Category: 2011

Taku River Sockeye Salmon Genetic Stock Identification Analysis for Commercial Samples

This proposal involves genetic analysis of tissue samples anticipated from the in-river commercial sockeye fishery on the Taku River in 2019. This activity was first supported by the Northern Fund in 2008 and makes use of the baseline samples collected with Northern Fund assistance from 2007-12.

This will identify the composition of the commercial harvest by stock groupings. In addition, when coupled with escapement counts from headwater counting fences (weirs), it will permit estimation of drainage-wide abundance for comparison with the mark-recapture estimate or other assessment methodology.

N19-I27 Taku River Sockeye Salmon Genetic Stock Identification Analysis of 2019 Commercial Samples Report

N16-I46 Taku Sockeye Genetic Stock Identification Report 2016

 

Estimation of Fraser River – South Thompson Age 0.3 Chinook Aggregate Escapement

The goal of the project is to estimate the spawning escapement of the Fraser River – South Thompson age 0.3 aggregate (ST0.3A Chinook). The ST0.3A escapement will be estimated using Coded Wire Tags (CWT), Genetic Stock Identification (GSI), and CWT exploitation rate indicator stock data from escapement and Fraser River fisheries. To achieve this objective, we will increase recovery of CWTs from Chinook carcasses in the Lower Shuswap River; conduct a high-precision mark-recapture project and CWT sampling in the Middle Shuswap River; collect age samples across the South Thompson watershed; produce a CWT release group of Middle Shuswap River smolts (to augment the Lower Shuswap indicator stock); and analyze GSI and age data from the Albion Test Fishery.

N18-VHP16 Estimation of 2015 – 2018 Escapements of the South Thompson 0.3 Chinook Aggregate using a Bayesian Model that Combines Data on CWT Recoveries and GSI_Report Title Page

 

Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques

The Skeena River is host to the second largest aggregate of Chinook salmon in British Columbia. While the aggregate is a PSC escapement indicator stock, there are no biologically based escapement goals for this population. This project provides an annual escapement estimate for the aggregate as well as for the large component stocks. The estimate produced is comparable with the historic estimates produced using an estimate of variance. The Tyee Test fishery, which has been conducted since 1955, provides data such as age information that is matched to the genetic information. The combination of stock specific escapements with age composition forms the basis for escapement goals and benchmarks.
The Kitsumkalum River hosts one of the major Chinook populations in the Skeena watershed, and is a PSC exploitation rate indicator stock. The mark-recapture estimate produced in in a separate project forms the cornerstone for the expansions of the stock compositions observed at the Tyee Test fishery.
The project consists of genetic analyses of samples from Chinook salmon caught at the Tyee Test fishery, and escapement data from the Kitsumkalum mark-recapture program. Chinook salmon scale samples will be collected from the Tyee Test Fishery and the DNA from the samples will be compared against genetic baselines from Skeena Chinook salmon populations. The proportion identified as Kitsumkalum Chinook will be expanded to generate escapement estimates for the Skeena River aggregate using the mark-recapture estimate of escapement for the Kitsumkalum population.

N19-I34 Chinook Escapement Estimation to the Skeena River Using Genetic Techniques 2019

N18-VHP09 Chinook Escapement Estimation to the Skeena River using Genetic techniques Report 2018

N17-VHP13 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques Report 2017

N16-I33 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques 2016. Year 8

N15-I27 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques 2015. Year 7

SSP14-09 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques 2014. Year 6

SSP13-06 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques 2013

SSP12-05 Chinook Salmon Escapement Estimation to the Skeena River using Genetic Techniques 2012. Year 4

SSP11-01 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic Techniques 2011. Year 3

SSP10-01 Chinook Salmon Escapement Estimation to the Skeena River Using Genetic techniques 2010. Year 2

SSP-4 Chinook salmon Escapement Estimation to the Skeena River using Genetic techniques (Year 1)

 

 

Burman River Chinook Salmon Mark-Recapture

Concern for West Coast Vancouver Island (WCVI) natural Chinook currently limits PSC fisheries in Southeast Alaska, the Haida Gwaii recreational fishery and particularly the Area F troll fishery in northern British Columbia and troll fisheries and some recreational fisheries on the WCVI. Although the Burman River is enhanced, the population is of sufficient size to estimate the escapement with precision, and thermally marked otolith sampling provides an estimate of the naturally spawned fraction.
The program will estimate the escapement of adult Chinook salmon to the Burman River, a PSC Chinook escapement indicator, using both closed population and open population mark-recapture techniques refined between 2009-2014. The project will also quantify age, sex and origin compositions. Estimates of abundance of the thermally marked hatchery fraction combined with a precise escapement estimate will provide important information to verify and support the WCVI Aggregate ratio estimation project by providing an independent reference point (the Burman River Chinook hatchery fraction, independent of Robertson Creek Hatchery stock) in the northern WCVI area.

S18-VHP11 Spawning escapements and origin of Chinook salmon at Burman River Report 2018

S17-VHP13 Burman River Chinook salmon mark-recapture 2017

S16-I17 Burman River Chinook Salmon Mark-Recapture Report 2016. Year 8

S15-I06 Burman River Chinook Salmon Escapement Indicator Mark-Recapture Experiment, 2015. Year 7

S14-I13 Burman River Open population mark-recapture estimation of ocean-type Chinook spawning escapements WCVI Report 2014

SSP13-01 Burman River Chinook Salmon Total Escapement Estimation Project, 2013

SSP12-01 Preliminary - Burman River Chinook Salmon Total Escapement Estimation Project, 2012

SSP11-06 Burman River Chinook Salmon Total Escapement Estimation Project, 2011

SSP10-03A Burman River Chinook Salmon Total Escapement Estimation Project, 2010

SSP-1A/B Burman River Chinook Salmon Total Escapement Estimation Project, 2009 (Year 1)

 

 

Tatsamenie Lake Sockeye Fry Extended Rearing and Smolt Enumeration

A sockeye enhancement program has been ongoing at Tatsamenie Lake since 1990. A review of the program was funded by the Northern Fund in 2005, and in 2008, the Northern Fund began supporting the Extended Sockeye Fry Rearing Project.
The fry were originally reared in lake pens, but because of a devastating disease outbreak, the project shifted to onshore rearing systems beginning in 2009. The egg to smolt survivals of the fed fry have been variable but have ranged from 10% to 70%, or 5 to 15 times compared to wild fry, depending on fry behaviour after outplanting. Assessment of adult production from this project is ongoing. Smolt to adult survivals of the reared fry will be definitively determined with the return of the corresponding adults in the coming years, but to date, the adult production from reared fry has been lower than expected. This project continues to test a technique that has the potential of increasing production for other small scale sockeye salmon enhancement projects as well as rebuilding the Tatsamenie Lake sockeye stock in low brood year cycles.
Also at Tatsamenie Lake, the Canadian Department of Fisheries and Oceans began a smolt enumeration program in 1996, and this ran continuously from 1998 through to 2011. The Northern Fund began supporting this program in 2012, and the two programs were combined in 2015. The combination allowed the Tatsamenie Lake sockeye smolt mark-recapture project to extend beyond its previous end date of June 30, through to the second week of September. This provides a more accurate smolt population estimate as well as increased precision of the estimated enhanced sockeye survival and production. This also allows for monitoring of potential early out-migration of the reared fry.

N19-E02 Tatsamenie Lake Sockeye Fry Rearing and Smolt Projects 2019 Report

N18-E07 Tatsamenie Lake Sockeye Fry Rearing and Smolt Report

N17-E01 Tatsamenie Lake Rearing Final Report

N16-E01 Tatsamenie Lake Sockeye Fry Rearing and Smolt Projects 2016

N15-E01 2015 Tatsamenie Lake Sockeye Fry Extended Rearing and Smolt. Year 11

N14-E01 2014 Tatsamenie Lake Sockeye Fry Extended Rearing. Year 10; N14-E06 2014 Tatsamenie Lake Smolt Project. Year 3

N13-E02 2013 Tatsamenie Lake Sockeye Fry Extended Rearing. Year 9

N13-E07 2013 Tatsamenie Lake Smolt Project. Year 2

Calibration of Assessment Methods for Fraser Sockeye Enumeration

Since 2007, with support from the Southern Boundary Restoration and Enhancement Fund, calibration work has been conducted on twenty-five Sockeye populations of various stream types in the Fraser and has led to the development of indices for aerially surveyed Sockeye populations on the following three stream types: i) medium sized, clear streams, ii) medium sized, partially turbid/tannic streams and iii) large sized, clear streams. Although this represents substantial progress, significant gaps still exist on the remaining stream types and lake spawning populations. Calibration work involves the comparison between estimates generated using high precision enumeration techniques (enumeration fences, sonar, and/or mark-recapture programs) and those generated using standard low precision visual techniques. As annual calibration opportunities on target populations are limited, calibration work over the long term will be required to satisfy the data requirements for all stream types.  The actual populations to be calibrated will be determined based on in-season estimates of abundance.

S18-FRP03 Calibration of Visual Assessment Methods for Fraser River Sockeye Salmon (Oncorhynchus nerka)

S17-I06 Calibration of Visual Assessment Methods for Fraser River Sockeye Salmon Year 9

S16-I21 Calibration of Visual Assessment Methods for Fraser River Sockeye Report 2016

S15-I01 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2015. Year 7

S14-I02 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2014. Year 6

S13-I01 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2013. Year 5

S12-I02 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2012. Year 4

S11-I04 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2011. Year 3

S10-I05 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2010

S07-I05 Calibration of Assessment Methods for Fraser Sockeye Enumeration 2007

 

Genetic changes associated with in-basin supplementation of a population of Sockeye salmon

This joint project by NOAA and the University of Alaska Fairbanks evaluates the long term fitness of hatchery and wild sockeye salmon within a small watershed in Southeast Alaska. Concern over preserving wild stock fitness in enhancement project watersheds has been expressed in the case of both the Pacific Salmon Commission (PSC) Transboundary River Plans on the Taku and Stikine Rivers, and the PSC Northern Boundary Treaty Area of Southern Southeast Alaska (Hugh Smith and MacDonald Lakes). Measurement of the fitness effects and potential impact of such enhancement projects is needed to avoid long term undesirable effects on wild stocks. Initial genetic sampling and trial fish culture work in 2008, 2009, and 2010 showed potential for utilizing microsatellite and single nucleotide polymorphism (SNP) markers to assess the parentage of Auke Lake sockeye and to identify the progeny of wild and enhanced fish, and this allows the evaluation of the survival and introgression, if any, of the enhanced fish into the wild population. Furthermore, we have demonstrated the ability to sample very close to 100% of the adult sockeye entering the system and provided a low impact design for sampling, capturing, maturing and spawning small numbers for use as brood stock in this study. During the summers of 2011, 2012 and 2013, we captured and held adult sockeye in the Auke Creek Research hatchery, and conducted experimental matings in all three years. We have incubated, cultured and released approximately 50,000 juvenile sockeye into Auke Lake in the springs of 2012, 2013, and 2014. Complete sampling of upstream migrating adult sockeye has occurred from 2008 thru 2015 and smolt sub-sampling has occurred in May and June of those years as well.

Beginning in 2016, additional objectives were added to cover the sampling, marking and recovery of coho salmon at Auke Creek. Because of the operational efficiencies and base support this was accomplished with a small budget increment. Auke Creek is the longest and most complete coho salmon time series in Southeast Alaska, and is used as an indicator of marine survival, harvest and productivity for coho in the region.

N17-I11 Genetic Changes Associated with In-basin Supplementation of Sockeye Report 2017

N16-I04 Genetic changes associated with in-basin supplementation of a population of sockeye (NOAA Component) 2016. Year 8

N15-I06 Genetic changes associated with in-basin supplementation of a population of sockeye salmon; Phase 3 (NOAA Component of Joint Proposal with UAF/ADFG McPhee/Gilk-Baumer). Year 7

N14-I05 Genetic Changes Associated with In-basin Supplementation of a Population of Sockeye Salmon; Phase 6 (NOAA Component of Joint Proposal). Year 6

N13-I05 Genetic changes associated with in-basin supplementation of a population of sockeye salmon; Phase 5, NOAA Component of Joint Proposal, Joyce (AFSC)

N12-I04 Genetic Changes Associated with In-basin Supplementation of Sockeye Salmon (NOAA Component). Year 4

N11-I10A Genetic Changes Associated with In-basin Supplementation of a Population of Sockeye Salmon; Phase 3 (UAF Component)

N10-I12 Genetic Changes Associated with In-basin Supplementation of a Population of Sockeye Salmon; Phase 2

N08-I26A Genetic Changes Associated with In-basin Supplementation of a Population of Sockeye Salmon; Feasibility (UA Fairbanks Component)

N08-I26B Genetic Changes Associated with In-basin Supplementation of a Population of Sockeye (NOAA Component)

 

Northern and Transboundary Sockeye Matched Scale-Tissue Sampling

Provisions of the 1999 Pacific Salmon Treaty (PST) specify abundance-based harvest sharing arrangements of Nass and Skeena River sockeye salmon returns for the U.S. and Canada. The United States is allowed to harvest a fixed percentage of the annual allowable harvest of Nass and Skeena sockeye stocks in Alaska’s District 101 gillnet and District 104 purse seine fisheries. Accurate estimates of the stock-specific catch in commercial fisheries of each nation are required to estimate the total return of these stocks and the percentage of each stock caught in treaty-limited fisheries.
Since 1982, scale pattern analysis (SPA), sometimes in conjunction with other biological markers, has been used to survey the weekly catch of Northern Boundary and Transboundary sockeye salmon stocks in Southeast Alaska fisheries. However, problems in accurately estimating stock-specific catches and total returns of sockeye salmon in the early years of the Pacific Salmon Treaty resulted in an extensive investigation, and it was concluded that improved stock identification techniques, such as genetic stock analysis, were needed to accurately evaluate effectiveness and improve, if possible, existing run reconstruction methods. Two blind tests of scale analysis vs. genetic analysis demonstrated that, while both techniques were accurate, the genetic analysis had higher precision and could also often identify many specific stocks, while scale analysis is limited to identifying a few stock-groups. Neither technique can identify enhanced fish where the brood stock came from wild stocks that are also present in the mixed stock fisheries; thus, otoliths are used in annual stock composition estimates and run reconstructions.
ADF&G proposes to continue collecting weekly otolith, tissue, and scale samples of sockeye from the Southeast Alaska commercial harvest in the District 101 gillnet and District 104 purse seine fisheries, among other districts and fisheries for projects that complement this program. Stock identification analysis using age composition, thermal mark presence, and new, more stock-discrete DNA techniques will be conducted at NOAA’s Auke Bay Laboratory. This project also complements the continuing work by DFO in Areas 3, 4 and 5.

N18-I06 Northern & Transboundary Sockeye Salmon Matched Scale-Tissue Sampling Report

N17-I07 Northern & Transboundary Sockeye Salmon Matched Scale-Tissue Sampling Report

N16-I05 Northern & Transboundary Sockeye Matched Scale-Tissue Sampling. Year 9

N15-I08 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 8

N14-I07 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 7

N13-I07 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 6

N12-I05 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 5

N11-I13 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 4

N10-I10 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 3

N08-I12 Northern and Transboundary Sockeye Matched Scale-Tissue Sampling. Year 2

N07-I25 Northern and Transboundary Sockeye Salmon Matched Scale-Tissue Sampling

 

Abundance Estimates for Stillaguamish River Chinook Salmon Using Trans-generational Genetic Mark Recapture

The primary objective of this trans-generational genetic mark-recapture (tGMR) project is to: 1) estimate the abundance of Chinook salmon spawners and effective breeders in the Stillaguamish River above the smolt trap site using genetic abundance methods. The secondary objectives of this study are to: 2) estimate the natural spawning Chinook salmon abundance by origin (hatchery or natural), sex and age, and 3) estimate a redd expansion calibration factor from historic redd-based escapement estimates and possible future redd counts. The data collected for this project also provide a genetic baseline for these population estimates, a genetic (parentage-based) estimate of the proportion of hatchery-origin spawners, and an estimate of relative reproductive success of hatchery spawners, because carcasses are classified by origin. Genetic sampling will be conducted during the fall spawning period, and smolt trapping will be conducted during the following spring.

S19-I08 Abundance estimates for Stillaguamish River Chinook salmon using trans-generational genetic mark recapture 2019 Report

S18-VHP12 Abundance estimates for Stillaguamish River Chinook salmon using trans-generational genetic mark recapture

S17-VHP17 2016 Broodyear Report Abundance estimates for Stillaguamish River Chinook salmon using trans-generational genetic mark recapture

VHP16-01: Abundance estimates for Stillaguamish River Chinook salmon using trans-generational genetic mark recapture 2015-2016

VHP15-06 Abundance Estimates for Stillaguamish River Chinook Salmon Using Trans-generational Genetic Mark Recapture. Year 1

SSP14-05 Abundance Estimates for Stillaguamish River Chinook Salmon. Year 5

SSP13-11 Abundance Estimates for Stillaguamish River Chinook Salmon. Year 4

 

 

Northern Boundary Area Sockeye Salmon Genetic Stock Identification

Provisions of the Pacific Salmon Treaty specify harvest sharing arrangements of Nass and Skeena River sockeye salmon returns for the U.S. and Canada. The United States is allowed to harvest a fixed percentage of the Annual Allowable Harvest of Nass and Skeena sockeye stocks in Alaska’s District 101 gillnet and District 104 purse seine fisheries. Accurate estimates of the stock-specific catch in commercial fisheries of each nation are required to estimate the total return of these stocks and the percentage of each stock caught in treaty-limited fisheries. Annual catches over or under the agreed percentage are made up for in subsequent years.

Until recently, the Alaska Department of Fish and Game (ADF&G) used scale pattern analysis successfully to estimate contributions of Nass, Skeena and Southeast Alaska sockeye stocks to fisheries in southern Southeast Alaska. Since  2006, the Auke Bay Laboratories has used genetic analysis for the Northern Boundary sockeye fisheries. Results from comparisons between stock composition using scales and genetic analysis show both methods provide accurate estimates of stock composition, although DNA analysis is able to discriminate stocks at a finer resolution than scales. An additional advantage of the DNA technique is that it does not require annual sampling to re-establish the escapement baseline.

The purpose of this project is to continue the genetic stock identification of the commercial sockeye catch in ADF&G District 101 gillnet fishery and District 104 seine fishery using the baselines developed by the ADF&G.

N18-I10 Northern Boundary Area Sockeye Genetic Stock Identification Report 2018

N17-I09 Northern Boundary Area Sockeye Genetic Stock Identification Report 2017

N16-I02 Northern Boundary Area Sockeye Genetic Stock Identification Report 2016

N15-I02 Northern Boundary Area Sockeye Salmon Genetic Stock Identification for 2015. Year 9 of 17

N14-I02 Northern Boundary Area Sockeye Salmon Genetic Stock Identification for 2014. Year 8

N13-I02 Northern Boundary Area Sockeye Salmon Genetic Stock Identification for 2013. Year 7

N12-I07 Northern Boundary Area Sockeye Salmon Stock Identification for 2012. Year 6

N11-I04 Northern Boundary Area Sockeye Genetic Stock Identification. Year 5

N10-I11 Northern Boundary Area Sockeye Salmon Genetic Stock Identification. Year 3

N08-I30 Northern Boundary Area Sockeye Genetic Stock Identification. Year 3

N07-I19 Northern Boundary Area Sockeye Genetic Stock Identification. Year 2.

N06-I12A Northern Boundary Area Sockeye Salmon Genetic Stock Identification

N06-I12B Northern Boundary Area Sockeye Salmon Genetic Stock Identification (ADFG)