FST between archaic and present-day samples

Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples

Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: 1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; 2) The product of the LD coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and 3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.

Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe

OBJECTIVES

The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.

MATERIALS AND METHODS

We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.

RESULTS

Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.

DISCUSSION

Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.