spawning seasons is depicted with a white circle.

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Table 4. Average size of potential lake trout spawning habitat at the Waukegan reef complex and
Julian’s reefs.
Substrate Area (m2
) Length (m) Width (m)
Waukegan
Boulder-cobble 625 44 20
Fractured bedrock debris 1749 81 41
Waukegan South
Scarp debris 255 38 18
Julian’s
Length (m)
0 20 40 60 80 100 120 140
Count
0
2
4
6
8
10
12
a)
Width (m)
0 10 20 30 40 50 60 70 80
Count
0
2
4
6
8
10
b)
Figure 6 Frequency distribution of potential lake trout habitat by feature a) length and b) width
derived from minimum bounding regions at Waukegan reef.
Waukegan South Reef
Initial interpretation of the sidescan sonar data showed extensive areas of sand mixed with
smaller areas of bedrock and coarse-grained cobble-boulder deposits. More detailed analysis
showed that the predominate substrate classes within the survey area for Waukegan South reef
were sand (89%), and to a lesser extent massive bedrock (6%) and boulder-cobble lag deposits
(3%;Table 5 and Figure 7). Areas interpreted as sand exhibit a rough acoustic (rippled) texture
that may be covered locally by scattered dreissenid shell debris and a thin veneer of flocculent
mud and/or pseudofeces. Some of the sand deposits surrounding the eastern portion of the
Waukegan South survey area are characterized by linear striping and show evidence of bedrock

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and/or glacial till showing through a thin veneer of sand. These deposits have been interpreted as
boulder-cobble lag deposits. These deposits are typically found adjacent to exposures of flat-
lying massive bedrock and/or areas of exposed fracture bedrock within the Waukegan South
survey area. Associated with these bedrock substrates are bedrock scarps, areas of scarp debris
and boulder-cobble deposits overlying both massive and fractured bedrock surfaces (Figures 7
and 8). Examples of backscatter characteristics and interpreted substrates found within the study
survey areas are illustrated in Figure 9. Potential habitat areas found at Waukegan South include
scarp debris (average area 255 m2
), fractured bedrock debris (264 m2
), and boulder-cobble piles
(514 m2
; Table 5); collectively, these substrates totaled to 34,081 m2
. Analysis of individual
substrate polygons revealed that potential habitat areas suitable for use as spawning habitat were
typically less than 70 m in length and 30 m in width (Figure 10).
area for Waukegan South reef. An asterisk is used to identify substrates determined to be
potential lake trout habitat.
Substrate Area (m2) Percent Area
Scarp 2012(m)
Scarp debris* 1529 0.03
Boulder cobble bedrock* 25676 0.51
Boulder-cobble lag 136458 2.73
Medium coarse sand 4437643 88.63

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Figure 7. Substrate and habitat interpretations from sidescan surveys for Waukegan South reef
located within Illinois waters of Lake Michigan; potential lake trout spawning habitat is outlined
in yellow. The inset map (lower right corner) represents a close-up of an area of fractured
bedrock that was targeted with deep-water egg traps during the 2009 and 2010 lake trout
spawning seasons. The portion of the survey area that appears within the inset map is outlined
with a black square, and the centroid of the egg trap site is depicted with a white circle.

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Figure 8. Map illustrating the presence of debris along a large bedrock scarp found within the
southern portion of the Waukegan South reef survey area.

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Figure 9. Sidescan sonar images illustrating the range of substrate types mapped on the
Waukegan reef complex and Julian’s reef in Illinois waters of Lake Michigan.

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Length (m)
0
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
Count
0
5
10
15
20
25
30
a)
Width (m)
0
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
Count
0
10
20
30
40
b)
Figure 10. Frequency distribution of potential lake trout habitat by feature a) length and b) width
derived from minimum bouding regions at Waukegan South reef.
Julian’s Reef
Initial interpretation of the sidescan sonar data showed extensive sand areas overlying massive
smooth bedrock surfaces with extensive exposures of fractured bedrock. More detailed analysis
showed that the predominate substrate classes within the survey area at Julian’s reef were
fractured bedrock (45%), sand with patchy dunes (43%), areas of striped sand (10%), and to a
lesser extent massive bedrock (1%). Areas of striped sand are interpreted to be a thin veneer of
sand overlying bedrock and/or glacial till similar to that described within the eastern portion of
the Waukegan South survey area. However, these areas were generally more fine grained (i.e.
less boulder-cobble size material) than at the Waukegan South survey area. Areas interpreted as
sand exhibit a rough acoustic (rippled) texture that may be covered locally by scattered
dreissenid shell debris and a thin veneer of flocculent mud and/or pseudofeces. Julian’s reef also
contains boulder-cobble deposits and fractured bedrock debris, but these substrates were much
less prevalent (<1%; Table 6 and Figure 11). The southeastern portion of Julian’s reef is
interesting because it not only contains scattered areas of coarse-grain substrate suitable for lake
trout spawning (boulder-cobble and bedrock debris deposits), but is also characterized by
numerous bedrock scarps that form linear, bench-like features (Figure 12). Edsall et al. (1996)
also described extensive bedrock with rubble substrate and linear bedrock ridges within the
southeastern portion of Julian’s reef. Potential habitat areas found at Julian’s reef include
boulder-cobble piles (average area 1085 m2
) and fractured bedrock debris fields (3609 m2
;Table
6); collectively these substrates totaled to 58,494 m2
. Analysis of individual substrate polygons
revealed that potential areas suitable for spawning were typically less than 150 m in length and
60 m in width (Figure 13). Fractured bedrock areas also have the potential to provide suitable
lake trout spawning habitat. However, due to the structural complexity associated with fractured
bedrock, the sidescan sonar data does not have the resolution to identify potential habitat areas
within fractured bedrock. It is anticipated that potential habitat areas within the larger extent of
fractured bedrock at Julian’s reef would consist of relatively small and discrete patches scattered
randomly across the reef.

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area for Julian’s reef. An asterisk is used to identify substrates determined to be potential lake
trout habitat.
Substrate Area (m2
) Percent Area
Scarp (linear feature) 2395(m)
Boulder-cobble bedrock* 15184 0.21
Medium-coarse striped sand 743138 10.21
Medium-coarse sand & patchy dunes 3098402 42.58

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Figure 11. Substrate and habitat interpretations from sidescan surveys for Julian’s reef located
within Illinois waters of Lake Michigan; potential lake trout spawning habitat is outlined in
yellow. The inset map (lower right corner) represents a close-up of two areas of boulder-cobble
that were targeted with deep-water egg traps during the 2009 and 2010 lake trout spawning
seasons. The portion of the survey area that appears within the inset map is outlined with a black
square and the centroid of the egg trap sites are depicted with white circles.

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Figure 12. Example of a bedrock scarp that form the linear, bench-like features within the
southeastern portion of Julian’s reef.
Length (m)
0 50 100 150 200 250 300 350
Count
0
2
4
6
8
10
a)
Width (m)
0 20 40 60 80 100 120 140
Count
0
2
4
6
8
10
12
14
b)
Figure 13. Frequency distribution of potential lake trout habitat by feature a) length and b) width
derived from minimum bouding regions at Julian’s reef.
Task 4: Bathymetric surveys
During 2011, bathymetry data was collected at both the Waukegan reef complex and Julian’s
reef. A single beam FURUNO echo sounder LS-6100 (200 kHz) with a thru-hull transducer and
Standard Horizon chart plotter (CP180) were used to collect bathymetry data. Data points
included water depth (0.1 m) and vessel position (in the form of latitude and longitude) and were
produced every 2-3 seconds. Vessel speed during bathymetry surveys was approximately 2.6 m/s
and allowed collection of a data point every 5.2-7.8 m along a survey line. Survey lines were
plotted in advance of each cruise and used to generate waypoints for vessel navigation. Data was
collected along a set of parallel survey lines spaced approximately 100 m apart at all survey sites.

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The bathymetry system allowed real-time display of data which aided vessel navigation and
allowed preliminary assessment of the data (Figure 15). Since bathymetric surveys were
conducted on multiple dates, data from the nearest NOAA water level gauging stations (Calumet
Harbor and Milwaukee) was used to correct bathymetric data for changing water surface
elevations (relative to chart datum; 176.02 m). Daily water level data taken from both gauging
stations (http://www.great-lakes.net/envt/water/levels/levels-cur/michwlc.html) was used to
approximate water levels within the survey area for a given survey date. The extent of the
bathymetry surveys conducted over both reefs and water level data for each sampling event are
summarized in Table 7.
Table 7. Summary of bathymetry surveys conducted at the Waukegan reef complex and Julian’s
reef during 2011 as well as average daily water levels at the nearest gauge stations.
Daily water level (m)
Reef
Survey
Dates
Line km
(nm) Calumet Milwaukee Mean
Δ from chart
datum
Waukegan July 7 40.0 (21.6) 176.321 176.300 176.311 0.290
Waukegan South Aug. 1 6.0 (3.2) 176.282 176.272 176.277 0.257
Waukegan Total 46.0 (24.8)
Julian’s (south) Aug. 30 55.0 (29.7) 176.209 176.211 176.210 0.190
Julian’s (north) Oct. 4 24.0 (13.0) 176.175 176.162 176.169 0.149
Julian’s Total 79.0 (42.7)
Figure 14. Real-time display of bathymetric data (uncorrected) over the Waukegan reef complex
(left) and Julian’s reef (right).
The corrected bathymetry data was imported into ArcScene, which allows 3D visualization of
GIS data. Interpolation procedures were performed using a Triangulated Irregular Network
(TIN). The TIN procedure uses Delaunay triangulation with voronoi polygons to determine
region of influence based on Euclidean distances between points and assumes the distances

21
impose an “attraction” on neighbors (Burrough and McDonnel 1998, Johhson et al. 2001). This
interpolation is local (i.e. only surrounding points are included in analysis) and its predicted
values are within the range of the data. Interpolation calculations were based on fitting a
spherical or most appropriate model to the variogram. Bathymetric data from all study sites were
displayed using 1-m depth contours and a vertical exaggeration value of 20 was used to aid
visualization of the z dimension. Then, coverages of substrate deemed suitable for lake trout
spawning were draped over the 3-D bathymetry surface and a TIN triangle (3D Analyst) was
used to calculate slope (degrees) of potential habitat areas found at the study sites. Then, the
Identify tool within ArcScene was used to locate areas where both substrate and slope (15-60°;
Marsden et al. 1995a; Fitzsimons et al. 2003) suitable for lake trout spawning were found.
Results of these analyses are presented below. Interactive, 3-D versions of Figures 15 and 16
were included with the report.
Waukegan Reef Complex
Water depths within the survey areas covering the Waukegan reef complex ranged from 37.6 to
54.5 m (Figure 15). In general, bathymetry throughout the survey areas was relatively gentle, and
water depth was shallowest within the western portion of the survey area and deeper in the
northeastern portion. The Waukegan reef complex lies in approximately 37-48 meters of water
and areas containing substrate suitable for lake trout spawning were found throughout this depth
range. Areas of suitable substrate within the Waukegan reef complex associated with 15-60º
slope were composed of boulder-cobble piles and fractured bedrock debris and were primarily
found clustered in the southeastern portion of the Waukegan reef survey area and the northern
portion of the Waukegan South survey area (Figure 16). The slope of these patches of potential
lake trout spawning habitat ranged from 15-53º and were found in 38-46 meters of water (Table
8).

22
Figure 15. A 3-dimensional depiction of water depth (1 m contours) overlaid with potential lake
trout spawning substrate (black areas) at the Waukegan reef complex.

23
Figure 16. Map of the Waukegan reef complex illustrating locations with substrate and slope
characteristics suitable for lake trout spawning (red circles).

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Table 8. Summary of sites associated with substrate and slope suitable for lake trout spawning at
the Waukegan reef complex. Coordinates are in UTM Zone 16N WGS 1984.
Substrate Latitude Longitude Depth
(m)
Slope (º)
Boulder-cobble 42.344511 -87.635394 46 33
Boulder-cobble 42.344506 -87.635553 46 15
Boulder-cobble 42.338678 -87.624394 40 15
Boulder-cobble 42.338650 -87.624394 40 15
Fractured bedrock debris 42.337119 -87.631039 38 15
Boulder-cobble 42.337003 -87.626150 42 15
Boulder-cobble 42.336597 -87.625547 42 32
Boulder-cobble 42.336567 -87.625806 42 20
Boulder-cobble 42.328369 -87.626672 43 15
Boulder-cobble 42.328303 -87.626656 43 24
Boulder-cobble 42.328092 -87.616611 43 15
Boulder-cobble 42.327911 -87.616911 43 25
Boulder-cobble 42.327036 -87.627797 44 24
Boulder-cobble 42.327011 -87.627606 43 24
Boulder-cobble 42.326489 -87.626800 43 17
Boulder-cobble 42.326472 -87.626797 43 53
Boulder-cobble 42.326386 -87.627528 43 26
Boulder-cobble 42.325886 -87.617186 46 26
Boulder-cobble 42.325681 -87.617503 47 17
Boulder-cobble 42.324625 -87.619353 46 15

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Julian’s Reef
Water depths within the Julian’s reef survey area ranged from 25.0 to 56.6 m (Figure 17).
Bathymetry changed relatively drastically throughout the survey area and the shallowest depths
were recorded in the central portion of the survey area, which corresponds to the crest of Julian’s
reef. Julian’s reef lies in approximately 25-45 meters and areas containing substrate suitable for
lake trout spawning were found throughout this depth range. Areas of suitable substrate
associated with 15-60º slope were composed of boulder-cobble piles and fractured bedrock
debris and were primarily found along the eastern portion of Julian’s reef (Figure 17). The slope
of these patches of potential lake trout spawning habitat ranged from 15-29º and were found in
34-42 meters of water (Table 9).
Figure 17. A 3-dimensional depiction of water depth (1 m contours) overlaid with potential lake
trout spawning substrate (black areas) at Julian’ reef.

26
Figure 18. Map of Julian’s reef illustrating locations with substrate and slope characteristics
suitable for lake trout spawning (red circles).

27
Table 9. Summary of sites associated with substrate and slope suitable for lake trout spawning at
Julian’s reef. Coordinates are in UTM Zone 16N WGS 1984.
Substrate Latitude Longitude Depth
(m)
Slope
(º
Boulder-cobble 42.216600 -87.525292 38 19
Boulder-cobble 42.214928 -87.525972 41 29
Boulder-cobble 42.214894 -87.525978 41 15
Boulder-cobble 42.214872 -87.525994 41 17
Boulder-cobble 42.213556 -87.527639 41 17
Boulder-cobble 42.212078 -87.528244 42 20
Boulder-cobble 42.209900 -87.530828 34 16
Boulder-cobble 42.209494 -87.531011 35 16
Boulder-cobble 42.209478 -87.530928 36 19
Boulder-cobble 42.208883 -87.532122 38 29

28
Task 5: Evaluation of egg deposition
During the summer of 2009, eighty deep-water egg traps were constructed following the design
of Riley et al. (2010). The
frame of each egg trap
consisted of a 48 cm diameter
hoop of 6 mm galvanized
steel (Figure 19). The body of
each trap was composed of a
cylindrical piece of 3 mm
mesh that was cinched closed
40 cm below of the frame
using two 18 cm cable ties.
Each trap was filled with 5 L
of 5 cm plastic ‘bio barrels’
manufactured by Aquatic Eco
Systems and then a 48-cm
diameter piece of 2-cm
polyethylene mesh was
fastened to the top of the
circular frame with cable ties.
The ‘bio barrels’ were added
to provide structure, aid
entrainment of eggs, and
hinder consumption of eggs
by predators able to penetrate
the polyethylene mesh lid.
Each trap was weighted with
two rings of 8-mm, 30 proof
galvanized chain. The top
chain was 150 cm long and
was fastened to the steel
frame with cable ties. Then, a
120 cm chain was attached
with cable ties to the mesh
body of the trap 15 cm below
the steel frame. Ten egg traps
were linked using nylon rope
with 2.4 m spacing between
each trap to create a gang;
total sample length of a gang
was 24 m. Four gangs were
deployed at both the
Waukegan reef complex and
Julian’s reef; two of these gangs were deployed on substrate deemed suitable for lake trout
spawning, while the other two gangs were deployed on substrate deemed not suitable. Suitability
Figure 19. Side (left panel) and top-view (right) of a deep-water egg
trap used to evaluate lake trout egg deposition during the 2009 and
2010 spawning seasons.
Figure 20. Egg trap and IDNR gill net sampling locations for the
Waukegan reef complex (left) and Julian’s reef (right). Egg trap sites
are depicted by a red square encompassed by yellow circle and IDNR
gill net sites are represented by red circles and lines.

29
of the substrate and selection of egg traps sites was based on initial interpretation
of sidescan sonar data
combined with historical
fish sampling data. The
location of suitable sites
and locations used for
historical gill net sampling
are provided for the
Waukegan Reef Complex
and Julian’s Reef in Figure
20. During 2009, egg traps
were deployed on October
20 and retrieved on
November 4. During 2010,
egg traps were deployed at
the same locations on
October 4 and retrieved on
November 2 (Figure 21).
Traps were disassembled back at the laboratory and examined for intact eggs and egg chorions.
No intact eggs or egg chorions were collected in either year. However, invasive quagga mussels
and round goby were collected during both years.
Task 6: Incorporate geo-referenced substrate and bathymetric data into Great Lakes GIS
All geospatial datasets are being sent to the Great Lakes GIS (GLGIS) and will be incorporated
into the Lake Michigan GIS framework which is maintained by the Institute for Fisheries
Research, University of Michigan, and Michigan Department of Natural Resources.
http://ifrgis.snre.umich.edu/projects/GLGIS/support_docs/html/lake_GISs/LMGIS_index.htm.
Executive Summary
High resolution substrate and bathymetric maps were created for the Waukegan reef complex
and Julian’s reef using geo-referenced sidescan sonar, single beam sonar, and underwater video
data. Although potential lake trout spawning habitat (desired substrate and slope) was found at
all study sites, these areas were relatively small and scattered across each reef. The small size
and patchy distribution of these areas made it very difficult to accurately sample and evaluate
egg deposition on both reefs. Additionally, underwater video footage indicated that both reefs are
extensively covered by dreissenid mussels and Cladophora spp. Thus, while suitable cobble-
boulder piles and debris deposits were identified at the study sites using sidescan sonar, the
extent to which these substrates may still provide suitable spawning habitat remains unknown.
Spawning lake trout reportedly are attracted to clean substrate (Marsden et al. 1995) and in
northeastern Lake Michigan lake trout egg deposition was shown to incrementally decrease as
coverage of dreissenids increased from < 5% to >70% (Claramunt et al. 2011). Taken together,
the small size of potential spawning habitat patches, along with extensive coverage of dreissenids
at both reefs may at least partially explain why no lake trout egg deposition was documented
during this study. Future research is needed to understand how these habitat alterations are
Figure 21. Deep-water egg traps on lake bottom shortly after
deployment at Waukegan reef during the 2010 lake trout spawning
season.

30
impacting lake trout spawning behavior and egg survival as well the possible importance of
nearshore areas for lake trout spawning.
Major findings
The objective of this study was to map the substrate and bathymetry of Waukegan and Julian’s
reefs and use this data to determine the location of potential lake trout spawning habitat. We also
set out to measure egg deposition at these locations in an effort to inform future lake trout
restoration work in Lake Michigan. Reconnaissance work at Waukegan reef revealed the
presence of multiple undescribed bedrock areas south of the area originally associated with
Waukegan reef. This region was added as an additional (third) study site and based on sidescan
sonar data, portions of this site as well as Waukegan and Julian’s reef contain areas that lake
trout may use as spawning habitat. The predominant substrates deemed suitable for spawning
within the three survey areas were boulder-cobble piles, fractured bedrock debris and scarp
debris. These substrates were found in relatively small quantities scattered across each study site,
which made it difficult to accurately sample potential spawning habitat for eggs and evaluate egg
deposition on these reefs. Potential lake trout habitat made up 1% (31,363 m2
) of the hard/coarse
substrates (excludes sand) found at Waukegan reef and 6% (34,081 m2
) of that at Waukegan
South reef; collectively potential lake trout habitat totaled 65,444 m2
within the Waukegan reef
complex. This newly described area (Waukegan South) contributed significantly to identification
of potential lake trout habitat in Illinois’s offshore waters and was the only study site were scarp
debris was found, which has been identified as good spawning habitat for lake trout in Lake Erie.
On Julian’s reef, potential lake trout habitat made up 2% (58,494 m2
) of the hard/coarse
substrates, but fractured bedrock areas found on Julian’s reef may also provide suitable lake trout
spawning habitat. The sidescan sonar data does not have the resolution to identify potential
habitat areas within fractured bedrock areas and it is anticipated that potential habitat within
fractured bedrock areas would consist of relatively small and discrete patches located randomly
across the reef. Overall, our results show that the Waukegan reef complex provides a significant
amount of potential lake trout spawning habitat and may contribute more to Illinois’s historical
spawning grounds than previously thought. Finally, all areas of potential spawning habitat found
within the survey areas are located adjacent to deeper water areas that are assumed to serve as
potential nursery habitat for lake trout in southern Lake Michigan.
Although suitable “substrate” near potential deep water nursery habitat was found at the study
sites using sidescan, more detailed inspection with an underwater camera indicated these areas
may no longer be suitable spawning “habitat” due to extensive coverage of dreissenids (D.
bugensis found in egg traps) and Cladophora spp. Inspection of deep water egg traps also
confirmed the presence of round goby at the study sites, but densities are unknown. A
comparison of the images Edsall et al. (1996) captured of cobble-boulder piles on Julian’s reef
during the 1990s and those captured during this study help to illustrate the major alteration
invasive species have brought about over the last decade. Currently, interstitial spaces, which are
essential for lake trout eggs to develop properly, may be clogged with fine silt and pseudofeces
from dreissenids. Round goby may also negatively impact the success of lake trout reproduction
on the study sites as they are a known predator of lake trout eggs. Therefore, while suitable
cobble-boulder piles and debris deposits were identified using sidescan sonar, the extent to which
these substrates may be compromised by sedimentation and invasives remains unknown. The

31
presence of lithophillic species can reduce energy associated with waves and currents over
coarse substrates causing an increase in siltation, especially in interstitial spaces which are
necessary for protection of lake trout eggs. Siltation may be augmented by dreissenid
pseudofeces. Siltation reduces the volume of interstitial space available and may suffocate eggs
that are deposited there. However, the extent of negative impact these alterations may have on
lake trout eggs has not been empirically tested and thus remains largely unconfirmed.
Taken together, the small size of the potential spawning habitat patches and major habitat
alteration by invasive species may explain the lack of egg deposition over suitable substrate at
Illinois’s deep water reefs. These and other deep water areas which were once thought of as
historical spawning grounds may no longer provide habitat suitable for successful spawning and
reproduction of lake trout. Similar work in Lake Erie suggested a shift in spawning at deep water
sites to high-energy nearshore areas, which are associated with a lower density of lithophillic
species and reduced siltation of interstitial spaces (Biberhofer et al. 2010). Similarly, Claramunt
et al. (2005) reported higher lake trout egg deposition in shallow water (1 m) despite availability
of spawning habitat in deeper waters (up to 9 m) and suggested this shallow water habitat, which
was relatively free of dreissenids, may have a greater potential to contribute to spawning success
than deeper water habitat. In southwestern Lake Michigan, exposed bedrock areas and manmade
structures within Illinois’s nearshore waters may now provide some of the best available
spawning habitat for lake trout. However, the densities of round goby in nearshore areas of
southwestern Lake Michigan have increased dramatically over the last several years (Sara
Creque INHS, personal communication, 2011) and their impact as egg predators might be
significant in these areas.
Management implications
Our results suggest that the Waukegan reef complex provides as much potential lake trout
spawning habitat as Julian’s reef. Additionally, catch rates of lake trout at Waukegan reef are
typically higher compared to Julian’s reef (Steve Robillard IDNR, personal communication,
2012). Thus, the Waukegan reef complex should be considered a significant portion of Illinois’s
offshore lake trout spawning grounds and as such should be considered as a possible additional
location for stocking lake trout within Illinois waters. Final data from sidescan sonar and
bathymetric surveys were provided to the IDNR for consideration of potential sites for their
annual lake trout spawning assessment surveys.
Future research
This project has provided valuable insights on the current status, quality and quantity of potential
lake trout spawning substrate on Illinois’s offshore reefs. It also provided the first detailed
substrate and bathymetry map of Waukegan reef; the last mapping of this reef was the
hydrographic map compiled from 1946 USACE soundings. However, due to the extensive
coverage of invasive species on these reefs it is now crucial to understand how these habitat
alterations are affecting lake trout spawning behavior, egg deposition and most importantly egg
survival rate.

32
Virtually no work has been done on lake trout nursery habitat and this lack of data severely
limits our ability to assess the importance of connectivity to spawning habitat. Thus, a suite of
studies to identify and evaluate lake trout nursery habitat and connectivity to spawning habitat
would be consistent with goals of the Great Lakes Fish and Wildlife Restoration Act of 2006 to
restore fish resources within the Great Lakes Basin and would involve rehabilitation of lake trout
in support of A Fisheries Management Implementation Strategy for the Rehabilitation of Lake
Trout in Lake Michigan and the Lake Michigan Fish Community Objectives.
Presentations
Redman, R., S. J. Czesny, and S. D. Mackey. 2010. An evaluation of lake trout (Salvelius
namaycush) spawning habitat: are southern Lake Michigan’s offshore reefs suitable?
International Association of Great Lakes Research, Toronto, ON (poster presentation).
An electronic version of this poster presentation was included with the hard copy of the report
(CD1).
Relevant images: Electronic versions of all imagery and photographs that appear within the
report were included with the hard copy of the report (CD 1).
Geographic region: All data collection was conducted in and around two bedrock reefs that lie
within Illinois waters of Lake Michigan: 1) Waukegan reef and 2) Julian’s reef. Below are
coordinates for boundaries of each reef; coordinates are in UTM Zone 16N WGS 1984 (decimal
degrees).
Reef Northwest Northeast Southeast Southwest
Waukegan Complex 42.350222
-87.651383
42.350027
-87.599222
42.304198
-87.599912
42.304795
-87.652035
Julian’s 42.234405
-87.547522
42.234405
-87.515363
42.205618
-87.515363
42.205617
-87.547522
Reports
Redman, R., S. D. Mackey, and S. J. Czesny. 2009. Evaluation of lake trout spawning reef
suitability in Illinois waters of Lake Michigan. First Annual Progress Report to the U.S.
Fish and Wildlife Service.
Redman, R. S. D. Mackey, and S. J. Czesny. 2010. Evaluation of lake trout spawning reef
suitability in Illinois waters of Lake Michigan. Second Annual Progress Report to the
U.S. Fish and Wildlife Service.
Redman, R. and S. J. Czesny. 2010. Exploring offshore reefs in Illinois waters of Lake
Michigan: Are they suitable for lake trout spawning? Illinois Natural History Survey
Reports. No. 403.
An electronic version of these completed reports and article was included with the hard copy of
the report (CD1).

33
References
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Erie. Great Lakes Fish and Wildlife Restoration Act Final Report. 24p.
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report.
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34
Meadows, G.A., S. D. Mackey, R. R. Goforth, D. M. Mickelson, T. B. Edil, J. Fuller, D. E. Guy,
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