Genetic monitoring of white sturgeon conservation aquaculture

For more information contact Andrea Schreier: amdrauch@ucdavis.edu

Background and Significance of Study

Kootenai Tribe of Idaho Conservation Aquaculture Program

The ESA-listed Kootenai River white sturgeon population has suffered from negligible recruitment for the past 20-30 years. 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 Because tissue samples have been archived for most adult sturgeon brought into the hatchery, the Tribe has a tissue archive of all or nearly all parents contributing offspring since the 1990s.

Genetic monitoring sturgeon project image

 

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. The program consists of an “in situ” and “ex situ” component.  For the “in situ” monitoring of conservation aquaculture, we are collecting microsatellite genotype data on all adult white sturgeon sampled by the Tribe in order to monitor changes in genetic diversity over time. The Tribe is striving to maximize genetic diversity in their conservation aquaculture program in order to preserve the population’s ability to adapt to changing environmental conditions. Additionally, we are using microsatellite data to conduct parentage analysis to determine family relationships among all adult sturgeon brought into the conservation aquaculture program as broodstock. By understanding how potential broodstock are related to each other, the Tribe can avoid inbreeding, or the crossing of close relatives that may reduce the fitness of the endangered population.

Previous work in the GVL used eight microsatellite loci to assign parentage full-sibling families whose parents were known. Low levels of genetic variation resulted in suboptimal assignment accuracy. We have optimized nine additional microsatellite loci and used these in combination with the previous eight loci to increase the accuracy of parentage assignment within known full-sib families produced by the Kootenai hatchery.

A third aspect of genetic monitoring includes monitoring of genome size. The recent discovery of individuals of abnormal ploidy in a commercially farmed population of white sturgeon indicates that some aspect of sturgeon culture is unintentionally inducing or supporting spontaneous autopolyploidy. As sturgeon culture techniques are similar for commercial and conservation aquaculture, this finding raised concerns that genome duplication could be induced in the Kootenai River conservation aquaculture program. We are working with the Tribe to develop sampling and analysis protocols to allow them to screen all families produced in the hatchery for spontaneous autopolyploidy. This work is described more fully under the project Spontaneous Autopolyploidy in Sturgeon Aquaculture.

Our most recent project on the Kootenai River white sturgeon conservation aquaculture program has been to determine how post-release mortality has altered genetic composition of hatchery-reared juveniles.  We synthesized data from the multi-agency Kootenai River white sturgeon juvenile monitoring program and our genetic monitoring database to characterize the variance in apparent survival among the 209 families released by the program.  If many families are extirpated after release into the Kootenai River, than our estimate of genetic diversity calculation based on wild broodstock genotypes will be biased low. If post-release mortality is significant and if environmental predictors of apparent post-release survival can be identified, hatchery practices can be altered to increase survival of more families and maximize genetic diversity conservation and Ne.

Upper Columbia River Conservation Aquaculture

The Genomic Variation Lab was funded by the Spokane Tribe of Indians to conduct two projects related to the white sturgeon conservation aquaculture program for Lake Roosevelt (US side of the Transboundary Reach of the Columbia River).  First, we genotyped the wild broodstock used in the program from 2001-2010 to determine how much genetic diversity was passed on to progeny released into Lake Roosevelt.  Next, we were asked to compare different approaches to sturgeon conservation aquaculture for their effectiveness at conserving genetic diversity in Upper Columbia River white sturgeon. The traditional approaches to sturgeon conservation aquaculture involve 1) capturing adults in spawning condition from the wild and either transporting them to a hatchery for spawning or 2) collecting gametes from spawning adults in the field for artificial spawning in the hatchery. Traditional approaches were used for white sturgeon conservation aquaculture in the Upper Columbia from 2001 – 2010. In 2010, Jason McClellan and Matt Howell of the Colville Confederated Tribes tested a new approach to sturgeon conservation aquaculture that involved the capture of down-migrating, naturally spawned larvae for rearing in the hatchery and release at larger sizes. This “repatriation” approach was conducted in 2010 and 2011, providing us an opportunity to compare survival and genetic diversity conservation between the two approaches.

Results

Kootenai Tribe of Idaho Conservation Aquaculture

By 2014, nearly 500 adult Kootenai River white sturgeon had been genotyped by the GVL, representing about ½ of the wild population. Within each year of genetic monitoring, wild broodstock used in the Kootenai Tribe of Idaho conservation aquaculture program possessed ~80-90% of the wild population’s neutral genetic diversity. A total of 96% of wild genetic diversity has been represented by broodstock. Seventeen microsatellite loci allow for highly accurate parentage assignment in hatchery families, although relatedness among adults (potential parents) in this small population can complicate parentage assignment of juveniles captured in the wild when year class is uncertain.

Our analysis of apparent survival revealed that only 55% of families released by the conservation aquaculture program are represented by progeny still at large in the Kootenai River. There was high variability in the reproductive success of parent pairs, with many families extirpated completely and some families leaving hundreds of offspring. We found a significant reduction in genetic diversity conservation within most years of the program relative to genetic diversity of year classes at the time of release. Ne (estimated from broodstock demographics) also declined significantly in most years of the program due to post-release mortality of juveniles. Because releases have been occurring for over a decade, however, there was no decline in overall genetic diversity conservation of the program.

Upper Columbia River conservation aquaculture

Thirteen microsatellite loci were used to genotype broodstock used from 2001-2010 and we compared genetic diversity levels in broodstock to that of wild adults in the Transboundary Reach of the Upper Columbia. We found that collectively, wild broodstock used between 2001 and 2010 represented 87% of alleles found in the wild population. We determined that approximately 100 wild broodstock were required to represent 90% of the neutral genetic diversity of the wild population.

Our comparison of traditional conservation aquaculture approaches to repatriation showed that greater genetic diversity was captured by repatriation, likely because more parents are represented by natural spawning events. In 2010, a year where both approaches were used, we found that repatriation conserved a significantly greater amount of genetic diversity than the traditional approach, even when 15 wild broodstock were used. We also found that ~200 surviving larvae were required to represent 90% of genetic diversity found in the wild population.

Future Work

Genetic monitoring of the Kootenai Tribe of Idaho white sturgeon conservation aquaculture program will continue in future years.  We are also interested in developing a genetic method for estimating effective population size, Ne, in this endangered population.  However, Ne estimation is complicated in this case not only by the species protracted, iteroparous life history but also the fact that their genomes are highly duplicated.  We are seeking collaborators interested in working with us to develop a new tool for estimating Ne from polysomic genetic data.

Collaborators

Shawn Young and Chris Lewandowski, Kootenai Tribe of Idaho

Sarah Stephenson, British Columbia Ministry of Forests, Lands and Natural Resource Operations

Pete Rust, Idaho Department of Fish and Game

US Fish and Wildlife Service

Spokane Tribe of Idaho

Jason McLellan and Matt Howell, Colville Confederated Tribes

 

Press

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.

Publications

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.  Submitted to Biological Conservation.

A manuscript describing our comparison of white sturgeon conservation aquaculture techniques is in preparation.