The geography of recent genetic ancestry across Europe

The geography of recent genetic ancestry across Europe

Peter Ralph, Graham Coop
(Submitted on 16 Jul 2012 (v1), last revised 19 Jul 2012 (this version, v2))

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

The variance of identity-by-descent sharing in the Wright-Fisher model

The variance of identity-by-descent sharing in the Wright-Fisher model

Shai Carmi, Pier Francesco Palamara, Vladimir Vacic, Todd Lencz, Ariel Darvasi, Itsik Pe’er
(Submitted on 21 Jun 2012)

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced a recent bottleneck. The detection of these IBD segments is now feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright-Fisher model. Using coalescent theory, we calculate the mean and variance of the total sharing between arbitrary pairs of individuals. We then study the cohort-averaged sharing: the average total sharing between one individual to the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution remains large even for large cohorts, implying the existence of “hyper-sharing” individuals. The presence of such individuals bears important consequences to the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD, and subsequently, in power to detect an association, when individuals are either randomly selected or are specifically the hyper-sharing individuals. Finally, we study the distribution of pairwise sharing and cohort-averaged sharing in the Ashkenazi Jewish population.