Origins of Greek Civilization: Minoans and Mycenaeans May 3, 2021 21:18:08 GMT
Post by Admin on May 3, 2021 21:18:08 GMT
Figure S1 Images of archaeological site Elati-Logkas (Log02, Log04), related to Table 2 and Document S1
(A) Elati-Logkas, view of the cemetery with burials covered by stones known as “periboloi.” (B) Elati-Logkas, Burial 80.1 (Log04) is a pit-grave in the circumference of an inner enclosure built from rough stones. The buried individual was in crouched position lying to the left side, with the hands bent and the palms supporting the skull. Inside the same walls, four other similar burials were excavated with no grave goods apart from only one flint stone blade in tomb 80.5. (C) Elati-Logkas, Burial 22.1 (Log02) is the main among three pithos-inhumations and one secondary burial inside the “peribolos 22.” The grave itself is bordered by rough stones, with the buried individual laid on a ceramic “stretcher.” Several vertical lines are still visible on the skeletal remains. The individual of the burial 22.1 was found in a supine position with the hands crossed on the abdomen, the legs bent in a crouched position to the left, and the skull turned to the right side. There were no grave goods found in the burial 22.1. Photo credits: Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture, Greece. Courtesy of Dr. Georgia Karamitrou-Mentessidi.
Six ancient Aegean whole genomes
The resulting depth of coverage for the Aegean BA genomes ranged between 2.6× and 4.9× (average: 3.7×) (Tables 2 and S1; and STAR Methods). The number of SNPs covered by at least one read is considerably higher for the six Aegean BA genomes than for the Aegean BA SNP capture data from Lazaridis et al., 2017 when considering the “1240K” SNP capture set (Mathieson et al., 2015) but also across an “intergenic region” SNP set defined in this study (Figure S2A). The latter includes ∼5,270,000 SNP sites located at least 20 kb away from annotated genes and CpG islands (STAR Methods). Note that whole genomes from the populations studied hereafter have more low frequency variants in the intergenic regions than were detected in the 1240K SNP set for the same regions (Figure S2B). This likely owes to the SNP ascertainment scheme in the latter (Clark et al., 2005).
Figure S2 Comparison of SNP capture and WGS data, related to Figure 4 and Tables 2 and S1
(A) Number of single nucleotide polymorphisms (SNPs) in the nuclear genomic data from this study (WGS data) in comparison with previously published BA genomic data from the Aegean. The number of covered SNPs across BA Aegeans based on two SNP sets are shown. On the left: the number of SNPs based on the 1240K SNP set (Dataset I) defined by the array used in Lazaridis et al., 2017 to enrich the libraries. On the right: the number of SNPs based on the intergenic regions defined for the ABC-DL analysis below (Dataset IV, STAR Methods). The green box plots (median indicated by a horizontal line and interquartile range indicated by the box) correspond to the number of SNPs among the BA Aegean data from present-day Greece (Lazaridis et al., 2017); the blue box plots correspond to the number of SNPs among the whole genome sequence (WGS) data from this study. (B) One-dimensional Site Frequency Spectrum (SFS) for the seven whole genomes used for demographic analyses (ABC-DL). The seven genomes included here are: Mik15 and Log04 from this study, YamnayaKaragash_ EBA (3,018-2,887 BCE) (de Barros Damgaard et al., 2018), KK1 (CHG; 7,745-7,579 BCE) (Jones et al., 2015), Bar8 (Neolithic Barçın; 6,122-6,030 BCE) (Hofmanová et al., 2016), Sidelkino (EHG; 9,386-9,231 BCE) (de Barros Damgaard et al., 2018), and S_Greek-1 (SAME3302732; modern Greek from Thessaloniki) (Mallick et al., 2016).STAR Methods In blue ("WGS") the SFS for the regions included in Dataset IV (STAR Methods). In red ("1240K") the SFS for the regions in Dataset IV restricted to the sites overlapping with the SNPs included in the 1240K array.
We observed typical ancient DNA damage patterns at the 5′ and 3′ termini of the DNA fragments, as well as short sequence reads (average length between 49.9 and 74.3 bases across genomes, after adaptor removal and mapping), attesting to the authenticity of the ancient data (Figure S3; STAR Methods). Across individuals, contamination rate estimates ranged between 0.6% and 1.1%, and between 0.01% and 1.49% when estimated using the X chromosome and mtDNA, respectively (Table 2).
Figure S3 Error rates, damage, and read length distributions for the WGS and nuclear capture data from this study, related to Figure 1 and Tables 2 and S1
(A) Error rate for whole genome sequencing before (lighter colors) and after (darker colors) trimming 5 bp from the extremities of the reads. Log02 was USERTM-treated. (B) Error rate for nuclear capture data for different mutation types. Columns 1 and 2 show transitions and column 3 shows transversions. (C) Read length distribution for whole genome sequencing. (D) Read length distribution for nuclear capture data. (E) Post-mortem damage pattern for whole genome sequencing (C to T and G to A substitutions). Dashed lines indicate partial data removal resulting from trimming 5 bp from the extremities of the reads. The color of each curve indicates the analyzed sample according to panel A. Log02 (dark green curve) was USERTM-treated. (F) Post-mortem damage pattern for nuclear capture data. Curves are colored according to panel B. See STAR Methods for details.