Epigenetic contributions to early life history variation in Chinook salmon
Notice bibliographique
Résumé
DNA methylation has been proposed as an epigenetic, evolutionary mechanism for acclimation, transgenerational plasticity, and local adaptation without changes in DNA sequence. In this thesis, I assess the highly targeted evolutionary nature of DNA methylation in Chinook salmon from the tissue to the population level, with important implications for organism survival and evolution. First, I developed a PCR-based bisulfite assay for Next-Generation sequencing for genes involved in growth, development, immune function, stress response, and metabolism (Chapter 2). Locus- and tissue-specific methylation was assessed in inbred and outbred Chinook salmon at two developmental stages (fry and yearling). This chapter established DNA methylation as a mechanism targeted to specific loci, tissues, levels of inbreeding, and developmental stages/environmental contexts. I assessed the role of DNA methylation in the propagation of maternal effects at three early developmental stages (egg, alevin, and fry; Chapter 3). Two 6x6 fully factorial Chinook salmon breeding crosses were used to estimate maternal effects. DNA methylation was assessed using bisulfite sequencing and both locus-specific and CpG-specific maternal effects were identified. This chapter established DNA methylation as a potential mechanism for the transmission of maternal effects, which can have important influences on offspring development and fitness. I quantified the effects of early environment on the genetic architecture of DNA methylation using 6x6 factorial crosses reared in two environments: a hatchery and a semi-natural channel (Chapter 4). Additive, non-additive, and maternal variance components, combined with environmental and GxE effects for DNA methylation were calculated. Rearing environment caused gene-specific plasticity in methylation, as well as differences in the genetic architecture of methylation. This chapter identified the importance of both genetic and environmental variation in controlling methylation, with important implications for methylation as an acclimation or adaptive mechanism. Finally, I characterized differences in locus-specific methylation among eight populations of Chinook salmon (Chapter 5). The significant population differences in locus-specific methylation were tested for correlation with environmental variables from natal streams, and pairwise FST estimates (microsatellite and SNP data). I identified no effects of rearing environment, but a weak among-population correlation between methylation and microsatellite FST indicating that genetic drift is influencing methylation. Population-level differences in DNA methylation suggest methylation may contribute to local adaptation and is certainly an important additional source of phenotypic variation. In conclusion, my doctoral research evaluated the role of DNA methylation from the tissue to the population level. My results support DNA methylation as a novel, potentially adaptive mechanism, contributing to normal organism function, transgenerational plasticity through maternal effects, plasticity, and population-level acclimation or adaptation.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,001 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».