Hypothesis status board

Built against MOSAiC commit 86432e3; upstream lock last updated 2026-10-07. Rules for adding a hypothesis are in CLAUDE.md.

Hypotheses
ID Tier Claim Status Layers Species Depends on
H01 1 Colony identity explains more gene-expression variance than season in all three species not supported genes Apul, Peve, Ptuh
H02 1 Transcriptional plasticity across the year ranks Acropora > Pocillopora > Porites supported genes Apul, Peve, Ptuh H01
H03 1 Seasonal expression responses are conserved across the three species at orthologous genes not supported genes Apul, Peve, Ptuh H02
H04 2 DNA methylation is more stable within colonies over time than gene expression inconclusive cpg, genes Apul, Peve, Ptuh H01
H05 2 Gene-body methylation is positively associated with expression level and negatively with its temporal variability supported cpg, genes, annotation Apul, Peve, Ptuh H04
H06 2 Seasonal change in gene-body methylation tracks seasonal change in expression at the same genes inconclusive cpg, genes, annotation Apul, Peve, Ptuh H04, H05
H07 2 Seasonal miRNA expression profiles are conserved across species for shared miRNA families inconclusive mirna Apul, Peve, Ptuh
H08 2 lncRNA-mRNA co-expression at a fixed correlation threshold exceeds a permutation null supported lncrna, genes Apul, Peve, Ptuh
H15 2 Seasonal gene-body methylation changes persist after temperature reverses, while expression changes revert inconclusive cpg, genes, temperature, annotation Apul, Peve, Ptuh H04, H05, H06
H16 2 Expression change precedes gene-body methylation change, not the reverse not supported cpg, genes, annotation, physiology Apul, Peve, Ptuh H05, H06
H17 2 lncRNAs co-vary with neighboring protein-coding genes more than with expression-matched distant genes, decaying with distance supported lncrna, genes, annotation Apul, Peve, Ptuh H08
H23 2 Acropora's excess seasonal expression plasticity is concentrated in low-methylation orthologs inconclusive cpg, genes, annotation Apul, Peve, Ptuh H02, H05
H24 2 Orthologs retain similar gene-body methylation ranks across species inconclusive cpg, genes, annotation Apul, Peve, Ptuh H05
H25 2 Beyond 2 kb, local co-expression is practically equivalent for lncRNA–gene and gene–gene pairs inconclusive lncrna, genes, annotation Apul, Peve, Ptuh H08, H17
H26 2 Distal lncRNA–mRNA co-expression predicts gene expression in held-out colonies not supported lncrna, genes, annotation Apul, Peve, Ptuh H08, H17
H09 3 Symbiont density and chlorophyll predict host gene-expression modules not supported genes, physiology Apul, Peve, Ptuh H01
H10 3 Symbiodiniaceae ITS2 community composition is fixed by colony and does not shift seasonally supported its2, physiology Apul, Peve, Ptuh
H11 3 Cumulative thermal exposure before sampling predicts expression of heat-stress orthologs withdrawn genes, temperature Apul, Peve, Ptuh H03
H12 3 Site nutrient context modulates the seasonal trajectory of host physiology inconclusive physiology Apul, Peve, Ptuh
H20 3 Colonies whose transcriptome lags current temperature lose biomass and calcification by the next timepoint withdrawn genes, temperature, physiology Apul, Peve, Ptuh H02, H11
H21 3 Colonies with higher constitutive stress-gene expression show smaller seasonal responses in those genes inconclusive genes Apul, Peve, Ptuh H02, H11
H27 3 Colonies with different stable ITS2 profiles follow different seasonal symbiont-density trajectories withdrawn its2, physiology Peve, Ptuh H10
H13 4 A single latent factor spanning all omics layers separates summer from winter samples not supported genes, mirna, lncrna, cpg, metabolomics, lipidomics Apul, Peve, Ptuh H01, H04
H14 4 Seasonal shifts in storage lipids and central metabolites track host biomass and calcification inconclusive lipidomics, metabolomics, physiology Apul, Peve, Ptuh
H18 4 Gene-body methylation and cis-lncRNA expression explain largely independent parts of within-colony expression change not supported cpg, lncrna, genes, annotation Apul, Peve, Ptuh H06, H17
H19 4 Colonies with higher methylome turnover have lower host biomass and storage-lipid reserves not supported cpg, genes, physiology, lipidomics, metabolomics Apul, Peve, Ptuh H04, H14
H22 4 Expression at one timepoint forecasts next-timepoint physiology at held-out sites better than physiology alone inconclusive genes, physiology Apul, Peve, Ptuh H09

Tiers

  1. Variance structure. Colony vs season vs site. Everything downstream depends on these.
  2. Regulatory layers. Methylation, miRNA, lncRNA.
  3. Phenotype and environment. Physiology, symbionts, thermal history, nutrients.
  4. Integration. Multi-omics factors and energetics.