Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews

Abstract

In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016. Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132–1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.

Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project

“…The Geographic Population Structure (GPS) algorithm is a recently devised admixture based tool for biogeographical analyses. While GPS has been demonstrated to be superior to other existing methods for tracing the ancestry of human populations [ 2 – 7 ], it may not be accurate for tracing ancestry of recently admixed individuals and groups (up to 1000 years before present) [ 2 , 8 ]. It relies on extrapolating the genomic similarity between the query and reference populations to infer the likely biogeographical affinity of the former using the geographic locations (latitude and longitude) corresponding to the latter as a reference.…”

The time and place of European admixture in Ashkenazi Jewish history

“…The first is that AJ genetics defies simple demographic theories. Hypotheses such as a wholly Khazar, Turkish, or Middle-Eastern origin have been disqualified [4–7, 17, 55], but even a model of a single Middle-Eastern and European admixture event cannot account for all of our observations. The actual admixture history might have been highly complex, including multiple geographic sources and admixture events.…”

The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish

“…Rejecting the theory of evolution may lead one to conclude that birds and bats are close relatives. By disregarding the literature on relexification and Jewish history in the early Middle Ages, authors (e.g., Aptroot, 2016 ; Flegontov et al, 2016 ) reach conclusions that have weak historical support. The advantage of a geo-localization analysis is that it allows us to infer the geographical origin of the speakers of Yiddish, where they resided and with whom they intermingled, independently of historical controversies, which provides a data driven view on the question of geographical origins.…”