Table 1.
Numbers of DNA methylation and RNA sequenced samples from each study location.
Fig 1.
Sampling locations and overview of DNA methylation and gene expression variation among the study samples.
(A) Colors indicate island populations: Mentawai, blue; Sumba, yellow; Korowai, red. PCA was performed on the top 10,000 most variable methylation probes and the top 1,000 most variable genes, determined by the sample-wide coefficient of variation. The first two axes of variation from the principal component analysis in the (B) RNA-seq-derived genotype data, (C) DNA methylation and (D) gene expression data after correcting for confounding effects are driven by between-island differences. Plotting shapes indicates sequencing/array batches.
Fig 2.
Inter-island differential expression and methylation trends.
Volcano plots of (A) differentially methylated probes and (B) differentially expressed genes between Sumba and Mentawai (green), Korowai and Sumba (orange), and Korowai and Mentawai (purple). Venn diagrams of DMPs (C) and DEGs (D) overlapping between different pairwise comparisons at an FDR-adjusted p value ≤ 0.01 and an absolute log2(FC) ≥ 0.5. Relationship between the log2(FC) of each probe (E) and gene (F) between Mentawai vs. Korowai and Sumba vs. Korowai. Probes and genes that were DMP or DEG between Mentawai and Korowai (purple), Sumba and Korowai (orange), or both comparisons (pink) are indicated. Smoothed conditional means based on generalized additive models are presented with 95% confidence intervals.
Fig 3.
Association between methylation and gene expression levels.
(A) Relationship between probe cluster DNA methylation and gene expression levels among the 1,282 probe clusters and associated genes identified by MethylMix. (B) Example of a single gene, SIGLEC7, which is both differentially expressed and differentially methylated between Sumbanese and the Korowai.
Fig 4.
Differential gene expression trends at the village level partially reflect inter-island trends.
(A) Sharing of village-level DEG signal across all possible inter-island contrasts. (B) Top 100 DEGs between Taileleu and the Korowai that are not DE between Madobag and the Korowai. (C) Top 100 DEGs between Wunga and the Korowai that are not DE between Anakalang and the Korowai.