The Status of Walleye in Nipigon Bay Area of Concern: 2012

Prepared for: Environment Canada

Prepared by: Terry Marshall

Marshall Consulting

March 31, 2013

Executive Summary

Walleye were once very abundant in Nipigon Bay, with thousands observed each spring congregating in the lower Nipigon River. Overfishing, habitat loss, and other stresses contributed to their decline in the early 1960s and some 50 years later this population has still not recovered to its past magnitude, although there have been vast improvements in ecosystem health.

Many projects have been carried out to monitor population recovery and to discover why this process has been so delayed. While no directed studies have been made to document changes in population abundance, inferences can be made based on the results of some of the other work.

Walleye stocks in the Nipigon system are currently quite healthy although they continue to exist at much lower levels of abundance than in the past. Growth rates are extremely rapid and mortality rates are low which suggest good reproductive potential. There are recent indications that the size of the population is increasing. A comparison to reference waterbodies with similarly degraded stocks reveals that the recovery process can be quite protracted and that walleye are slowly reaching their new equilibrium in Nipigon Bay.

Telemetry studies suggest that two discrete stocks of walleye may now exist, one residing in the upper river and Lake Helen area and the other in the lower river and Nipigon Bay. Additional genetic analyses must be carried out to confirm this finding. A benchmarking of the existing walleye population is required to allow assessment of future change.

Contents

Executive Summary ...... ii 1 Introduction ...... 1 2 A brief overview of walleye stocks in Lake Superior ...... 1 3 Factors related to the walleye decline in Nipigon Bay ...... 3 3.1 Exploitation ...... 3 3.2 Habitat degradation ...... 4 3.3 Sea lamprey control ...... 4 4 Rehabilitation Efforts ...... 5 4.1 Stocking ...... 5 4.2 Habitat restoration ...... 6 5 Recent research, assessment and monitoring studies ...... 7 5.1 Genetics of stocks ...... 7 5.2 Telemetry studies: Seasonal movement and habitat use ...... 7 5.3 Walleye spawning observations and drift netting: Nipigon River ...... 10 5.4 Walleye and northern pike abundance: Lake Helen/Polly Lake ...... 11 5.5 Fish community assessment: Lake Helen ...... 11 5.6 Electrofishing surveys: Nipigon Bay and River ...... 13 5.7 Fish community index netting: Nipigon Bay ...... 14 5.8 Walleye population assessment: Nipigon Bay ...... 15 6 Status of walleye stocks and their habitat in the Nipigon system ...... 16 6.1 Reference sites ...... 16 6.1.1 Recovery of collapsed populations ...... 16 6.1.2 Status indictors ...... 18 6.2 Walleye population status ...... 18 6.3 Walleye habitat status ...... 20 7 Information needs ...... 21 7.1 Genetic analysis of stocks ...... 21 7.2 Population monitoring and assessment ...... 21 8 Conclusions ...... 22 9 Acknowledgements ...... 23 10 References ...... 24

iii

1 Introduction

Nipigon Bay was designated an Area of Concern (AOC) in 1987 under the Canada-United States Great Lakes Water Quality Agreement. The degradation of fish populations and the loss of fish habitat were beneficial use impairments (BUI) identified in Stage 1 of the Remedial Action Plan (RAP). A recent review of the BUIs determined that further assessment is required to evaluate the health of fish populations within and adjacent to the AOC (Environment Canada 2010).

One of the fish populations that had been greatly reduced in numbers is that of walleye (Sander vitreus). Over-harvesting, degraded habitat, pollution and the construction of dams have been identified as possible contributing factors.

There have been a number of research and assessment studies in recent years supported by the RAP process to learn more about walleye and their use of existing habitat and to monitor their population recovery. Ontario Ministry of Natural Resources (OMNR) Nipigon District, OMNR Upper Great Lakes Management Unit, OMNR Aquatic Research and Development Section, Anishinabek/Ontario Fisheries Resource Centre and the Red Rock Indian Band have all contributed to this field work.

In this paper the results of these studies are reviewed and synthesized to provide a status report on the walleye population in the Nipigon Bay AOC. The recovery process is explained and comparisons are made to reference sites in which walleye are at different stages of recovery. Additional data needs and field studies required to complete our understanding of this population are identified.

2 A brief overview of walleye stocks in Lake Superior

The walleye populations of Lake Superior have always been relatively small and widely scattered due to limited amounts of available habitat (Schneider and Leach 1977). Within this lake they are confined to shallow embayments and the estuaries of moderate to large rivers which afford suitable conditions for spawning and the protection of juvenile fish. Historically, the three largest stocks of walleye were found in Black Bay and Nipigon Bay in Ontario, and in the St. Louis River at Duluth, Minnesota (MacCallum and Selgeby 1987). Smaller populations occur elsewhere around the lake, where smaller rivers and protected bays provide appropriate habitat.

Exploitation has been an ongoing source of stress to these walleye populations, with commercial harvest records going back to about 1870 (Figure 1). In the early years, most of the harvest came from Michigan and Wisconsin waters, but from about 1920 onward harvest was largely from Ontario, with Black Bay contributing about 90% of the yield until the collapse of its

1 walleye fishery in 1968 (Schneider and Leach 1977; Schram et al. 1991). In Nipigon Bay, an increase in the commercial walleye harvest occurred in the late 1940s as lake trout stocks declined through overexploitation and sea lamprey predation (Lawrie and Rahrer 1972). Following a number of years of high harvest in the 1950s, the walleye population declined catastrophically with no harvest reported from 1966 onward. The Whitefish Bay stocks were also fished commercially at the Goulais River and in Batchawana Bay until their decline in the early 1970s (Schram et al. 1991).

Figure 1: Historical harvest of walleye in Lake Superior (Schram undated).

As a result of these intense fisheries, along with pervasive habitat degradation, walleye fisheries declined across Canada at this time. Country-wide, the annual catch of walleye fell from 9,090,909 kg in 1955 to about 2,954,500 kg in 1971 (Hartman 2009).

The populations that persisted all lacked a commercial fishery. This included the smaller Thunder Bay populations near the mouths of the Current, Kaministiquia, Pine, and Pigeon rivers. Schram et al. (1991) reported these to have been only lightly fished by anglers with all populations appearing stable, although habitat loss has subsequently been identified as an issue (Solec 2012). The St. Louis population was the only large stock of walleye to survive this period and continues to be one of the healthiest stocks in the lake (Solec 2012). Interestingly, it too was not commercially fished as the walleye had an objectionable flavour attributed to chlorophenolic products released from upstream paper mills (Margenau and Schram 1982; MacCallum and Selgeby 1987).

3 Factors related to the walleye decline in Nipigon Bay

There has been much debate over what was responsible for the dramatic decline in the walleye population in Nipigon Bay. A number of factors have been suggested, including overfishing and habitat degradation (Ryder 1968, Wilson et al. 2007). Sea lamprey control may also have played a role. Kelso and Cullis (1996) provide a detailed timeline of these various perturbations.

3.1 Exploitation

At the time of collapse of the walleye population in Nipigon Bay, less was understood about the dangers of overfishing, with the feeling that fish populations were able to compensate for large reductions in their abundance. In 1956, in a review of walleye dynamics in the Nipigon River during the peak of commercial harvest, Ryder (1956) reported “. . . the commercial catch has increased immensely over the past two years, thus reducing the competitive factor among the pickerel themselves. The drastic reduction of lake trout . . . removes a competitive factor making more food available to the pickerel. It might be concluded then, that the present rate of exploitation is far below the maximum catch that could be taken to improve the quality of the population. . . . the harvest has not yet approached the point where optimal benefits to the pickerel population and subsequently to the angler are received.” This proved to be false, as the walleye population rapidly declined over the next few years.

In Nipigon Bay, the commercial harvest was a classic example of fishing a stock down to insignificance. Within this bay, walleye were very concentrated post-spawn, and gillnet and poundnet operations targeted them very effectively. The gillnet catch-per-unit-effort (CUE) remained extremely high through the latter period (1959-63) of reduced abundance, revealing the efficiency of the fishermen as they became more attuned to the fish’s seasonal movements (Ryder 1968). In addition, a substantial angling fishery also existed (Schram et al. 1991).

The walleye catch in Nipigon Bay from all commercial gear during the eight peak years of harvest prior to the collapse (1951-1959, 1956 excluded) totalled 97,245 kg (Figure 2). The average weight of walleye in the catch can be assumed to be similar to that reported for the Black Bay harvest, which was 0.87 kg (P. Addison, pers. comm.). This then translates into an annual harvest of about 14,000 walleye which when related to the estimated population size of 41,000 mature fish (Ryder 1968) implies an annual exploitation rate of 34% (or higher, including the angling harvest). While this high of an exploitation rate may arguably be sustainable in more southern locales (Schmalz et al. 2011), it has never proven to be the case in the colder waters of Ontario (Baccante and Colby 1996).

Nipigon Bay and the Nipigon River were closed to commercial fishing for walleye in 1984 and to angling in 1989, along with the Jackfish River.

18000

16000

14000

12000

10000

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Harvest (kg)

6000

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0 1948 1950 1952 1954 1956 1958 1960 1962 1964 1966 1968 1970 1972 Year Figure 2: Commercial harvest of walleye from Nipigon Bay (Zones 10 and 11) between 1948 and 1972 (E. Berglund, pers. comm.).

3.2 Habitat degradation

In a historical review of Nipigon Bay walleye, Wilson (1991) detailed the many habitat alterations that affected this population. The logging industry contributed through damming, deforestation, sedimentation, the accumulation of wood fibre, bark, and other organic matter from historic log drives, and DDT contamination. The creation of hydroelectric generating stations segmented the Nipigon River isolating fish populations and the altered flow regimes affected stream bank stability, sediment load and the quality of fish and wildlife habitat. Effluent discharges from municipal sewage treatment plants and a kraft pulp and paper mill were also implicated in the demise of the walleye fishery (Ryder 1968).

3.3 Sea lamprey control

An electric barrier on the Jackfish River was operated by the Sea Lamprey Control Center for three years beginning in 1959. Besides restricting walleye and other fish from moving up the river, it also caused direct mortality with an estimate of 700 walleye killed during its first year of operation alone (R. Ryder pers. comm., cited in Wilson 1991).

It is unknown how the use of lampricide in later years affected walleye, although there were reports of significant mortality of many different species of fish in the Nipigon and Jackfish rivers following lampricide treatments in the 1960s and 1970s (Wilson 1991). While early life stages of walleye are thought to be considerably more resistant than sea lamprey ammocoetes to TFM lampricide (Seelye et al. 1987), recent kills of post spawning adult walleye have been reported following TFM treatment (McChesney 2008; Preddice 2009).

4 Rehabilitation efforts

In 1991, the historic loss and continued low abundance of walleye in Nipigon Bay was identified as a Beneficial Use Impairment (BUI) in the Nipigon Bay Remedial Action Plan (RAP) Stage 1 document (Cullis et al. 1991). Through the RAP process, multiple actions were identified and implemented in an effort to restore walleye in the Nipigon River including the stocking of adult walleye (Cullis et al. 1995). The Nipigon River walleye stock was later recognized as one of 14 priority areas for walleye rehabilitation around Lake Superior in “A Rehabilitation Plan for Walleye Populations and Habitats in Lake Superior” (Hoff 2002).

4.1 Stocking

A stocking program was initiated in 1978 as an approach to rehabilitate the walleye population of Nipigon Bay and continued until 1992 (Wilson 1991). Initially eggs were stocked, then fingerlings and fry, and finally adult walleye were transferred into the bay (Table 1).

The source of eggs for the stocking program varied through the years, but included Current River, Onaman Lake, and Lake Nipigon. Stocking sites included Jackfish River, Condon Island, and three sites on the Nipigon River: the Lake Helen access, the highway bridge, and the river mouth.

An adult stocking program began in 1986, with 2,686 fish transferred from Savanne Lake over a four year period. A further 12,100 fish were obtained from Lac des Mille Lac , Georgia Lake and Lake Nipigon and stocked in the bay from 1990 to 1992 (Wilson et al. 2007).

Table 1: Stocking history for Nipigon Bay walleye (data from Wilson 1991, Wilson et al. 2007, and R. Swainson, pers. comm.).

Year Number Life Stage Source 1978 261,000 Eggs 1979 1,170,000 Current River

1,364,000 1980 20,800 Fingerlings 500,000 Eggs 1981 3,700 Fingerlings 1,461,000 Eggs Onaman Lake 1982 11,755 Fingerlings 2,450,000 Eggs 1983 347 Adults 350,000 Fertilized Eggs Current River 1984 200,000 Eyed eggs Onaman Lake 757,000 Fry Lake Nipigon 4,000,000 Fry 1985 Lake Nipigon 1,800 Fingerlings 425,000 Fry 1986 556 Savanne Lake 1987 421 Savanne Lake 1988 1209 Onaman Lake Savanne Lake 1989 968 Adults Trapnarrows Lake 1990 3500 Lac des Milles Lac 1991 4400 Lac des Milles Lac 1992 4200 Georgia Lake Lake Nipigon

4.2 Habitat restoration

There has been considerable progress in addressing environmental concerns in the Nipigon Bay AOC. This has included the development of a bioengineered marina at Red Rock, which features armour stone breakwalls that provide public access and fish and wildlife habitat; the development and implementation of the Nipigon River Water Management Plan, which has provided a workable solution to water use conflicts arising from regulated flows; and the realignment of Clearwater Creek and Kama Creek, which restored valuable brook trout habitat in the AOC. The ‘historic’ spawning grounds and the ‘Old Mill Site’ wetland on the lower river were rehabilitated through the removal of logs, pilings and debris. Domtar Packaging Ltd. upgraded its treatment technology in 1995 to improve the quality of its wastewater discharged to Nipigon Bay (and ceased operation in 2006). In 2012, the township of Nipigon incorporated secondary treatment to its water pollution control plant.

In 2004, Environment Canada completed an assessment of the sediment contaminants in Nipigon Bay. The findings suggest that the soil contaminants near the vicinity of the pulp and paper mill have reduced to a point that the concentrations are suspected to have no or limited impact on the benthos (Richman 2004). A recent inventory of benthic macroinvertebrate communities in the Nipigon system suggests a high quality habitat indicative of a highly oxygenated, unimpaired environment (Deacon 2011).

5 Recent research, assessment and monitoring studies

5.1 Genetics of stocks

A genetic assessment of walleye in Nipigon Bay and Black Bay was carried out by Wilson et al. (2007) using microsatellite DNA analysis. They found that the juvenile stocking and adult transfers from the four source populations1 differed substantially in their contributions to the re-established population. There was little indication that the stocking efforts up to 1991 (Table 1) provided any enhancement to the current population, as it lacked genetic information from the Current River, Savanne Lake, Onaman Lake, or Lac des Mille Lac stocks.

However, the analysis did show that fish from nearby Georgia Lake and Lake Nipigon (Ombabika Bay), with interbreeding between these groups, contributed substantially to the population. It is now known that Georgia Lake walleye were the product of an earlier Onaman Lake introduction (R. Swainson, pers. comm.), so this further complicates the picture.

Most interestingly, a stock of walleye of unknown parentage also exists in abundance (Wilson et al. 2007). Unfortunately, genetic information from the historic population from Nipigon Bay does not exist, so there are no genetic benchmarks for comparison. In the absence of historical data, it could not be determined whether these fish represented remnants of the original population, stocking from another source, or dispersers from unknown wild populations.

5.2 Telemetry studies: Seasonal movement and habitat use

A multi-year walleye telemetry study was carried out within the Nipigon River system by OMNR Nipigon District beginning in 2006 and continuing to the present as part of the effectiveness monitoring program for the Nipigon River Water Management Plan. Walleye used in this study were captured at a number of different locations on the Nipigon River in the fall, once water temperatures had cooled, to minimize stress on the fish. External radio transmitters were most commonly used, although internal transmitters were inserted into some walleye. Over the

1 It is now known that adult fish from Trapnarrows Lake were also stocked in Nipigon Bay in 1989 (R. Swainson, pers. comm.), but this population was not included in the Wilson et al. (2007) genetic analysis.

7 course of this study, a total of 120 walleye were fitted with transmitters, as follows: 2006-2009 – 33 fish, 2010 – 25 fish, 2011 – 38 fish, and 2012 – 24 fish. A number of northern pike and lake sturgeon were also implanted with transmitters.

Walleye were commonly tracked by boat although a helicopter was also used at critical times. A base station was established at the Nipigon River highway bridge in 2007 and in more recent years (2011-2012) at Alexander Dam, Sawmill Point on the lower Nipigon River, and at the Jackfish River railway bridge to provide a continuous record of tagged fish in the vicinity.

The objective of this study was to determine water flows and depth used by spawning walleye in order to provide protection through amendments to the Water Management Plan. The study was expected to provide information on spawning locations, movement patterns, and habitat use at different times of the year, but it also had the potential to reveal information about the discreteness of walleye spawning stocks.

The idea of two different stocks of spawning walleye inhabiting the Nipigon River was a question put forward back in the mid 1950s before the walleye population collapse (Ryder 1956). Polly Lake anglers considered the stock to be singular and worried that the increased commercial harvest of walleye in Nipigon Bay may have adverse effects on their fishery, while the commercial industry claimed that there was no concern as two different stocks existed. Ryder (1956) investigated the issue by following 1025 walleye tagged in the lower river during the spawning run in May 1956. He found that the majority of these fish moved up into the Polly Lake area for the summer (with some exceptions that instead travelled to the Jackfish and perhaps the Gravel River), then returned to the lower Nipigon River in the early fall, and then moved to Nipigon Bay to overwinter. He concluded from this that a single population existed. The movement pathways described by Ryder (1956) and the seasonal use by walleye are illustrated in Figure 3.

The current telemetry study challenges this single stock hypothesis. Instead, it suggests that two discrete stocks of walleye currently inhabit the Nipigon River, separated by the Highway 11/17 bridge. In general, walleye captured and implanted in the upper portion of the river (Alexander Falls, Polly Lake, upper Lake Helen) displayed different patterns of seasonal movement and habitat use than those tagged in the lower river ( highway bridge to river mouth) (Figure 4).

Walleye that are found in the upper river in the fall spend a portion of their time in the river itself and the rest of the year in either Lake Helen or Polly Lake. A common pattern is apparent. Walleye enter the upper Nipigon River in the spring, presumably to spawn. Following this, a few remain in the river but most return to the warm waters of Lake Helen and Lake Polly for the summer. They then move back to the river in the fall to feed, and return once more to Lake Helen to overwinter. These fish will be referred to as the Upper River/Lake Helen stock.

Figure 3: Movement patterns and seasonal use of habitat described by Ryder (1956). The solid yellow line illustrates the primary pathways while the dashed lines show alternate pathways taken by a minority of fish.

Walleye found in the lower river in the fall display a radically different pattern of seasonal movement. Most members of this Lower River/Nipigon Bay stock enter the Jackfish River in the spring to spawn, then spend the early summer in Nipigon Bay. In late summer and fall they return to the lower Nipigon River to feed, then head back to the bay to overwinter. Some of these fish may instead spawn in the traditional areas in the lower Nipigon River or, alternatively, travel to the Gravel River or Pays Plat area, but they tend to follow the standard pattern of movement at other times of the year.

Further genetic analysis is required to definitively determine if these stocks represent discrete spawning populations of walleye.

Figure 4: Movement patterns and seasonal use of habitat inferred from recent telemetry studies. Note differences between the Upper River/Lake Helen stock (yellow) and the Lower River/Nipigon Bay stock (red).

5.3 Walleye spawning observations and drift netting: Nipigon River

Observations on where walleye and other species spawn in Nipigon River have been made by OMNR Nipigon District staff over the past 25 years. These observations involve walking the shoreline or cruising by boat while shining a high intensity light beam which reflects in the eyes of walleye.

Walleye are occasionally seen during the spawning season at the historic spawning site downriver from the highway bridge, but these sightings are infrequent and the number of fish is very few. Spawning activity was first evident here back in the 1990s and as recent as 2012 with 10 spawning walleye observed (R. Swainson, pers. comm.). However, drift netting immediately below this site over the past two or three years has failed to ever detect any larval walleye.

Walleye are commonly seen through the spawning period, at times actively performing the rituals, at various sites in the upper river including Bass Creek. Also, large numbers of walleye have been observed in the upper Jackfish River at this time of year.

5.4 Walleye and northern pike abundance: Lake Helen/Polly Lake

OMNR Nipigon District and Red Rock First Nation, with support from Anishinabek/Ontario Fisheries Resource Centre, carried out a four year trapnetting and tagging study on Lake Helen and Polly Lake during the spring of 2006-2009 as a component of the effectiveness monitoring program for the Nipigon River Water Management Plan. The goal was to assess the relative abundance of walleye and northern pike and provide information regarding their age structure, growth and mortality (McKee 2008; Swainson 2010).

While considerable effort was put into the trapnetting study, relatively few walleye were captured (see McKee 2008 and Swainson 2010 for sampling details and net locations). A total of 266 overnight sets were made during these 4 years through the period of May 9th to July 8th capturing a total of 193 walleye, resulting in an average CUE of 0.72 walleye per lift.

A rough Schumacher population estimate (Ricker 1975) can be made using these data, although confidence limits are very broad due to the small sample size with few recaptured fish. A total of 5,030 adult walleye are estimated to be present in this part of the Nipigon River system. Growth rates were observed to be high with the continuous representation of age classes ranging from 2-13 demonstrating at least some reproduction in all years and suggesting a degree of stability to this population (Figure 5, 6).

5.5 Fish community assessment: Lake Helen

In 2010, the Anishinabek/Ontario Fisheries Resource Centre, supporting the Red Rock First Nation, completed a Fish Community Index Netting (FCIN) project on Lake Helen to determine the status of key members of the fish community, with a focus on commercial and recreational species (McKee 2010).

The program was carried out in September, at water temperatures of 14-16 oC, following the standard FCIN netting protocol. Only 44 walleye were captured in the 20 sets, resulting in a CUE of 2.2 fish/net. Considering the style of gillnets used and the time of year and ignoring the difference in depth strata, catches could be roughly comparable to what might have been achieved following the Fall Walleye Index Netting (FWIN) protocol. When compared to FWIN results across northwestern Ontario, a mean catch of 2.2 fish/net indicates a low abundance, well within the lower 25% quartile (Morgan et al. 2003). On the positive side, one-third of these fish were aged at 1-2 years, suggesting that continuous recruitment into the system is occurring.

Number of fish

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Age Figure 5: Age frequency of walleye sampled in trapnetting study on Lake Helen and Polly Lake.

Number of Fish

0 265 295 325 355 385 415 445 475 505 535 565 595 625 655 Total Length (mm) Figure 6: Length frequency of walleye sampled in trapnetting study on Lake Helen and Polly Lake.

Assuming that the CUE:density relationship is roughly similar between the FCIN catch and that from FWIN nets, a CUE of 2.2 fish/net would translate into a density of about 2.5 walleye/ha (P. Addison, pers. comm.). The upper river/Lake Helen/Polly Lake chain covers an area of about 2,000 ha which then implies a population size of roughly 5,000 walleye. This is admittedly a very crude estimate, however it is closely aligned to that obtained independently through the mark-recapture study reported above.

5.6 Electrofishing surveys: Nipigon Bay and River

The first electrofishing surveys in the Nipigon River were carried out between 1991 and 1995 (Bray 1996). These were conducted at night at select sites using a boat electrofisher with the purpose of monitoring the abundance of small fish. The surveys were carried out during late summer and fall at 10 sites, although all sites were not sampled each year. Seven of these sites were located in the lower Nipigon River and the other three at Red Rock (see Addison and Chicoine (2007) for maps of these sites).

As walleye were also vulnerable to this gear (two fish captured in 1993), the OMNR Upper Great Lakes Management Unit began a repeat of this survey starting in 2000 and continued until the present. The original 10 sites were assessed along with an additional 24 sites, but once more, all sites were not sampled in all years and some years were missed altogether. The objectives of this project were to monitor the relative abundance and population demographics of walleye during the rehabilitation process. Addison and Chicoine (2007) describe the early results of this project and provide maps of the additional sample sites.

In addition to providing catch per unit effort data, life history parameters for walleye were also recorded during these electrofishing surveys. This provides valuable information on growth, condition, and mortality rates of these fish, and informs us as to the status of the walleye population today.

The surveys reveal that there are many old fish in the population, with ages up to 15 years in these small samples, which suggests relatively low mortality rates. Also, growth rates are extremely high, and walleye exhibit very good condition with much greater weight at length than the general Ontario population. The reproductive potential of these large fish should be great.

Equally important to note are changes in the abundance of walleye as reflected by the electrofishing CUE. After being relatively flat in the 1990s, positive improvements are evident in recent years (Figure 7).

0.10

0.08 Year:CUE: y = -7.1893 + 0.0036*x; r = 0.8154, p = 0.0004; r2 = 0.6649

0.06

0.04

CPUE (fish/minute)

0.02

0.00

1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 Year Figure 7: Geometric mean catch per unit effort for walleye from electrofishing surveys, summed across all sampling sites

5.7 Fish community index netting: Nipigon Bay

Fish Community Index Netting (FCIN) is a standardized annual fisheries independent survey that is carried out during the summer by the OMNR Upper Great Lakes Management Unit. It consists of multimesh gillnets set in random locations within select depth strata in the large bays of Lake Superior. It is used to assess trend through time relative abundance and the population dynamics of the offshore fish community in Canadian waters of Lake Superior, with emphasis on lake whitefish and lake trout. However, other members of the fish community including walleye are vulnerable to the fishing gear, so it can provide information around changes in their abundance as well.

This program was carried out annually in Thunder Bay and Nipigon Bay (2009-2012) and in Jackfish Bay and Peninsula Harbour (2010-2012). No walleye were caught in the FCIN gear in Nipigon Bay in any year. Walleye were captured in at least some nets in some years at each of the other locations (E. Berglund, pers. comm.). This further attests to the low abundance of walleye within the Nipigon Bay area.

5.8 Walleye population assessment: Nipigon Bay

A trapnetting study was carried out by OMNR Nipigon District in June 2011 to provide basic demographics of the walleye stock in Nipigon Bay. Two nets were fished for four days and a total of 282 walleye were captured, representing a CUE of 35.3 fish/net/day.

This study revealed that a small but healthy population of walleye exists in the bay. A wide range of ages were noted, ranging from 2-15, with many old fish present (Figure 8). This is indicative of a population subject to a low rate of mortality.

These walleye are also extremely large, with over 25% of the fish sampled exceeding 700 mm in length (Figure 9). This signifies a very high rate of growth.

Number of fish Number

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Age (yrs) Figure 8: Age frequency of walleye sampled in 2011 trapnetting study on Nipigon Bay.

Number of Fish

0 315 355 395 435 475 515 555 595 635 675 715 755 795 835 875

Total Length (mm)

Figure 9: Length frequency of walleye sampled in 2011 trapnetting study on Nipigon Bay.

6 Status of walleye stocks and their habitat in the Nipigon system

6.1 Reference sites

6.1.1 Recovery of collapsed populations

Information on a number of other collapsed or recovering walleye populations2 was assembled as a means of putting the recovery process of the Nipigon Bay population in perspective (Table 2).

2 In all cases, rainbow smelt were also present in these waterbodies which is an important consideration if making comparisons. The Nipigon Bay east area has the greatest biomass of rainbow smelt documented in Canadian waters of Lake Superior (Yule et al. 2008). This species was also found to be generally of larger body size in this part of the lake. The presence of a large and abundant prey such as rainbow smelt has a positive influence on walleye growth energetics. In western US reservoirs, growth rate increases of up to 50% have been documented once rainbow smelt became a large part of the walleye diet (Johnson and Goettl 1999; Graeb et al. 2008). On the other hand, rainbow smelt may also compete with and prey on age-0 walleye which in some instances can significantly reduce their density (Mercado-Silva et al. 2007).

Table 2: Reference waterbodies and the status of their walleye population.

Waterbody Year of Recovery Current status Authority collapse period (yrs) Lake Nipissing ongoing n/a declining OMNR 2012a; G. Morgan, pers. comm. Ombabika Bay 1995 18+ no recovery OMNR 2012b; (Lake Nipigon) R. Salmon, pers. comm. Nipigon Bay 1966 47+ early recovery this report Black Bay 1968 45+ early recovery E. Berglund, pers. comm. Shoal Lake 1981 32+ mid recovery Mosindy 2012 Rainy Lake (N. Arm) 1964 40 recovered McLeod and Rob 2009

Recovery of a collapsed walleye population takes a considerable period of time. In a controlled experiment in the early 1980s, walleye in Henderson Lake in northwestern Ontario were fished down to 6% of their adult biomass (Reid 1985). Recovery of this population took 21 years, even though the fish community was very simple and fishing mortality was kept to zero (Amtstaetter 2004). Nipigon Bay and the reference lakes support a more complex fish community and changes have occurred to most of these communities through the course of recovery. Also, in each of these cases there has been some residual fishing occurring which is known to further constrain recovery.

Rainy Lake (North Arm) represents an example of a recovered walleye population. This took 40 years to accomplish and the first improvements were not noted until 30 years had passed. Shoal Lake may be considered in the middle stages of recovery, 32 years after the collapse of the population. The first improvements were not seen here until 25 years had passed. Ombabika Bay is showing no signs of recovery 18 years after the collapse of the fishery (R. Salmon, pers. comm.).

The lengthy recovery period for Nipigon Bay and Black Bay walleye is not that unusual in light of these other examples. The fish community is more complex in Lake Superior, with many other top predators competing for the same prey resources, including lake trout, brook trout, rainbow trout, chinook salmon, coho salmon and northern pike. There have been many shifts in the relative abundance of these various species over the last 50 years.

The forage base has also altered dramatically through these years (Gorman et al. 2011) and invasive species such as the spiny water flea (Bythotrephes longimanus) have caused changes to the food web which are not fully understood. In addition, white pelicans and cormorants are reported to be increasing in the Nipigon Bay area (R. Swainson, pers. comm.).

6.1.2 Status indictors

A change in population abundance is the primary flag when monitoring the health of a species. Unfortunately, there are no estimates available of walleye abundance within the Nipigon Bay AOC since the early studies by Ryder (1956). Even so, inferences can be made based on evidence from the studies that have been done.

Table 3: Indicators of walleye population status for reference waterbodies. Mortality rates represent Robson-Chapman estimates from age 4 through 10. Authorities are as indicated in Table 2.

Waterbody Abundance Mean Age Mortality Size @ Age 10 (yrs) (A) (mm) Lake Nipissing moderate, declining 1.7 31.6 567 Ombabika Bay low, no change 3.3 31.5 594 Upper River/Lake Helen low, increasing 6.5 29.6 625 Lower River/Nipigon Bay low, increasing 9.3 21.8 671 Black Bay low, increasing 4.5 25.6 607 Shoal Lake moderate, increasing 4.3 46.8 644 Rainy Lake (N. Arm) high, stable 5.0 38.6 619

Table 3 illustrates how abundance has changed, or is currently changing, in the reference populations. It also provides information on the mean age, annual mortality, and growth rate of walleye. These attributes are all useful in judging the health of a population.

Growth rates for the Lower River/Nipigon Bay walleye were the highest recorded for any of the recovering populations (Figure 10). While the Upper River/Lake Helen walleye follow a similar growth trajectory, this is delayed by a year or more. By age 5, these fish reach a size similar to Ombabika Bay walleye, which were successfully stocked in the bay in the 1990s (Wilson et al. 2007). The Lower River/Nipigon Bay walleye grow at a faster rate, resembling that of Black Bay walleye, an original Lake Superior stock. This fact adds more support to the two-stock theory, and suggests that the upper river population may be the result of stocking while the lower river walleye may be the remnants of the original population, or the ‘unknown’ population discussed in Wilson et al (2007).

6.2 Walleye population status

Much can be inferred about the status of the walleye in the Nipigon system through a synthesis of the information provided through the various studies that have been carried out. From this we can surmise the following:

800

700

600

500

400

Total Length (mm)

Lake Helen 300 Nipigon Bay Rainy (N. Arm) Black Bay Nipissing 200 Shoal L. Ombabika Bay

100 0 2 4 6 8 10 12 14 16 18 20 Age (years)

Figure 10: Growth rates of Nipigon Bay AOC walleye in relation to walleye from other reference sites. Growth cannot be broken down by sex for Nipigon Bay fish, so combined sexes were used for this comparison.

1. Abundance remains low

Walleye were once observed in the thousands on the lower Nipigon River in the vicinity of the railway bridge during April and May (Wilson 1991). Ryder (1956) reported that these fish could be captured in quantity at this location with seine or dip nets. Spawning observations carried out since 1988 by OMNR Nipigon District reveals that very few fish are found here today.

Fish community assessment projects carried out on Lake Helen/Polly Lake by the Anishinabek/Ontario Fisheries Resource Centre also reported low catches of walleye, both in trapnets and gillnet gear. Electrofishing surveys carried out at standard sites by OMNR Upper Great Lakes Management Unit verifies that this species remains at low abundance and the lack of walleye in their FCIN catches provides further evidence of this.

A very rough estimate of 5,000 walleye can be made for Lake Helen based on FCIN catches and a trapnet mark/recapture study. No estimates are possible for Nipigon Bay walleye.

2. Density is increasing

The electrofishing surveys, while revealing low abundance, indicate that improvements are occurring with walleye CUEs generally increasing over the last decade or so. While not

quantitative, records of spring spawning observations also reveal that greater numbers of walleye have been seen in recent years. In addition, anecdotal reports from anglers tell of increased incidental catches of walleye in Nipigon River through to Polly Lake (R. Swainson, pers. comm.).

3. Growth rates are very high

The 2011 trapnetting survey on Nipigon Bay provided information on the size and age of a large sample of walleye. It was found that these fish are growing at a very rapid rate and reaching a large maximum size (Figure 9). The fish community assessment studies show that the Lake Helen/Polly Lake walleye also exhibit rapid growth (McKee 2008) although less than that of the Nipigon Bay stock (Figure 10).

Walleye generally display rapid growth in recovering populations as competition is low and food resources are not limiting. High growth rates are evident for all the reference populations, however the Nipigon Bay fish stand out with this population reaching the greatest size at age 10 (Table 3). A succession of warm summers and a forage base comprising large and abundant rainbow smelt have likely contributed to this rapid growth.

4. Mortality is very low

The trapnetting data also provides evidence that the walleye in Nipigon Bay are long-lived (Figure 8) with a very high mean age of 9.3 years, much greater than the other reference populations. These ages were determined using dorsal spines, which if anything would underestimate ‘true’ age (S. Mann, pers. comm.). The lack of missing year classes reveals that recruitment has been constant and successful in all years.

This slow reduction in numbers with age translates into a very low annual rate of total mortality of 21.8% (Table 3). Mortality rates are up to twice this in the other reference populations. Recovery of degraded populations has always been enhanced when mortality is maintained at a low rate.

6.3 Walleye habitat status

There have been considerable improvements to the aquatic habitat in the Nipigon Bay AOC. Remediation has been done to shorelines and near-shore area, water quality has been much improved through municipal and industrial treatment facilities, and water levels and flows on the Nipigon River are now controlled through a water management plan.

The ‘historical’ walleye spawning area below the highway bridge was cleared of logs and debris as part of the early remediation efforts, although additional logs have accumulated here and should be removed (R. Swainson, pers. comm.). While a thin layer of algae-like material coats the rubble at this site, it was examined and found to be suitable as walleye spawning and

20 nursery habitat (Colby 2007). Other improvements to walleye habitat include enhancements of spawning sites at Bass Creek and at Polly Lake.

In general, the aquatic habitat is of excellent quality in the Nipigon Bay AOC and should not be an impediment to the recovery of walleye populations.

7 Information needs

7.1 Genetic analysis of stocks

In their genetic assessment of walleye in Nipigon Bay, Wilson et al. (2007) found that a stock of walleye of unknown parentage exists in abundance and appears to be successfully reproducing. They speculated that this could be the result of strays from another wild population and suggest that there could have been other undocumented tributaries of Lake Superior in which walleye spawned.

Recent telemetry studies have provided evidence that two discrete stocks of walleye may exist. The Lower River/Nipigon Bay stock is known to run up the Jackfish River in the spring, presumably to spawn. Perhaps these fish represent the remnants of the original population, or are the stock of ‘unknown’ heritage that Wilson et al. (2007) discovered, while the Upper River/Lake Helen stock are the progeny of recently stocked fish.

Additional genetic analysis is required to answer this question. Tissue samples from upper and lower river walleye have been gathered for this purpose.

7.2 Population monitoring and assessment

An estimate of the size of the walleye population is required to benchmark the current status and allow future evaluation of improvements or reductions in this number. If genetic analysis determines that two discrete populations exist, the size of each must be determined independently.

This would normally be done through a Fall Walleye Index Netting (FWIN) project, which is the standard approach for assessing walleye populations in Ontario. The FCIN survey carried out in Lake Helen in September 2010 and recommended to be repeated on a two-year cycle (McKee 2010) may serve as a surrogate for a FWIN to monitor the Upper River/Lake Helen stock.

Better yet, a FWIN survey could replace FCIN as the standard sampling protocol for the Upper River/Lake Helen stock if walleye assessment was the primary goal. If an evaluation of the entire fish community is of similar importance, Broad-scale Fish Community Monitoring (BsM)

21 may be another alternative (Sandstrom et al. 2010). These netting programs would be repeated at intervals that were deemed necessary by management staff.

However, for the Lower River/Nipigon bay stock a FWIN may not be effective due to the unique migratory nature of this population, with walleye congregating in the lower river in the fall when this netting would normally be done out in the bay. Alternatively, the size of this population may be better established through a mark-recapture study. Fish could be caught and tagged during the spawning run up the Jackfish River, and a later trapnetting project in Nipigon Bay or the lower Nipigon River could be used to assess the ratio of marked to unmarked fish.

Because the sex of walleye can normally be determined at spawning time, information could also be gathered on size and age of both males and females. Some smaller fish would have to be sacrificed to determine age of maturity.

8 Conclusions

There have been many changes in the 50+ years since Ryder`s (1956) early studies and the collapse of the walleye fishery in Nipigon Bay. There have been drastic shifts in the composition of the aquatic community, along with significant improvements to nearshore habitat within the bay, and recent changes to the thermal properties of the area brought about by climate warming. Together, these present a new environment for walleye to which they continue to adapt. This process appears to have promoted the development of two separate stocks of walleye in the Nipigon system.

We have a new population (or two) of walleye here today, different from the historic population in terms of its genetics, its spawning behaviour, and its annual movement patterns and use of habitat. This population is thought to be at a relatively low level of abundance compared with historic estimates, but quite healthy in all other respects. Growth rates are rapid and mortality is low. Together these traits suggest that large, rapidly maturing fish are present and have the potential to produce quantities of offspring in the future. Clean, high quality substrate is available in unobstructed spawning areas in both the Nipigon and Jackfish rivers and is not constraining recovery.

On the basis of this evidence, it is recommended that the BUI status of the walleye population and their habitat in the Nipigon Bay AOC be updated to ‘Not Impaired’.

The 40,000 fish target for walleye recovery may never be achieved in light of all the changes observed in this ecosystem (Colby 2007). All that can be done to accomplish this has been done. Maintaining fishing mortality at a low level will help the walleye population expand to achieve its new equilibrium.

9 Acknowledgements

I thank Darryl McLeod, Tom Mosindy, Albertina Vanogtrop, Rick Salmon, George Morgan, and Kim Armstrong for supplying information on reference walleye populations. Rob Swainson (Nipigon District), Eric Berglund (Upper Great Lakes Management Unit) and Kim Tremblay (Anishinabek/Ontario Fisheries Resource Centre) were very helpful in providing data from their respective field programs. The report also benefited from discussions with Ken Cullis, Marilee Chase, and Pete Addison, along with earlier conversations with Dick Ryder. Reviewers of the report included Sarah Da Silva, Rob Swainson, Marilee Chase, and Ken Cullis.

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