Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for

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bicicleur 2

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Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay),
that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun
sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites
hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the
identification of previously undiscovered variants.

tree + map.jpg

I'm impressed.
 
bicicleur2: Glad you posted this. Very interesting. I went to https://www.biorxiv.org/content/10.1101/2021.02.19.431761v1 and some of the authors are providing some takeways, one of which it shows a 2 path movement of Neolithic Farming into Western Europe or I guess sort of confirms it, obviously from the same Neolithic Anatolians.
 
Link to the paper:
https://www.biorxiv.org/content/10.1101/2021.02.19.431761v1

"[FONT=&quot]Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe."



[/FONT]
 
"Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe."

"When we plotted all of the samples in our study on a map of Europe, a phylogeographic patternclearly emerged. The H2d individuals are all found along the so-called inland/Danubian route intoavailable under aCC-BY-NC-ND 4.0 International license.(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is madebioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431761; this version posted February 19, 2021. The copyright holder for this preprint11central Europe, and all but one of the H2m individuals are found along the so-calledMediterranean route into Western Europe, the Iberian Peninsula and ultimately, Ireland. Thesolitary H2m individual (LEU019) found in central Germany is dated to the Late Neolithic/EarlyBronze Age context, postdating the Neolithic expansion by 2000-3000 years. Archaeological andmtDNA evidence of an eastward expansion of Middle/Late Neolithic groups such as Michelsberg(Jeunesse 1998; Küßner 2016, Beau et al. 2017) could potentially explain this singlegeographically outlying observation."

They need to go back and apply this method to all the ancient Italian samples.
 
not just ancient Italian samples

if this proves to be reliable and applicable to all ancient samples, there is a lot of work to do
it would enhance our understanding of the prehistory and classical times a lot

e.g. if they would do the same with haplogroup I, it is very likely they'll find the same link between the mediterranean route (EN Iberia/France) and some Y-clades LN/EBA Germany/Czechia via Michelsberg

they also could find when and where, and which Y-clades made the link between Iberian Bell Beaker and steppe Beaker
 
or who introduced the chalcolithic in Vinca, and who in Iberia?
who were the first semites?
where did the Globular Amphora come from?
which clades are in Khvalynsk, and what is their relation with later IE clades?

so many mysteries that could be clarified with a little luck if we have better resolution on Y-DNA along with reliable TMRCA
 
It is time to ditch the idea that the Neolithic farmers that ventured into Europe were 100% derived from Anatolian Neolithic farmers. Different cultures mean different people. In the Levant, the Philistines had a different culture, different religion, different burial customs, a different script and a different language, eventually in 200 years they were genetically changed into Canaanites, but kept their culture until they were deported to Mesopotamia.

As far as haplogroup H2, I have learned something I did not know before with Neolithic farmers.
 
Ozzie said:
It is time to ditch the idea that the Neolithic farmers that ventured into Europe were 100% derived from Anatolian Neolithic farmers. Different cultures mean different people. In the Levant, the Philistines had a different culture, different religion, different burial customs, a different script and a different language, eventually in 200 years they were genetically changed into Canaanites, but kept their culture until they were deported to Mesopotamia.

As far as haplogroup H2, I have learned something I did not know before with Neolithic farmers.
Click to expand...

The Philistines typically are dated from 12th century before Christ to around 600 BC. The Neolithic Farmers are way older and while you are correct, the Anatolian Farmers were not 100% from the local Anatolian HG, they were 80/90% from local Anatolian sources and 10-20% from other sources, CHG/Iran and Levant. 3 very good papers on Anatolian Farmers

Feldman et al 2019 documents the 80/90 to 10/20% admixture from the sources I noted sequencing 8 Neolithic Anatolians.

https://www.nature.com/articles/s41467-019-09209-7

Lazaridis et al 2016 document the same admixture that Feldman later confirmed. Figure 1 I think is really nice in plotting out how all these populations plot relative to each other.

https://www.nature.com/articles/nature19310

Kilinc et al 2016 provides a similar plot that Lazaridis et al 2016 Figure did, but they plotted modern Populations with the Ancient samples. Figure 2 in my opinion indicates the following 1) All those Anatolian EEF samples are genetically similar or comparable to each other. 2) All of them fall into the Southern European Cluster.

https://www.cell.com/current-biology/fulltext/S0960-9822(16)30850-8
 
When Anatolian farmers started expanding into NW Anatolia and the Balkans, they had 2 novelties they didn't have before in Cantral Anatolia : cattle and pottery.
It means they had met and admixed with some pastoralist tribes just before expansion. IMO those pastoralist tribes were haplo J and T coming from the eastern Taurus Mountains.
It would be nice if this novel Y-chromosome capture technique could find out their subclades.
Something else : in a recent study it appeared that the Boncuklu populations were not the direct ancestors of EN Anatolia (they split around 9,8 ka)
Higher resolution in G2a2 sublcades could help us here too.
 
https://en.wikipedia.org/wiki/Leubingen_tumulus



Y Haplogroup
R1b - LEU001.A0101
T1a - LEU002.A0101
G2a - LEU003. A0101
I2a1 - LEU005.A0101
R1b - LEU007.A0101
R1a - LEU011.A0101
R1B - LEU012.A0101
H2 - LEU019.A0101
R1B - LEU024.A0101
R1a - LEU027.A0101
R1a - LEU033.A0101
R1B - LEU041.A0101
R1a - LEU047.A0101 R1b1A
- LEU160
- LEU047.A0101 R1b2
- LEU1601


p.s
i see one T
torzio salento
 
kingjohn said:
https://en.wikipedia.org/wiki/Leubingen_tumulus

Y Haplogroup
R1b - LEU001.A0101
T1a - LEU002.A0101
G2a - LEU003. A0101
I2a1 - LEU005.A0101
R1b - LEU007.A0101
R1a - LEU011.A0101
R1B - LEU012.A0101
H2 - LEU019.A0101
R1B - LEU024.A0101
R1a - LEU027.A0101
R1a - LEU033.A0101
R1B - LEU041.A0101
R1a - LEU047.A0101 R1b1A
- LEU160
- LEU047.A0101 R1b2
- LEU1601


p.s
i see one T
torzio salento
Click to expand...

Thanks KingJohn, ... interesting :)
 
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