Genetic Monitoring of White Sturgeon Conservation Aquaculture
The Genomic Variation Lab (GVL) is continuing work with the Kootenai Tribe, using genetic techniques to inform the management of the Kootenai River white sturgeon population.
Kootenai Tribe of Idaho Program
Background and significance of study
Kootenai River white sturgeon population, listed as an endangered Distinct Population Segment under the Endangered Species Act, has experienced negligible recruitment since the 1960s. The Kootenai Tribe of Idaho initiated a conservation aquaculture program for this population in 1992 to maintain it in the absence of natural reproduction. Currently, nearly all recruitment is thought to be derived from the aquaculture program. Because tissue samples have been archived for most adult sturgeon brought into the hatchery, the Tribe has a tissue archive of all or nearly all parents contributing offspring since the 1990s.
The Genomic Variation Lab (GVL) has used genetic tools to monitor the conservation aquaculture program in collaboration with the Kootenai Tribe and other co-managing agencies (US Fish and Wildlife Service, Idaho Fish and Game, BC Ministry of Water, Land, and Resource Stewardship). The program consists of an “in situ” and “ex situ” component. For the “in situ” monitoring of conservation aquaculture, we are collecting genotype data on all adult white sturgeon sampled by the Tribe to monitor changes in genetic diversity over time. The Tribe is striving to maximize genetic diversity in their conservation aquaculture program to preserve the population’s ability to adapt to changing environmental conditions. These data can also be used to understand how potential broodstock are related to each other, allowing the Tribe can avoid inbreeding, or the crossing of close relatives that may reduce the fitness of the endangered population.
Another aspect of genetic monitoring involves using a newly developed white sturgeon SNP panel to perform parentage-based tagging using genotypes of broodstock and their offspring
released from the hatchery at a very young age. To learn more about this project, see “Developing Parentage-Based Tagging to Improve White Sturgeon Conservation Hatchery Methods”
A third aspect of genetic monitoring includes monitoring of genome size. In 2011, the GVL discovered the commercial and conservation aquaculture of sturgeon can lead to production of individuals of abnormal genome size, spontaneous autopolyploids. After helping the Kootenai Tribe of Idaho manage spontaneous autopolyploidy for several years, they now are screening all indivduals released from the hatchery themselves using Coulter counter technology, validated by PhD student Aviva Fiske for sturgeon ploidy monitoring.
Dr. Shawn Young and Nate Jensen of the Kootenai Tribe of Idaho Native Fish Conservation Aquaculture Program oversee collection of tissue samples for this research. Each year the GVL collaboratively revisits with the Tribe what genetic monitoring work will be performed in future years.
Andrea’s work with the Kootenai River white sturgeon conservation aquaculture program was highlighted in a documentary film. The film can be rented or purchased here.
Idaho Power Corporation Program
In the mid 2010s, sturgeon conservation aquaculture programs began to explore repatriation-based conservation aquaculture. In repatriation, biologists collect eggs and larvae from natural spawning events, bring them back to a hatchery, rear them until they are large enough to experience high survival in the wild, and release them. Matt Thorstensen used the Idaho Power conservation aquaculture program for the Bliss Reach of the Snake River to determine which method preserved the most genetic diversity and represented the most spawners. Matt found that repatriation represented much more diversity and represented far more spawners that broodstock based aquaculture. His work also helped us better understand the limitations of progeny array reconstruction (inferring a pedigree without parents) for estimating the number
of spawners contributing to a year class.
Number of alleles data from Table 2 of Thorstensen et al. (2019) shows how larvae sampled for repatriation have similar numbers of microsatellite alleles as a wild year class (sampled at age 1
in 2011) despite a much smaller sample size. Repatriation year classes have more genetic diversity than broodstock based conservation aquaculture in 2016 and 2017. So few broodstock
were used because only a small number of large bodied (sexually mature) adults can be held in captivity for spawning.
Matt’s work was based on microsatellite genotypes but now that we have a SNP panel available for white sturgeon, we are exploring the extent to which it improves progeny array reconstruction accuracy. Young of year collected from the Bliss Reach for Idaho Power
Company’s repatriation program are one of many datasets being used for this study led by PhD students Peter Johnson and Aviva Fiske)
Ken Lepla, Phil Bates, and Jake Hughes from the Idaho Power Corporation collected samples and provided funding for this work over the years.
On the upper Columbia River, white sturgeon spawn annually in substantial numbers, but the ensuing larvae die off such that no natural recruitment is detected. This recruitment failure
has been occurring for several decades and results from anthropogenic change to the river. To mitigate this issue, wildlife managers collect eggs and larvae from wild spawning events, rear
them in aquaculture, and repatriate them to the river as juveniles, at which point they can survive. As this conservation aquaculture program perpetuates the population, capturing the breadth of native genetic diversity and avoiding genetic drift is a top goal. I am conducting a genetic analysis of aquaculture juveniles and wild adults to evaluate the extent to which this goal is being achieved. My approach centers on estimating family structure, using tetraploid
single nucleotide polymorphism (SNP) markers obtained through genotyping in thousands by sequencing (GTseq). By using maximum-likelihood methods to reconstruct sibships among aquaculture juveniles, we can estimate total and effective numbers of wild spawners represented, which reflect the potential for genetic drift. As a fraction of collected offspring die in aquaculture, I’m conducting sibship reconstruction with and without these individuals to
quantify the impact that such mortalities have on spawner representation and thus diversity capture. With samples from a significant portion of the population of wild adults, I’m furthermore conducting parentage analysis to quantify offspring contributions by specific spawners. Broadly, I’m using novel genetic resources and tools to evaluate a large-scale conservation aquaculture program for an iconic species.
Schreier, A. D., J. Rodzen, S. Ireland, and B. May. 2012. Genetic techniques inform conservation aquaculture of the endangered Kootenai River white sturgeon, Acipenser transmontanus. Endang. Species Res. 16:65-75. (pdf)
Schreier, A., S. Stephenson, S. Young, and P. Rust. Post-release genetic monitoring is necessary to evaluate genetic diversity conservation in captive and supportive breeding programs. Biological Conservation 192:74-81. (pdf)