University of California, Berkeleyが行った、5万年前のネアンデルタール人の女性の足の指の骨から採取されたDNAを用いた これまで行われたものとしてはもっとも完璧なネアンデルタール人のゲノム解析の結果から、 ネアンデルタール人は少なくヨーロッパとアジアにいた4種類の異なる初期人類との間で異種交配が行われてことが判った。
Specimens in Level G3 (38,000-45,000 years bp), the lowest hominin-bearing level, are Neanderthals and are associated with exclusively Mousterian artifacts. Specimens in Level G1 (32,000-34,000 years bp) represent the most recent Neanderthals at the site and are associated with both Mousterian and Upper Paleolithic stone tools. Hominins in Level F (31,000-28,000 years bp) are associated with Aurignacian and according to researchers look a little like both AMH and Neanderthal. Hominins in Level D (less than 18,500 years bp, the uppermost hominid-bearing strata in the cave, are associated with Gravettian culture artifacts, and represent only anatomically modern humans.
この研究では、スペイン北部の通称「骨の穴(Sima de los Huesos)洞窟」で発見された人骨のDNAが解析・比較されています。 「骨の穴洞窟」では少なくとも28個体分となる30万年以上前の更新世中期の人骨が多数発見されており、 「骨の穴洞窟」は世界最多の更新世中期の人骨が発見された遺跡となります。 「骨の穴洞窟」はスペイン北部のアタプエルカ丘陵地にある複雑な洞窟群の一つで、古人類学では有名な遺跡です。
Table S8.6: Summary of lineage specific homozygous deletions identified along the Neandertal-Denisova branch.
lineage bp loci Neandertal-Denisova 141723 35 Neandertal 646519 77 Denisova 723582 100
Deletions
We next assessed lineage specific fixed/homozygous deletions in the Altai Neandertal and Denisova individual identifying 212 regions encompassing a total of 1.5Mbp of sequence lost along these lineages (Table S8.5 attached, Table S8.6). Among these loci, 17 exon deletions were identified on the archaic lineages (Table S8.7), including complete loss of the GSTT1, MRGPRG, and C11orf36 genes and partial loss of the GSTTP2 and SPINK14 genes along the Denisova-Neandertal ancestral lineage. Each of GSTT1, MRGPRG and C11orf36 show copy number polymorphism among modern humans and GSTT1 shows strong continental population stratification with Asian populations having higher frequency of loss (Figure S8.5).
Figure S8.5: Copy number genotypes of the GSTT1 gene in 675 diverse humans from the 1000 Genomes Project, the Denisova, Neandertal and three non-human great ape genomes. Asian populations show a higher frequency of homozygous and hemizygous deletions than African or European populations.
Supplementary Information 12 Population size changes and split times
(i) Findings ? The Altai Neandertal was inbred and its ancestral population size was low. ? We estimate that Neandertals and Denisovans split 381-473 kya (assuming μ = 0.5×10-9/bp/year). ? We estimate that archaic and modern humans split 550-765 kya (assuming μ = 0.5×10-9/bp/year). ? We estimate that the Neandertal/Denisovan split time was 58-86% of that from modern humans.
Table S12.1: Relative estimates of heterozygosity from three methods Altai/other ratio GATK calls mlrho SAMtools Altai/Denisova 82% 89% 95% Altai/Karitiana 31% 30% 34% Altai/San 16% 16% 19%
This revealed that Neanderthal DNA sequences and those of present-day humans share common ancestors on average about 800,000 years ago and that the population split of Neanderthal and modern human ancestors occurred 270,000?440,000 years ago
This has shown that all Neanderthals studied so far share a common mtDNA ancestor on the order of 100,000 years ago10, and in turn, share a common ancestor with the mtDNAs of present-day humans about 500,000 years ago10, 18, 19 (as expected, this is older than the Neanderthal?modern human population split time of 270,000?440,000?years ago estimated from the nuclear genome8)
In 2008, the distal manual phalanx of a juvenile hominin was excavated at Denisova Cave. This site is located in the Altai Mountains in southern Siberia, and is a reference site for the Middle to Upper Palaeolithic of the region where systematic excavations over the past 25?years have uncovered cultural layers indicating that human occupation at the site started up to 280,000?years ago20. The phalanx was found in layer 11, which has been dated to 50,000 to 30,000?years ago. This layer contains microblades and body ornaments of polished stone typical of the ‘Upper Palaeolithic industry’ generally thought to be associated with modern humans, but also stone tools that are more characteristic of the earlier Middle Palaeolithic, such as sidescrapers and Levallois blanks21, 22, 23.
Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils2, 3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6, 7, 8.
Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9, 10, an eastern Eurasian sister group to Neanderthals.
Our results pave the way for DNA research on hominins from the Middle Pleistocene.
Inferred time to the most recent common ancestor (TMRCA) of the modern human, Neanderthal, chimpanzee and bonobo mtDNAs, as well as divergence estimates for human/chimpanzee and bonobo/chimpanzee mtDNA (continuation of Table 1)
. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes10, 11, 12.
Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture1, 2. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci1, 3, 4, 5, 6, 7, 8. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans9. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes10, 11, 12. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%).
Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.