Computational population genetics, clearly explained

Among the unreleased samples in the Akbari et al. dataset is an individual (IID: I25719) rumoured to be from Kish, dated in the supplementary table to the Early Dynastic III period, around 2450 BCE. His Y-DNA haplogroup is G-FT19860, a downstream branch of G2a, one of the main paternal lineages associated with Anatolian Neolithic farmers, and his mtDNA haplogroup is R0a1a. The sample has decent coverage: 598,059 “compatibility” SNPs were called, 645,472 were missing. ...

Among the Akbari et al. dataset, there is a previously unreported individual (Sample IID: I41584/I41584_preQC) potentially from Anatolia. His terminal Y-DNA subclade is Y148982/Y106006 (TMRCA ~3100 BCE according to FTDNA), a lineage that also includes most modern West Asian and Near Eastern V1636 samples. His maternal haplogroup is HV29d1, also according to FTDNA. ...

Ust-Ishim is a sample identified from only a femur bone pulled out of eroding sand on the banks of the Irtysh River in western Siberia in 2008. Later analysis established that the bone belonged to a man estimated to have lived around 45,000 years ago. His genome is one of the earliest Upper Paleolithic WGS genomes. Neither Clearly East- nor West Eurasian What makes this sample particularly interesting is that he does not fall clearly into either the East or West Eurasian category. The initial Fu et al. study placed him before, or approximately at, the separation of subsequent eastern and western Eurasian populations, which include all modern Eurasian populations. Later graph modelling reached essentially the same conclusion; the best fit placed Ust-Ishim slightly towards the West Eurasian branch, but the uncertainty overlapped the East-West split. ...

To convert raw DNA data from 23andMe, AncestryDNA, MyHeritage, or FamilyTreeDNA (FTDNA) to PLINK binary format (.bed, .bim, .fam), you will have to first convert the raw file to 23andMe format. You can then convert it with PLINK 1.9 using --23file. Converting Raw DNA to 23andMe Format with AWK Windows users can use WSL to access awk; see How to Download the AADR Dataset (Linux & WSL). If your DNA file is already in 23andMe format, skip this section. ...

I was inferring genetic traits of ancient individuals, among them the “Cheddar Man”, whose pigmentation phenotype I thought was well established from his genotype. However, most of the 58 trait markers I was checking for could not be called reliably (with MAPQ ≥30 and base quality ≥30). Most markers had no reads at all, several others were supported by only a single read. This included markers like HERC2/OCA2 rs12913832 for eye colour, likewise SLC24A5 and SLC45A2 used to infer skin pigmentation. ...