Limits...
Upper Palaeolithic genomes reveal deep roots of modern Eurasians.

Jones ER, Gonzalez-Fortes G, Connell S, Siska V, Eriksson A, Martiniano R, McLaughlin RL, Gallego Llorente M, Cassidy LM, Gamba C, Meshveliani T, Bar-Yosef O, Müller W, Belfer-Cohen A, Matskevich Z, Jakeli N, Higham TF, Currat M, Lordkipanidze D, Hofreiter M, Manica A, Pinhasi R, Bradley DG - Nat Commun (2015)

Bottom Line: We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland.While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum.CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

View Article: PubMed Central - PubMed

Affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Dublin 2, Ireland.

ABSTRACT
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Show MeSH

Related in: MedlinePlus

Genetic structure of ancient Europe.(a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected11 onto the first two principal components defined by selected Eurasians from the Human Origins data set1. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called12345679 (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components12 for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4660371&req=5

f1: Genetic structure of ancient Europe.(a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected11 onto the first two principal components defined by selected Eurasians from the Human Origins data set1. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called12345679 (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components12 for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.

Mentions: Kotias and Satsurblia, the two CHG, are genetically different from all other early Holocene (that is, Mesolithic and Neolithic) ancient genomes1234568910, while Bichon is similar to other younger WHG. The distinctness of CHG can be clearly seen on a principal component analysis (PCA) plot11 loaded on contemporary Eurasian populations1, where they fall between modern Caucasian and South Central Asian populations in a region of the graph separated from both other hunter gatherer and EF samples (Fig. 1a). Clustering using ADMIXTURE software12 confirms this view, with CHG forming their own homogenous cluster (Fig. 1b). The close genetic proximity between Satsurblia and Kotias is also formally supported by D-statistics13, indicating the two CHG genomes form a clade to the exclusion of other pre-Bronze Age ancient genomes (Supplementary Table 2; Supplementary Note 3), suggesting continuity across the Late Upper Palaeolithic and Mesolithic periods. This result is mirrored in western Europe as Bichon is close to other WHG in PCA space (Fig. 1a) and outgroup f3 analysis (Supplementary Fig. 1), belongs to the same cluster as other WHG in ADMIXTURE analysis (Fig. 1b), and forms a clade with other WHG to the exclusion of other ancient genomes based on D-statistics (Supplementary Table 3; Supplementary Note 3). Thus, these new data indicate genomic persistence between the Late Upper Palaeolithic and Mesolithic both within western Europe and, separately, within the Caucasus.


Upper Palaeolithic genomes reveal deep roots of modern Eurasians.

Jones ER, Gonzalez-Fortes G, Connell S, Siska V, Eriksson A, Martiniano R, McLaughlin RL, Gallego Llorente M, Cassidy LM, Gamba C, Meshveliani T, Bar-Yosef O, Müller W, Belfer-Cohen A, Matskevich Z, Jakeli N, Higham TF, Currat M, Lordkipanidze D, Hofreiter M, Manica A, Pinhasi R, Bradley DG - Nat Commun (2015)

Genetic structure of ancient Europe.(a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected11 onto the first two principal components defined by selected Eurasians from the Human Origins data set1. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called12345679 (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components12 for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660371&req=5

f1: Genetic structure of ancient Europe.(a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected11 onto the first two principal components defined by selected Eurasians from the Human Origins data set1. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called12345679 (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components12 for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.
Mentions: Kotias and Satsurblia, the two CHG, are genetically different from all other early Holocene (that is, Mesolithic and Neolithic) ancient genomes1234568910, while Bichon is similar to other younger WHG. The distinctness of CHG can be clearly seen on a principal component analysis (PCA) plot11 loaded on contemporary Eurasian populations1, where they fall between modern Caucasian and South Central Asian populations in a region of the graph separated from both other hunter gatherer and EF samples (Fig. 1a). Clustering using ADMIXTURE software12 confirms this view, with CHG forming their own homogenous cluster (Fig. 1b). The close genetic proximity between Satsurblia and Kotias is also formally supported by D-statistics13, indicating the two CHG genomes form a clade to the exclusion of other pre-Bronze Age ancient genomes (Supplementary Table 2; Supplementary Note 3), suggesting continuity across the Late Upper Palaeolithic and Mesolithic periods. This result is mirrored in western Europe as Bichon is close to other WHG in PCA space (Fig. 1a) and outgroup f3 analysis (Supplementary Fig. 1), belongs to the same cluster as other WHG in ADMIXTURE analysis (Fig. 1b), and forms a clade with other WHG to the exclusion of other ancient genomes based on D-statistics (Supplementary Table 3; Supplementary Note 3). Thus, these new data indicate genomic persistence between the Late Upper Palaeolithic and Mesolithic both within western Europe and, separately, within the Caucasus.

Bottom Line: We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland.While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum.CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

View Article: PubMed Central - PubMed

Affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Dublin 2, Ireland.

ABSTRACT
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Show MeSH
Related in: MedlinePlus