返回列表 回复 发帖

Assessing the relationship of ancient and modern populations

AbstractGenetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequencing more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.

http://www.biorxiv.org/content/early/2017/03/04/113779?%3Fcollection=
...
we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.
Tocharian_2 发表于 2017-3-5 16:23
总体上作者所表达的意思是可以成立的,但是因为个别辞语表达不到位,会造成一些令人混淆之处。
比如他本文所说的“the most ancient Europeans”主要是指旧石器时代的欧洲人(包括罗马尼亚oase古人、GoyetQ-2、GoyetQ53-1、Villabruna古族群、El Miron、瑞士古游猎者族群等),迟至去年大量的检测结果我们已经清楚,这些欧洲‘古人’并非都对现代欧洲人的基因做出了明显的贡献。其中,Villabruna古族群与瑞士古游猎者族群对现代欧洲人贡献非常明显,特别是瑞士古族群对现代中北欧的血统贡献最多,平均而言高达30%左右,因此绝不能简单的说the most ancient Europeans appear to have had the smallest effective,这是具有误导性的。


  当然,作者也承认,新石器的农业人口对现代欧洲人的血统影响巨大,这个是符合事实的。
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...
本帖最后由 imvivi001 于 2017-3-7 12:24 编辑

对于这篇论文,有一些爱好者们提出了一些不同看法,其中一位这样评论说:
The big problem I see here is "Similarly, we only consider a single ancient population at a time, albeit with multiple samples. Ideally, ancient samples would be embedded in complex demographic models that include admixture, detailing their relationships to each other and to modern populations [Patterson et al., 2012, Lipson and Reich, 2017]."

Clearly no single population is going to be ancestral to "Europeans" - CEU. Of those they test Bell Beaker Germany would likely be closest... but even then will this one Bronze Age set of samples have all the variants to converge with CEU's ancestors via their model? Heterozygosity will be higher in modern Europeans from pooling distinct isolated populations that existed at, e.g. Bronze Age time period (which may have been quite similar in terms of the major components we think about).

(To some extent I got an impression here (perhaps wrongly) that they were thinking of these populations as having broken off at some point from a single population who were the single true ancestors of CEU, and then to have gone through greater drift and smaller population than the real ancestors... but of course that wouldn't make any sense.)March 5, 2017 at 6:48 AM


对此,作者 Joshua Schraiber 如是回复:

   Hey y'all, I'm the author of the preprint. You're absolutely right---the lack of signal of direct ancestry in Europe is primarily a result of the fact that modern Europeans are extremely mixed, so the result is really not super exciting. Frankly, the model is misspecified for Europeans, but Europe happens to be the place where there's the most ancient data so I thought it would the most interesting demonstration of the way the method works.I also absolutely agree that CEU are not a particularly good stand-in for "all Europeans". I mostly chose them as an example in the paper because they are often used as the default European stand-in, and I couldn't figure out a nice way to present results from, e.g., all the 1000 Genomes EUR populations simultaneously.

I'll take the thoughts here into account and try to think of a better way to present the empirical results in a revision. Honestly, I'm a theoretician; the thing I think is the coolest in the manuscript is the diffusion theory in the methods :)
March 5, 2017 at 11:02 AM

很明显,作者也承认他的表述存在一些误导性,主要还是源自对现代欧洲人的选样问题,也没有充分考虑欧洲血统在历史长河中的分分合合因素,这个因素上面的那位评论者已经援引赖希氏团队最新的成果予以阐述了(Lipson and Reich, 2017,也是前不久我与大家在本坛本栏目热烈讨论的那篇论文)当然,对于作者在文中重点推广的diffusion theory,我们需要认真地学习一下,估计也是一个比较好的新视野~
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...
关于,目前一些专业工作者对欧洲血统前后延续性的误读,我之前已经根据当今主流大咖们的最新科研成果予以纠偏了,如下:
      这篇来自中国社会科学报的采访报道存在一些明显的偏差。比如说,并不是早期的欧洲人没有给后人留下基因,事实上,论文清楚地指出很早之前的古欧洲奠基者人群一度在长达1万4千年多年间几乎消失了,之后在长达冰期即将结束前的旧石器时期再度出现在欧洲,而且把他们的基因流传给了其后直至今天的的欧洲人。
     另外,这篇由代表中科院人类起源重点实验室的付大美主创、携手国际多家知名专业机构同时汇集了当今国际分子人类学最豪华阵容学者所完成的业内重磅力作,还揭示了一个令所有参与者都感到非常惊讶的发现,那就是现代欧洲人最主要的先祖,以Villabruna古族群为代表的欧洲人直系先祖,不仅早在旧石器结束前就“沾染”了来自近东入群的血统,而且,其中一部分人还居然具有与 ...
imvivi001 发表于 2017-2-18 02:59
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...
返回列表
baidu
互联网 www.ranhaer.org