Paleogenomics of Upper Paleolithic to Neolithic European hunter-gatherers
Looks like the data is available shortly so maybe it needs a dedicated thread.
Eurasia has been populated by modern humans for over 45,000 years and for the vast majority of their time they relied on a foraging lifestyle. Our knowledge of the genetic relatedness and structure of European hunter-gatherers is, however, still limited, because dedicated studies are challenged by the scarce availability and poor molecular preservation of human remains from that period. Here we analyze 356 ancient hunter-gatherer genomes including new genomic data of 116 individuals from 14 countries in western and central Eurasia, dating between 35,000 and 5,000 years ago (35-5 ka). We identify a new genetic ancestry profile in individuals associated with the Upper Paleolithic Gravettian from western Europe, which is distinct from contemporaneous groups related to this archeological culture in central and southern Europe. However, it resembles that of preceding individuals associated with the Aurignacian and survives during the Last Glacial Maximum (LGM, ~25-19 ka) in human populations from southwestern Europe, associated with the Solutrean and later Magdalenian, which re-expanded northward and northeastward after the LGM. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups during the LGM, alongside a north-to-south expansion of Epigravettian-associated populations. From at least 14 ka, a lineage related to this culture expands from the south across the rest of Europe largely replacing the Magdalenian-associated gene pool. After a period of limited admixture across the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, also characterized by marked differences in inherited phenotypic traits.
Pasting analysis from the news discussion thread here just to have it in the dedicated spot.
Ok here's a cursory overview of the new samples and what I think they represent... (low coverage = unusable, poor coverage = don't use standalone, maybe ok grouped with similar samples)
EHG from Russia and Baltics
JAZ001, KAR001 (poor coverage), KVH001&002 (001 poor coverage), MN2001/2002/2003, MNN (3 good quality, 1 poor coverage, 3 low coverage), MUR001 (5 mediocre coverage, 1 poor coverage, 1 low coverage), UOO - tons of samples, VSL (2 decent samples, 1 poor coverage)
WHG of the Bichon/Loschbour/Isles variety
AAT001, ACR001 (low coverage), DOG (001&002 good coverage, 003-010 low coverage), FMR001 (poor coverage), KGH006, MAF001, MPR001, OKL001&002
Miscellaneous European WHG
AC16 - GrottaContinenza-like
AMI001&002 - Central European WHG (Germany/Poland/Hungary)
CRN001&002 - Iberian HG similar to Chan
CRW001 - Looks quite close to Denmark HG
DOB001 - Close match Germany_BadDurrenberg_HG
DON005&006 - WHG of some kind, either early or Central European (low coverage)
DRI001 - WHG (Denmark/Germany)
GFW (5 good coverage samples out of 7) - WHG (Denmark/Germany)
IGR001 - Ukrainian HG likely
OST001-003 - Not quite sure, Balkan-WHG maybe?
PRD001 - IronGates-like (poor coverage)
STO001 - GrottaContinenza-like
VO (3 decent samples, 2 poor coverage) - Ukrainian HG likely
WCX - Denmark HG? (low coverage)
WOL001 - Similar to Hungary-WHG (poor coverage)
Magdelanians
LMA001 (low coverage), MAZ003
Previously published samples not given labels in this set
- BER001 (EHG - poor coverage)
- PES001: Arkhangelsk EHG
- SRA62: Irish WHG
- RIP001: higher coverage version of Tagliente
Other not particularly revelatory samples
BRM001 - Western EEF with high WHG (poor coverage)
CIO001 - Cioclovina or something remarkably similar (low coverage)
DLV005&006 - Vestonice, very closely related to the others if not duplicates.
RIE002 - no idea (low coverage)
LPI002 - Late Aurignacian? (low coverage)
LRO001 - GoyetQ116_1 like (low coverage)
PIN004 - Late Aurignacian? (low coverage)
Now for the exciting stuff
FRL006 - Looks like GoyetQ116_1 (complete with high Ust-Ishim & BachoKiro affinity) but more relevant to later Magdelanians. Good enough coverage, ~600k snps.
GER002&003 - Similar to FRL006 (002 = low coverage, 003 = poor coverage)
GOY (3 low coverage, 1 poor coverage) - Looks to be Gravettian period at Goyet site. Not particularly high affinity to anyone, likely mixed between late-GoyetQ116_1 types and Vestonice-like ancestry of a type more relevant to WHG.
MAZ001 - Tough to make heads or tails of this, superficially looks like it could be a Dzudzuana but then again it's such poor coverage it could be a 3-toed sloth. Assuming MAZ003 the Magdelanian is from the same given the matching MAZ label, that either means MAZ001 is indeed a 3-toed sloth or he came from North Africa.
ORM001 - GoyetQ116_1 like
PA12 - Similar to Vestonice, but slightly higher affinity to BK1653 and WHG
TTK001 - Extremely interesting. Very ANE, no discernable East-Asian, no discernable WHG. Lower paleo-Euro affinity than MA1/Yana, equal Native American affinity to MA1. Highest affinity is to Tarim_EMBA. Possible connection to Iran_N/CHG. Paleolithic Central Asian? Coverage is mediocre but not awful ~230k snps.
Quite surprising to see AAT001 as R-M269, looks like a good coverage, very typical WHG. The number of y-calls there seems low compared to it's coverage, maybe something to that...
AAT001
"Ireland_Killuragh_HG.SG" 40.05
"Loschbour.DG" 27.05
"Germany_Falkenstein_HG" 21.4
"Germany_Bottendorf_HG" 10.8
"Ethiopia_Mota_4500BP.SG" 0.7
Columns:,Anatolia_Boncuklu_N.SG,Anatolia_Barcin_N. SG,Iran_TepeAbdulHosein_N.SG,Iran_Wezmeh_N.SG,CHG. SG,Taforalt,ElMiron,Spain_Chan_HG.SG,Bichon.SG,Ita ly_GrottaContinenza_HG.SG,RUS_Arkhangelsk_HG.SG,RU S_Samara_Sidelkino_HG.SG,Afanasievo_KarasukIII.SG, Yamnaya_Kazakhstan_Karagash.SG,Botai.SG,Andaman_10 0BP.SG,Jomon.SG,RUS_Primorsky_DevilsCave_N.SG,RUS_ Irkutsk_Shamanka_EN.SG,RUS_Irkutsk_AngaraRiver_LN. SG,RUS_Irkutsk_Sokhter_LN.SG,RUS_Yakutia_Kamenka2_ LN.SG,RUS_Krasnoyarsk_Nefteprovod_BA.SG,Peru_RioUn callane_1800BP.SG,Bahamas_SouthAndros_Ceramic.SG
A lot of low coverage samples turning up weird calls, probably contamination.
Some of the very good coverage samples have disproportionately low # of y-calls coupled with unexpected haplogroups (maybe female?)
Also update to the OST site. Blatterhohle-like situation.
OST2 = ~77% WHG (56% Denmark, 16% Germany, 6% Ireland), ~23% EEF.
AMI = I was mistaken before, these look like the Iberian HG Canes.
Pasting analysis from the news discussion thread here just to have it in the dedicated spot.
Ok here's a cursory overview of the new samples and what I think they represent... (low coverage = unusable, poor coverage = don't use standalone, maybe ok grouped with similar samples)
EHG from Russia and Baltics
JAZ001, KAR001 (poor coverage), KVH001&002 (001 poor coverage), MN2001/2002/2003, MNN (3 good quality, 1 poor coverage, 3 low coverage), MUR001 (5 mediocre coverage, 1 poor coverage, 1 low coverage), UOO - tons of samples, VSL (2 decent samples, 1 poor coverage)
WHG of the Bichon/Loschbour/Isles variety
AAT001, ACR001 (low coverage), DOG (001&002 good coverage, 003-010 low coverage), FMR001 (poor coverage), KGH006, MAF001, MPR001, OKL001&002
Miscellaneous European WHG
AC16 - GrottaContinenza-like
AMI001&002 - Central European WHG (Germany/Poland/Hungary)
CRN001&002 - Iberian HG similar to Chan
CRW001 - Looks quite close to Denmark HG
DOB001 - Close match Germany_BadDurrenberg_HG
DON005&006 - WHG of some kind, either early or Central European (low coverage)
DRI001 - WHG (Denmark/Germany)
GFW (5 good coverage samples out of 7) - WHG (Denmark/Germany)
IGR001 - Ukrainian HG likely
OST001-003 - Not quite sure, Balkan-WHG maybe?
PRD001 - IronGates-like (poor coverage)
STO001 - GrottaContinenza-like
VO (3 decent samples, 2 poor coverage) - Ukrainian HG likely
WCX - Denmark HG? (low coverage)
WOL001 - Similar to Hungary-WHG (poor coverage)
Magdelanians
LMA001 (low coverage), MAZ003
Previously published samples not given labels in this set
- BER001 (EHG - poor coverage)
- PES001: Arkhangelsk EHG
- SRA62: Irish WHG
- RIP001: higher coverage version of Tagliente
Other not particularly revelatory samples
BRM001 - Western EEF with high WHG (poor coverage)
CIO001 - Cioclovina or something remarkably similar (low coverage)
DLV005&006 - Vestonice, very closely related to the others if not duplicates.
RIE002 - no idea (low coverage)
LPI002 - Late Aurignacian? (low coverage)
LRO001 - GoyetQ116_1 like (low coverage)
PIN004 - Late Aurignacian? (low coverage)
Now for the exciting stuff
FRL006 - Looks like GoyetQ116_1 (complete with high Ust-Ishim & BachoKiro affinity) but more relevant to later Magdelanians. Good enough coverage, ~600k snps.
GER002&003 - Similar to FRL006 (002 = low coverage, 003 = poor coverage)
GOY (3 low coverage, 1 poor coverage) - Looks to be Gravettian period at Goyet site. Not particularly high affinity to anyone, likely mixed between late-GoyetQ116_1 types and Vestonice-like ancestry of a type more relevant to WHG.
MAZ001 - Tough to make heads or tails of this, superficially looks like it could be a Dzudzuana but then again it's such poor coverage it could be a 3-toed sloth. Assuming MAZ003 the Magdelanian is from the same given the matching MAZ label, that either means MAZ001 is indeed a 3-toed sloth or he came from North Africa.
ORM001 - GoyetQ116_1 like
PA12 - Similar to Vestonice, but slightly higher affinity to BK1653 and WHG
TTK001 - Extremely interesting. Very ANE, no discernable East-Asian, no discernable WHG. Lower paleo-Euro affinity than MA1/Yana, equal Native American affinity to MA1. Highest affinity is to Tarim_EMBA. Possible connection to Iran_N/CHG. Paleolithic Central Asian? Coverage is mediocre but not awful ~230k snps.
Quite surprising to see AAT001 as R-M269, looks like a good coverage, very typical WHG. The number of y-calls there seems low compared to it's coverage, maybe something to that...
AAT001
"Ireland_Killuragh_HG.SG" 40.05
"Loschbour.DG" 27.05
"Germany_Falkenstein_HG" 21.4
"Germany_Bottendorf_HG" 10.8
"Ethiopia_Mota_4500BP.SG" 0.7
Columns:,Anatolia_Boncuklu_N.SG,Anatolia_Barcin_N. SG,Iran_TepeAbdulHosein_N.SG,Iran_Wezmeh_N.SG,CHG. SG,Taforalt,ElMiron,Spain_Chan_HG.SG,Bichon.SG,Ita ly_GrottaContinenza_HG.SG,RUS_Arkhangelsk_HG.SG,RU S_Samara_Sidelkino_HG.SG,Afanasievo_KarasukIII.SG, Yamnaya_Kazakhstan_Karagash.SG,Botai.SG,Andaman_10 0BP.SG,Jomon.SG,RUS_Primorsky_DevilsCave_N.SG,RUS_ Irkutsk_Shamanka_EN.SG,RUS_Irkutsk_AngaraRiver_LN. SG,RUS_Irkutsk_Sokhter_LN.SG,RUS_Yakutia_Kamenka2_ LN.SG,RUS_Krasnoyarsk_Nefteprovod_BA.SG,Peru_RioUn callane_1800BP.SG,Bahamas_SouthAndros_Ceramic.SG
A lot of low coverage samples turning up weird calls, probably contamination.
Some of the very good coverage samples have disproportionately low # of y-calls coupled with unexpected haplogroups (maybe female?)
Also update to the OST site. Blatterhohle-like situation.
OST2 = ~77% WHG (56% Denmark, 16% Germany, 6% Ireland), ~23% EEF.
AMI = I was mistaken before, these look like the Iberian HG Canes.
An R1b M 269 among a full fledged WHG population? What is the date of the sample?
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Originally Posted by Kale
