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Friday, June 29, 2012

Ancient DNA from Iberian Mesolithic hunter-gatherers

A paper in Current Biology reports on the partial genome sequences of two 7,000-year-old Mesolithic skeletons from a cave in northwestern Spain. It shows that these hunter-gatherer samples fall outside the range of contemporary European genetic variation, but are much more similar to present-day Northern Europeans than Iberians.

They also seem to be closely related to prehistoric hunter-gatherers from as far away as the Baltic region, because like them they belong to mtDNA haplogroup U. That's basically the angle that Science Now has taken in covering the story:

Although the first farmers spread quickly across Europe, trading and exchanging culture across thousands of kilometres, many researchers had assumed that Mesolithic nomadic hunter-gatherers lived in small, isolated bands with little contact over long distances. But the genetic picture, Lalueza-Fox says, suggests "highly mobile" groups that kept in touch and interbred continent-wide.

These are interesting outcomes, because modern-day Northern Europeans, all the way from the Atlantic to the Volga, commonly share a very robust "ancestral" cluster when analyzed with the ADMIXTURE program. This cluster usually peaks in Lithuanians and other Baltic groups, and is difficult to break down (see here). Also, it correlates very well with clusters that peak in Swedish hunter-gatherers analyzed recently by Skoglund et al. (see here). As a result, I have no doubt now that this modern ADMIXTURE cluster is largely of Mesolithic hunter-gatherer origin, and its widespread range in Europe today is at least partly due to the fact that hunter-gatherers from across Europe were very similar genetically.

Unfortunately, the Iberian hunter-gatherers weren't compared to modern-day Lithuanians. Instead, the authors used the samples from the 1000 Genomes Project as references. However, it seems they oversampled the Finns when running their intra-European PCA. This showed clearly that these Finns were different from other Europeans, largely due to fairly recent founder effect and genetic drift, but provided very little information about the hunter-gatherers (marked "Brana" below).

The global PCA was more informative, because it wasn't skewed by the Finns, who were still there, but didn't have enough influence to dominate things at global level. Remarkably, this analysis showed that the prehistoric Iberians were shifted towards both East Asia and Sub-Saharan Africa relative to modern-day Europeans.

However, I suspect that if many more Mesolithic samples were present on that plot, things would look somewhat different. It’s difficult to say how different though. We’ll have to wait and see when more ancient samples come in.

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic [1,2,3,4,5,6,7,8,9,10] is poorly understood, both due to the scarcity of human remains from that period [11,12,13,14,15,16,17,18] and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns [19,20,21,22]. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain) [23]. The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

Sánchez-Quinto et al., Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers, Current Biology, 28 June 2012 doi: 10.1016/j.cub.2012.06.005

Monday, June 25, 2012

Long IBD gives clues to migrations across Europe from the Iron Age to the present (aka. SMBE 2012 abstracts)

The Society for Molecular Biology and Evolution (SMBE) is holding its annual conference this week, and has released a PDF of abstracts of the presentations at the meeting. Most of these presentations are yet to be published as articles in journals, but after a bit of Googling, I think I located one of them online. Luckily, it just happens to be the one I’m most interested in…

Long IBD in Europeans and recent population history

Peter Ralph, Graham Coop
UC Davis, Davis, CA, USA

Numbers of common ancestors shared at various points in time across populations can tell us about recent demography, migration, and population movements. These rates of shared ancestry over tens of generations can be inferred from genomic data, thereby dramatically increasing our ability to infer population history much more recent than was previously possible with population genetic techniques. We have analyzed patterns of IBD in a dataset of thousands of Europeans from across the continent, which provide a window into recent European geographic structure and migration.

Unfortunately, the link doesn’t include much data, but has lots of impressive graphics. I’ve put together a small selection of these, focusing on…surprise, surprise…Poland. Basically, the larger the circle, the more Identity-by-descent (IBD) shared:

I think t’s very clear from the results that the Polish sample shares a lot of fairly recent IBD with many groups from across Europe, and especially those from north and east of the Alps. Most of these segments were certainly spread by various Indo-European groups, including the Slavs.

The authors have attempted to estimate the ages of the admixtures, and divided the results into three periods. The outcomes for Poland appear very accurate based on what we know from history and archaeology, although keep in mind that East Slavic individuals are missing from this part of the analysis. I’ve also included the graphics for Italy (IT) and Iberia (Iber), for comparison. The results for these two Southern European regions look much more conservative, and I suspect that’s due to their larger effective population sizes, plus the Alps and Pyrenees acting as strong barriers to gene flow from the north.

At the 0-540 ya period, Poles don’t share much with anyone except with each other and Germans. This makes sense, considering, for instance, the heavy migration of Poles from regions under Prussian occupation to the German industrial areas of the Ruhr and Saxony. These people were quickly Germanised and absorbed by the locals. Today, only their Polish sounding names and diluted genes remain.

I think the 555-1500 ya graphic very clearly shows the effects of the Slavic expansion, probably at least partly from the territory of modern Poland. I suspect the same expansion can also be seen on the 1515-2353 ya graphic. But here we can also likely see the effects of several other major population movements, including migrations of the Celts and Germanics. In any case, looking at all those large “Slavic” bubbles in the Balkans, I’m reminded of this quote from Procopius.

Illyria and all of Thrace, that is, from the Ionian Gulf to the suburbs of Constantinople, including Greece and the Chersonese, were overrun by the Huns, Slavs and Antes, almost every year, from the time when Justinian took over the Roman Empire; and intolerable things they did to the inhabitants. For in each of these incursions, I should say, more than two hundred thousand Romans were slain or enslaved, so that all this country became a desert like that of Scythia.

Eventually, the Slavs stopped raiding the Balkans and settled there permanently. Many became subjects of the Roman Empire.

It’d be fascinating if an IBD analysis like this was carried out on an expanded dataset, including many more samples from Northern and Eastern Europe, as well as West and Central Asia. We know there were movements of people from Europe deep into Asia during the metal ages, and learning more about these events could help us unravel the origins of such enigmatic groups as the early Indo-Europeans.

Actually, there’s another abstract in that SMBE selection, and this one is dealing with Identical by State (IBS) tracts in Europeans. It claims there’s been” no significant gene flow between Europeans and Asians within the past few hundred generations”. That sounds like a reasonable statement, but only in the context of the 1000 Genomes samples these scientists compared, which I assume included Europeans vs. South and East Asians. So like I say, what we really need is a study of IBD or IBS, or both, that looks at a wider variety of groups from West and Central Asia, because that’s where most of the relatively recent mixing took place.

Reconstructing demographic histories from long tracts of DNA sequence identity

Kelley Harris1, Rasmus Nielsen1,2

1UC Berkeley, Berkeley, CA, USA, 2University of Copenhagen, Copenhagen, Denmark

There has been recent excitement and debate about the details of human demographic history, involving gene flow that has occurred between populations as well as the extent and timing of bottlenecks and periods of population growth. Much of the debate concerns the timing of past admixture events; for example, whether Neanderthals exchanged genetic material with the ancestors of non-Africans before before or after they left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past genetic exchanges, along with population divergence times and changes in effective population size. To achieve this, we look at the length distribution of regions that are shared identical by state (IBS) and maximize an analytic composite likelihood that we derive from the sequentially Markov coalescent (SMC). Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method its power by influencing the distribution of shared IBS tracts. However, since IBS tracts are directly observable, we do not need to infer the precise locations of IBD tracts. In this way, we can accurately estimate admixture times for relatively ancient events where admixture mapping is not possible, and in simulated data we show excellent power to characterize admixture pulses that occurred 100 to several hundred generations ago. When we study the IBS tracts shared between and within the populations sequenced by the 1000 Genomes consortium, we find evidence that there was no significant gene flow between Europeans and Asians within the past few hundred generations. It also looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians in a population-specific way, though there may have been admixture between Africans and an ancestral non-African population.

See also...

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

Wednesday, June 20, 2012

First direct evidence of genetic continuity in West and Central Poland from the Iron Age to the present

I've just been sent a fascinating thesis on the mtDNA of Iron Age and Medieval samples from Poland. It suggests direct genetic continuity between Iron Age samples belonging to the Przeworsk and Wielbark Cultures, of what is now West and Central Poland, and present-day Poles. Here's the English summary, and a map of the sites under study:

For many years the origin of the Slavs has been the subject-matter in archaeology, anthropology, history, linguistics and recently also modern human population genetics. By now there is no unambiguous answer to a question where, when and in what way the Slavs originated. For the purposes of this dissertation, the analysis of ancient human mitochondrial DNA was applied. The ancient DNA was isolated from 72 specimens which came from Iron-Age and medieval graveyards from the area of current Poland. Ancient mtDNA was extracted from two teeth from each individual and reproducible sequence results were obtained for 20 medieval and 23 Iron-Age specimens. On the basis of HVR I mtDNA mutation motifs and coding region SNPs each specimen was assigned to a mitochondrial haplogroup. The obtained results were used together with other ancient and modern populations to analyse shared haplotypes and population genetic distances illustrated by multidimentional scaling plots (MDS). The differences on genetic level and quite high genetic distances (FST) between medieval and Iron-Age populations as well as significant number of shared informative haplotypes with Belarus, Ukraine and Bulgaria may evidence genetic discontinuity between medieval and Iron Ages. From the other side, the highest number of shared informative haplotypes between Iron-Age and extant Polish population as well as the presence of subhaplogroup N1a1a2, can confirm that some genetic lines show continuity at least from Iron Age or even Neolithic in the areas of present day Poland. The results obtained in this work are considered to be the first ancient contribution in genetic history of the Slavs.

Below is an MDS from the thesis, based on data corrected for the effects of potential relatives in the Iron Age sample. I don't think it's a particularly useful way of judging the intra-European affinity of the two ancient Polish groups, mostly because the samples are small, and contemporary North, Central and East Europeans don't differ very much in terms of mtDNA. Nevertheless, we can see that both the Iron Age (Okres Rzymski) and Medieval (Sredniowiecze) samples fall within the range of modern European mtDNA diversity. On the other hand, the German Neolithic LBK sample (Neolit LBK Niemcy) clearly does not, because it's sitting at the far right of the plot, away from the main European cluster. This dichotomy between the genetic structure of the LBK farmers and modern Europeans has been demonstrated in previous studies, but the reasons for it are still a mystery.

Interestingly, modern Poles are closer to an Iron Age sample from Denmark (Okres Zelaza Dania) than to the Polish Iron Age set. However, as per the summary above, the author also compared the frequencies of the most informative haplotypes among the modern and ancient samples, and found that extant Poles are the closest group to the Polish Iron Age remains, followed by Balts, Swedes and Baltic Finns. Below is a table showing those results.

According to the author, these matches might hint at Baltic, Germanic and Finno-Ugric influences in the Polish Iron Age population. Perhaps, but in my opinion, they're simply in line with geography, and reflect the general North European character of maternal lineages shared by populations from around the Baltic, both today and during the Iron Age.

The results for the Medieval Polish sample are more intriguing, because they're somewhat out of whack with geography. Its best matching modern groups are Belorussians, Ukrainians and Bulgarians. This might suggest that, during the early middle ages, the territory of present day Poland experienced an influx of groups from what are now Belarus and Ukraine, who then melted into the gene pool of the natives of Polish Iron Age descent. However, conversely, it might mean that Belorussians, Ukrainians and Bulgarians descend in large part from fairly specific medieval groups from the area of modern Poland.

In any case, whether present day Polish territory saw some migrations from the immediate east during the Medieval period or not, this preliminary look at ancient Polish mtDNA suggests long-standing genetic continuity in the region. What it clearly doesn't show is a complete, or almost complete, population replacement in the areas between the Oder and Bug rivers during the migration period.

Indeed, the thesis results put into doubt past notions that the Przeworsk and Wielbark cultures were of Germanic origin.

The (mtDNA) haplogroup missing from both the Iron Age and medieval samples from the territory of modern Poland was haplogroup I. In contemporary Slavic populations, this haplogroup is found at levels ranging from 1.2% in Bulgarians to 4.8% in Slovaks. It was also recorded at high levels in ancient remains from Denmark. It showed a frequency of 12.5% in an Iron Age sample, and 13.8% in a medieval sample. Melchior et al. 2008 suggest that haplogroup I might have been more common in Denmark and Northern Europe during that period. Therefore, the lack of this haplogroup in ancient DNA from the territory of modern Poland, might mean that the Przeworsk and Wielbark cultures should not be identified with Germanic populations.

I'm sure more ancient DNA studies are on the way looking at the origins of Slavs and Poles. Indeed, if the Y-chromosomes of Przeworsk and Wielbark remains are successfully tested, I won't be surprised if they look fairly typical of modern Poles, with a decent representation of R1a1a-M458, which is the most common Y-chromosome haplogroup in Poland today.

Anna Juras, Etnogeneza Słowian w świetle badań kopalnego DNA, Praca doktorska wykonana w Zakładzie Biologii Ewolucyjnej Człowieka Instytutu Antropologii UAM w Poznaniu pod kierunkiem Prof. dr hab. Janusza Piontka

Friday, June 15, 2012

Ancient mtDNA from the Dnieper-Donets cultural complex

A new paper at the Journal of Human Genetics reports on the mtDNA gene pool of the Dnieper-Donets (DD) cultural complex of Neolithic Ukraine. The authors were able to confirm the presence of the following haplogroups in the ancient remains from the Mariupol-type sites along the Dnieper: two H, two C, one C4a2, one U5a1a and one U3. So, three out of the seven samples belonged to haplogroup C, which is a Siberian-specific marker.

We've already had a sneak peek at these results thanks to a thesis abstract published last year by the Grand Valley State University (see here). The presence of mtDNA C among the DD remains suggests that the North Pontic steppe was formerly inhabited by genetically heterogeneous groups, and part of their ancestry came from Siberia.

The fact that Siberian-specific mtDNA lineages are very rare in Ukraine today, means that something must have happened there since the Bronze Age that basically wiped them out.

Alexey G Nikitin et al., Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe, Journal of Human Genetics, advance online publication, 7 June 2012; doi:10.1038/jhg.2012.69