Eurasian Genetics

The Onge versus other Indian & SE Asian ASI proxies

The Onge versus other Indian & SE Asian ASI proxies

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. Although short stature and dark pigmentation can be prevalent among some […]

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Diploid Genotyping Low to Medium Coverage Ancient DNA – Part 1

Diploid Genotyping Low to Medium Coverage Ancient DNA – Part 1

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 genomes is also compared their diploid counterparts which were processed […]

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Alternate methods of analysis using ADMIXTURE & PCAs

Alternate methods of analysis using ADMIXTURE & PCAs

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 outline some of the benefits of placing upper thresholds  on […]

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An Admixture Calculator for Eurasians

An Admixture Calculator for Eurasians

Genealogical testing companies use highly admixed references In other posts, I have mentioned the problems with ancestry proportion tests from genealogical testing companies such as 23andMe, AncestryDNA, and FTDNA, and how useless the test results can be for describing the population history and admixture for individuals from various parts of Eurasia. For example, what does it mean if you are say from Pakistan, and the […]

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A detailed look at East & North Eurasian Gene Flow to South & West Asians

A detailed look at East & North Eurasian Gene Flow to South & West Asians

Here I perform a detailed analysis of East and North Eurasian gene flow to South, South-Central, and West Asians by doing a one-to-one comparison of genomes sampled at about 404,000 Single Nucleotide Polymorphism (SNP) positions, using the program BEAGLE. To do this I utilize many genomes from northern and eastern Asia publicly available from the Estonian Biocentre. The results from my analysis are very surprising […]

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Characterising private and shared signatures of positive selection in 37 Asian populations

Characterising private and shared signatures of positive selection in 37 Asian populations

A new paper by Liu et al1 examines patterns of genetic diversity and positive natural selection, and finds that populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Here is their abstract: “The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a […]

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23andMe’s New Admixture Date Estimator

23andMe’s New Admixture Date Estimator

I received a couple of inquiries asking what my thoughts were on the recently introduced 23andMe “Admixture Date Estimator”, which is detailed in their White Paper no. 23-14. Their theory appears mathematically and statistically sound, and appears to be heavily based on the size and distribution of the segments in your genome, however, the model assumes that admixture is inherited in a single pulse, which […]

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Elevated Eurasian Steppe Ancestry in Kurds

Elevated Eurasian Steppe Ancestry in Kurds

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, 20122. The output of qpDstat is informative about the direction […]

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