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以古代及現代基因組重建人類歷史

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发表于 2013-9-28 04:18 | 显示全部楼层 |阅读模式
本帖最后由 natsuya 于 2013-9-28 13:01 编辑

Reconstructing the Human Past using Ancient and Modern Genomes


PONTUS SKOGLUND

Abstract

Skoglund, P. 2013. Reconstructing the Human Past using Ancient and Modern Genomes. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1069. 68 pp. Uppsala. ISBN 978-91-554-8744-7. The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modernday contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.
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 楼主| 发表于 2013-9-28 04:18 | 显示全部楼层
 楼主| 发表于 2013-9-28 04:35 | 显示全部楼层


常染色體分析圖示:越靠左邊者越接近現代南歐人,越靠右邊者越接近現代北歐人。

波羅的海島嶼中石器獵人:St. Förvar(灰點)
瑞典新石器獵人:Ajv52、Ajv53、Ajv58、Ajv59、Ajv70(藍點)
瑞典新石器農民:Ire8、Gok2、Gok4、Gok5、Gok7(紅點)
冰人Oetzi:Tyrolean Iceman(粉紅點)
西班牙中石器獵人:La Brana1、La Brana2(灰點)
 楼主| 发表于 2013-9-28 13:14 | 显示全部楼层
本帖最后由 natsuya 于 2013-9-28 13:16 编辑

有關尼人和丹人的未發表內容:

Some time after the emergence of early modern humans in Africa, their descendants expanded into Eurasia, and it has been suggested that they absorbed gene flow from archaic humans on at least two occasions: from Neandertals and from Denisovans further in the east (Green et al. 2010; Reich
et al. 2010). However, the distribution and extent of this ancestry has not
been investigated in a large set of worldwide human populations. To address
this, we overlapped genomic data from the Neandertal and Denisovan draft
genomes with genotypes from more than a thousand individuals from across
the globe from which we had information on half a million genetic markers
in the genome (Altshuler et al. 2010; Li et al. 2008b; Surakka et al. 2010).
Previous analyses had suggested that Neandertal ancestry was uniformly
distributed in Eurasia and the Americas, whereas Denisova ancestry was
restricted to Oceania (Reich et al. 2010). In Paper II, we performed principal component analysis on the chimpanzee, Neandertal, and Denisova genomes, and projected the present-day human populations on the resulting
axes of variation. We found that genetic affinity to the two archaic humans
increased from west to east in Eurasia, in contrast to previous suggestions.

However, using simulations we also showed that a serial founder model of
increasing genetic drift from west to east could produce a similar pattern in
data with ascertainment bias for common alleles (such as the empirical data
analyzed), but some southeast Asian populations affinities to archaic humans
(in particular Denisovans) were difficult to reconcile with this expectation
(see below). Recent analysis of the complete high-coverage Denisova genome have partly confirmed this view, arguing for a higher degree of archaic
Neandertal-related ancestry in East Eurasia (~1.7%) compared to West Eurasia (~1.0%) (Meyer et al. 2012). In our analysis we also found that on the
East Asian mainland, southern populations showed significantly higher degree of genomic affinity to the Denisova genome compared to northern populations. In the light of the Central Siberian location of Denisova cave, this
casts new light on the previously puzzling observations that Denisovan ancestry was completely restricted to the Oceanian islands, and absent from
mainland East Asia (Reich et al. 2010; Reich et al. 2011).
Our study suggests that the original admixture event could have taken place on the mainland, but the genetic traces may have been subsequently diluted by later migrations.
Denisovans share a common origin with Neandertals, but were genetically
differentiated from Neandertals in Europe and the Caucasus (Reich et al.
2010). In Paper V, we obtained a complete mitochondrial genome sequence
from a Neandertal in Okladnikov cave, close to the Denisova cave, and show
that its mtDNA lineage is basal to all published complete Neandertal
mtDNA sequences from Central and Western Europe.
However, robust conclusions about Neandertal population structure and their genetic history with
Denisovans will require more genomic information from both populations.
These studies will also provide more information on when and how admixture with modern humans took place.
 楼主| 发表于 2013-9-28 13:40 | 显示全部楼层
In Paper II, we performed principal component analysis on the chimpanzee, Neandertal, and Denisova genomes, and projected the present-day human populations on the resulting
axes of variation. We found that genetic affinity to the two archaic humans
increased from west to east in Eurasia, in contrast to previous suggestions.


In Paper II,該研究分析黑猩猩、尼人、丹人、現代人基因組,與之前的研究論點相反的是,該研究發現現代歐亞人群當中與尼人及丹人的親緣性是由西往東逐漸升高。

In our analysis we also found that on the East Asian mainland, southern populations showed significantly higher degree of genomic affinity to the Denisova genome compared to northern populations. In the light of the Central Siberian location of Denisova cave, this
casts new light on the previously puzzling observations that Denisovan ancestry was completely restricted to the Oceanian islands, and absent from mainland East Asia (Reich et al. 2010; Reich et al. 2011).


該研究分析發現,丹人的基因影響不僅見於大洋洲人群,同樣發現於東亞大陸人群,而且東亞南部人群的丹人成份還顯著高於東亞北部人群。

In Paper V, we obtained a complete mitochondrial genome sequence
from a Neandertal in Okladnikov cave, close to the Denisova cave, and show
that its mtDNA lineage is basal to all published complete Neandertal
mtDNA sequences from Central and Western Europe.


In Paper V,該研究取得西伯利亞Okladnikov洞穴的阿爾泰尼人mtDNA完整基因組序列,此阿爾泰尼人生前居住的洞穴在地理上十分接近先前發現的丹人洞穴。透過分析此阿爾泰尼人的mtDNA,發現其mtDNA單倍群相較其他歐洲中西部的尼人mtDNA單倍群,更處於尼人mtDNA tree的根部位置,意味著阿爾泰尼人的mtDNA單倍群較早於其他尼人分開的。
发表于 2013-9-28 16:45 | 显示全部楼层
尼人成份又降下来啦,降到2%不足了。剩下的只有用建人来补了
发表于 2013-9-28 17:58 | 显示全部楼层
还没仔细看,但方法和工具的不同,上下差一些很正常,admixture在CHB、JPT平均是3.2%,23andme用的那个工具是2.9%。
 楼主| 发表于 2013-9-28 22:00 | 显示全部楼层
尼人成份又降下来啦,降到2%不足了。剩下的只有用建人来补了
hercules 发表于 2013-9-28 16:45
大力兄說的建人應該跟丹人(Denisovan)是一回事吧?
发表于 2013-9-29 13:35 | 显示全部楼层
大力兄說的建人應該跟丹人(Denisovan)是一回事吧?
natsuya 发表于 2013-9-28 22:00
是的,俄语t、d在i、e之前是要腭化的,Putin港台译作普亭,大陆译作普金。
发表于 2013-9-29 13:46 | 显示全部楼层
Denisova的俄语正确音译应该是杰尼索瓦。
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