Tag: structure

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model

… Read the rest “Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component”

Human ancestry: how to work your own PCA, ADMIXTURE analyses for human evolutionary and genealogical studies

yamna-corded-ware-bell-beaker

I wrote two days ago in the post anouncing the revised version (October 2017) of the Indo-European demic diffusion model, about dumping the information I had on doing PCA and ADMIXTURE analyses as ‘drafts’, without reviewing them, in the new section of this website called Human Ancestry.

I had some time today to review them, and to correct gross mistakes in the texts, so that they might be more usable now…

I began to work with free datasets to see if I could learn something more about results of recent Genetic research by working with the available … Read the rest “Human ancestry: how to work your own PCA, ADMIXTURE analyses for human evolutionary and genealogical studies”

Neolithic and Bronze Age Basque-speaking Iberians resisted invaders from the steppe

gaul-asterix

Good clickbait, right? I have received reports about this new paper in Google Now the whole weekend, and their descriptions are getting worse each day.

The original title of the article published in PLOS Genetics (already known by its preprint in BioRxiv) was The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods, by Martiniano et al. (2017).

Maybe the title was not attractive enough, so they sent the following summary, entitled “Bronze Age Iberia received fewer Steppe invaders than the rest of Europe” (also in Phys.org. … Read the rest “Neolithic and Bronze Age Basque-speaking Iberians resisted invaders from the steppe”