Iron Age and Anglo-Saxon genomes from East England reveal British migration history

Abstract

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo--Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole--genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo--Saxon period). We use present--day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today's British are more similar to the Iron Age individuals than to most of the Anglo--Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo--Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo--Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Na-Dene populations descend from the Paleo-Eskimo migration into America

“…Europeans or Africans were used as alternative outgroups in this study. Since we expected a decay of a recent ancestry signal at higher allele frequencies 12 , all statistics were calculated separately for alleles of various frequencies: occurring 2, 3, 4, … and up to 20 times among 2,412 haploid chromosome sets, which corresponds to frequencies from 0.08% to 0.83%.…”

“…Text 1. Rarecoal is a software that implements a fast algorithm to estimate the joint site frequency spectrum for rare alleles in hundreds of samples 12 . Since the initial report, we have improved the software and added pulse-like admixture events as a new feature (see Methods).…”

“…Rare variants, i.e. those occurring at a global frequency of less than 1%, have been shown to have more power to resolve subtle relationships than common variants 12, 18 . We calculated allele sharing counts (ASC) and their standard deviations for each American population (a modern group or an ancient genome) and the Siberian or Arctic meta-populations (Fig.…”

“…1) and a recently developed coalescent method, Rarecoal 12 , which relies on rare alleles and for which we developed a new extension to include admixture. In parallel, we generated new genotyping data from Siberian populations, and inferred and dated admixture events using GLOBETROTTER, a tool relying on autosomal haplotype data 13 .…”

Genetic Time Travel

“…A recent study on Pleistocene human remains across Europe provided genetic evidence for a previously unknown population turnover in Europe at the end of the last Ice Age, 14,000 years ago, highlighting how genetic studies can reveal unsuspected events in human history (Posth et al 2016). Ancient and present-day genomic data will also provide new perspectives on historically documented events such as the Anglo-Saxon invasion of Great Britain by allowing estimates of the number of migrants and the reconstruction of admixture patterns (Schiffels et al 2016).…”