A worthwhile improvement would be to apply a clustering algorithm like I did back in January over the fastIBD output; that way, one does not have to arbitrarily partition Europe into regions, but have the partitions jump out of the data.
A different idea to confirm the scenario presented in this paper would be to drill into different European populations. For example, in the case of the Italians, it would be worthwhile to identify whether there are particular sub-populations with likely Greek or Albanian ancestry who share an excess of IBD with modern Greeks and Albanians.
Population averages may mask such interesting patterns lurking in the data. For example, sub-clusters within populations can be identified with both fineSTRUCTURE and fastIBD, and the corresponding clusters can be assessed with supervised ADMIXTURE to detect how they differ from each other. For example, using this technique, I was able to infer 3 sub-clusters within the ethnic Greek population:
- pop8 (mainland Greek) with ~23% North_European
- pop11 (Greek Cypriot) with ~5% North_European
- pop14 (Cretan, islander, mainland+Asia Minor) with ~12% North_European
- I have also a strong hunch based on a few half Pontic Greek+half mainland Greek data points that unmixed Pontic Greeks would be related to pop22 (Northeastern Anatolia) with ~5% North_European
Interestingly, ~5% North_European levels would be similar to those of Armenians who are the closest linguistic cousins of the Greeks within the Indo-European family, as well as the the Anatolian Turkish cluster pop13 at ~9%.
Overall, it would appear that some mainland Greek groups received some input as the result of the medieval Slavic intrusions, since the mainland North_European excess appears as a "wedge" within the South Italy/Sicily/Crete/Anatolia/Armenia arc and the fastIBD pattern of sharing suggests that this is due to fairly recent connections.
As I have pointed out before, one limitation of the method of counting shared blocks of ancestry is that it does not disclose the directionality of gene flow. For example, gene flow between Germans and Slavs is detected in this study, which could be ascribed to Germans living in eastern Europe and/or to Slavs becoming acculturated Germans as a result of living within Germanic states or intermarrying with them prior to the age of the nation state.
Finally -and most interestingly- I hope that similar haplotype-based methods can be applied to a wider dataset, because, as it is becoming clear, Europe has not been isolated from Asia or Africa during its long history. The authors mention "Slavic or Hunnic" as an explanation for the pattern of shared ancestry in eastern Europe, but it is only by including Asian groups that we can detect the existence of real Hunnic (or Avar, or Mongol, or Pecheneg, or, ...) ancestry.
Moreover, I am confident that the Bronze Age is well within the power of haplotype-based methods to detect IBD. For example, South Asian populations clearly show differential patterns of affiliation with modern West Eurasian groups, most of which can date to no later than the Bronze Age. Together with the gradual incorporation of the new ancient DNA genomes that are bound to be coming our way soon, it seems that our picture of not only recent history, but also of late prehistory is bound to become much sharper.
The geography of recent genetic ancestry across Europe
Peter Ralph, Graham Coop
(Submitted on 16 Jul 2012)
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.