... and (sadly) do not care to cite my lowly blog.
From the new paper's Methods:
To infer the putative ancestral populations, we applied ADMIXTURE46 in an unsupervised mode to the filtered data set. This analysis uses a maximum likelihood approach to determine the admixture proportions of the individuals in question assuming they emerged from K hypothetical populations. We speculated that our method will be the most accurate when populations have uniform admixture assignments. In choosing the value of K that seemed to best satisfy this condition, we experimented with different Ks ranging from 6 to 12. We identified a substructure at K=10 in which populations appeared homogeneous in their admixture composition. Higher values of K yielded noise that appeared as ancestry shared by very few individuals within the same populations. ADMIXTURE outputs the speculated allele frequencies of each SNP for each hypothetical population.
Using these data, we simulated 15 samples for each hypothetical population and plotted them in a PCA analysis with the Genographic populations. We observed that two hypothetical populations were markedly close to one another, suggesting they share the same ancestry and eliminated one of them to avoid redundancy. The remaining nine populations were considered the putative ancestral populations and were used in all further analyses.
Given nine admixture proportions for a sample of unknown geographic origin obtained using ADMIXTURE’s supervised approach with the nine putative ancestral populations, we calculated the Euclidean distance between its admixture proportions and the N reference populations (GEN). All reference populations were sorted in an ascending order according to their genetic distance from the sample.I'm sure my readers, and users of DIYDodecad know exactly why this is a carbon-copy of the tools I developed for the Dodecad Project. But, in any case...
The most exciting use of "zombies" is to convert unsupervised ADMIXTURE runs into supervised ones. In unsupervised mode, ADMIXTURE treats all individuals alike, and tries to infer their ancestral proportions. In supervised mode, some individuals are treated as "fixed" (belonging 100% in one of K ancestral components), and the ancestry of the rest is inferred.
The idea is fairly simple: run an unsupervised ADMIXTURE analysis once to generate allele frequencies for your K ancestral components; then generate zombie populations using these allele frequencies; whenever you want to estimate admixture proportions in new samples run supervised ADMIXTURE analysis using the zombie populations.... and the first post on the Oracle which shows how to find proximity to a population by calculating Euclidean distance in the space of admixture proportions between reference populations and a test individual (and also considers mixtures of populations).
I am flattered that the zombie approach has been copied and tested, but I doubt that all of the paper's 32 authors were unaware of the previous publication of the gist of their "new" method.
Nature Communications 5, Article number: 3513 doi:10.1038/ncomms4513
Geographic population structure analysis of worldwide human populations infers their biogeographical origins
Eran Elhaik et al.
The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700?km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50?km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing.