Data from: Conservation aquaculture of wild-origin offspring preserves genetic diversity in an endangered population of white sturgeon
Data files
Feb 25, 2025 version files 9.75 MB
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README.md
2.92 KB
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UCR_WS_genotypes_adults.xlsx
1.52 MB
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UCR_WS_genotypes_offspring.xlsx
8.23 MB
Abstract
Conservation aquaculture programs that release fish to supplement wild populations can potentially capture greater genetic diversity by collecting offspring as embryos and larvae from wild spawning events than by producing them conventionally from broodstock. A conservation aquaculture program for the endangered white sturgeon population of the Upper Columbia River initially utilized wild broodstock for 14 years before fully transitioning to rearing wild-origin offspring in 2014. Here we evaluated the performance of this program in capturing the wild population’s genetic diversity since transitioning to wild-origin offspring. We analyzed genotypes of 325 tetrasomic single nucleotide polymorphism (SNP) markers in more than 5,000 offspring reared from 2014 through 2020 and over 1,000 wild adults from the population. Genetic diversity statistics were highly similar between each offspring year class and the wild adult population. We inferred sibship structure to estimate the total number of spawners (Ns) and effective number of breeders (Nb) represented within each year class and found values as high as 932.5 (95% CI 876-989) and 146.3 (95% CI 144-149), respectively, far surpassing the numbers included as broodstock. We further estimated Ns and Nb for three-year classes with their individuals that died in aquaculture and found that on average, the mortality rate of 33.2% decreased Ns by 21.5% and Nb by 7.9%. Finally, we analyzed relationship coefficients to identify full-sibships spanning collection sites and found them in one year class, comprising 0.27% of all full-sibling pairs that year, demonstrating that the separate sites display negligible redundancy with respect to sibling families collected. Our results illustrate a robust performance by this program in representing the wild population’s diversity compared to broodstock approaches and support the adoption of utilizing wild-origin offspring in other conservation aquaculture programs when feasible.
https://doi.org/10.5061/dryad.fqz612k2m
Description of the data and file structure
These data consist of two Excel spreadsheets with the tetrasomic SNP genotypes analyzed in this study. UCR_WS_genotypes_offspring.xlsx contains genotypes of offspring that were collected from the wild as neonates, reared in aquaculture, and released as juveniles. UCR_WS_genotypes_adults.xlsx contains genotypes of adults in the wild population that were sampled during a long-term capture-mark-recapture (CMR) study.
File: UCR_WS_genotypes_offspring.xlsx
Description:
Full genotypes for 325 tetrasomic SNPs per sample. Ungenotyped SNPs are indicated by ‘na’.
Offspring sample IDs have a structure of multiple sections separated by underscores (e.g. BY14_FDR_345, BY14_WAN_G1_0001):
- The first section consists of ‘BY’ or ‘MT’ followed by a two-digit number. ‘BY’ indicates individuals that survived in aquaculture to be released, while ‘MT’ indicates individuals that died in aquaculture. The two-digit number indicates the year in which the individuals were collected from the wild (e.g. 19 = 2019).
- The second section is a capitalized three-letter code that indicates the location of the collection. ‘FDR’ refers to China Bend at FDR Lake in Washington. ‘HKS’, ‘KIN’, and ‘WAN’ refer to Hugh Keenleyside Dam, Kinnaird, and Waneta Dam, respectively, which are all in British Columbia.
- Samples from British Columbia sites have a third section consisting of ‘G#’, which indicates the spawning group (event) number from which that individual was collected. This section is absent in Washington samples; their spawning events are unknown as these individuals were collected as drifting larvae downstream of spawning events.
- All samples end with a number distinguishing samples within years/locations/groups.
File: UCR_WS_genotypes_adults.xlsx
Description: Full genotypes for 325 tetrasomic SNPs per sample. Ungenotyped SNPs are indicated by ‘na’.
Samples from adults captured in Washington have an ID structure of three sections separated by underscores (e.g. FDR_2009_078):
- The first section is ‘FDR’ for all samples, indicating FDR Lake as the general location of capture
- The second section is the four-digit year of capture and sample preservation.
- The third section is the sample number.
Samples from adults captured in British Columbia have a slightly different ID structure:
- The first section indicates the year in which the individual was captured and sampled
- The final section indicates the sample number
- Some samples have a middle section indicating the season of capture (F = fall, Sp = spring), or that the individual was captured for hatchery broodstock (‘BS, only 2014).
These genotypes were assembled through GTseq with the white sturgeon panel developed by Delomas et al. 2021.