May 20, 2013

More population structure in the Netherlands (Lao et al. 2013)

There was a recent article on the topic by Abdellaoui et al., and here is another one.

Investigative Genetics 2013, 4:9 doi:10.1186/2041-2223-4-9

Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history

Oscar Lao et al.

Abstract (provisional)

Background

The presence of a southeast to northwest gradient across Europe in human genetic diversity is a well-established observation and has recently been confirmed by genome-wide single nucleotide polymorphism (SNP) data. This pattern is traditionally explained by major prehistoric human migration events in Palaeolithic and Neolithic times. Here, we investigate whether (similar) spatial patterns in human genomic diversity also occur on a micro-geographic scale within Europe, such as in the Netherlands, and if so, whether these patterns could also be explained by more recent demographic events, such as those that occurred in Dutch population history.

Methods

We newly collected data on a total of 999 Dutch individuals sampled at 54 sites across the country at 443,816 autosomal SNPs using the Genome-Wide Human SNP Array 5.0 (Affymetrix). We studied the individual genetic relationships by means of classical multidimensional scaling (MDS) using different genetic distance matrices, spatial ancestry analysis (SPA), and ADMIXTURE software. We further performed dedicated analyses to search for spatial patterns in the genomic variation and conducted simulations (SPLATCHE2) to provide a historical interpretation of the observed spatial patterns.

Results

We detected a subtle but clearly noticeable genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern and a southern group. Furthermore, we observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands, similar to earlier findings from across Europe. Simulation analyses indicate that this genomic gradient could similarly be caused by ancient as well as by the more recent events in Dutch history.

Conclusions

Considering the strong archaeological evidence for genetic discontinuity in the Netherlands, we interpret the observed clinal pattern of genomic diversity as being caused by recent rather than ancient events in Dutch population history. We therefore suggest that future human population genetic studies pay more attention to recent demographic history in interpreting genetic clines. Furthermore, our study demonstrates that genetic population substructure is detectable on a small geographic scale in Europe despite recent demographic events, a finding we consider potentially relevant for future epidemiological and forensic studies.

Link

13 comments:

Jim said...

Unsurprisingly this tracks with the language geography.
http://en.wikipedia.org/wiki/File:Germanic_Languages.PNG

That geogrpahy does not have to reflect settlement patterns, only patterns of intercommunication (and intermarriage).

terryt said...

"we interpret the observed clinal pattern of genomic diversity as being caused by recent rather than ancient events in Dutch population history".

More likely to be the result of the accumulation of a whole series of genetic waves rather than just a single one. Again we see an example of the Garden of Eden syndrome: the desire to see everything in simplified form.

Rokus said...

Well, this is funny. Genetic evidence is not in line with archeological interpretations and now the geneticists found that it isn't in line with recorded recent population events either. However, according to their evaluation once upon a time some ill-defined "recent events" should confirm that the archeological interpretation must be right anyway. Future investigation should thus prove the current results on recent population history wrongin order to turn the absence of evidence for continuous population into true evidence of absence. Am I dreaming? Something must be wrong here!

Actually, geological investigation already produced maps (Peter Vos) that show most of the Netherlands was never submerged since the last glacial maximum. The known marshes in the west were only submerged incidentally, while some geological structures ("donk") remained as islands that never submerged at all. One such "donk" was Molenaarsgraaf, a known (~Veluwe) Bell Beaker site, in the middle of an ancient region full of other donks in the Rhine delta. Those whose ancestors derive from donks in the near (Noordeloos, Uitwijk) or wider (Vlaardingen) neighborhood often attest R1b-Z14, the oldest branch of R1b-U106. I find it hard to believe that recent immigrants brought a selective and diverse subset of this rare haplogroup into this region.

The Rhine delta was a place where continuous subduction and rapid sedimentation don't facilitate the search for continuous habiation at all. People could have moved a just few hundred yards while their previous settlement became drenched and covered with a few meters of virgin layers of sediments. Strictly spoken this indeed isn't exactly "continuous habitation", though per definition the geological nature of the region already invalidates any claim or pleas for strong archeological evidence of absence.

eurologist said...

As in the other paper, the researchers make the great omission of not including neighboring areas. I realize they state they want test on the microscale - but you cannot draw any conclusion with respect to the time frame without including German and Belgium samples.

The boarders are quite recent artifacts, with both known historical migrations/ expansions and re-filling of areas destroyed by plagues and wars. However, on a just slightly wider scale, most areas were re-populated by genetically very similar neighboring people.

So, you might find an element in the Netherlands that is well-established and ancient in Frisia farther east, or in the Emsland, the Grafschaft, or adjacent regions of North Rhine-Westphalia. Alternatively, post-Roman Frank and related movements south (and their timing) might be confirmed in Belgium.

Finally, as much as I distrust molecular clocks, nowadays you can do some timing from segment size statistics or uniparental DNA that might help a lot.

Dr Rob said...

Well said, Terry ; & Rokus; & Euro

Retiarius said...

What do they mean by "strong archaeological evidence for genetic discontinuity"? Discontinuities in the kinds of pots or discontinuities in the physical types?

And why not compare the modern Dutch DNA to that of ancient skeletons found in the country? Then speculations about how recent or how old the genetic distributions seen are can be more meaningful.

mr. Knows When said...

@Rokus, that's fuzz about nothing

Maybe they simply realize that you have to go back in time step by step to see ant pattern.

Grognard said...

Retiarius, people don't like to have their "legitimacy" questioned, that's the only reason I can think of for relatively few DNA tests on ancient skeletons to date.

But the picture seems to say most of europe is pretty discontinuous from the few we have info on.

Retiarius said...

Grognard, thanks for the reply.

Indeed/yet, I think they could just as easily have phrased their conclusion as follows (i.e. completely the other way around):

"Considering the strong archaeological evidence for genetic discontinuitIES in the Netherlands , we interpret the observed clinal pattern of genomic diversity as being caused by RELICTUAL AND INHERITED patterns of ANCIENT population distributions."

Discontinuities do not imply full population replacements. Especially discontinuities in something as non-genetic as pot-making traditions -- hence my original question.

What I suggest is no more an arbitrary "flip of the coin" than the researchers picking the obverse side -- i.e. "recent" (and unelaborated further, despite greater historical record) events instead of "ancient" ones. Indeed, I claim that the ancient DOCUMENTED discontinuities offer a better explanation than the researchers' adduced, yet further apparently left as UNELABORATED "recent events/discontinuities"...

I think they just went for their interpretation with what sounds more palatable to the "we're all the same" crowd: the idea that our differences are recent and shallow. Their conclusion also carries water for the nerve-calming, soporific ideas of gradualism which permeate Academia at present.

terryt said...

"I think they just went for their interpretation with what sounds more palatable to the 'we're all the same' crowd: the idea that our differences are recent and shallow".

That's a perspective I hadn't thought of before, but it does explain a lot about usual interpretations of evidence.

Retiarius said...

A question for @Dienekes.

I am just getting into DNA matters and it seems to me that genetic analyses of ancient human specimens are still somewhat of a scientific rarity (mid-2013). My question is: does there exist some nice database or web portal that assembles all that ancient DNA information? Or is one reduced to building one's own "catalogue" of data of interest up by fishing odd bits and bites out of disparate scientific papers?

Thanks in advance.

Simon_W said...

Good, but restricted to Eurasia:

http://www.buildinghistory.org/distantpast/ancientdna.shtml

There's also a compendium on ancient Y chromosome studies here:

http://dienekes.blogspot.ch/2008/05/ancient-y-chromosome-studies.html

Studies on autosomal aDNA are still rare.

Retiarius said...

Many thanks, Simon_W !