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Science: A high-coverage Neandertal genome from Croatia

本帖最后由 Ryan 于 2017-11-5 14:48 编辑

A high-coverage Neandertal genome from Vindija Cave in Croatia

To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.





http://science.sciencemag.org/content/358/6363/655
She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size.

不见得是因为尼人人口少。更有可能是因为尼人近亲结婚现象严重。以前的文章看就是的。
从图一可知,黑人杂和度高但人口少于非黑人。
极品猥琐凤凰眼镜生物党棍左棍五毛愤青爱国
八代贫农根正苗
远山劲松傲然孤独千秋万代一统浆糊
图4也有问题。左边说新几内亚人尼人基因最多。右边说东亚人尼人基因最多。
极品猥琐凤凰眼镜生物党棍左棍五毛愤青爱国
八代贫农根正苗
远山劲松傲然孤独千秋万代一统浆糊
本帖最后由 imvivi001 于 2017-11-5 10:07 编辑

很好! 再次印证我之前关于亚欧大陆现代智人各种成分尤其是东西两大成分的形成过程的推测。
与付团队刚刚发表的田园洞古人报告相比,本文只说到四种亚欧‘尼人’成分(其中包括丹人),而付团队提到六种~
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
3# 一统浆糊
看是否可以去NCBI再BLAST一下这个克罗地亚‘尼人’的基因片段,特别是与schizophrenia相关的片段,说不定可以发表一篇好论文呢~
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
很好! 再次印证我之前关于亚欧大陆现代智人各种成分尤其是东西两大成分的形成过程的推测。
与付团队刚刚发表的田园洞古人报告相比,本文只说到四种亚欧‘尼人’成分(其中包括丹人),而付团队提到六种~
imvivi001 发表于 2017-11-3 12:25
原来付本人也在这个团队之中,还有其它好几个马普所的大牛~
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
早几个月的另一篇关于这几个尼人的检测分析报告(paabo老师也参与其中)

Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition  http://www.pnas.org/content/114/40/10606

作者:Thibaut Devièsea,1, Ivor Karavanićb,c, Daniel Comeskeya, Cara Kubiaka, Petra Korlevićd, Mateja Hajdinjakd, Siniša Radoviće, Noemi Procopiof, Michael Buckleyf, Svante Pääbod, and Tom Highama

Abstract
Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000–29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ~32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe.
We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1–G3.
    These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size.

不见得是因为尼人人口 ...
一统浆糊 发表于 2017-11-3 10:23
估计还是人口规模的因素。如果人口规模大,自然择偶空间就大,allele的多样性自然就出来了。

另外,好像之前有研究表明,尼人的生育能力差于现代智人(文章一下子找不到了,谁有的话,可以分享一下),如果是这样的话,那两个人种相处,长期以往,我们的现代智人先祖就会把我们的尼人与丹人先祖‘取代掉’~
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
另外,这个古人的时间段也有一些特殊,正好是意大利超级火山爆发的前后,会不会正好是爆发之后,所以造成人口规模急剧下降?
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
Humans and Neanderthals Branched off 600,000 years ago Due to an Incompatible Y Chromosome | Ancient Origins  http://www.ancient-origins.net/n ... compatible-y-020804


8 APRIL, 2016 - 21:51 作者:
MARK MILLER


Humans and Neanderthals Branched off 600,000 years ago Due to an Incompatible Y Chromosome

Neanderthals and humans branched off about 600,000 years ago, possibly because of genetic incompatibility in the context of the Y chromosome, a team of researchers has announced.
There was some interbreeding between Homo sapiens and Neanderthals around 100,000 to 60,000 years ago, previous research has shown.
The latest research speculates that male children conceived between a Homo sapien woman and a Neanderthal man would have resulted in miscarriage, an article in New Scientist says. The research posits that the most recent common ancestor between humans and Neanderthals lived around 590,000 years ago. This time frame is compatible with other researchers’ estimates.

A model of an adult Neanderthal male head and shoulders on display in the Hall of Human Origins in the Smithsonian Museum of Natural History in Washington, D.C. ( CC BY SA 2.0 )

“Neanderthal genes have been found in our genomes, on X chromosomes, and have been linked to traits such as skin color, fertility and even depression and addiction,” the article states. “Now, an analysis of a Y chromosome from a 49,000-year-old male Neanderthal found in El Sidrón, Spain, suggests the chromosome has gone extinct seemingly without leaving any trace in modern humans. This could simply be because it drifted out of the human gene pool or, as the new study suggests, it could be because genetic differences meant that hybrid offspring who had this chromosome were infertile – a genetic dead end.”
The study offered  that the woman’s immune system may have attacked the fetuses that had the Neanderthal Y chromosome due to incompatibility. Over time, the consistent miscarriages could have led to the absence of these genes in modern humans.


Stanford University’s Fernando Mendez led the research, published in the American Journal of Human Genetics , comparing ancient and modern humans, Neanderthal, and chimpanzee Y chromosomes. New Scientist says they determined mutations in four genes that could have prevented the Y chromosome to pass from Neanderthal fathers to the hybrid children.
“Some of these mutations could have played a role in the loss of Neanderthal Y chromosomes in human populations,” Mendez said.

Relationship of Neanderthal Y Chromosome to Those of Modern Humans. The genealogy (red tree) can be parsimoniously explained as mirroring the population divergence (gray tree). The researchers find no evidence for (a) a highly divergent super-archaic origin of the Neanderthal Y chromosome, (b) ancient gene flow post-dating the population split, or (c) relatively recent introgression of a modern human Y chromosome into the Neanderthal population. ( Mendez et al. )

An October 2015 article by Darren Curnoe on The Conversationreported much the same about the Y chromosome. Curnoe said:
“Over the past half-decade, ancient DNA research has revealed some surprising aspects to our evolutionary history during the past 50,000 years. Perhaps the most startling of these has been the extent to which the ancestors of living people across the planet interbred with other closely related species of human. […] One particularly interesting example compared the genome of a female Neanderthal with 1,000 contemporary human ones from across the world and found clear evidence for negative selection. Mapping the DNA of Neanderthals against this large number of human genomes also showed that there were vast ‘deserts’ of Neanderthal ancestry. One million base pairs compared across the autosomes (i.e. other than the X or Y chromosomes) showed four windows in Europeans and 14 in East Asians where around 0.1% of the DNA was Neanderthal. The human Y chromosome is also known to be lacking Neanderthal DNA suggesting strong natural selection against hybrid males, who were likely to have been infertile.”
In January 2016, a paper published in The American Journal of Human Genetics said other studies have found that modern human immunitywas boosted by interbreeding with what the authors call “archaic humans.” The genes the authors studied, human toll-like receptors, were possibly passed down to modern humans when they and Neanderthals interbred around 50,000 years ago.

Comparison of Modern Human and Neanderthal skulls from the Cleveland Museum of Natural History. (Deriv) ( CC BY SA 2.0 )

Researchers have estimatedthat 1 to 6 percent of modern Eurasian genes came from now extinct hominins, including the Denosivans and Neanderthals.
Featured Image: An artist’s depiction of a family of Neanderthals. Source: Public Domain
By Mark Miller

(如果看不到图片,可打开文章链接直接查看)
物格而后知至,知至而后意诚,意诚而后心正,心正而后身修,身修而后家齐,家齐而后国治,国治而后天下平...
3# 一统浆糊
看是否可以去NCBI再BLAST一下这个克罗地亚‘尼人’的基因片段,特别是与schizophrenia相关的片段,说不定可以发表一篇好论文呢~
imvivi001 发表于 2017-11-3 12:39
有道理!
极品猥琐凤凰眼镜生物党棍左棍五毛愤青爱国
八代贫农根正苗
远山劲松傲然孤独千秋万代一统浆糊
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