Pallantides
10-03-2012, 08:29 PM
http://www.genetics.org/content/early/2012/09/06/genetics.112.145037.abstract
Ancient Admixture in Human History
Nick Patterson et al.
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred, and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses, and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples where they provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present day Basques and Sardinians, and the other related to present day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean ‘Iceman’.
http://blogs.discovermagazine.com/gnxp/files/2012/09/euro.png
We estimate an admixture date of 4150 ± 850 B.P. Our standard errors computed using a block jackknife (block size=5cM) are uncomfortably large here.
However this date must be treated with great caution. We obtained a data set from the Illumina iControl database (http://www.illumina.com/science/icontroldb.ilmn) of ‘Caucasians’ and after curation have 1,232 samples of European ancestry genotyped on an Illumina SNP array panel. We merged the data with the HGDP Illumina 650Y genotype data obtaining a data set with 561, 268 SNPs. Applying rolloff to this sample with HGDP Karitiana and Sardinians as sources, we get a much more recent date of 2200 ± 762 years B.P.
Ancient DNA studies have documented a clean break between the genetic structure of the Mesolithic
hunter-gatherers of Europe and the Neolithic first farmers who followed them. Mitochondrial
analyses have shown that the first farmers in central Europe, belonging to the Linear Pottery culture
(LBK), were genetically strongly differentiated from European hunter-gatherers (BRAMANTI
et al., 2009), with an ‘affinity’ to present day Near Eastern and Anatolian populations (HAAK
et al., 2010). More recently, new insight has come from analysis of ancient nuclear DNA from
three hunter-gatherers and one Neolithic farmer who lived roughly contemporaneously at about
5000 years B.P. in what is now Sweden (SKOGLUND et al., 2012). The farmer’s DNA shows a
signal of genetic relatedness to Sardinians that is not present in the hunter-gatherers who have
much more relatedness to present-day northern Europeans. These findings suggest that the arrival
of agriculture in Europe involved massive movements of genes (not just culture) from the Near
East to Europe and that people descending from the Near Eastern migrants initially reached as far
north as Sweden with little mixing with the hunter-gatherers they encountered. However, the fact
that today, northern Europeans have a strong signal of admixture of these two groups, as proven
by this study and consistent with the findings of (SKOGLUND et al., 2012), indicates that these two
ancestral groups subsequently mixed.
Ancient Admixture in Human History
Nick Patterson et al.
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred, and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses, and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples where they provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present day Basques and Sardinians, and the other related to present day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean ‘Iceman’.
http://blogs.discovermagazine.com/gnxp/files/2012/09/euro.png
We estimate an admixture date of 4150 ± 850 B.P. Our standard errors computed using a block jackknife (block size=5cM) are uncomfortably large here.
However this date must be treated with great caution. We obtained a data set from the Illumina iControl database (http://www.illumina.com/science/icontroldb.ilmn) of ‘Caucasians’ and after curation have 1,232 samples of European ancestry genotyped on an Illumina SNP array panel. We merged the data with the HGDP Illumina 650Y genotype data obtaining a data set with 561, 268 SNPs. Applying rolloff to this sample with HGDP Karitiana and Sardinians as sources, we get a much more recent date of 2200 ± 762 years B.P.
Ancient DNA studies have documented a clean break between the genetic structure of the Mesolithic
hunter-gatherers of Europe and the Neolithic first farmers who followed them. Mitochondrial
analyses have shown that the first farmers in central Europe, belonging to the Linear Pottery culture
(LBK), were genetically strongly differentiated from European hunter-gatherers (BRAMANTI
et al., 2009), with an ‘affinity’ to present day Near Eastern and Anatolian populations (HAAK
et al., 2010). More recently, new insight has come from analysis of ancient nuclear DNA from
three hunter-gatherers and one Neolithic farmer who lived roughly contemporaneously at about
5000 years B.P. in what is now Sweden (SKOGLUND et al., 2012). The farmer’s DNA shows a
signal of genetic relatedness to Sardinians that is not present in the hunter-gatherers who have
much more relatedness to present-day northern Europeans. These findings suggest that the arrival
of agriculture in Europe involved massive movements of genes (not just culture) from the Near
East to Europe and that people descending from the Near Eastern migrants initially reached as far
north as Sweden with little mixing with the hunter-gatherers they encountered. However, the fact
that today, northern Europeans have a strong signal of admixture of these two groups, as proven
by this study and consistent with the findings of (SKOGLUND et al., 2012), indicates that these two
ancestral groups subsequently mixed.