Our study seeks to answer several pressing ecological and conservation questions:

• How do the genetic relationships among salmonid populations correlate with the geological history of the North Cascades?
• Have ancient glaciers and shifting river networks influenced gene flow and population structure?
• How have modern hatchery practices affected the genetic diversity of native trout populations?

These questions are central to understanding long-term species persistence, especially in a rapidly changing environment.

Our recently completed genetic assessment revealed that native salmonid populations in the upper Skagit River are genetically distinct from those found below the Skagit Gorge—the lowest dam in the system. This discovery has catalyzed our current investigation, aimed at tracing the genetic identities of native trout to guide effective conservation and management strategies.

We’re currently collaborating with City Light and other project partners to define key research priorities and agree on shared methodologies. This consensus-driven approach ensures scientific rigor while aligning with broader conservation goals in the basin.

Although the study is grounded in academic research, its implications extend to real-world decision-making. As policymakers and stakeholders consider the reintroduction of anadromous (ocean-going) salmonids upstream of current barriers, it is critical to understand the genetic composition of resident fish and the consequences of non-volitional fish passage for long-term species health.

Our work in the Skagit River Basin with Seattle City Light has been deeply rewarding. We thank our collaborators, including HDR for their technical leadership, and City Light for their ongoing support and commitment to ecological stewardship. Stay tuned for future updates as we continue to uncover the genetic legacy of the Skagit’s native fish.

Let’s Start Your Project. Contact Us

The post Unraveling the Genetic History of Native Salmonids in the Upper Skagit River appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Let’s Start Your Project. Contact Us

The post Investigation of Winter-Run Chinook Salmon Vital Rates appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Average yearly false positive rate for winter run (i.e. calling a fish winter run when it wasn’t) at South Delta diversions fish protection facilities (salvage) during 1996-2010 was 56%, although error rates varied considerably within a season.  For 2011-2014, average yearly false positive rates at the CVP salvage have been 58% – 80%, with rate >85% during recent years of drought. There is reason to believe that observations from salvage may reflect general inaccuracy that would apply to IEP monitoring programs, which collect upwards of 100,000 Chinook Salmon juveniles annually.  Further there is indication that identification of spring run in IEP surveys is also problematic (i.e. ~2/3 false positive rate) using length-at-date criteria. These error rates compromise interpretations from compliance monitoring activities regarding listed Chinook Salmon populations.

Project Objectives

The primary objectives of this work is the genetic classification (to race; ESU or winter vs. not winter) of Chinook Salmon captured from SWP and CVP fish protection facilities and IEP monitoring programs. The population-of-origin is determined for juveniles by comparing their genotypes to reference genetic baselines in order to quantify the number and distribution of true ESA-listed (genetic) winter and spring runs categorized by length-at-date criteria models.  The overarching goal of this work is to directly target (and reduce) one source of uncertainty in the estimation of loss for listed Chinook Salmon (but primarily winter run) at South Delta fish salvage facilities and from IEP compliance monitoring. Additionally, this project intends to develop the means to scale (increase) genotyping capacity without dramatically altering current cost projections.

Let’s Start Your Project. Contact Us

The post Genetic Identification of Salmonids to Inform Central Valley Project Operations and Bay-Delta Monitoring appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

A parental genotype database was created by genotyping all adult (carcass) samples. Each carcass was associated with either a restored or unrestored site.  Maximum likelihood methods were employed to assign or relate out migrating juvenile genotypes to adult genotypes in order to determine spatially explicit recruitment patterns. Results directly link the genotype of the juveniles coupled with the meta-data of the rotary screw trap (fish size, outmigration timing) to genotype of parents taken from the carcass surveys from both restored and unrestored sites. This analysis documented recruitment from enhanced sites and provided a recruitment metric (juveniles per female) for both restored and unrestored sites.

Let’s Start Your Project. Contact Us

The post Quantifying the Benefits of Habitat Restoration appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Overview

Present monitoring programs were not designed to derive population estimates of Delta smelt. Thus, estimating Delta smelt annual population size (N) has proven challenging due to difficulties in estimating gear efficiencies and sampling in all potentially occupied habitats.  Additionally, reliance on an abundance index has hindered the ability to evaluate the role that water exports may play in Delta smelt population dynamics.(1) The ongoing activities of regulators and stakeholders provide (2) information and biological material on which (3) genetic measures can be made. There is an alternative to using an abundance index for assessing Delta Smelt population status.  From a conservation and population recovery stand point, the effective population size ( N_e ) is a critical metric to know over time (4), as there are agreed upon thresholds where genetic impact (long term viability) would be minimized (5) – the so called 50/500 rule.  Further, the N_e is measurable, which would provide credible and useful information for assessing impacts of water operations to Delta smelt (1).

Information regarding Delta smelt N_e is limited, which was stated as a critical information gap in review of Delta smelt Long-term Operations Opinions Reasonable and Prudent Alternatives.  The information that did exist prior to this study showed N_e had approached the threshold where long-term population persistence could be impacted (N_e ~ 1000).

Relevance

Calculating this alternative population size measure will increase the information content produced from current monitoring activities, adding value without increasing “take”.  Additionally, scientifically defensible population size measures could directly inform deliberations about water operation impacts on Delta smelt and population recovery performance measures.

Results

Genetic results were derived by Cramer Fish Sciences, Genidaqs, with data measures independently corroborated by project partner Dr. Mandi Finger.  CFS analyzed N=995, N=534, N=678, and N=421 Delta Smelt tissues from year classes 2011, 2012, 2013, and 2014, respectively.  These collections represent a majority of Delta Smelt encountered during those years and are archived (as DNA).  Observed genetic diversity was high and individual year classes did not differ genetically from each other.  The effective population size was estimated for each year class using published methods.  At this time, there is no population genetic evidence supporting the hypothesis that N_e of Delta Smelt is below 1000.

Genidaqs – Conclusions and Interpretation

The implication of the genetic diversity and N_e information is that a large number of Delta Smelt remain in the San Francisco Estuary system.  The current disparity between Delta Smelt abundance indices and N_e is a concern as it may indicate existing monitoring programs will have difficulty adequately representing Delta Smelt abundance, distribution or habitat needs.

The trend in Delta Smelt N_e – as of the 2014 year class – is above the threshold where fitness related (quantitative) genetic diversity is expected to be lost each generation through genetic drift (i.e., N_e > 500).  Despite the positive result that the Delta Smelt gene pool is expected to retain quantitative genetic diversity at its present size, the resiliency of Delta Smelt is low because the species occupies a restricted geographic range and largely has an annual reproductive cycle.  The Delta Smelt species is recoverable if habitat is provided that is consistent with its life-history requirements.

Let’s Start Your Project. Contact Us

The post Delta Smelt Population Size Metrics Derived from Genetic Measures appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.