DISCUSSION Earlier this month the much awaited Bronze Age Indus Valley Civilization (IVC) paper on the Harappan genomes was released (1). Unfortunately, only one of the sampled skeletons yielded usable DNA fragments. The main conclusions of the paper, which relied primarily on this single sequenced genome, named I6113, and 11 previously sequenced BA individuals in …
DISCUSSION We are proud to announce the availability to the public of our latest genetic admixture inference program named SAPDA (Shared Ancestral Population Defining Alleles). Eurasians, whether Europeans or Asians, are genetically very similar to each other, with genetic similarities far outweighing any differences they have. Most Eurasians have descended from a few thousand individuals …
SAPDA – A new publicly available admixture inference program Read More »
New program for ancestry calculation
ABSTRACT The flood of recently sequenced ancient DNA has tremendously increased our understanding of demography of various Eurasian modern populations. Thanks to the recently sequenced genomes in Damgaard et al, Narasimhan et al, Olaide et al, Lazaridis et al, and Mathieson et al, and the suite of tools within Admixtools, detailed in Patterson et al …
Impact of the Iron Age Saka and Scythians on the demography of Kurds Read More »
DISCUSSION You have just obtained your results from a commercial ancestry result test such as 23andMe and it shows that you are 94% W Asian with 1% E Asian. Does this mean that you only have a tiny1% geneflow from some E Asian population? You think to yourself this does not seem right especially if …
How to interpret your ancestry admixture results Read More »
BACKGROUND Over the past decade various tools have been developed for ancient DNA analysis and assessing shared drift between populations. Some programs such as STRUCTURE, ADMIXTURE are allele frequency based. Others such as Reich Lab’s ADMIXTOOLS use both allele frequencies as well as direct allele comparisons. Others yet such as IBS and IBD compared genomes …
In progress: A method for improving accuracy in specific shared drift tests Read More »
OVERVIEW The overwhelming majority of published ancient DNA (aDNA) are pseudo-haploid genomes. This study focuses on the suitability and accuracy of these pseudo-haplodized aDNA genomes for various types of downstream analysis, such as those involving admixture allele frequency studies, as well as Identity-by-Decent (IBD) analyses and analyses using formal methods. The accuracy of pseudo-haploid aDNA …
Diploid Genotyping Low to Medium Coverage Ancient DNA – Part 1 Read More »
DISCUSSION The Onge are an endangered relic population with only about 100 surviving members, who inhabit the Andaman Islands in the Indian Ocean. They are classified as Negritos, and are related to Negritos from neighboring NE India, Burma, Cambodia, and Indonesia. The unifying physical characteristics of Negritos are short stature, curly hair, and dark pigmentation. …
The Onge versus other Indian & SE Asian ASI proxies Read More »
Here I investigate how much more genetic drift Kurds share with various ancient Eurasian Steppe samples, in comparison with some of their geographic neighbors. I do this formally using D-Statistics (Dstats) from ADMIXTOOLS1, a software bundle, readily available from the Reich Labs website at Harvard University. ADMIXTOOLS has been fully described in Patterson et al, …
The use of PCAs and ADMIXTURE program is widespread in the study of population histories, although the most common way those programs are used, using all available SNPs, including common variants, pruned for maximizing the genotype rate among samples in the dataset, may not be best for accurately inferring shared drift amongst populations. Here I …
Alternate methods of analysis using ADMIXTURE & PCAs Read More »