PDA

View Full Version : Anatolia is the source of the European Neolithic



Angela
01-01-16, 22:40
Well, sort of, and we sort of knew... This is the Kumtepe sample.

See:Omrak et al
http://www.cell.com/current-biology/abstract/S0960-9822%2815%2901516-X
Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool "Summary
Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [ 1–5 ]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [ 6–9 ]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [ 10 ]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia’s central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic."

That's all I've got folks, because it's behind a pay wall at Science Direct. If someone has access, let us know what's new. I can't even seem to get access to the data and figures.

Tomenable
02-01-16, 00:01
It's always good to get reassured but they did not hurry up. :)

Fire Haired14
02-01-16, 02:14
It sounds like their Neolithic Anatolians might be mixed, with mostly EEF but also some CHG or something else.

Angela
02-01-16, 02:56
It sounds like their Neolithic Anatolians might be mixed, with mostly EEF but also some CHG or something else.

You mean this statement, yes?

"We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus."

I wondered about this too. Do they just mean that Near Eastern and Caucasus populations also descend from the Anatolian farmers to a certain extent, or do they mean that something CHG like had started moving into the northwestern Anatolia?

When their first statement about their paper on Kumtepe came out I remember that there was something ambiguous then too. I speculated at the time as to whether perhaps subsequent Neolithic flows might have been slightly different from the Early Neolithic ones. There's that J2 and E-V13 that shows up.

These are their "highlight points":

"


•Kum6 shows a strong population continuity with present-day Sardinia
•Kum6 expresses connections to the central Eurasian gene pool
•Kum6 shares notable affinity with the Iceman, a 5,300-year-old southern European
•Genetic affinities to both East and West suggest continuous contact with Anatolia"


On the old Dodecad runs Oetzi had some "Caucasus". Does any CHG show up in any of the amateur analysis for Oetzi?

Fire Haired14
02-01-16, 03:40
Here's info from someone else who has access.

Summary of info:

>To Neolithic Turkey Genomes: Kum6 from 6700 BP at high coverage and Kum4 from 5500-4800 BP and of low coverage. So, we can only get good info from Kum6.

>D-stats and TreeMix show close affinity between Otzei and Kum6.

>In Admixture EEF is a mixture of Orange, Blue, and Green components. Blue peaks in hunter gatherers and Steppe, it's a Euro-centered component and from shared ancestry in WHG and EHG. The Orange is a EEF-specfic component that peaks in them and today peaks in West and South Europe. The Green one peaks in the Middle East.

>Kum6 is a typical EEF, except he scores high in Green. He lacks the South Asian centered Pale component which looks like it came from HG So, he doesn't have CHG, but he might have sometype of common ancestry with West Asians, maybe via EEF contribution to West Asians.


http://i67.tinypic.com/28mh0sw.jpg

http://i65.tinypic.com/23gxlx3.jpg


RESULTS:

* Kum6 carries the H2a3 mitochondrial haplogroup (both females, the other Kum4 was not typed)

* The Anatolian Kum6 individual falls close to the early and middle Neolithic European farmers, showing a tendency toward modern-day Near Eastern populations. Interestingly, Kum6 does not group with any modern-day Anatolian populations. These results were confirmed by outgroup f3 statistics where, among modern-day groups, Kum6 shows the greatest genetic similarity to Sardinians, Greeks, and Cypriots, whereas modern-day Anatolian populations display lower levels of genetic affinity to Kum6 (Figure 2). Kum6 also falls between modern-day West Asians and Europeans when additional modern-day populations are included in the analysis

* For a model with nine clusters (K = 9; results for higher numbers of clusters are similar, Figure S3), three major ancestry components were observed in the ancient individuals. The first one (blue), observed as the main component in all hunter-gatherers, is also found as a minor contribution to all farmers, which is in line with the observed admixture from hunter-gatherers into farmers [3]. The second (orange) and the third (green) components were observed mostly in farmers to varying degrees (5%–68% and 0.06%–45% for K = 9, respectively). The orange component is mainly found in present-day Western Europeans, whereas the third component (green) is mostly found in the modern-day Near East and Caucasus, and the highest proportion of this third component among Neolithic individuals was observed in Kum6 (45% for K = 9). The notion that this component is West Asian is also supported by its presence in a Bronze Age Armenian sample (51%), which contains less than 2% of the orange component. Interestingly, this ‘‘West Asian’’ component (green) is not related to the potential genetic material brought to Europe by migration during the Bronze Age and recently connected to the Yamnaya culture [19, 24], visualized in Figure 3 as light blue, and it is observed in high frequency in modern-day people from southern Asia. The elevated ‘‘West Asian’’ affinity of Kum6 is likely to be the cause of the genetic differentiation observed between Kum6 and all other ancient farmers shown in the PCA plot (Figure 1B.).

* A clear decline was observed in the values of the green component over time (average of _29% in Early Neolithic, _14% in Middle Neolithic, and 2% in Late Neolithic), which is consistent with increased admixture with hunter-gatherer groups [3]. Our results suggest that the two ancestry components of ancient farmers (orange and green in Figure 3) were established at an early stage, probably before the first farmers expanded into Europe, and were maintained in Europe up until the end of Middle Neolithic and that both components are present in various modern-day European populations. Therefore, these observations directly link the early European Neolithic gene pool to western Anatolia.

* We computed D statistics [20] to further investigate additional genetic relationships between ancient Europeans with
sufficient sequencing coverage (>13) and Kum6. All proposed tree topologies where the Tyrolean Iceman [20] was included as one of the in-groups were rejected (2 < jZj < 4.6), suggesting gene flow or a more recent shared ancestry between Kum6 and the Tyrolean Iceman (Figure 4A). A similar tendency was observed with a Middle Neolithic Hungarian farmer [23], (co1), contemporary with the Tyrolean Iceman, resolution due to the low coverage of Kum6 and Co1. The observed genetic affinity between the Tyrolean Iceman and Kum6 could be interpreted as additional contacts between western Anatolia and Neolithic Europe at a later stage. This scenario is congruent with mitochondrial [29] and archaeozoological [30] studies, as well as the archaeological indications of multiple waves of contact between the Balkans and Anatolia.

* Furthermore, the Bronze Age Yamnayan component suggested to be a part of the Corded ware expansion [19, 24] is
not present in Kum6, and thus is not producing any increased affinity to the ancestors of the Yamnaya culture from north of the Caucasus (D-Denisovan, Yamnaya_RISE; Kum6, early farmer), all Z > _1.7).

* Contacts to the east, independent of Yamnaya ancestry [19, 24] are, however, supported by (1) higher affinity
of Kum6 to some Bronze Age Asian cultures when compared to Mesolithic Europeans and (2) higher affinities of Bronze Age Asians(BA Armenia) to Kum6 compared to early Neolithic Europeans (Table S5).


* "A comparison of Kum6 to an Asian Upper Paleolithic individual (Ust-Ishim [27]) and a European Upper Paleolithic sample (Kostenki14 [28]) confirms that Kum6 shows more affinity to early Europeans (Z = 5). Stronger affinities of Kostenki14 to Kum6 than to early Neolithic Europeans (Table S5), however, suggest that Kum6 contains genomic components not found in early Neolithic Europeans. Kum6 is also grouped with farmers in a model-based
population-tree analysis [34] (Figure 4B.), and the inferred migration edges point to the same conclusion as the D statistics results, as well as manifest the expected signals from previously published observations [3, 4].

* "Interestingly, the genetic similarity to the Tyrolean Iceman and the eastern component detected in Kumtepe indicate an intense entanglement of contacts from the East and into Europe, with western Anatolia at the center. Most modern-day European populations display ancestries from Mesolithic hunter-gatherers, early Neolithic farmers, and in some cases traces of additional admixture from different sources [3, 4, 23, 24] (Figure 3). Modern-day Anatolian groups display a variety of admixture traces originating from groups in the Middle East, Central Asia, and Siberia, which
cause Kum6 to be genetically more similar to modern-day Europeans than to modern-day Anatolians.

Fire Haired14
02-01-16, 04:02
Ginormous migrations came to Turkey after 5,000 years ago. We know that for a fact now. The way to investigate what that change is, is by testing the relationship between Turkey and West Asians and Europeans, and how it compares to their relationship with EEF. If Turkish are significantly close to some ancients or moderns, that means Turkey received migration from people similar to those ancients or moderns after 5,000 years ago. CHG is definitely apart of the change but the change is probably more complicated.

I don't think our concepts based on ancient DNA: CHG, EHG, etc., etc. or components in ADMIXTURE can explain it. We have to get new data, mostly from formal stats. We have no ancient DNA from West Asia, outside of CHG and BA Armenia, so we don't really know what's going on there. They relate to the European types of ancestry: EEF, WHG, Steppe, etc., but it's a distant relationship. I don't like putting Bedouin as the "Orignal EF reference", because their relationship with EEF might only go back to paleolithic times.

Fire Haired14
02-01-16, 04:14
When their first statement about their paper on Kumtepe came out I remember that there was something ambiguous then too. I speculated at the time as to whether perhaps subsequent Neolithic flows might have been slightly different from the Early Neolithic ones. There's that J2 and E-V13 that shows up.

It's possible. We know most J/E1b came in after EEF first came, but that's it. Kum6's relationship with Otzei and West Asians has nothing to do with CHG, so maybe he is related to J/E1b.

I just looked at "haplotype-analysis" on modern Europeans which is used to track recent ancestry, and there's no connection with Italy and Balkans. Instead Italy, according to this test, has most recent ancestry with Other Italians, France, Spain(inclu. Basque), and Sardinians. This could be a Cardial connection. According to the test Italy has as much recent ancestry with Balkans as with East Europe and Scandinavia.

That relates to J/E1b because Italy and Balkans share that, but don't have a lot of recent ancestry(according to that test). If E1b/J arrived recently, like in historical times, and they received migration from the exact same people, then they'd be close in that test. Also, Ashkenazi Jews and Italians don't share a lot of recent ancestry in that test. So, Ashkenazi Jews probably aren't mostly Italian.

Angela
02-01-16, 05:01
It's possible. We know most J/E1b came in after EEF first came, but that's it. Kum6's relationship with Otzei and West Asians has nothing to do with CHG, so maybe he is related to J/E1b.

I just looked at "haplotype-analysis" on modern Europeans which is used to track recent ancestry, and there's no connection with Italy and Balkans. Instead Italy, according to this test, has most recent ancestry with Other Italians, France, Spain(inclu. Basque), and Sardinians. This could be a Cardial connection. According to the test Italy has as much recent ancestry with Balkans as with East Europe and Scandinavia.

That relates to J/E1b because Italy and Balkans share that, but don't have a lot of recent ancestry(according to that test). If E1b/J arrived recently, like in historical times, and they received migration from the exact same people, then they'd be close in that test. Also, Ashkenazi Jews and Italians don't share a lot of recent ancestry in that test. So, Ashkenazi Jews probably aren't mostly Italian.


I don't think they are (mostly Italian, that is). That's just the pet theory of Sikelliot, who is perhaps tired of posting pictures of Sicilians in dark nightclubs? I wouldn't know, as I don't go near theapricity with a ten foot pole. He has apparently migrated over to anthrogenica to push his pet theory. Dienekes did an IBD analysis years ago that showed no gene sharing between Jews and Italians in historical times. Ashkenazim, and Sephardim to some extent, just share similar percentages of ancient ancestral groups as south Italians and a few even plot pretty close to Tuscans on PCA's. (Behar's) Some people still haven't grasped that plotting near one another on a PCA or even having similar percentages on certain Admixture components doesn't mean there's been recent gene sharing. From what I remember it was Greeks and Cypriots who showed some level of sharing with Ashkenazim, although I don't know if this new analysis shows that.

I'm not sure about this no sharing between the Balkans and Italy, because that would directly contradict Ralph and Coop as to IBD sharing. How could that be explained?
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555

"There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya. An exception is that Italy and the neighboring Balkan populations share small but significant numbers of common ancestors in the last 1,500 years, as seen in Figures S16 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s016) and S17S17 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s017). , as seen in Figures S16 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s016) and S17S17 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s017). "

That makes sense historically because of the Albanian migrations into southern Italy, and also perhaps some migration from the Balkans and Greece after the Fall of Constantinople.

Also, what do you mean by the Balkans? Do you include Greek in that, or just populations like Croats and Serbs?

Oh, Fire-Haired, is there a spreadsheet for this haplotype analysis?

Fire Haired14
02-01-16, 06:03
I'm not sure about this no sharing between the Balkans and Italy, because that would directly contradict Ralph and Coop as to IBD sharing. How could that be explained?
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555

"There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya. An exception is that Italy and the neighboring Balkan populations share small but significant numbers of common ancestors in the last 1,500 years, as seen in Figures S16 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s016) and S17S17 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s017). , as seen in Figures S16 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s016) and S17S17 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555#pbio.1001555.s017). "

That makes sense historically because of the Albanian migrations into southern Italy, and also perhaps some migration from the Balkans and Greece after the Fall of Constantinople.

Also, what do you mean by the Balkans? Do you include Greek in that, or just populations like Croats and Serbs?

Oh, Fire-Haired, is there a spreadsheet for this haplotype analysis?

Romanians were the only Balkan reference. Thanks for the link to the paper. There's no spreadsheet it's a picture (https://sites.google.com/site/fennobga/CLAggrWorld240413.png). I already took notes on all of it here (https://docs.google.com/spreadsheets/d/1o9M3dL19KhWJKz1TC0enC1Qfk1AcMf2FjPnr690HJSs/edit#gid=0). The results make sense. The only place there's been a lot of recent gene flow between far-away places is East Europe, probably because of Slavs.

Fire Haired14
02-01-16, 08:43
Full Paper (http://www.cell.com/cms/attachment/2042476822/2055464038/mmc2.pdf)
Supp Info (http://www.cell.com/cms/attachment/2042476822/2055464037/mmc1.pdf)

Angela
02-01-16, 19:10
Full Paper (http://www.cell.com/cms/attachment/2042476822/2055464038/mmc2.pdf)
Supp Info (http://www.cell.com/cms/attachment/2042476822/2055464037/mmc1.pdf)

Thanks, Fire Haired. I have to read it all again, but those admixture graphs in the main paper look fakakta to me. If you're going to use some ancient samples why not use CHG? Wasn't it out yet?

Also, as to one of your prior points, didn't the amateur analysis show a few percent CHG in the Barcin samples? If that's right, why so sure there's none here?