1. Objectives

Two major goals are described in the Research Narrative: (a) evaluate the nature and extent of genetic changes in out-planted hatchery stocks, and (b) quantify the genetic impact of out-planting on targeted and non-targeted natural stocks. Three objectives are also listed in the previous proposal in Taurus: (a) monitor population genetic relationships within and among populations of Chinook salmon and steelhead in the Snake River Basin; (b) determine the degree to which supplemented populations affect non-supplemented populations of Chinook and steelhead; and (c) monitor relative reproductive success of hatchery and wild Chinook and steelhead in the Snake River Basin.

These tasks are clearly defined, measurable, testable, and relevant to the Program. The Research Narrative notes that the project is flexible with no set end-point and will terminate when co-managers and subbasin planners agree that critical uncertainties (CUs) have been satisfied and there is no longer the need to monitor the effects of supplementation.

Although these studies continue to provide valuable information to Snake River subbasin planners and co-managers, it seems that some of the original objectives have been adequately addressed. The ISRP recommends that the proponents specify new objectives or refine existing hypotheses that can be tested in the future. For example, we recommend that future studies focus on clarifying genetic (rather than ecological) mechanisms for reduced RRS and the extent to which hatchery supplementation limits the ability of small wild salmon and steelhead populations to adapt to changes in their local environments.

2. Methods

The study has mostly relied on a well-developed microsatellite DNA (GAPS) protocol but recently transitioned to Single Nucleotide Polymorphisms (SNPs) in concert with other major genetic-monitoring programs in the Basin. A time-series approach is being used to study general trends in genetic diversity, population structure, and effective population sizes of Chinook salmon and steelhead in the Snake River basin, together with more focused studies of RRS of hatchery and wild origin fish at three study locations. Sampling and analytical protocols are clearly documented in the Annual Reports through links to resourcemonitoring.org websites. Standard methods are being used, and statistically reliable results are being produced. Confidence intervals or significance test probabilities are provided to support most conclusions. Efforts are still underway to document and complete analyses following the recent transition from GAPS microsatellite markers to SNP markers; publication of up-to-date results is expected later in 2018.

A notable strength of this project is the deliberate effort to replicate RRS studies in different locations with different species. However, two complications that warrant further discussion are the small initial population size of the study populations and the high level of interbreeding that has occurred prior to and during the investigation. These complicating factors could be expected to reduce the power to detect real differences in reproductive success between hatchery and natural origin spawners. The ISRP is concerned that findings to date, which indicate that RRS is not significantly less than 1 for Chinook salmon at the Catherine Creek and Lostine River sites, may underestimate the effects of hatchery supplementation in more natural Chinook salmon populations. It would be useful to consider how the history of pHOS and PNI in these study populations is influencing results.

3. Results

This project has clarified evolutionary relationships among salmon populations in the Snake River and provided new insights on demographic, ecological, and evolutionary processes in these populations. Collaboration and sharing of information among partners seem excellent. Sampling efforts are coordinated closely with other BPA-funded projects to best leverage the available resources and incur the least disturbance possible to the fish being sampled. The project has generated 43 reports and publications and continues to inform management actions. Key findings include:

Population structure and diversity studies: Supplementation efforts in the Salmon and Grande Ronde rivers appear to have had a minimal effect on the genetic diversity of Chinook salmon populations over the time frame of this project. Results indicate no general decline in heterozygosity or allelic richness in 2,400 individuals sampled over a 3-4 generation time span in 8 of 9 Chinook salmon populations examined in the Salmon River. Similarly, heterozygosity or allelic richness did not decline in any of the Grande Ronde populations examined and actually increased in some populations (e.g., Lookingglass Creek, Upper Grande Ronde River, and Wenaha River). The estimated effective number of breeders has been stable, tracking trends in total population size, except in Lookingglass Creek where the number of breeders has declined in recent years. Introgression from the Rapid River Hatchery stock was particularly noticeable in the early 1990s, but it appears to have had a substantial effect on only two of the native populations (i.e., Lookingglass Creek and the upper Grande Ronde River) despite ample opportunities for introgression to occur. All seven of the native populations sampled have maintained their levels of within-population genetic diversity throughout the sampling period.

Relative reproductive success studies: In the steelhead study at Sheep Creek, the overall geometric mean reproductive success of hatchery origin fish was only 0.4 relative to their natural counterparts, measured both from juvenile and adult offspring. Hatchery males and females both continued to do poorly relative to wild counterparts, even after 2005 when new procedures were adopted to move hatchery fish upstream to reduce the concentration of hatchery-origin spawners remaining near the weir.

In contrast, no evidence of differential reproductive success was detected between natural-origin (NO) and hatchery-origin (HO) Chinook spawning in Catherine Creek over the adult spawn years 2002-2013, whether measured with juvenile offspring (geometric mean RRS = 1.05) or adult offspring (geometric mean = 0.96).

An important finding of this study is that RRS based on juvenile offspring appears to be comparable to that based on adult returns. If confirmed, this conclusion could justify quicker and statistically more robust evaluations of RRS given the greater speed and ease of collecting large samples of juveniles as opposed to scarcer adults. This type of monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations.

Overall, these projects illustrate that HO and NO interactions can be similar in some locations and species, yet strikingly different in others. Consequently, results from a single study should not be applied across all species and programs. The ultimate goal of these studies is to investigate the causal mechanisms behind any observed deficits in RRS. The more that can be learned about factors determining RRS, the more managers will understand the effects of supplementation, and the more they will be able to achieve the stated goals of sustainably increasing natural production.

4. 2017 Research Plan uncertainties validation

The Research Narrative indicates that the proponents agree with the summary in the 2017 Uncertainties Database regarding critical uncertainties being addressed by the project. In summary, the project directly addresses C1.2, C1.3, C1.4 and C1.5 and indirectly addresses C1.1, F1.1, F1.4 and F3.6.

The ISRP advises the proponents to specify new objectives or refine existing hypotheses that can be tested in the future. Three suggestions for refocusing the studies of relative reproductive success (RRS) are to: (a) investigate how the history of pHOS and PNI in the study populations has influenced RRS values. The ISRP is concerned that findings to date that RRS is not significantly less than 1 for Chinook salmon at the Catherine Creek and Lostine River sites may underestimate the effects of hatchery supplementation in more natural Chinook salmon populations. (b) focus on genetic effects rather than known ecological effects arising from differences in the distribution of hatchery and natural origin spawners. For example, efforts should be made to eliminate known differences in spawner distribution in Sheep Creek, first by resolving issues with the acclimation pond, and then as necessary, manipulating fish numbers transferred over the weirs. (c) evaluate the extent to which hatchery supplementation might limit the ability of small wild salmon and steelhead populations to adapt to changes in their local environments.

Comment:

This is a well-developed and well-designed proposal to increase our understanding of the effects of artificial propagation on salmonid populations. The project is credited with pioneering many of the genetic monitoring tools now widely used by salmon researchers. It has consistently provided valuable information to regional managers and helped others within and outside of the Basin to address issues raised in FCRPS BiOp RPAs and the Fish and Wildlife Program.

The proponents have responded thoughtfully to questions raised by the ISRP in the last review (ISRP 2018-8), and plan to continue to address these issues through ambitious new research described in the current proposal. We continue to encourage the proponents to find ways to: (1) evaluate the contingent historical effects of low initial population sizes and low proportionate natural influence (PNI) in the study populations; (2) identify the genetic versus environmental causes of reduced relative reproductive success (RRS) in steelhead; and (3) move the acclimation site in Little Sheep Creek to control for environmental effects on RRS which are now understood.

1. Objectives, Significance to Regional Programs, and Technical Background

The proposal includes 15 clearly defined objectives that are implicitly quantitative (i.e., include metrics). Of these, 12 were added, in part to address a qualification arising from the previous ISRP review (ISRP 2018-8). The ISRP's concerns have now been addressed.

The proposal clearly explains why this project was initiated and how it addresses two biological objectives identified in previous FCRPS Biological Opinions and four critical uncertainties in the Fish and Wildlife Program.

Nine deliverables all involve quantitative assessments, and each is linked to at least one objective. Seven of the new objectives are not associated with any deliverable, but these cases, the objective is itself a very specific task that could be considered as a deliverable.

No specific timelines are provided but should be included in work plans, annual reports, and future proposals. The proponents point to the continuing need to monitor genetic changes, to extend time series to improve statistical power to detect differences in reproductive success, and to identify heritable effects in the second generation. In some cases, the tasks are expected to occur annually (e.g., genetic monitoring of reference populations and evaluations of RRS). In other cases, specific endpoints could not be established without some preliminary results (e.g., objectives 11 -15 to develop new genetically based monitoring tools).

Results will aid in understanding and mitigating the genetic risks of using artificial propagation in salmon and steelhead recovery. A particularly important issue, to be addressed in part by Objectives 6 and 8, is to understand how the history of hatchery supplementation affects RRS. RRS values measured in the study populations might be misleading (biased high relative to more natural populations) if the natural origin population had historically experienced significant domestication and/or bottlenecks of low effective population size.

2. Results and Adaptive Management

The project has consistently met its objectives and provided tribal, state, and federal agencies with genetic monitoring information. It has clarified evolutionary relationships among salmon populations in the Snake River and provided new insights on demographic, ecological, and evolutionary processes in these populations. Results from the project are being used within the region to make management decisions.

This type of monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations. Overall, these projects illustrate that hatchery origin and natural origin interactions can be similar in some locations and species, yet strikingly different in others. The ultimate goal of these studies is to investigate the causal mechanisms behind any observed deficits in RRS. The more that can be learned about factors determining RRS, the more managers will understand the effects of supplementation, and the more they will be able to achieve the stated goals of sustainably increasing natural production. A key research issue is the extent to which hatchery supplementation limits the ability of small wild salmon and steelhead populations to adapt over time to local environments.

Some findings from these RRS studies raise questions that might be possible to answer in subsequent reports. Why did RRS of male Chinook in Catherine Creek (adult to juvenile stage) continually increase over time (Fig. 6)? More generally, how does cumulative low PNI and low population size influence RRS results? How should we expect RRS to differ among supplemented streams given contingent historical differences in the initial abundance of natural spawners and cumulative PNI? It would be useful to consider how the history of PNI and bottlenecks in natural population size varies among the RRS study populations.

Collaboration and sharing of information among partners seem excellent. Sampling efforts are coordinated closely with other BPA-funded projects to best leverage the available resources and incur the least disturbance possible to the fish being sampled. The project has created a valuable long-term genetic database of broad interest to managers and researchers throughout the Basin and elsewhere. Project results have been presented through 43 peer-reviewed publications, conference presentations, and presentations to the Council.

Besides supplying information that will inform regional policies and management actions, the proponents have exhibited adaptive management in meeting their own objectives. For instance, since the project began in 1989, it has benefited from two major decisions to change the types of genetic variation being surveyed—from metabolic proteins encoded by DNA (allozymes) which required lethal sampling, to selectively neutral mutations in microsatellite DNA which could be assayed non-lethally, and recently to Single Nucleotide Polymorphisms (SNP) which include both neutral and adaptive genes.

The current proposal continues the quest to explore, develop, and implement genetically based monitoring tools. Warm temperatures in some streams have reduced opportunities to collect DNA samples. The proponents are now testing the possibility of obtaining allele frequency data for population profiles directly from eDNA in water samples, in lieu of using individual fish when environmental conditions prevent field sampling. Additionally, the proponents plan to look for microhaplotypes associated with the SNPs currently being assayed as a way to increase the statistical power of pedigree assessments for RRS studies.

3. Methods: Project Relationships, Work Types, and Deliverables

A time-series approach is being used to study general trends in genetic diversity, population structure, and effective population sizes of Chinook salmon and steelhead in the Snake River basin, together with more focused studies of RRS of hatchery and wild origin fish at three study locations. Sampling and analytical protocols are clearly documented in the annual reports through links to the PNAMP website. Standard methods are being used, and statistically reliable results are being produced.

A notable strength of this project is the deliberate effort to replicate RRS studies in different locations with different species. However, two complications are the small initial population size of the study populations and the high level of interbreeding that has occurred prior to and during the investigation. These complicating factors might reduce the power to detect differences in reproductive success between hatchery and natural origin spawners. The proponents acknowledge this concern from our previous review (ISRP 2018-8) and have added new objectives to clarify their intentions to investigate the issue.

The proponents also recognize the limitations imposed by continued use of the existing juvenile acclimation site, which results in hatchery steelhead homing to the lower river and disproportionately spawning in poor quality substrate. This known environmental cause of reduced RRS (poor spawning habitat) must be eliminated or controlled to better elucidate genetic mechanisms causing reduced RRS. It is not clear why stakeholders are reportedly reluctant to move the Little Sheep Creek acclimation site to areas in the upper watershed with better spawning habitat. One potential solution might be to release study steelhead from a new acclimation site in the upper watershed while continuing to release non-study steelhead at the existing site to maintain fishing opportunities for stakeholders.

This project began in 1989 with the goal of assessing evidence of hatchery spawning and introgression with wild Snake River spring/summer Chinook and steelhead using allozyme (protein) technology. The project transitioned to employing DNA microsatellites as the genetic marker prior to the 2007-2009 proposal cycle and is starting to explore using DNA single nucleotide polymorphisms (SNPs). In addition to the original approach of evaluating allele frequencies in hatchery stocks and looking for “signatures” of these alleles in natural populations with different levels of hatchery presences in the spawning mixture, relative reproductive success investigations are underway in the Grande Ronde River subbasin.

Field sampling to obtain fin clips from fish in hatcheries and natural locations takes place annually, but samples are not analyzed unless requested from local managers. Based on information provided during the proposal presentation, about 10% of the effort is dedicated to sample collection, about 25% on analysis of samples for allele frequency comparisons, and 65% on relative reproductive studies. The ISRP concludes that the annual sampling and archiving of fin tissue is important and needs to continue, that refinements are needed in the development and execution of the comparative allele frequency effort, and that the relative reproductive studies are needed.

There are several qualifications that the proponent should address during this project cycle:

Qualification 1: Formal plans for performing the comparative allele frequency analyses needs to be developed. The work should clearly be linked and integrated with the Columbia River hatchery effects team and the LSRCP. The current approach is to wait for co-managers to ask them questions, and then initiate analysis. The efficacy of the approach should be examined.

Qualification 2: They should increase coordination of QA/QC of the relative reproductive studies sample collections to ensure field practice is consistent with the assumptions of their investigations. It is disappointing that the Chinook relative reproductive success work in the Lostine lost 8 years of effort because of fish handling mistakes at a weir.

Qualification 3: They need a better described plan for the examination and potential transition from microsatellites to SNPs.

1. Purpose, Significance to Regional Programs, Technical Background, and Objectives

The general purpose of this ongoing and long-term project is reasonably stated. The problem statement provides the rationale for the project, including the general need for genetic monitoring. The explanation of hatchery uncertainties, genetic risk, and hatchery reform, however, is very general. The link of this proposal to the uncertainties is not well developed. The statement regarding using the multivariate breeders equation, “These methods can be used with the molecular studies proposed here to elucidate the fundamental selective pressures that determine successful supplementation” seems an overstatement without many more details on what selective pressures are to be assessed.

The proposal would be improved with more detailed explanation of how SNPs would be used and interfaced with the existing data sets built using other methodologies.

There were three clearly stated objectives, with deliverables listed for each.

Project Objectives:

Objective 1. Monitor population genetic relationships within and among populations of Chinook salmon and steelhead in the Snake River Basin.

The objective is okay, especially monitoring the genetic relationships through time. No indication is made anywhere in the proposal how often the data needs to be collected. Every year? Every five? In how many populations? These topics are developed in the Anadromous Salmon Monitoring Strategy (ASMS), but not discussed in the proposal. No table has been provided of how much genotyping has actually been completed.

Objective 2. Determine the degree to which supplemented populations affect non-supplemented populations of Chinook and steelhead.

This was the original objective and approach to evaluate hatchery influences on natural populations. The analytical methods do not seem to have been updated to reflect recent development – for example using STRUCTURE to dissect the relationships among individuals in a spawning population. The text reads almost identical to Objective 1. The framework for the analysis and its application to management decisions needs to be developed in more detail.

Objective 3. Monitor relative reproductive success of hatchery and wild Chinook and steelhead in the Snake River basin.

These are important analyses, but the explanation of the range of contrasts possible and how these investigations fit into the AHSWG framework for evaluating supplementation are absent.


2. History: Accomplishments, Results, and Adaptive Management

The explanation of the financial performance and history and contract deliverables history and performance is adequate.

The project has been ongoing since 1989 and has modified its methods of genotyping fish in tandem with development of PCR and expanded DNA methodologies. Initially the project used allozymes (proteins) in a very simple analysis of allele frequency comparisons among hatchery populations and natural populations with and without hatchery-origin adults. Currently the project genotypes fish using microsatellite loci and is exploring the utility of Single Nucleotide Polymorphisms (SNPs). The project has also expanded the analysis to estimates of effective population size (Ne), and estimates the effective number of breeders (Nb), although the presentation does not provided details on the scope of these analyses. The project has also expanded to include relative reproductive success (RRS) investigations of hatchery steelhead in the Imnaha River and Chinook salmon in tributaries of the Grande Ronde River.

Allozyme data from this project was used in the original status reviews of steelhead (Busby 1996) and Chinook (Myers 1998). The proposal states, although explanation is inadequate, that data from this project was used by the Interior Columbia Basin TRT to establish the population structure for recovery program development. It is not clear whether the data used was allozyme or microsatellite genotypes. There are many peer-reviewed publications, but many are on topics with peripheral management application.

The major results achieved is a list, some duplicates, and many do not clearly relate to the application of the primary objectives – stock structure of Snake River steelhead and Chinook salmon, and the effects of hatchery interactions with natural spawning populations. There is a long list of major results listed (many quite interesting) and of publications, but how these results and publications combine to influence change is unclear.

The adaptive management section reports that this project informed ICTRT population boundaries (see above) that have been used in the FCRPS BiOp and recovery planning. The proposal reports that boundaries have not changed much from initial work. There was an early management decision (1993) to discontinue using Rapid River spring Chinook in the Grande Ronde hatchery programs. Finally, based on the relative reproductive success of hatchery steelhead in the Imnaha River, new management rules have been developed regarding the total number (HOR, NOR) and hatchery fraction passed above the weir for natural spawning in Little Sheep Creek, Imnaha River subbasin.

No actual data are presented. A statement is provided regarding a decreasing trend in effective population size, and there is limited reporting of reduced RRS in steelhead and equivalent RRS in Chinook. The ISRP would need more extensive presentation of the data to judge its adequacy. No definitive future application of the stock structure, Ne, and Nb data is presented.

In response to the questions about prior ISRP reviews, the answers seemed accurate, but the same principal question(s) remain. Some data has been used, but not a huge use. The ISRP asks again, how much more data on stock structure are needed to manage Snake River steelhead and Chinook?

The RRS studies are not presented in sufficient depth to arrive at a conclusion at whether they will substantially contribute to the management decisions regarding hatchery production. An RRS study by itself (contrast of hatchery versus natural fish) is not particularly informative to answer the question of supplementation effectiveness. These studies do make important contributions to analysis of the demography of the supplemented population, but they do not identify whether supplementation is adding natural-origin adults in the following generation and they do not inform the long-term fitness effects of interbreeding between hatchery and natural fish. For both of these important management questions contrasts to non-supplemented reference locations or among pedigree groups beyond just hatchery and wild are needed. The proposal does not provide a connection to the Anadromous Salmonid Monitoring Strategy, the Ad Hoc Supplementation Work Group recommendations, or the up-coming NOAA review of hatchery program HGMPs.

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging)

Project relationships are listed as “None”, but then there is a good section explaining additional relationships, including quite a number of other BPA-funded projects.

The lab also seems to have ongoing working relationship with other genetics entities in the region – likely due to the high quality of researchers on the project.

For geographic region a number of hatchery and field collection and tagging projects are identified. The Idaho Department of Fish and Game and CRITFC work with parental based tagging (PBT) and genetic analysis of individuals at Lower Granite Dam are not mentioned. Although this project is sampling fish from throughout the Snake Basin, it is not clear this work is coordinated with the more recent SNP investigations to collect VSP information for Snake Basin anadromous salmon.

Regarding similar work, a number of RRS investigations are identified, and other SNP work is mentioned. Differences and similarities as well as consistency with other investigations are not provided. Particularly, the RRS work in the Hood River and planned in the Methow involve more than just contrasts of hatchery and natural fish. In this proposal, the types of contrasts, their interpretation, and management implication are not well developed. Coordination with other SNP efforts in the Snake Basin is not provided. In particular, the CRITFC stock identification project seems to duplicate the stock structure activities in this proposal.

Regarding Emerging Limiting Factors, this does not really apply here and the proposal covers it adequately. The question is posed for restoration actions where emergent factors might compromise the outcome.

RME issues are not addressed. No response to tagging report issues is given with regard to genetic methodologies.

4. Deliverables, Work Elements, Metrics, and Methods

The linkage of the deliverables, especially the methods and results, to the BiOp and Fish and Wildlife Program monitoring strategies is not well developed. It is not clear how much of the data collected by this project will be used in management, and in what time frame. For example, they report the observation that effective population size is decreasing, but no options for management are identified, and no explicit connection to recovery planning or management is developed.

Tracking population relationships through time is worthwhile, but how many populations need to be surveyed, and how often, is not considered.

Sampling methods could be described in more detail. Also, details on how the results might be analyzed, as well as the metrics used for determining project success is unclear.

This project began in 1989 with the goal of assessing evidence of hatchery spawning and introgression with wild Snake River spring/summer Chinook and steelhead using allozyme (protein) technology. The project transitioned to employing DNA microsatellites as the genetic marker prior to the 2007-2009 proposal cycle and is starting to explore using DNA single nucleotide polymorphisms (SNPs). In addition to the original approach of evaluating allele frequencies in hatchery stocks and looking for “signatures” of these alleles in natural populations with different levels of hatchery presences in the spawning mixture, relative reproductive success investigations are underway in the Grande Ronde River subbasin. Field sampling to obtain fin clips from fish in hatcheries and natural locations takes place annually, but samples are not analyzed unless requested from local managers. Based on information provided during the proposal presentation, about 10% of the effort is dedicated to sample collection, about 25% on analysis of samples for allele frequency comparisons, and 65% on relative reproductive studies. The ISRP concludes that the annual sampling and archiving of fin tissue is important and needs to continue, that refinements are needed in the development and execution of the comparative allele frequency effort, and that the relative reproductive studies are needed. There are several qualifications that the proponent should address during this project cycle: Qualification 1: Formal plans for performing the comparative allele frequency analyses needs to be developed. The work should clearly be linked and integrated with the Columbia River hatchery effects team and the LSRCP. The current approach is to wait for co-managers to ask them questions, and then initiate analysis. The efficacy of the approach should be examined. Qualification 2: They should increase coordination of QA/QC of the relative reproductive studies sample collections to ensure field practice is consistent with the assumptions of their investigations. It is disappointing that the Chinook relative reproductive success work in the Lostine lost 8 years of effort because of fish handling mistakes at a weir. Qualification 3: They need a better described plan for the examination and potential transition from microsatellites to SNPs. 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives The general purpose of this ongoing and long-term project is reasonably stated. The problem statement provides the rationale for the project, including the general need for genetic monitoring. The explanation of hatchery uncertainties, genetic risk, and hatchery reform, however, is very general. The link of this proposal to the uncertainties is not well developed. The statement regarding using the multivariate breeders equation, “These methods can be used with the molecular studies proposed here to elucidate the fundamental selective pressures that determine successful supplementation” seems an overstatement without many more details on what selective pressures are to be assessed. The proposal would be improved with more detailed explanation of how SNPs would be used and interfaced with the existing data sets built using other methodologies. There were three clearly stated objectives, with deliverables listed for each. Project Objectives: Objective 1. Monitor population genetic relationships within and among populations of Chinook salmon and steelhead in the Snake River Basin. The objective is okay, especially monitoring the genetic relationships through time. No indication is made anywhere in the proposal how often the data needs to be collected. Every year? Every five? In how many populations? These topics are developed in the Anadromous Salmon Monitoring Strategy (ASMS), but not discussed in the proposal. No table has been provided of how much genotyping has actually been completed. Objective 2. Determine the degree to which supplemented populations affect non-supplemented populations of Chinook and steelhead. This was the original objective and approach to evaluate hatchery influences on natural populations. The analytical methods do not seem to have been updated to reflect recent development – for example using STRUCTURE to dissect the relationships among individuals in a spawning population. The text reads almost identical to Objective 1. The framework for the analysis and its application to management decisions needs to be developed in more detail. Objective 3. Monitor relative reproductive success of hatchery and wild Chinook and steelhead in the Snake River basin. These are important analyses, but the explanation of the range of contrasts possible and how these investigations fit into the AHSWG framework for evaluating supplementation are absent. 2. History: Accomplishments, Results, and Adaptive Management The explanation of the financial performance and history and contract deliverables history and performance is adequate. The project has been ongoing since 1989 and has modified its methods of genotyping fish in tandem with development of PCR and expanded DNA methodologies. Initially the project used allozymes (proteins) in a very simple analysis of allele frequency comparisons among hatchery populations and natural populations with and without hatchery-origin adults. Currently the project genotypes fish using microsatellite loci and is exploring the utility of Single Nucleotide Polymorphisms (SNPs). The project has also expanded the analysis to estimates of effective population size (Ne), and estimates the effective number of breeders (Nb), although the presentation does not provided details on the scope of these analyses. The project has also expanded to include relative reproductive success (RRS) investigations of hatchery steelhead in the Imnaha River and Chinook salmon in tributaries of the Grande Ronde River. Allozyme data from this project was used in the original status reviews of steelhead (Busby 1996) and Chinook (Myers 1998). The proposal states, although explanation is inadequate, that data from this project was used by the Interior Columbia Basin TRT to establish the population structure for recovery program development. It is not clear whether the data used was allozyme or microsatellite genotypes. There are many peer-reviewed publications, but many are on topics with peripheral management application. The major results achieved is a list, some duplicates, and many do not clearly relate to the application of the primary objectives – stock structure of Snake River steelhead and Chinook salmon, and the effects of hatchery interactions with natural spawning populations. There is a long list of major results listed (many quite interesting) and of publications, but how these results and publications combine to influence change is unclear. The adaptive management section reports that this project informed ICTRT population boundaries (see above) that have been used in the FCRPS BiOp and recovery planning. The proposal reports that boundaries have not changed much from initial work. There was an early management decision (1993) to discontinue using Rapid River spring Chinook in the Grande Ronde hatchery programs. Finally, based on the relative reproductive success of hatchery steelhead in the Imnaha River, new management rules have been developed regarding the total number (HOR, NOR) and hatchery fraction passed above the weir for natural spawning in Little Sheep Creek, Imnaha River subbasin. No actual data are presented. A statement is provided regarding a decreasing trend in effective population size, and there is limited reporting of reduced RRS in steelhead and equivalent RRS in Chinook. The ISRP would need more extensive presentation of the data to judge its adequacy. No definitive future application of the stock structure, Ne, and Nb data is presented. In response to the questions about prior ISRP reviews, the answers seemed accurate, but the same principal question(s) remain. Some data has been used, but not a huge use. The ISRP asks again, how much more data on stock structure are needed to manage Snake River steelhead and Chinook? The RRS studies are not presented in sufficient depth to arrive at a conclusion at whether they will substantially contribute to the management decisions regarding hatchery production. An RRS study by itself (contrast of hatchery versus natural fish) is not particularly informative to answer the question of supplementation effectiveness. These studies do make important contributions to analysis of the demography of the supplemented population, but they do not identify whether supplementation is adding natural-origin adults in the following generation and they do not inform the long-term fitness effects of interbreeding between hatchery and natural fish. For both of these important management questions contrasts to non-supplemented reference locations or among pedigree groups beyond just hatchery and wild are needed. The proposal does not provide a connection to the Anadromous Salmonid Monitoring Strategy, the Ad Hoc Supplementation Work Group recommendations, or the up-coming NOAA review of hatchery program HGMPs. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) Project relationships are listed as “None”, but then there is a good section explaining additional relationships, including quite a number of other BPA-funded projects. The lab also seems to have ongoing working relationship with other genetics entities in the region – likely due to the high quality of researchers on the project. For geographic region a number of hatchery and field collection and tagging projects are identified. The Idaho Department of Fish and Game and CRITFC work with parental based tagging (PBT) and genetic analysis of individuals at Lower Granite Dam are not mentioned. Although this project is sampling fish from throughout the Snake Basin, it is not clear this work is coordinated with the more recent SNP investigations to collect VSP information for Snake Basin anadromous salmon. Regarding similar work, a number of RRS investigations are identified, and other SNP work is mentioned. Differences and similarities as well as consistency with other investigations are not provided. Particularly, the RRS work in the Hood River and planned in the Methow involve more than just contrasts of hatchery and natural fish. In this proposal, the types of contrasts, their interpretation, and management implication are not well developed. Coordination with other SNP efforts in the Snake Basin is not provided. In particular, the CRITFC stock identification project seems to duplicate the stock structure activities in this proposal. Regarding Emerging Limiting Factors, this does not really apply here and the proposal covers it adequately. The question is posed for restoration actions where emergent factors might compromise the outcome. RME issues are not addressed. No response to tagging report issues is given with regard to genetic methodologies. 4. Deliverables, Work Elements, Metrics, and Methods The linkage of the deliverables, especially the methods and results, to the BiOp and Fish and Wildlife Program monitoring strategies is not well developed. It is not clear how much of the data collected by this project will be used in management, and in what time frame. For example, they report the observation that effective population size is decreasing, but no options for management are identified, and no explicit connection to recovery planning or management is developed. Tracking population relationships through time is worthwhile, but how many populations need to be surveyed, and how often, is not considered. Sampling methods could be described in more detail. Also, details on how the results might be analyzed, as well as the metrics used for determining project success is unclear.

Our project applies directly to Recommendation II from the 2008 Ad Hoc Supplementation Workgroup Final Report, calling for the “Implementation of a genetically-based relative reproductive success (RRS) study to quantify short-term impacts of supplementation on productivity, targeting a representative range of supplementation project strategies.”   Long before recent planning processes, we initiated reproductive success studies based on pedigrees (circa 1995) and applied them to systems of relevance to BPA and LSRCP (1999, Imnaha River steelhead).  Enthusiasm among state and tribal biologists in the sub-basin planning process led to addition of the Northeast Oregon Chinook captive brood stocks.  Our studies set the standard for this class of work, and text passages from our proposals were excerpted verbatim into sub-basin plans.  We can think of no higher recommendation than the confidence of our colleagues on the sub-basin planning teams.  Consistent with direction from comanagers, we propose to continue our 4 RRS projects in the Grande Ronde and Imnaha basins.  These will allow managers to evaluate RS of hatchery and natural fish in each system.  Specifically, they can monitor and evaluate changes to various supplementation strategies and transition from captive brood to conventional hatchery stocks, e.g., percent natural fish passed above the weir, total number of fish passed each year, percent natural fish in the supplementation broodstock, etc.  Our peer-reviewed, published research provides unique new insight into density dependence and competition between and among hatchery and natural fish.  Our steelhead study is the longest temporal series of its kind and will be pivotal to the implementation of SNP analysis, comparing the results we measure with each technique.  We are unclear about what “redundancies” might exist with other RRS studies in the Snake River Basin, as the results from one supplementation program are not necessarily applicable to another program, even from neighboring systems.  Indeed, that is the importance of coordinating this class of study.  Given that each system has its own unique characteristics, multiple RRS projects allow us to compare the effects of those characteristics to RS of hatchery and natural fish.  There are no geographically redundant RRS studies to ours (at the presumably relevant sub-basin level), and every one of our studies is in direct response to the request of managers and recovery planners—those are the folks we serve.  We have ongoing contact with other Snake River RRS studies to ensure that we are using relevant and cutting-edge analysis techniques, but it bears recognizing that we have little control over what new studies have been funded since 1999, when we began our pedigree work, and certainly not since 1989 when, in collaboration with comangers, we began the first studies of genetic monitoring and RRS of hatchery fish in the wild.

 

The newly formed CRHEET workgroup calls for increased coordination of hatchery review and assessment processes.  We applaud that goal, having been an active facilitator among the other genetics laboratories since the early 1980s.  No laboratory has done more than ours over a longer period of time to facilitate communication and cooperation and data sharing among geneticists and managers (also see data availability discussion below).  We are working closely with other agencies doing RRS studies, and particularly with the startup of the SNP work as part of our ongoing studies (both RRS and genetic monitoring).  There is a multi-agency effort (coordinated by Ken Warheit and Sewall Young--WDFW, Lisa and Jim Seeb—UW SAFS, and Bill Templin—ADFG) to develop SNP loci and analytical techniques, and we are active participants, recently hosting an international meeting.  We also consult regularly with Shawn Narum of CRITFC as well as Mike Ford in our own NWFSC who are actively developing SNP assays and testing them in ongoing genetic monitoring projects funded by BPA.  

 

The RM&E Workgroup expressed concern that our data are “not electronically available.” As indicated above, our lab has been a leader in data standardization and sharing.  We’ve led the West Coast salmon genetics community and indeed the world in international data standardization and distribution through a shared access database and web application, hosted at the Northwest Fisheries Science Center.  Most of the Columbia River data currently available were generated and submitted by BPA-funded laboratories.  The GAPS database and SPAN steelhead data that we host at no cost to BPA is undoubtedly the largest single repository of BPA genetic data.  Truly raw genetic data are vast graphics files that are of no value to anyone without extensive analysis.  However, we’ve gone far beyond normal measures to assure that appropriate data are available to whomever can benefit.  In sum, all useful data are available electronically for any reasonable use—if not instantaneously, on a shared access database, then by request in near real time.

Although the proposal is fundable, the ISRP emphasizes that the results need to be used in regional analytical forums; e.g., NOAA's Technical Recovery Teams (TRTs). The proposal could be improved by showing how the data from this project have guided adaptive management of recovery and implementation strategies.

Technical and scientific background: There is good explanation of the need to use this data to assess the natural spawning by hatchery salmon and steelhead in the Grande Ronde and Imnaha subbasins. Testable hypotheses are included. It is less clear how more genetic data can serve to guide TRTs and others in the broader survey of populations.

Rationale and significance to subbasin plans and regional programs: Five uncertainties from the Fish and Wildlife Program are identified in the narrative as being addressed by this proposal. The uncertainty over relative fitness of hatchery fish spawning in the wild (point 1) is well presented by the proposal. The remainder of the uncertainties are either questionably justified (point 2), partially covered (3 and 5), or not clear (4). The project could be strengthened by integration between this project and the monitoring and evaluation it supports for other agencies and tribes and by clarifying these applications of the data.

Project history: The history of the project is well described, and the milestones properly identified. The sponsors have a good track record of publications in the peer reviewed scientific literature. Less compelling is the evidence that the information being developed is making its way to guiding management decisions.

Objectives: It is not clear from the bulleted list below biological objective 1 (Describe demographic, evolutionary, and population genetic relationships) what demographic relationships mean or how they will be assessed. Evolutionary and population genetic relationships are clear, however.

Information transfer: The sponsors publish peer-reviewed work on salmon genes and lead development of standardized protocols for cross validating genetic data. There is little evidence however, that management decisions have been guided by the work to date. For example, has the captive broodstock work in the Grande Ronde been thought about differently, or the use of captive broodstock justified or reinforced as a result of the data collected by this project? The sponsors themselves note that more effort has been requested by cooperators to assist with information transfer. Data from this project have been used extensively by the Interior Columbia Technical Recovery Teams (TRT) to develop the independent populations and ESU boundaries for the Snake system. The ISAB was critical of the depth to which that data was analyzed in the TRT work. The sponsors only cite Myers (1998) and Busby (1996) as status reviews that used data from the project. Those references are now outdated, and new status reviews have been performed. It would be useful for the sponsors to identify how the recent NOAA hatchery review and status review update used data from this project.