The last pieces of a puzzling early meeting

doi:10.1126/science.abe2766

GSTDTAP > 气候变化

DOI	10.1126/science.abe2766
	The last pieces of a puzzling early meeting
	Mikkel Heide Schierup
	2020-09-25
发表期刊	Science
出版年	2020
英文摘要	Since the sequencing of the first Neanderthal and Denisovan genomes, genetic evidence has revealed an increasing number of admixture events between Homo sapiens and these archaic humans. However, scientists have lacked detailed information about Y chromosome sequences from our two closest relatives. Now, on page 1653 of this issue, Petr et al. ([ 1 ][1]) report intricate DNA sequencing data for Y chromosomes from less-than-well-preserved bones of male Neanderthals and Denisovans. Most scientific focus has been on genetic admixture from Neanderthals into H. sapiens ∼40,000 to 60,000 years ago (soon after the so-called main out-of-Africa event) (see the figure). This meeting resulted in the 1.5 to 2% of the Neanderthal-genome fragments present in the nuclear genomes of all non-Africans today ([ 2 ][2]). Gene flow between H. sapiens and Neanderthals was initially surprising, because earlier studies of mitochondrial DNA found no signs of gene flow ([ 3 ][3]). Furthermore, the sex chromosomes display a different pattern from that of autosomes, with no introgression of Neanderthal Y chromosomes into H. sapiens and less-than-expected introgression of the X chromosome. Because mitochondria and Y chromosomes represent single nonrecombining entities, they may have been lost by random genetic drift. The mitochondrion is transmitted by mothers alone, whereas Y chromosomes are transmitted from father to son. Thus, the lack of introgression of one or the other (but not both) could also result from sex differences between who had children together (for example, no mitochondria transfer occurs if Neanderthal fathers, but not mothers, contributed genetic material). Subsequent to these studies, evidence has accumulated that suggests a much earlier meeting between H. sapiens and Neanderthals in which the main gene flow went in the opposite direction ( H. sapiens to Neanderthals), first based on nuclear genomes ([ 4 ][4]) and later from mitochondrial data ([ 5 ][5]) (see the figure). This event affected only Neanderthals and not Denisovans. The gene flow to the nuclear genome was likely only 3 to 6% ([ 6 ][6]). However, all sequenced Neanderthal mitochondria are much more similar to the human mitochondrion than either are to the Denisovan mitochondrion, suggesting a total replacement of this organelle and evidence that H. sapiens females contributed to gene flow. The event has been difficult to date, but an upper bound of about 350,000 years ago can be derived from the genetic divergence of the mitochondrion and a lower bound of about 150,000 years ago from evidence that this gene flow event is shared among all sequenced Neanderthals. Until the new study by Petr et al. , archaeologists had only limited Y chromosome data from two Neanderthals ([ 7 ][7]) and no information on exchanges of Y chromosomes during the early meeting. The main reason is that the three fully sequenced Neanderthal individuals ([ 8 ][8]–[ 10 ][9]) and the single fully sequenced Denisovan individual ([ 11 ][10]) all happen to be females; no bones with a similar quality of noncontaminated DNA from archaic males were identified. Thus, Petr et al. used a capture-based DNA sequencing approach to enrich for Y chromosome sequences in less well-preserved bones from males. They succeeded in getting usable Y chromosome sequences from three male Neanderthals and two male Denisovans. The results mirror exactly the findings from the mitochondrion study—complete replacement of Neanderthal Y chromosomes (and no replacement of Denisovan Y chromosomes) with H. sapiens Y chromosomes (see the figure). The molecular dating falls well within the estimates from the mitochondrion and nuclear studies, making it a parsimonious explanation that all admixtures are from the same event. The new study solves important questions but fosters even more new ones. It unequivocally shows that both male and female H. sapiens contributed to gene flow, suggesting that both H. sapiens and Neanderthal populations accepted children of mixed heritage. Researchers do not yet have genetic evidence from H. sapiens bones outside of Africa for the period in question, but it seems likely that they will show evidence of Neanderthal admixture. There are no genetic traces of the H. sapiens population from the meeting 350,000 to 150,000 years ago in present day humans except for small pieces of the genome that H. sapiens eventually got back from Neanderthals in the much later meeting. A rapid and total replacement of both the Y chromosome and mitochondrion seems too much of a coincidence to be driven by chance alone, especially given the relatively small contribution of H. sapiens to the Neanderthal nuclear genome. Some form of natural selection must have contributed. It is as yet anyone's guess what the selective agent might have been. Because both the Y chromosome and mitochondrion are inherited as nonrecombining units, it is exceedingly difficult to locate targets of natural selection on them. ![Figure][11] Gene flow in two meetings (Top) A small group of Homo sapiens left Africa for Europe (red arrow), where they transferred genes to Neanderthals (blue arrow) and later went extinct. (Bottom) A second, larger group of Homo sapiens left Africa for Europe (thick red arrow), where they received genes from Neanderthals who later went extinct (blue arrow, flow in opposite direction). The tables show the amount of each type of genetic material transferred after the two migrations. ka, thousand years. GRAPHIC: X. LIU/ SCIENCE Neanderthals likely had a much lower population size than H. sapiens during the 500,000 to 700,000 years of separation ([ 9 ][12]), making Neanderthals more prone to the accumulation of harmful genetic variants. Petr et al. use simulations of accumulations of deleterious variants on the Neanderthal Y chromosome that cause it to have a lower fitness than the H. sapiens Y chromosome. The results show that under reasonable parameter assumptions, this process could explain the replacement; but the authors emphasize that this is a possibility and not proof. By the same argument, scientists could expect selection for the H. sapiens fragments in the nuclear genome. However, this is not suggested from the low percentage of H. sapiens fragments in the Neanderthal nuclear genome. Thus, other selective forces private to the Y chromosome might be at play. Recent results suggest complex replacements of modern human Y chromosomes after the last out-of-Africa event, which are indicative of recurrent positive selection by an unknown agent ([ 12 ][13]). Y chromosomes have very fast and structurally complex evolution ([ 13 ][14]), and their variation is associated strongly with male fertility. The introgression patterns of X, the Y chromosome partner, also differs notably between the two gene flow events, with Neanderthal accepting more H. sapiens X chromosomes in the early meeting and vice versa in the later meeting. This is the same qualitative pattern seen for the Y chromosome. Thus, another possibility is that the X and Y chromosomes of H. sapiens and Neanderthals did not fit well together during male meiosis, and this affected male fertility. Sequencing of male Neanderthal bones from the critical period between 150,000 and 300,000 years ago might resolve these questions. 1. [↵][15]1. M. Petr et al ., Science 369, 1653 (2020). 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领域	气候变化 ; 资源环境
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引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/296478
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Mikkel Heide Schierup. The last pieces of a puzzling early meeting[J]. Science,2020.
APA	Mikkel Heide Schierup.(2020).The last pieces of a puzzling early meeting.Science.
MLA	Mikkel Heide Schierup."The last pieces of a puzzling early meeting".Science (2020).