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Thursday, July 19, 2012

Long IBD gives clues to migrations across Europe from the Iron Age to the present - take 2

That Ralph and Coop study on intra-European IBD sharing I blogged about recently (see here) is now out as a preprint. It's a really nice read for those interested in European population genetics, and shows things from a perspective rarely offered in other studies. Here are a few quotes that caught my eye:

Work from uniparentally inherited markers (mtDNA and Y chromosomes) has improved our understanding of human demographic history (e.g. Soares et al., 2010). However, interpretation of these markers is difficult since they only record a single lineage of each individual (the maternal and paternal lineages, respectively), rather than the entire distribution of ancestors. Genome-wide genotyping and sequencing datasets have the potential to provide a much richer picture of human history, as we can learn simultaneously about the diversity of ancestors that contributed to each individual’s genome.


In this paper, we analyze those rare long chunks of genome that are shared between pairs of individuals due to inheritance from recent common ancestors, to obtain a detailed view of the geographic structure of recent relatedness. To determine the time scale of these relationships, we develop methodology that uses the lengths of shared genomic segments to infer the distribution of the ages of these recent common ancestors. We find that even geographically distant Europeans share ubiquitous common ancestry even within the past 1,000 years, and show that common ancestry from the past 3,000 years is a result of both local migration and large-scale historical events.


In contrast, within samples from the UK and nearby regions we see negative correlation between numbers of blocks shared with Irish and numbers of blocks shared with Germans. From our data, we do not know if this substructure is also geographically arranged within the UK. However, an obvious explanation of this pattern is that individuals within the UK di er in the extent of their recent Irish ancestry, and that individuals with less Irish ancestry have a larger portion of their recent ancestry shared with Germans. This suggests that there is variation across the UK { perhaps a geographic gradient { in terms of the amount of Celtic versus Germanic ancestry.

Individuals usually share the highest number of IBD blocks with others from the same population, but with some exceptions. For example, individuals in the UK share more IBD blocks on average, and hence more close genetic ancestors, with individuals from Ireland than with other individuals from the UK, and Germans share similarly more with Polish than with other Germans. In figure 3 we depict the geography of rates of IBD sharing between populations, i.e. the average number of IBD blocks shared by a randomly chosen pair of individuals. Above, maps show the IBD rate relative to certain chosen populations (maps, above), and below, all pairwise sharing rates are plotted against the geographic distance separating the populations. It is evident that geographic proximity is a major determinant of IBD sharing (and hence recent relatedness), with the rate of pairwise IBD decreasing relatively smoothly as the geographic separation of the pair of populations increases.


The fact that most people alive today in Europe share nearly the same set of (European, and possibly world-wide) ancestors from only 1,000 years ago seems to contradict the signals of long term, albeit subtle, population genetic structure within Europe (e.g. Novembre et al., 2008; Lao et al., 2008). These two facts can be reconciled by the fact that even though the distribution of ancestors (as cartooned in Figure 1B) has spread to cover the continent, there remain differences in degree of relatedness of modern individuals to these ancestral individuals. For example, someone in Spain may be related to an ancestor in the Iberian peninsula through perhaps 1000 different routes back through the pedigree, but to an ancestor in the Baltic region by only 10 different routes, so that the probability that this Spanish individual inherited genetic material from the Iberian ancestor is 100 times higher. This allows the amount of genetic material shared by pairs of extant individuals to vary even if the set of ancestors is constant.


One of the striking patterns we see is the relatively high level of sharing of IBD between pairs of individuals across eastern Europe, as high or higher than that observed within other, much smaller populations. Furthermore, the numbers of short (older) IBD blocks shared between different populations is constant regardless of the geographic distance separating the two, as shown in figure 3. This is consistent with these individuals having a comparatively large proportion of ancestry drawn from a relatively small population that expanded over a large geographic area, ancestry which we date to 1,000-2,000 years ago (see figures 4, 5, and S8).


This evidence is consistent with the idea that these populations derive a substantial proportion of their ancestry from various groups that expanded during the "migration period" from the fourth through ninth centuries (Davies, 2010). This period begins with the Huns moving into eastern Europe towards the end of the fourth century, establishing an empire including modern-day Hungary and Romania; and continues in the fifth century as various Germanic groups moved into and ruled much of the western Roman empire. The Slavic populations expanded beginning in the sixth century, probably from somewhere in the area between the Baltic, Black, and Adriatic seas (Barford, 2001).

The only point I'll argue about with the authors is their suggestion that the high IBD sharing across Central and Eastern Europe might be of Hunnic origin. The Huns probably facilitated migrations across Europe, via their military and political activities, but I doubt they inundated Europe with their own IBD.

The eastern IBD most likely derives from near the Baltic, because its spread shows a very strong correlation with the "North European" autosomal component seen in my project and elsewhere. This component reaches very high frequencies in Balto-Slavs, including individuals from eastern Poland, Ukraine and Belarus, where most scholars put the Slavic homeland.

It also matches closely the geographic peaks of two Y-DNA haplogroups commonly found in Slavs today - R1a-Z283 and I2. So I think it's pretty clear that it's mainly a signal of the early Slavic dispersals.


Peter Ralph, Graham Coop, The geography of recent genetic ancestry across Europe, Populations and Evolution, arXiv:1207.3815v2 [q-bio.PE]