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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide <t>methylation</t> scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.
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The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide methylation scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.

Journal: Evolutionary Applications

Article Title: Investigating food production‐associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

doi: 10.1111/eva.13743

Figure Lengend Snippet: The demographic characteristics of the 34 ancient genomes used in this study and their genome‐wide methylation scores. (a) The excavation locations of ancient individuals are included in this study. Color coding indicates subsistence type. (b) Left panel: Violin plots of the methylation score (MS) data related to ancient individuals included in this study. The brown and blue points indicate the mean and the median, respectively. The x ‐axis shows the log2‐transformed MS values. The y ‐axis represents the ancient individuals. Right panel: Zoomed‐in version of the left panel. (c) The distribution of mean MS per individual on CpG islands and genomic sites representing shelves, shores, and open seas.

Article Snippet: To this end, we utilized methylation differences documented between modern‐day HGs and agriculturalists in Central Africa, measured in whole blood samples using bisulfite treatment and the Illumina 450K array (Fagny et al., ).

Techniques: Genome Wide, Methylation, Transformation Assay

Violin plots of X chromosome methylation estimates in female and male ancient genomes. The y ‐axes show chrX MS values divided by the mean autosomal MS for the same individual. Left Panel: ChrX MS values of all 34 paleogenomes for 12 females (XX) and 22 males (XY). The MS values for females and males were pooled after normalizing by dividing the chrX MS values by the mean autosomal MS value for the same individual. Right Panel: ChrX MS values from NF individuals from Marchi et al. . These genomes were chosen to remove the possible influence of other factors (different laboratory and subsistence type effects) on chrX methylation estimates.

Journal: Evolutionary Applications

Article Title: Investigating food production‐associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

doi: 10.1111/eva.13743

Figure Lengend Snippet: Violin plots of X chromosome methylation estimates in female and male ancient genomes. The y ‐axes show chrX MS values divided by the mean autosomal MS for the same individual. Left Panel: ChrX MS values of all 34 paleogenomes for 12 females (XX) and 22 males (XY). The MS values for females and males were pooled after normalizing by dividing the chrX MS values by the mean autosomal MS value for the same individual. Right Panel: ChrX MS values from NF individuals from Marchi et al. . These genomes were chosen to remove the possible influence of other factors (different laboratory and subsistence type effects) on chrX methylation estimates.

Article Snippet: To this end, we utilized methylation differences documented between modern‐day HGs and agriculturalists in Central Africa, measured in whole blood samples using bisulfite treatment and the Illumina 450K array (Fagny et al., ).

Techniques: Methylation

Representative genes with the most significant differential methylation signals in linear mixed model analyses, related to subsistence type, tissue, and sex. The x ‐axis represents the factors while the y ‐axis represents the mean MS values per gene per individual. (a) Genes chosen using models with “individual” as random factor. Left panel: ICAM5 (subsistence type p < 0.01). Middle panel: ATPB1 (tissue type p < 0.01). Right panel: CEP135 (genetic sex p = 0.02). (b) Genes chosen using models with “laboratory‐of‐origin” as random factor. Left panel: TOX2 (subsistence type p = 0.006). Middle panel: PCDHA2 (tissue type p = 0.03). Right panel: RCOR1 (genetic sex p = 0.04).

Journal: Evolutionary Applications

Article Title: Investigating food production‐associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

doi: 10.1111/eva.13743

Figure Lengend Snippet: Representative genes with the most significant differential methylation signals in linear mixed model analyses, related to subsistence type, tissue, and sex. The x ‐axis represents the factors while the y ‐axis represents the mean MS values per gene per individual. (a) Genes chosen using models with “individual” as random factor. Left panel: ICAM5 (subsistence type p < 0.01). Middle panel: ATPB1 (tissue type p < 0.01). Right panel: CEP135 (genetic sex p = 0.02). (b) Genes chosen using models with “laboratory‐of‐origin” as random factor. Left panel: TOX2 (subsistence type p = 0.006). Middle panel: PCDHA2 (tissue type p = 0.03). Right panel: RCOR1 (genetic sex p = 0.04).

Article Snippet: To this end, we utilized methylation differences documented between modern‐day HGs and agriculturalists in Central Africa, measured in whole blood samples using bisulfite treatment and the Illumina 450K array (Fagny et al., ).

Techniques: Methylation

Pairwise comparisons of HG‐agriculturalist DNA methylation differences between ancient and present‐day human datasets.

Journal: Evolutionary Applications

Article Title: Investigating food production‐associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

doi: 10.1111/eva.13743

Figure Lengend Snippet: Pairwise comparisons of HG‐agriculturalist DNA methylation differences between ancient and present‐day human datasets.

Article Snippet: To this end, we utilized methylation differences documented between modern‐day HGs and agriculturalists in Central Africa, measured in whole blood samples using bisulfite treatment and the Illumina 450K array (Fagny et al., ).

Techniques: DNA Methylation Assay