Pottery from East Kalimantan sites and Borneo’s Pottery Chronology

Poster presented at the “South-east Asia: Human Evolution, Dispersals and Adaptation” session of the International Union of Prehistoric and Protohistoric Sciences conference, 1–7 september 2014, Burgos, Spain

Overview of site frequency spectrum (SFS).

Histogram showing the SFS for Denisovan, Neanderthal and non-archaic variants A) before and B) after the variant filtering steps. C) Histogram showing the SFS for aSNPs (Neanderthal + Denisovan) and the matched background set of naSNPs. (PDF)</p

Functional validation of the regulatory impact of Denisovan variants near <i>OAS2</i> and <i>OAS3</i>.

A) The genomic region encompassing the eight Denisovan variants associated with OAS2 and OAS3. The top two tracks display patterns of DNase Hypersensitivity sites in Blood and immune T cells as well as in HSC and B cells [34]. Tested variants are shown along with their calculated Δ PWM. Bottom tracks display the chromatin state information for the same tissues; B) the distribution of the log2 RNA-seq counts per million in whole blood for OAS2 and OAS3 between the Korowai and the people of Mentawai, from [57]; C) the relative expression changes between Denisovan and non-archaic alleles, or between the alternative and the reference allele for positive control (rs9283753) [45], in two Papuan LCLs. Asterisks mark significant differences from 1, BH-corrected p p ≤ 0.001; ** = 0.001 p ≤ 0.01; * = 0.01 p ≤ 0.05.</p

Table reporting the primer and oligo sequences used in the <i>in-vitro</i> validation.

(XLSX)</p

Biological processes putatively affected by SNPs within immune-related CREs.

For each ancestry the figure shows A) the overlap between the putative sets of target genes for each ancestry; B) the semantic similarity score estimates between the set of significantly enriched GO terms.</p

Distribution of common-to-high-frequency aSNPs falling within CREs across 18 tissues.

Patterns of enrichment across the 18 different tissue types in Roadmap Epigenomics for the set of common-to-high-frequency aSNPs annotated within chromatin states associated with CREs, relatively to the matched background set of naSNPs. Histograms on top indicate the mean number of variants calculated across all cell types belonging to each tissue. Asterisks indicate BH-corrected Fisher’s exact test p-values: * = p ≤ 0.05, ** = p ≤ 0.01; *** = p ≤ 0.001; **** = p ≤ 0.0001 (for full statistical results see S7 Table).</p

Distribution of Neanderthal aSNPs identified within EUR across chromatin states and tissues.

Figure showing the patterns of enrichment across A) the 15 chromatin states for the entire set of Neanderthal aSNPs B) the 18 different tissues for the set of cis-regulatory Neanderthal variants segregating at common-to-high-frequencies in EUR. OR are computed relatively to the matched background set of naSNPs. Histograms on top indicate the mean number of variants annotated within each chromatin state (A) or within each tissue (B). The mean is respectively calculated across all 111 cell types and across the cell types belonging to each tissue. Asterisks indicate BH-corrected Fisher’s exact test p-values p ≤ 0.0001; *** = 0.0001 p ≤ 0.001; ** = 0.001 p ≤ 0.01; ** = 0.01 p ≤ 0.05. (PDF)</p

Table reporting the GO enrichment results for the set of genes targeted by Denisovan, Neanderthal and non-archaic variants.

(XLSX)</p

File reporting the genomic location of all non-archaic variants used in this study.

(TXT)</p

Table reporting the enrichment results for the entire set of archaic variants annotated within each chromatin state.

(XLSX)</p