A field guide to population genetics

Computational population genetics, clearly explained

Posts on genetic data, ancient DNA, and the methods used to study ancestry and human history.

01 / DATA PREPARATION Start with the AADR dataset → Download and convert genetic data for analysis. 02 / F-STATISTICS Run f-statistics in Python → Calculate f-statistics and test models in Python. 03 / MODELS Running qpAdm models → Test ancestry hypotheses with ADMIXTOOLS2 in R.

Latest Posts

Interpreting f4-Statistics with AdmixPy

f4-statistics can be used to measure the covariance between allele-frequency differences across two pairs of populations. A value around zero implies that the two population pairs are symmetrically related, while a non-zero value implies excess allele sharing between one of the cross-pairs. Theory and formula An f4-statistic is the average, across SNPs, of the product of the allele-frequency differences between two pairs of populations: f4(A,B;C,D)=Ei[(pA,i−pB,i)(pC,i−pD,i)] f_4(A,B;C,D)=\mathbb{E}_i\left[(p_{A,i}-p_{B,i})(p_{C,i}-p_{D,i})\right] f4(A,B;C,D)=Ei[(pA,i−pB,i)(pC,i−pD,i)]Multiplying out results in: ...

A Potential Early Dynastic Kish G2a Individual (I25719) with Upper Mesopotamian Neolithic Ancestry

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. ...

A Potential Bronze Age Anatolian-Derived V1636 Sample (I41584)

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: A 45,000-Year-Old Genome at the East–West Eurasian Split

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. ...

Convert 23andMe, AncestryDNA, MyHeritage & FTDNA Raw DNA to PLINK (BED/BIM/FAM)

PLINK Awk

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. ...

Genetic Traits of Loschbour: Appearance, Height, Blood Type, and More

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. ...

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