March 24, 2012

Report on the symposium on Modern Human Genetic Variation

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)

13 comments:

celeres said...

Thank you for the link. Very useful.

mooreisbetter said...

I've postulated before that the triune Indo-European caste system (of farmers, warriors, and priests) (which survived in various forms into many civilizations at the dawn of writing) and perhaps even our cultural acceptance of the Holy Trinity concept were both cultural relics from our collective memories from what were initially ethnic separations in European culture.

It appears clear that different tribes in Europe experienced cycles of: farmers "taking over" or more accurately "crowding out" hunter-gatherers. When that occurs, as studies in Africa have shown, the farmers become the elites. But as we well know, admixture then occurs (or side by side living) and it only makes logical sense that the non-farmer culture, with their greater height, traditions of free time before farming, etc become a part of society, perhaps specialized, that values the professional warrior ethos.

In due course, these partly civilized cultures then attack the primarily farning cultures, and reverse things, establishing themselves as dominant. Rinse, repeat.

If you freeze history at the intersection of prehistory and historical writing, you have Italics with strong traditions of yeoman farmers dropping the plough and having to pick up the sword (cf Cincinnatus story). You have Germanics with a tradition of lazing around, much free time, no farming, and essentially being professional warriors.

I believe in those cultures, the bulk of the population was represented with those values, but of course, castelike stratification existed in IE civilizations from Ireland to the Indus, with all strains represented and probably blended genetically eventually.

Initially though (in Central and Eastern Europe), you probably had castes of R1a and I1 hunters and warriors, and E3b, J2, and G farmers and pastoralists, and I2 druids and priests.

Annie Mouse said...

"With most extant European populations appearing genetically intermediate between the two Neolithic groups"

This consistent with expansion from the South, not the East. And with continuity, as the presumably Scandinavian extant populations remain "intermediate". It says nothing about whether or not the Southern European populations were already present in Europe when the neolithic arrived. And in Iberia it is looking like the Neolithic arrived from North Africa, not along the northern Mediterranean.

"Maghrebi origin of early south Iberian Neolithic" by Sanchez.

Sanchez also says "The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast". This leads me to wonder if some knowledge of agriculture was already widespread, but that it only took off when the climatic conditions were right. Starting in the south and moving north with the climate change.

Australian aboriginal people remained hunter gatherers because the climate was not suitable for primitive farming. They had cultural contact with farming communities. The Papuans developed an odd sort of farming of their rain forests that was almost unrecognizable.

terryt said...

"modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans".

And, presumably, before that. Exactly as I've been suggesting for years. Great to see the idea being gradually widely accepted.

"Provocatively, he finds higher rates of introgression in Asians compared to Europeans".

Another suggestion I made years ago, to much derision I might add.

eurologist said...

You have Germanics with a tradition of lazing around, much free time, no farming, and essentially being professional warriors.

moreisbetter,

That makes no sense at all. I'd suggest you do some reading of European history and pre-history that includes recent European work. Firstly, Central and Western Europe had agriculture not significantly later than Italy (i.e., over 7,000 ya). Secondly, during the bronze and early iron age, southern and central Germany (Hallstatt: culturally but not necessarily linguistically Celtic) was relatively rich, culturally roughly an equal to Italy, and strongly militarized.

Conversely, there are no weapons found in the graves of the much poorer early iron age northern to central German Jastorf culture (culturally and linguistically Germanic).

I think the earliest farmers were in part overrun much earlier, roughly at the collapse of LBK, from groups at the fringe. It will definitely be interesting to see where extant Europeans fall - but my expectation is that northern Europeans group more closely with the pre-neolithic population, and Central Europeans somewhere in between, with a cline going to Southern Europe (with northern Italy perhaps 60-80% neolithic).

eurologist said...

It says nothing about whether or not the Southern European populations were already present in Europe when the neolithic arrived.

Exactly, the agriculturalist at first could have been largely Balkan - we don't know at this point. From the varied mtDNA, it appears they picked up further local genes along their way. And in the south, it is reasonable to assume that pre-neolithic Balkans were very similar to the inhabitants of Italy.

So, it's at least three (or four, including a perhaps different Iberian/Atlantic population) components that need to be disentangled - it's not just some simple-minded concept of homogeneous pre-neolithic Europeans versus west Asian agriculturalists.

apostateimpressions said...

> 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. <

I think that is what we all expected really. Note though, to say that Neo HGs are closer to modern NEs doesnt imply that modern NEs are closer to Neo HGs. From that bare fact, modern NEs could lie anywhere on a continuum between Neo HGs and SEs.

Further, when it is said that Neo farmers are closer to modern SEs, does that mean that they are closer to them than to any other group including West Asians or just that they are closer to them than to NEs? Anyway, if they are closest to modern SEs, that still doesnt tell us where they came from in the first place.

> You have Germanics with a tradition of lazing around, much free time, no farming, and essentially being professional warriors. [...] you probably had castes of R1a and I1 hunters and warriors <

I was looking at paintings of Odin the other night and I was struck by how Odin looks like both a hunter and an IE warrior on his horse and with his wolves and his spear/ sword. And indeed he has both roles in mythology, as the (I think) War Chief and as the Lord of the Hunt. It would make sense if hunters who were used to hunting and killing animals adopted a mobile warrior lifestyle. Farmers would be adapted to a more peaceful and settled way of life.

eurologist said...

I was looking at paintings of Odin the other night and I was struck by how Odin looks like both a hunter and an IE warrior on his horse and with his wolves and his spear/ sword. And indeed he has both roles in mythology, as the (I think) War Chief and as the Lord of the Hunt. It would make sense if hunters who were used to hunting and killing animals adopted a mobile warrior lifestyle. Farmers would be adapted to a more peaceful and settled way of life.

This is all fantasy. In reality, and well-documented by more than a hundred year of extremely detailed research, the people occupying much of what is now northern and central Germany as well as the Netherlands and much of Poland were poor, poorly-armed farmers surrounded by bronze-aged and iron-aged bullies who controlled trade and resources, and set up armed trading posts. This core Germanic region did not become militarized until very lathe La Tene/ Roman times, when it had to so as to not be subject of slave trade and raiding of agricultural resources for others' armies.

Archaeology clearly demonstrates that unlike the neighboring (cultural) Celts and Romans in the South, this was an egalitarian society, without casts, and without a warrior class.

apostateimpressions said...

> This is all fantasy. <

It is thought that Odin represents an earlier Proto-Germanic hunter-gatherer cult that was adopted by later sedentary cults. Odin is a warrior god who takes over from Tyr as the chief war god at some point during the Migration Age. He clearly is both a wanderer and a hunter, the Lord of the Hunt in fact as well as a warrior. The Germanic tribes originated about 1800 BCE out of the Indo-European Corded-Ware (Battle Axe) Culture on the north German plain and moved into southern Scandinavia as the people of the Nordic Bronze Age (1700 BCE-600 BCE). It is thought that remnants of Bronze Age religion survive in Germanic and Norse mythology. Bronze Age carvings depict a warrior figure with either an axe or a hammer and this is thought to be Thor. Another figure is depicted with a spear and this could be either Odin or Tyr as both are associated with this weapon. Other carvings show canoes used for war. Many artefacts of bronze and gold have been found from the period, including bronze axes and swords. Some of the Germanics moved southward into Holland and northern Germany because of climate changes between 850-650 BCE. From the Germanic Iron Age in Scandinavia, northern Germany and Holland (fifth to first century BCE) we have iron swords, shield bosses, spearheads and knives found among other iron and bronze artefacts. The Germanic tribes expanded south, east and west in the second and first centuries BCE, with Roman writers recording that Germanic tribes invaded Gaul, Italy and Spain by the late second century. The German chieftain Armin led his forces to defeat three Roman legions in 9 AD and the Germans continued to expand to occupy most of the territory of modern Germany by 100 AD. The Germans broke into Roman lands around 260 AD and continued to move south-west with the decline of Rome from 395. German tribes conquered France, Belgium, Luxemburg, England, Austria, Spain, Northern Italy and made their way into Northern Africa, the Balkans and Anatolia. The Germans went on to rule central Europe for a thousand years as the Holy Roman Empire of the German Nation.

Fanty said...

"Archaeology clearly demonstrates that unlike the neighboring (cultural) Celts and Romans in the South, this was an egalitarian society, without casts, and without a warrior class."

So, is there any news on the suposed "Germanic/Celtic wars"? 400 or so BC?

In wich the Germanics from Northgermany advanced into the Celtic Southgermany and drove them into Gaul (Tacitus) or assimilated them (late 20th century idea of what happend)

Did it happen or didnt it?
Isnt this one of the many examples of technological inferior Barbarians crushing an advanced civilation? Like the Mongols (iliterate herders)conquered China (the greatest civilisation that exististed til that moment)and Persia?

Isnt the whole "Germanic Invasions" a story about illiterate, dirty Barbarians swinging clubs, putting themselfs as ruling class over high developed civilisations?

Why do we assume that the farmers had been the rulers?

In the middle age, farmers had been bondslaves to anchestors of Germanic raiding parties.
. He comes once per year and gets half of the corn. ;-)


A ruler doesnt plant

Måns Sjöberg said...

"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".

So those farmers didn't replace everybody else, at least not in northern Europe. I guess things developed in different ways in different parts of the world.

"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."

The hunter-gatherers of that time and place were ex-farmers who had abandoned farming - mostly an east Swedish fenomenon called the Pitted Ware Culture.

Dienekes said...

So those farmers didn't replace everybody else, at least not in northern Europe. I guess things developed in different ways in different parts of the world.

We don't know at present what is the contribution of the different groups to extant populations, only that most of them are "intermediate".

The hunter-gatherers of that time and place were ex-farmers who had abandoned farming - mostly an east Swedish fenomenon called the Pitted Ware Culture.

There is a strong differentiation between farmers and PWC people:

http://dienekes.blogspot.com/2009/09/modern-scandinavians-descended-from.html

So it can't be said that PWC are farmers who abandoned farming; there is a clear genetic difference.

Måns Sjöberg said...

The PWC had contacts across the Baltic Sea. Maybe that's what made them different.