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Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring

Citation

Durland, Evan; De Wit, Pierre; Langdon, Chris (2021), Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring, Dryad, Dataset, https://doi.org/10.5061/dryad.2z34tmpn5

Abstract

Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favor of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity in oysters, while also inherently sheltering genetic load within populations.

Methods

Pooled samples of oyster larvae  (n=200-3000) were collected at various points during development (days 0,2,6,10,14,22).  DNA was extracted in bulk, converted to 2bRAD libraries (BCGI enzyme) and sequenced on an Illumina Hiseq (SE 50bp reads). 

Usage Notes

Please see manuscript for bioinformatic approaches and associated github page: 

GitHub - E-Durland/oyster-poolseq: Methods for library preparation and bioinformatic analysis of pooled DNA data from larval oyster samples

Please see README file for description of the files.

Funding

Oregon Sea Grant, Oregon State University, Award: NA14OAR4170064 (R/SAQ-20)

Agricultural Research Service, Award: 2072-31000-004-00D (CRIS Project Number)