The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods.
The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods.
复制标题
DOI：
10.1371/journal.pgen.1006852
复制
发表时间：
2017-07
期刊：
影响因子：
4.5
通讯作者：
Bradley DG
中科院分区：
文献类型：
--
作者：
Martiniano R;Cassidy LM;Ó'Maoldúin R;McLaughlin R;Silva NM;Manco L;Fidalgo D;Pereira T;Coelho MJ;Serra M;Burger J;Parreira R;Moran E;Valera AC;Porfirio E;Boaventura R;Silva AM;Bradley DG
我们分析了从新石器时代中期（公元前4200-3500年）到青铜时代中期（公元前1740-1430年）来自葡萄牙的14个古代个体的新基因组数据（0.05 - 2.95倍），并将这些个体与已发表的古代欧亚人的全基因组二倍基因型进行了计算。虽然在整个地区向农业过渡的过程中明显存在不连续性，但基于单倍型的敏感分析表明，当地狩猎采集者对后来的伊比利亚新石器时代人口有很大程度的贡献。从分析古代和现代基因组的单倍型共享、d统计和y染色体谱系可以发现，在青铜时代也有更微妙的基因涌入。然而，这种渗透的有限性与第三个千年北欧的主要草原迁移形成鲜明对比，并与伊比利亚半岛非印欧语言的生存相呼应。在整个欧洲，个体身高的基因组估计的变化也与这些主要的文化转变有关，而祖先成分继续与现代身高差异相关。最近的古代DNA研究表明，在新石器时代向青铜时代过渡期间，从草原到中欧和北欧的大规模迁徙对基因产生了重大影响。在伊比利亚，在物质文化和丧葬仪式层面上的考古变化在这一时期得到了报道，然而，与这种文化转变相关的遗传影响尚未得到估计。为了调查这一点，我们对来自葡萄牙的新石器时代和青铜时代的样本进行了测序，并将其与其他古代和现代个体进行了比较。对古代样本的大数据集进行全基因组植入，使检测古代样本群体结构和选择的灵敏方法成为可能。我们揭示了葡萄牙新石器时代和青铜时代样本之间微妙的遗传差异，表明与其他欧洲地区相比，伊比利亚的人口流入明显减少。此外，我们预测了古代人的身高，这表明新石器时代的身高减少了，并受到后来的混合因素的影响。最后，我们研究了重要性状的强选择特征及其起源时间。
We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, the genetic impact associated with this cultural transformation has not yet been estimated. In order to investigate this, we sequence Neolithic and Bronze Age samples from Portugal, which we compare to other ancient and present-day individuals. Genome-wide imputation of a large dataset of ancient samples enabled sensitive methods for detecting population structure and selection in ancient samples. We revealed subtle genetic differentiation between the Portuguese Neolithic and Bronze Age samples suggesting a markedly reduced influx in Iberia compared to other European regions. Furthermore, we predict individual height in ancients, suggesting that stature was reduced in the Neolithic and affected by subsequent admixtures. Lastly, we examine signatures of strong selection in important traits and the timing of their origins.
登录
查看更多内容
影响因子：
9.8
作者：
Balaresque P;Bowden GR;Adams SM;Leung HY;King TE;Rosser ZH;Goodwin J;Moisan JP;Richard C;Millward A;Demaine AG;Barbujani G;Previderè C;Wilson IJ;Tyler-Smith C;Jobling MA
通讯作者：
Jobling MA
影响因子：
3
作者：
Korneliussen TS;Albrechtsen A;Nielsen R
通讯作者：
Nielsen R
DOI：
10.1126/science.1243518
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hellenthal G;Busby GBJ;Band G;Wilson JF;Capelli C;Falush D;Myers S
通讯作者：
Myers S
影响因子：
4.5
作者：
Berg JJ;Coop G
通讯作者：
Coop G
影响因子：
64.8
作者：
Fu Q;Li H;Moorjani P;Jay F;Slepchenko SM;Bondarev AA;Johnson PL;Aximu-Petri A;Prüfer K;de Filippo C;Meyer M;Zwyns N;Salazar-García DC;Kuzmin YV;Keates SG;Kosintsev PA;Razhev DI;Richards MP;Peristov NV;Lachmann M;Douka K;Higham TF;Slatkin M;Hublin JJ;Reich D;Kelso J;Viola TB;Pääbo S
通讯作者：
Pääbo S