Collections of DNA baseline tissues from Chinook Salmon in the North Coast of in 2004

Ivan Winther

Fisheries & Oceans Canada Science Branch, Pacific Region 417-2nd Avenue West Prince Rupert, British Columbia V8J-1G8

February, 2005

A project funded by the Northern Boundary and Transboundary Rivers Restoration and Enhancement Fund 2004.

ii CONTENTS

Abstract...... iii List of Tables ...... iii List of Figures...... iii Introduction...... 1 Methods...... 2 Results...... 2 Discussion...... 3 Acknowledgements...... 3 References...... 4 Tables...... 5 Figures...... 6 Appendix...... 8

North Coast Chinook DNA Baseline NP4 iii

ABSTRACT

Tissue samples were collected from 495 chinook salmon (Oncorhynchus tshawytscha) across 13 different spawning populations in the North Coast of British Columbia for the purpose of augmenting the existing genetic baseline. The samples represent 10 new populations in the baseline and 3 populations that were previously sampled. The most significant samples come from the Kitlope River (120), the Ishkheenickh River (88) and the Kateen River (75).

LIST OF TABLES

Table 1. Inventory of chinook tissue samples collected for DNA analysis in the North Coast of British Columbia prior to this study...... 5

Table 2. Chinook tissue samples collected in 2004 by stream...... 6

LIST OF FIGURES

Figure 1. Location of tissue punch collected from chinook salmon...... 6

Figure 2. Map of the North Coast of British Columbia showing the approximate locations of the sampling sites...... 7

North Coast Chinook DNA Baseline NP4 1

INTRODUCTION

This project was designed and funded to collect tissue samples from populations of chinook salmon to augment existing collections of genetic material with the ultimate objective of forming a complete baseline of genetic material for the range of the species. The collections will support existing genetic baselines for chinook salmon in Canada and the United States of America. A coast-wide microsatellite deoxyribonucleic acid (DNA) baseline is under development by a consortium of American laboratories and Fisheries & Oceans Canada called “Genetic Analysis of Pacific Salmonids (GAPS)” (Moran, et. al., 2004). Chinook tissue samples will be collected and shared within GAPS according to the practices outlined by the Bilateral Chinook Technical Committee of the Pacific Salmon Commission (CTC, 2004). Collections of baseline genetic material allow for further refinement of chinook population units relevant to planning and management (i.e. management units, conservation units or evolutionarily significant units). Genetic stock identification methods can be used to determine stock composition of fisheries and stock specific catch estimates. Accurate stock identification from mixed stock samples requires complete baselines for estimating relative contribution by each component stock. This project considers chinook salmon bearing streams in British Columbia’s northern coast, essentially rivers and streams draining into Canadian waters of the Pacific Ocean north of 53º north latitude. The project area is bounded to the south by the height of land between the Kitlope and Kimsquit River watersheds. The study area extends north to the border between Canada and Alaska. Inland, the northern boundary of the study area was formed by Stikine and watersheds. The eastern boundary of the study area is the watershed. British Columbia’s northern coast is home to over 90 streams known to have spawning populations of chinook salmon. Among these are the large watersheds of the Skeena and Nass Rivers and their tributaries and a number of smaller independent coastal streams. A single endemic population of chinook salmon exists on the Queen Charlotte Islands (QCI) in the Yakoun River. Baseline tissues are complete for this population. The is the 3rd largest river occurring entirely in British Columbia with a drainage area of 21,100 km2 (Canada, 1985). Much of the river is extremely turbid and glacial. Most observations of spawning chinook come from clear tributaries or the confluence of clear tributaries with the mainstem. Radio telemetry studies conducted in 1992 revealed a number of previously unrecorded spawning sites (Koski et. al., 1993). The is the second largest river occurring entirely in British Columbia with a drainage area of 54,400 km2 (Canada, 1985). It is typical of large chinook producing rivers with a small number of large tributaries producing most of the chinook and a large number of smaller populations contributing to the diversity within the system. The majority of the chinook production in the Skeena comes from the large lake stabilized systems of the Kitsumkalum, Morice, Bear and Babine Rivers. Full (>200) baseline samples exist for these populations but there are several intermediate sized populations and a large number of small tributaries with relatively small chinook populations that have not been sampled. Many of the smaller coastal drainages do not have populations of chinook salmon. Among the small systems with chinook populations, many have less than a hundred spawners. The smaller populations are finite but logistically difficult to sample since only a portion of the population could be caught in any one year. Thus tissue collections will require several years of sampling to meet the objective of 200 tissues per population. Some populations are so small and remote that sampling is impractical at this time.

North Coast Chinook DNA Baseline NP4 2 Tissue samples for the purposes of DNA baseline data have been collected from chinook populations in the North Coast since 1991, most collections occurred after 1995 by Fisheries & Oceans Canada crews or contractors. Complete samples have been collected from most of the large chinook spawning populations in the North Coast, however, many remote or smaller spawning populations have not been sampled. A total of 16 streams have tissue collections from over 200 individual chinook salmon. Another 8 streams have collections from between 100 and 200 individuals and 10 streams have collections from less than 100 chinook (Table 1.).

METHODS

Streams were initially selected based on the size of the chinook population, whether any enhancement had occurred in the system and whether there were existing baseline samples available for the stock. Highest priority was assigned to large, wild populations without baseline samples or incomplete (<200) baseline samples. Appendix 1 lists known North Coast spawning populations of chinook salmon and their relative size based on mean escapement counts in the 1980’s. This time series was applied in an attempt to account for recent changes in escapement estimation. The data provide a very rough estimate of relative size for the priority setting exercise. A number of groups work on salmon enumeration within the study area. Their help was solicited to identify opportunities and to collect chinook tissue samples. Each was provided with the list of priority sites for chinook tissue samples in their area and the logistical considerations for the collections were discussed. Preferred samples for DNA baselines come from adult chinook collected in the location where they will spawn. Adult chinook salmon were caught using tangle nets, dip nets, beach seines or by angling. They were caught as close to spawning as possible or after spawning without disturbing actively spawning fish. The fish were released after sampling. A common paper punch was used to collect tissue samples from the operculum of the chinook salmon being sampled (Figure 1.). One tissue sample was collected from each chinook. Tissues were preserved in a solution of 95% non-denatured ethanol. Data on the geographic location, date, and sampler accompanied each sample. Samples were forwarded to the Fisheries & Oceans Canada, Molecular Genetics Laboratory at the Pacific Biological Station in Nanaimo.

RESULTS

A list of target populations was developed for the 2004 chinook tissue sampling project. The list included the Khutzeymateen, Ishkheenickh, Kiteen, Kitsault, Iknouk and Bell-Irving Rivers in Area 3, the Zymoetz (Copper), Skeena mainstem, Lakelse, Shegunia, Khyex, Kispiox tributaries (Nangeese, Sweetin, Stephens), Nanika and Kasiks Rivers in Area 4 and the Kitlope, Kemano, Dala, Brim, Kowesas, Wahoo Rivers in Area 6. Tissue samples were collected from a total of 495 individual chinook from 13 spawning locations. This total includes single tissues collected from the Oweegee River and Kumealon Creek. The Oweegee sample is added to the existing baseline of 219 chinook. The Kumealon sample is the first from that system. Table 2 lists the 2004 tissue collections by stream. None of the new systems sampled met the target of 200 tissues. Approximate locations of sampling sites appear in Figure 2. Details of the collections follow by river. Khutzeymateen River: This remote location required helicopter access. Park permits were also required. 75 tissue samples were collected from the Kateen River tributary. North Coast Chinook DNA Baseline NP4 3 Ishkheenickh River: 88 tissue samples were collected. Kiteen River: 5 tissue samples were collected. Zymoetz (Copper) River: Sampling opportunities were identified in the main-stem and in some tributaries (Thomas creek and Salmon creek). 21 tissue samples were collected from Thomas Creek but subsequent sampling opportunities were negatively influenced by warm weather and rain which raised water levels. Skeena River main-stem: Spawning chinook were collected using tangle nets above the confluence of the Kitsumkalum River. Timing was critical as the chinook must be spawning to ensure that passing stocks do not form part of the sample. 23 tissues were collected. Kitlope River: The Kitlope River is very glacial and observations of chinook are typically limited to the outlet of Kitlope Lake. This site was accessed twice in 2004, once by float plane and jet boat and once by a transport vessel and jet boat. Exceptionally good water conditions early in September allowed for the observation of chinook on redds over 1 km downstream of the lake outlet. Spawning chinook observed during an over-flight lead to the subsequent collection of over 100 samples. A total of 120 chinook tissues were collected. Kispiox River Tributaries: 62 chinook tissue samples were added to the existing 105 samples from Kispiox River mainstem. The following samples were collected from Kispiox tributaries: 32 from Slamgeesh River, 46 from Sweetin River, 8 from Suskwa River and 13 from Harold Price Creek. Collections were attempted in the Iknouk, Gitsegukla and Shegunia Rivers but no chinook were caught in these systems. An over-flight of the Lakelse River found no opportunities for sampling chinook. Collections were not attempted in the Kemano, Kitsault and Bell-Irving Rivers.

DISCUSSION

Attempts have been made to collect tissue samples from chinook in most North Coast systems in the past. Complete DNA baselines exist for systems that are readily accessible with large chinook populations or systems that have crews working on them. The remaining systems have significant challenges to sampling chinook either due to their location or the size of the stock present. Most of these systems are small or glacial and the availability of chinook to sample is highly dependent on water conditions. Tissue samples from several new spawning populations will be added to the DNA baseline as a result of the work in 2004. Most significant are samples from the Kitlope, Ishkheenickh, and Khutzeymateen Rivers.

ACKNOWLEDGEMENTS

Tissue samples from the Nass River tributaries, the Ishkheenickh and Kiteen Rivers, were collected by Nisga’a Fisheries staff. Tissue samples from the Kispiox River tributaries were collected by Gitxsan Watershed Authorities staff. The Terrace Salmonid Enhancement Society collected tissues from the Skeena River mainstem and Thomas Creek.

North Coast Chinook DNA Baseline NP4 4 REFERENCES

Canada. Energy, Mines and Resources Canada. Surveys and Mapping Branch. 1985. Canada - Drainage Basins, The National Atlas of Canada, 5th ed. Map Scale 1:7 500 000. Ottawa. (atlas.gc.ca).

Chinook Technical Committee, Pacific Salmon Commission. 2004. Sample exchange of DNA extractions. To: Principal Investigators in the PSC coastwide DNA baseline development project. unpublished letter.

Koski, W.R., M.R. Link and K.K. English. 1993. Distribution, timing and numbers of Chinook salmon returning to the Nass River watershed in 1992. LGL Ltd. Sidney B.C. unpublished report.

Moran, P., M. Banks, T, Beacham, C. Garza, S. Narum, M. Powell, L. W. Seeb, R. L. Wilmot, and S. Young. 2004. Genetic Analysis of Pacific Salmonids (GAPS): Development of a Standardized Microsatellite DNA Database For Stock Identification of Chinook Salmon. Chinook funding proposal submitted to the US Chinook Technical Committee for funding under the budget increment associated with the U.S. Letter of Agreement. unpublished.

North Coast Chinook DNA Baseline NP4 5

TABLES

Table 1. Inventory of chinook tissue samples collected for DNA analysis in the North Coast of British Columbia prior to this study. Area Locale Stream Years Sampled # samples 1 QCI Yakoun River 1987 1989 1996 2001 201 3 Nass River Bowser River 1996 1 3 Nass River Cranberry River 1995 1996 1997 164 3 Nass River Damdochax River & Lake 1995 1996 1997 257 3 Nass River Kincolith River 1996 1999 287 3 Nass River Kwinageese River 1991 1995 1996 1997 299 3 Nass River Meziadin River & Lake 1995 1996 1997 195 3 Nass River Oweegie Creek & Lake 1995 1996 1997 219 3 Nass River Seaskinnish Creek 1995 1996 1997 99 3 Nass River Snowbank Creek 1996 54 3 Nass River Teigen Creek 1996 1997 30 3 Nass River Tseax River 1995 1996 2002 180 3 Khutzeymateen River 2002 3 3 Portland Inlet Kwinamass River 2000 2001 2002 362 4 Prince Rupert Kloiya River 2001 2003 146 4 Skeena River Babine River 1994 1995 1996 266 4 Skeena River Bear River 1991 1995 1996 177 4 Skeena River Bulkley River - Upper 1991 1996 1998 1999 585 4 Skeena River Cedar River* 1996 116 4 Skeena River Ecstall River 1995 2000 2001 2002 2003 293 4 Skeena River Exchamsiks River 1995 11 4 Skeena River Gitnadoix River 2002 2003 42 4 Skeena River Kispiox River 1979 1985 1989 1991 1995 105 4 Skeena River Kitsumkalum River - Above Canyon 1991 1998 2001 190 4 Skeena River Kitsumkalum River - Below Canyon 1991 1995 1996 1998 2001 457 4 Skeena River Kitwanga River 1991 1996 2002 2003 288 4 Skeena River Magar Creek 1995 24 4 Skeena River Moonlit Creek 1995 1996 1998 83 4 Skeena River Morice River 1991 1995 1996 228 4 Skeena River Sustut Lake 1995 1996 1999 2001 2002 441 4 Skeena River Zymoetz River - Lower 1995 2003 8 6 Kitimat Arm Hirsch Creek 1998 1999 2000 474 6 Kitimat Arm Kildala River 1996 1997 1998 1999 2000 441 6 Kitimat Arm Kitimat River 1996 1997 1998 482

North Coast Chinook DNA Baseline NP4 6 Table 2. Chinook tissue samples collected in 2004 by stream. Area Locale Stream DNA samples collected in 2004 3 Nass River Oweegie Creek & Lake 1 3 Nass River Kiteen River 5 3 Nass River Ishkheenickh River 88 3 Portland Inlet Khutzeymateen River (Kateen tributary) 75 4 Skeena River Sweetin River 46 4 Skeena River Suskwa River 8 4 Skeena River Slamgeesh River 32 4 Skeena River Skeena River - Mainstem 23 4 Skeena River Kispiox River 62 4 Skeena River Harold Price Creek 13 4 Skeena River (Zymoetz) Thomas Creek 21 5 Kumealon Creek 1 6 Gardner Canal Kitlope River 120

FIGURES

Figure 1. Location of tissue punch collected from chinook salmon.

North Coast Chinook DNA Baseline NP4 7

Figure 2. Map of the North Coast of British Columbia showing the approximate locations of the sampling sites. 1 Ishkheenickh River 7 Thomas Creek (Zymoetz system) 2 Kiteen River (Nass system) 8 Kitlope River 3 Oweegee Creek 9 Suskwa River, Harold Price Creek 4 Slamgeesh River 10 Kumealon Creek 5 Khutzeymateen River (Kateen trib.) 11 Kispiox River, Sweetin River 6 Skeena River at Terrace

North Coast Chinook DNA Baseline NP4 8

APPENDIX

Appendix 1: Average chinook escapement data for streams in the North Coast of British Columbia. Area Stream Avg 90's Avg 80's # DNA Comment samples prior to 2004 4 Kitsumkalum River - Below Canyon 11,522 12,714 457 4 Bear River 11,278 10,480 177 6 Kitimat River 16,386 9,904 482 4 Morice River 17,889 7,800 228 3 Cranberry River 2,697 2,500 164 4 Kispiox River 5,170 2,381 105 4 Ecstall River 630 2,005 293 3 Damdochax River & Lake 2,166 1,550 257 6 Kildala River 4,167 1,470 441 3 Kwinageese River 1,863 1,383 299 1 Yakoun River 2,210 1,265 201 6 Kitlope River 160 1,100 3 Tseax River 866 935 180 4 Cedar River* 564 890 116 3 Meziadin River & Lake 659 797 195 6 Kemano River 48 705 4 Zymoetz River 374 695 8 4 Kitwanga River 1,538 677 288 4 Kitsumkalum River - Above Canyon 909 640 190 6 Dala River 534 520 4 Skeena River - Mainstem 925 500 3 Ishkheenickh River 216 459 4 Babine River 572 410 266 4 Bulkley River - Upper 833 400 585 4 Slamgeesh River 400 4 Sustut Lake 665 380 441 3 Khutzeymateen River 183 365 3 3 Seaskinnish Creek 335 355 99 4 Johnston Creek 138 355 Ecstall system 4 Shegunia River 81 327 3 Kincolith River 711 320 287 3 Kwinamass River 255 315 362 3 Iknouk River 30 263 3 Oweegie Creek & Lake 291 228 219 4 Kloiya River 184 228 146 3 Kiteen River 412 220 4 Lakelse River 91 217 4 Nangeese River 338 215 4 Clear Creek 109 213 4 Sweetin River 181 198 4 Stephens Creek 48 180 4 Khyex River 117 149 6 Brim River 17 148 3 Kitsault River 50 120 4 Date Creek 32 113 4 Nanika River 474 107 3 Teigen Creek 9 101 30 4 Magar Creek 105 90 24 4 Kitseguecla River 75 86 6 Foch Creek 5 85 4 Suskwa River 43 82 5 Kumealon Creek 52 78 4 Mccully Creek 40 75 6 Kowesas River 25 73 4 Kasiks River 87 72 6 Wahoo River 110 70 4 Gitnadoix River 38 65 42 6 Gilttoyees Creek 20 55 4 Maxan Creek 20 50 4 Boucher Creek 2 50 North Coast Chinook DNA Baseline NP4 9 3 Snowbank Creek 50 54 4 Exchamsiks River 116 49 11 4 Dog-Tag Creek 44 4 Zymagotitz River 24 38 6 Khutze River 41 37 4 Mcqueen Creek 35 4 Exstew River 60 31 6 Tsaytis River 1 31 4 Buck Creek 80 29 4 Coldwater Creek 21 28 4 Deep Creek 7 25 4 Fiddler Creek 25 4 Big Falls Creek 24 4 Kadeen Creek 24 23 4 Erlandsen Creek 25 22 Zymagotitz system 3 Tchitin River 221 22 4 Harold Price Creek 50 20 4 Club Creek - Lower 19 4 Fulton River 9 18 4 Shawatlan Creek 16 6 Kiltuish River 11 4 Johanson Lake 104 10 4 Diana Creek 10 6 Quaal River 4 3 4 Kleanza Creek 8 2 6 Bish Creek 2 4 Johnston Lake 2 6 Aaltanash River 1 1 3 Bell-Irving River 4,303 3 Anudol Creek 565 4 Limonite Creek 135 Zymoetz system 4 Thomas Creek 135 Zymoetz system 4 Nichyeskwa River 50 4 Simpson Creek 30 4 Club Creek - Upper 6 4 Salmon Run Creek 4 Moonlit Creek 83 Kitwanga system 4 Shilahou Creek 3 Bowser River 1 Nass system 6 Hirsch Creek 474 Kitimat system

North Coast Chinook DNA Baseline NP4