Clik here to view.
Analyzing the North African cluster
Continuing with the Intra-African genome-wide analysis, I wanted to further explore the 'North African' Cluster that appeared to be wide spread from East to North and West Africa, 408 individuals out...
View ArticleClik here to view.
Afrasans in a Genome-Wide context.
A subset of the Intra-African dataset I have includes Afrasans, or Afroasiatic speakers. Afroasiatic is typically divided into 6 major categories or groups; Semitic, Berber, Egyptian, Chadic, Cushitic...
View ArticleClik here to view.
TreeMix analysis on the African Dataset
Thanks to a commenter going by the moniker 'Eze', who notified me the other day of a new program called Treemix, in which it infers “patterns of population splitting and mixing from genome-wide allele...
View ArticleClik here to view.
Introducing Yemenis into the Afrasan dataset.
This is about an observation made when I introduced the Yemenis (from Behar (2010)) into an ADMIXTURE analysis of the Afrasan Dataset (x Mozabites). At K=5 the dataset behaves as expected, i.e similar...
View ArticleClik here to view.
A Supervised Global ADMIXTURE Run
A supervised ADMIXTURE run, assumes that certain populations within a given dataset are 100% of a certain ancestry, so for instance, given one wants to run ADMIXTURE at K=10 in supervised mode, then 10...
View ArticleClik here to view.
Reconstructing ancient mitochondrial DNA links between Africa and Europe
AbstractMitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs...
View ArticleClik here to view.
Cross Validating and K Selection
There are two ways of choosing a K value for any given dataset that one wishes to perform an ADMIXTURE run on, one is to throw a dart at a random set of numbers and hope it works out for the very best,...
View ArticleClik here to view.
A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root
Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical...
View ArticleClik here to view.
PGDSpider: an automated data conversion tool.
"The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between...
View ArticleClik here to view.
Converting 23andME raw data into PLINK format
A commenter requested that I post the script I use to convert 23andME raw data to the required PLINK format that can be then used for ADMIXTURE computations, there are several ways to do this using...
View ArticleClik here to view.
A Novel Solution For Dating The Origin Of Language.
A paper published by C. Perreault and S. Mathew in PLOS ONE outlines a new method of dating the origin of language in Africa, and therefore the origin of language of all humans.The method starts by...
View ArticleClik here to view.
Age of the Association between Helicobacter pylori and Man
When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts....
View ArticleClik here to view.
Video Commemorates Emperor Menelik II and the Battle of Adwa
The latest buzz is from a newly made and well produced video by singer/song writer Teddy Afro commemorating the Battle of Adwa and Emperor Menelik II, which just recently hit the Ethiopian air waves,...
View ArticleClik here to view.
Finding the TMRCA of Ethiopian YDNA lineages using an ASD method.
I have been lately working on computing TMRCAs using an ASD or average square difference method on publicly available Y-STR haplotypes. The premise for finding the TMRCA using the ASD method is quite...
View ArticleClik here to view.
Intra African Genome-Wide Analysis, V2
See Also : Intra African Genome-Wide Analysis, V1Finally got some more badly needed genome-wide data from East Africa. 12 sets of populations were added, 9 Afroasiatic (3 Omotic, 4 Cushitc, 2 Semitic)...
View ArticleClik here to view.
The World At K=2
The most basic Autosomal genetic division of the world is between Africans and Out of Africans (OOA), this is not only seen on global PCA or MDS maps , where the first PC separates Africans from non...
View ArticleClik here to view.
Evaluating the 'clinality' of a global Dataset.
Population discontinuities in a data-set produce strange results in Model based algorithms like ADMIXTURE, for example in a global data-set, sampling only discontinuous populations for the most part...
View ArticleClik here to view.
Anuak YDNA
Low resolution Anuak YDNA from Naser Ansari Pour et. al, I expect the BT*(xDE,KT) to be likely haplogroup B-M150 for the most part.E1b1a7, is old nomenclature from 2010, with the defining SNP for the...
View ArticleClik here to view.
Phylogeographic analysis of human Y chromosome diversity in eastern Africa
Cruciani F1,*, Ippoliti M1, Massaia A1, D'Atanasio E1, Moral P2, Coppa A3, Trombetta B1, Sellitto D4, Pascone R5, Scozzari R11Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma,...
View ArticleClik here to view.
Berber YDNA
Decent resolution composite Berber YDNA from The Berber and the Berbers, Genetic and linguistic diversities, Jean-Michel Dugoujon et. al (2009)Phylogeny of the 29 biallelic MSY markers (in bold)...
View Article