Temporal genetic change in North American Pacific oyster populations suggests caution in seascape genetics analyses of high gene-flow species
Bibliographic record
Abstract
MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 565:79-93 (2017) - DOI: https://doi.org/10.3354/meps12009 Temporal genetic change in North American Pacific oyster populations suggests caution in seascape genetics analyses of high gene-flow species Xiujun Sun1,2, Dennis Hedgecock1,* 1Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA 2Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China *Corresponding author: dhedge@usc.edu ABSTRACT: The Pacific oyster Crassostrea gigas was, for decades, massively introduced to North America from Japan and established large, self-recruiting populations in the Pacific Northwest of the USA and Canada. A previous study of mtDNA variation revealed little population genetic structure among populations from British Columbia and Washington State. Here, we used samples from that study, more recent samples from 2 of the same localities, and 2 additional samples, including 1 from Japan, to investigate spatial and temporal genetic variation at 52 mapped, coding, single-nucleotide polymorphisms (SNPs) assayed by high-resolution melting (HRM). Little variation was detected among North American populations, which, as a group, are distinct, perhaps adaptively so, from oysters in Hiroshima, Japan. However, significant excesses of heterozygotes with respect to random mating expectations and of pairwise linkage disequilibria revealed that North American populations are not in Hardy-Weinberg (random mating) equilibrium. Moreover, genetic changes over 10 to 21 yr in 2 localities are substantial, despite high gene flow, and are as large as spatial variance per generation. These results caution against basing connectivity or seascape genetic analyses on snapshots of spatial population structure in high gene-flow species. Because migration and selection are ruled out as causes of temporal genetic change, random genetic drift is the most parsimonious explanation. This implies effective population sizes (Ne) of hundreds to a few thousands, orders of magnitude smaller than the natural abundance (N) of this oyster. These low Ne:N ratios are compatible with the hypothesis of sweepstakes reproductive success. KEY WORDS: Crassostrea gigas · Single nucleotide polymorphism · High-resolution melting · Linkage disequilibrium · Genetic variance · Effective population size · Sweepstakes reproductive success Full text in pdf format Supplement 1 Supplement 2 PreviousNextCite this article as: Sun X, Hedgecock D (2017) Temporal genetic change in North American Pacific oyster populations suggests caution in seascape genetics analyses of high gene-flow species. Mar Ecol Prog Ser 565:79-93. https://doi.org/10.3354/meps12009 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 565. Online publication date: February 17, 2017 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2017 Inter-Research.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".