Report on the symposium on Modern Human Genetic Variation

This image shows the chronology of the Neolithic wave of advance in Europe. The arrow corresponds to the Y-direction in the model. Credit: http://iopscience.iop.org/1367-2630/12/12/123002/pdf/1367-2630_12_12_123002.pdf



The following text is taken from the http://dienekes.blogspot.com/


Joshua Akey summarizes the talks of a recent symposium at the Swedish Royal Academy of Sciences. Two bits of information stand out from his report. The first:

In another talk focused on demography, Mattias Jakobsson (Uppsala University, Sweden) presented novel data on the impact of the agricultural revolution on the genetics of contemporary European populations. Specifically, Jakobsson and colleagues obtained nearly 250 Mb of sequence from three 5,000-year-old remains of Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia. Analysis of these sequences in the context of the present day European gene pool suggests that the spread of agriculture involved the northward migrations of farmers. Thus, these data provide the most direct and compelling support for the demic diffusion model of agriculture (as opposed to cultural diffusion) described to date.

It seems I have my answer to the what's next question. Jakobsson has been doing some interesting work on the demography of human emergence and dispersal, so it will be interesting to see not only the novel sequences from these Neolithic Scandinavians, but also how they fit into existing models of demic diffusion.

The second bit of information:

Similarly, Jeff Wall (University of California San Francisco, USA) described a novel method for inferring archaic admixture, which he applied to publicly available whole-genome sequence data generated by Complete Genomics. Provocatively, he finds higher rates of introgression in Asians compared to Europeans. An advantage of Wall’s method is that it does not require an archaic genome to infer introgression, and thus he was able to also test the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors. Strikingly, Wall indeed did find evidence of archaic admixture in African genomes, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.

I guess that I shouldn't throw explanation #1 out the window yet. Wall was involved in the recent paper on archaic African admixture, which only looked at a small subset of the genome, so it is nice to see that he is now working with full genomes, and that the race to data mine complete genomes for archaic admixture is afoot.

The book of abstracts is online at the symposium site. The Jakobsson paper does seem to agree with our emerging picture of a non-local origin of northern European farmers as well as greater survival of pre-farming populations in the northern periphery of Europe, but it will be interesting to see where exactly extant populations fall on the farmer-hunter/gatherer continuum.


Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Northern Europe
Mattias Jakobsson

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden

The prehistoric spread of farming in Europe has garnered intense interest for almost a century, and was one of the first questions to which population genetic data was used to investigate demographic hypotheses. However, the impact of the agricultural revolution on the European gene pool remains largely unknown. We obtained 249 million base pairs of quality-filtered human autosomal sequence data from some 5,000 year-old remains of three Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia, the northernmost fringe of agricultural practice at the time. Applying novel methods to study population structure based on low genome-coverage data, we find that Northern European Neolithic farmers are most similar to modern-day southern Europeans, contrasting sharply to Neolithic hunter-gatherers who are most similar to extant individuals from northern Europe. With most extant European populations appearing genetically intermediate between the two Neolithic groups, our results suggest that migration from the south by a genetically distinct group of humans accompanied the spread of agriculture to geographic regions where hunting and gathering was the mode of subsistence, but that admixture eventually shaped modern-day patterns of genomic variation.

Archaic admixture in the human genome
Jeff D Wall

Department of Epidemiology & Biostatistics, University of California, San Francisco, USA

We describe a method that uses patterns of linkage disequilibrium in extant human populations to identify regions of the genome that were inherited from ‘archaic’ human ancestors, such as Neandertals, Homo erectus or H. floresiensis. We validate this approach using two recently published archaic human genomes, and show that several ancient admixture events must have occurred, both within and outside of Africa. We also explore differences in the amount of archaic admixture across different contemporary human populations.


Finally, here is the meeting report:

Investigative Genetics 2012, 3:7 doi:10.1186/2041-2223-3-7

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation

Joshua M Akey

LINK (PDF)

Intro - Some general concepts

The position of the mesolithic and neolithic has evolved over time. A neolithic culture being one with refined stone tools, sedentary and agricultural practices, etc. The classic neolithic culture of europe is the LBK, which has the complete 'package' and there should be know arguement about whether this was a culture or not.

The problem is that during the late mesolithic across a much larger area of europe the transitional process was not so abrupt, and as the archaeological reports indicate you have situations where archaeologist argue

1. Abrupt neolithization, or sudden neolithic occupation.

2. A transition or replacement of a site where a definite
point is reached where neolithization is evident and largely
incontroverable.

3. A mesolithic/neolithic transition that the crossover point is not
definable with confidence


As it turns out improvements in archaeological sampling are seeing more of the 2nd and 3rd catagories. This should not be surprising since the Mesolithic was brought into archaeology as a sought after transtion between paleolithic and neolithic peoples and then the late paleolithic has been carved into epipaleolithic and
earlier periods. As soon as you see the mesolithic catagory widely accepted archaeologist start focusing more on this transitional period. Now we see a focus toward the middle and late transitions in the mesolithic to the neolithic. As a result you have authors tiptoeing around defining neolithic sites as they do not
have all the classical elements that are seen in other sites.


Problem with the boundary definition is proximity. Apriori proximity should not have to play, but human culture is not static, and a neolithic culture has its preferences, so that it might move into a place K and develope it, or it might move into an occupation region L and admix or displace, or move into a region M adjacent to L and over time spread and diffuse into L. One has to look at the various strategies over time. Some examples for example in Portugal and Iberia neolithization looks to me to be opportunistic. There is a neolithization process going on that is taking time some places are evolving faster than others, at the same time
there is the sudden appearance or transition at some sites to a neolithic people, and the reasoning by archaeologist is often to explain the opportunity as it presented itself. For example in the north of Spain, it is rationalized that the neolithizing peoples did not see much opportunity on the steep slopes of the mountains that are just off the coast, so that the focus stopped short of northern spain moved inland.
Whereas a slow process of overland trade brought neolithization to northern Spain with a protracted boundary. This example was chosen to get into an area of discussion where the genetic impact and classical neolithization argument is avoided and whose impact on the larger europe is not deemed, by me, to be important. When we talk about Southeast Europe, in this case east Adriatic coast, neolithic package appears suddenn with the element that were unknown to mesolithic populations of the area. Other problem is the lack of quality data and archaeological sites of the entire mesolithic period.

The other issue of proximity is technology and obstructions (or surmounting obstructions). The definition of cultural capability for transportation is hard to define, evidence is spurious, and implicit evidence is almost as common in primative peoples or more so than in neolithic peoples. Barriers can appear and disappear, opening of barriers is not neccesarily and exact science, interpretation of plausibility is a combination of assumptions of technology and assumptions of geological and oceanography. Who has proximity to do what is of concern and what seems likely genetically may seem impossible by other concerns or vice versa.


The critical issue of previous threads needs to be addressed in an open frame work of question answering. Namely who or what cultures neolithicized other cultures and by what processes?

The other issue is whether all mesolithic cultures were neccesarily transitional, or whether the transition resulted from unidirectional, by and large, cultural flow. Those that have read the literature pretty much know the answer, those that haven't should read the literature. There is too much information for me to post on
the matter and so the next thread will deal with information that supports my current points of view, there is alot more information that support other areas of concern and there is simply no means for me to deal with these, my concern as plainly stated has been the food, food storage, and genetics. Therefore the discussion will only be productive if questions are answered via a pre-reading of the literature.