Tag Archives: coho

Automating procedures for the forecasting of terminal run and escapement of Chinook, coho and chum salmon stocks using open-source statistical software

The annual exercise of forecasting terminal run or escapement is a critical aspect of management and conservation of salmonids coastwide. This project involves the completion of an automated computer program (henceforth called “ForecastR”) relying on the open-source statistical software R to generate age-specific forecasts using a variety of generic models including (i) simple and complex sibling regressions with the ability to include environmental covariates, (ii) time series models such as ARIMA, exponential smoothing, and na├»ve models, and (iii) mechanistic models such as average return rate models that depend on auxiliary data such as the number of outmigrant juveniles, the number of hatchery fish released or the number of spawners.

S18-VHP15A ForecastR: tools to automate forecasting procedures for salmonid terminal run and escapement

S16-I11 Automating procedures for forecasting of terminal run and escapement of Chinook, Coho and Chum salmon stocks using open-source statistical software

 

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)

 

Skeena River CWT Equipment Procurement

The Skeena Fisheries Commission (SFC) is made up of five First Nations who do fisheries work within their respective traditional territories in both the Skeena and Nass Watersheds. They include the Gitxsan, Gitanyow, Wet’suwet’en, Lake Babine Nation and Lax Kw’alaams. Currently, both the Gitxsan and Gitanyow conduct annual coho coded-wire tag (CWT) projects in the Skeena Watershed to monitor coho abundance, estimate smolt production, fisheries exploitation and to determine Skeena coho ocean survival. These programs are important because the information collected improves fisheries managers’ abilities to manage coho salmon stocks in the Skeena River by better understanding exploitation rates in U.S. and Canadian fisheries. It also allows managers to determine ocean survival rates for upper and middle Skeena coho stocks because both the Gitxsan and Gitanyow programs accurately enumerate all marked and unmarked returning adult coho annually (fence operations), something that is often not available in many other CWT programs in BC.
SFC is requesting funds from the PSC Northern Fund to purchase CWT equipment. SFC will retain ownership of the equipment in the event that it is decided by SFC commissioners/technical experts that the equipment could be put to better use within one of the other areas where our signatory First Nations conduct works. Any decision to move the equipment for use in another part of the watershed would be done in consultation with the GFA.

 

Boundary Area Coho Escapement

The Hugh Smith Lake coho salmon population is substantially exploited by mixed-stock fisheries in both the U.S. and Canada and is, therefore, a key indicator stock used to monitor total adult abundance and escapements, and the pattern and intensity of exploitation by these fisheries on populations in the northern boundary area. It is the only system in the southern portion of Southeast Alaska where a total count (with back-up mark-recapture estimate) of coho salmon escapement has been routinely collected since 1982. Its location 70 km southeast of Ketchikan makes it a particularly strategic indicator stock for boundary area fisheries. It has also been one of three key indicator stocks used to measure the overall abundance of wild coho salmon available to the Alaska troll fishery and to measure the exploitation rate by the fishery.
Escapement projections are made from both the cumulative weir count and estimation models based on recovery of coded-wire tags to provide real-time information for management of fisheries for escapement. Peak helicopter survey counts at other Boundary Area streams provide an index with greater coverage that complements higher resolution assessment at Hugh Smith Lake.

N19-I04 Boundary Area Coho Escapement 2019 Report

N18-I03 Boundary Area Coho Escapement Report

N17-I04 Boundary Area Coho Escapement Report 2017

N16-I57 Boundary Area Coho Escapement Report 2016

 

Hugh Smith Lake Coho Smolt Enumeration and Marking

The Hugh Smith Lake coho salmon population is substantially exploited by mixed-stock fisheries in both the U.S. and Canada and is, therefore, a key indicator stock used to monitor total adult abundance and escapements, and the pattern and intensity of exploitation by these fisheries on populations in the northern Boundary Area. Its location 70 km southeast of Ketchikan makes it a particularly strategic indicator stock for boundary area fisheries. It has also been one of three key coded-wire tagged indicator stocks used to measure the exploitation rate by the Alaska troll fishery and to estimate the overall abundance of wild coho salmon available to the fishery. Timely escapement projections are made from both the cumulative weir count and estimation models based on recovery of coded-wire tags to provide real-time information for management of fisheries for escapement goals.
The Hugh Smith Lake coho salmon population has been the only long-term, continuously operated wild coho indicator stock project in the northern boundary area, with a record of catch, escapement, smolt production, marine survival, and age composition estimates dating from 1982. The proposal would continue to fund operation of a smolt weir to enumerate and coded-wire tag coho salmon smolts emigrating from Hugh Smith Lake to generate total population estimates, including total smolt production, marine survival, exploitation rate, and catch by area, time, and gear type. Coho smolt estimates and tag recovery rates in the Southeast Alaska troll fishery will be used to generate inseason estimates of marine survival and total adult abundance for fishery management. Estimates of brood year smolt production and adult return by age class will be used to evaluate and refine the biological escapement goal. Counts and samples of sockeye salmon smolts are also obtained at the smolt weir and have been used to evaluate escapement goals and effectiveness of sockeye salmon stock enhancement efforts. The proposed project will continue a core stock assessment program needed to manage fisheries for coho salmon in the northern Boundary Area.

N16-I58 Hugh Smith Lake Coho Smolt Estimation and Marking Report Year 1 of 2

Exploitation rate estimation for coho salmon in south coast marine fisheries using genetic stock identification

In 2014, an exploitation rate cap on Interior Fraser River (IFR) coho in Canadian fisheries was increased from 3% to 16% in response to improved status and rebuilding of these stocks as well as fishery needs. Pre-season predicted fishery impact on IFR coho was generally determined using historic (1986-97) exploitation and coded wire tag (CWT) recovery rates┬áscaled by current effort, which have changed over time, so current CWT recoveries do not provide a measure of fishery impact. Instead, DNA will be used to estimate the number of ‘wild’ unmarked IFR coho caught in fisheries which would provide an independent estimate of exploitation rate.

Development of a High Resolution SNP Baseline for Stock Identification of Coho Salmon

Genotyping by sequencing, or GBS, is a new type of DNA sequencing technology that allows the genotype of an individual to be determined by direct DNA sequencing. This new direct method of genotyping individuals will radically change stock identification, as several hundred markers per individual can be routinely screened for genotyping at a cost equivalent to or lower than that currently prevailing in stock identification applications. Screening more markers also provides increased resolution for stock identification.
The Molecular Genetics Laboratory (MGL) at the Pacific Biological Station in Nanaimo, BC, has assembled a panel of primers far in excess of any previous or current stock identification application in Coho Salmon by any agency. Application of this panel to a limited number of populations in southern British Columbia has indicated substantial differentiation among populations. GBS will clearly be the method of choice for Coho Salmon stock identification in the near future, as very high resolution estimates of stock composition will be available from this technique.
This project proposes to survey 40 populations of Coho Salmon in northern and central British Columbia with the aforementioned panel of primers, and evaluate the utility of the method for applied stock identification. This information will be merged with data from southern British Columbia populations that will be collected under a $10 million, 4-year Genome Canada project supported in part by Fisheries and Oceans Canada and in which the MGL is participating. A high-resolution stock identification baseline should thus be available for populations throughout British Columbia, and the GBS technology will allow new applications in stock identification, as it may be possible to identify individual Coho Salmon to specific populations (either hatchery or wild) if the baseline is adequate for the problem.

N16-I28 Development of a High Resolution SNP Baseline for Stock Identification of Coho Salmon Report 2016