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Post by Admin on Jul 7, 2017 19:33:19 GMT
 The Bulletin of the International Association for Paleodontology recently published the study. The researchers analyzed four isolated but associated mandibular teeth on the left side of the Neanderthal's mouth. Frayer's co-authors are Joseph Gatti, a Lawrence dentist, Janet Monge, of the University of Pennsylvania; and, Davorka Radovčić, curator at the Croatian Natural History Museum. The teeth were found at Krapina site in Croatia, and Frayer and Radovčić have made several discoveries about Neanderthal life there, including a widely recognized 2015 study published in PLOS ONE about a set of eagle talons that included cut marks and were fashioned into a piece of jewelry.  Even though the teeth were isolated, previous researchers were able to reconstruct their order and location in the male or female Neanderthal's mouth. Frayer said researchers have not recovered the mandible to look for evidence of periodontal disease, but the scratches and grooves on the teeth indicate they were likely causing irritation and discomfort for some time for this individual. They found the premolar and M3 molar were pushed out of their normal positions. Associated with that, they found six toothpick grooves among those two teeth and the two molars further behind them. The features of the premolar and third molar are associated with several kinds of dental manipulations, he said. Mostly because the chips of the teeth were on the tongue side of the teeth and at different angles, the researchers ruled out that something happened to the teeth after the Neanderthal died. Past research in the fossil record has identified toothpick grooves going back almost 2 million years, Frayer said. They did not identify what the Neanderthal would have used to produce the toothpick grooves, but it possibly could have been a bone or stem of grass.  The evidence from the toothpick marks and dental manipulations is also interesting in light of the discovery of the Krapina Neanderthals' ability to fashion eagle talons fashioned into jewelry because people often think of Neanderthals as having "subhuman" abilities. "It fits into a pattern of a Neanderthal being able to modify its personal environment by using tools," Frayer said, "because the toothpick grooves, whether they are made by bones or grass stems or who knows what, the scratches and chips in the teeth, they show us that Neanderthals were doing something inside their mouths to treat the dental irritation. Or at least this one was." |
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Post by Admin on Jul 9, 2017 19:32:36 GMT
:format(webp)/cdn.vox-cdn.com/uploads/chorus_image/image/55569277/HST_Femur.0.jpg) It’s not entirely clear when humans and Neanderthals split — and there are conflicting answers in ancient DNA. The 124,000-year-old leg bone offers scientists a peek at the DNA animals get primarily from their mothers, tucked away in the cells’ energy generators. It looked a lot more human-like than it should, according to scientists led by Cosimo Posth at the Max Planck Institute for the Science of Human History. We knew already that human ancestors interbred with Neanderthals. Even today, we can see signs of the inter-species hookups in the genomes of people with European ancestry. We also know that genes flowed in the opposite direction: DNA from a 130,000-year-old Siberian Neanderthal included chunks that looked human. /cdn.vox-cdn.com/uploads/chorus_asset/file/8797361/Stadel_Excavation_1937.jpg) But that’s weird: humans didn’t engage in mass migration from Africa, their home turf, to Europe, Neanderthal territory, until 75,000 years ago. Early human-like DNA suggests that a female ancestor of modern humans gave birth to a Neanderthal several hundred thousand years before humans and Neanderthals were first thought to meet. Does that mean a small group of archaic humans left Africa early, and interbred before the big migration? Today’s findings, in the journal Nature Communications, suggest that it could. It’s an interesting and provocative explanation, says Joshua Schraiber, a population geneticist at Temple University who was not involved in the research. And both he and Posth are eager to see if further genetic analyses back it up. |
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Post by Admin on Jul 11, 2017 19:49:36 GMT
 Figure 1: Archaic and modern humans' mtDNA and nDNA evolutionary scenarios. a) Pictures of the HST femur, (b) map of archaeological sites where complete mtDNA from archaic humans were reconstructed, (c) maximum parsimony tree of 54 modern human (collapsed), 18 Neanderthal, 3 Denisovan and 1 Sima de los Huesos mtDNAs built with coding region only and 98% partial deletion. Grey node numbers refer to bootstrap support after 1,000 iterations. Tree rooted with a chimpanzee mtDNA (not shown). (d) Schematic comparison of the nDNA (wide lines) with the mtDNA (thin lines) phylogenies of Neanderthals, Denisovans and modern humans. In c,d, colour legend for individual symbols and node numbers is illustrated in the horizontal time line. Node numbers in rectangular boxes are divergence times estimated in this study (Table 1), while in oval boxes are dates estimated in Prüfer et al.5 and Meyer et al.3 in thousand years before present. Red and blue tree branches represent supposed African and Eurasian distribution, respectively. In recent years, an increasing number of mitochondrial DNA (mtDNA) and nuclear genome (nDNA) data from archaic human remains have reshaped the understanding of evolutionary relationships among various hominin groups. Mitochondrial genomes provided evidence for at least two distinct mtDNA branches associated with Neanderthals and Denisovans, respectively, suggesting a sister group relationship between modern humans and Neanderthals with Denisovans as a basal mtDNA outgroup1,2,3,4. However, nDNA data revealed that Neanderthal and Denisovan populations separated only after their divergence from the lineage leading to modern humans2,5,6,7,8. The estimate for the population split time between the two archaic hominin groups and modern humans was calculated to 765,000–550,000 years ago (765–550 ka) based on a recent estimate of the genome-wide human mutation rate5. Furthermore, analyses of Y-chromosome data from a male Neanderthal returned an age of 806–447 ka for the divergence of Neanderthal and modern human Y-chromosome lineages9. These time intervals largely overlap, suggesting that the Neanderthal Y chromosome differentiated through the population split from the most recent common ancestor (MRCA) of modern humans and Neanderthals. In contrast, the corresponding divergence time for mtDNA has been dated to ∼400 ka (95% highest posterior density (HPD), 498–295 ka)10,11 and was thus found to be considerably younger compared to the time estimates obtained from autosomal and Y-chromosome data.  In addition, nDNA analyses of the Middle Pleistocene hominins from the Sima de los Huesos site in northern Spain confirmed their closer affinity to the Neanderthal lineage8, suggesting that at least by ∼430 ka, Neanderthals and Denisovans had already diverged (Fig. 1d). However, in contrast to genome-wide data, the Sima de los Huesos mtDNA was found to branch off with the deeply divergent Denisovan mtDNA lineage3. The phylogenetic discrepancies could be reconciled if the mtDNA of early Neanderthals was indeed Denisovan-like and was subsequently replaced by a more derived mtDNA lineage. Therefore, a genetic introgression event from African hominins into the early Neanderthal population that gave rise to the ‘Late Pleistocene’ Neanderthal mtDNA lineage has been proposed8. This event must have occurred after archaic and modern human populations diverged. However, the exact timing of the proposed gene flow is unknown and merely based on possible archaeological evidence for contacts between African and Eurasian populations8. While genomic evidence showed that gene flow between lineages as divergent as modern humans and Neanderthals took place12,13 in both directions14, it is unclear whether such small-scale phenomena were sufficient to explain the complete replacement of the initial Neanderthal mtDNA pool (found in Sima de los Huesos) by a Middle Pleistocene human lineage from Africa. Moreover, the temporal placement of such admixture event into Neanderthal populations is still under debate, partly due to the limited availability of additional archaic DNA. Therefore, an assessment of the feasibility of such a replacement as well as the availability of more ancient specimens is required to conclude whether the African introgression hypothesis is a viable one and to refine its time boundaries. |
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Post by Admin on Jul 13, 2017 19:13:59 GMT
MtDNA Neanderthal diversity In a previous study2, the mtDNA diversity among seven Neanderthals, three Denisovans and 311 modern humans were compared through the Watterson’s estimator θw, resulting in the lowest mtDNA distance within Neanderthals. The value decreased even further when 10 additional Neanderthal mtDNAs available in the literature were included (1.37 × 10−3), which confirms the small population size of late Neanderthals26 (Supplementary Table 4). However, by adding the HST mtDNA in the Neanderthal group the θw estimation almost doubled to 2.50 × 10−3. Although the value is still below the results obtained from the three Denisovan sequences (3.46 × 10−3), the HST mtDNA exhibits an average pairwise nucleotide distance to the other Neanderthal mtDNAs of 104 (89–111) positions (Fig. 2 and Supplementary Table 5). These values are greater than among any Denisovan mtDNA pair and are in the upper range of the modern human worldwide pairwise distance distribution (Fig. 2). This shows that HST belongs to a mtDNA branch highly divergent from the one represented in other Neanderthals (Altai branch) and overall Neanderthal mtDNA diversity was larger than that assumed previously.  Figure 2: Archaic and modern humans' mtDNA diversity. The pairwise nucleotide distance over its frequency (in logarithmic scale) is measured among 311 worldwide modern human, 17 Neanderthal, 3 Denisovan and 18 Neanderthal (including HST) mtDNAs. Points on the x axis represent one sequence pair comparison. The Neanderthal mtDNA effective population size (Ne) through time was estimated in a Bayesian statistical framework33 under the simplified assumption they belonged to a panmictic population with a fixed mutation rate previously calculated with ancient modern human mtDNAs as calibration points10 (Supplementary Note 4). The reconstructed skyline plot describes a Ne reduction through Middle and Late Pleistocene, reaching the lowest mean value at around 42 ka (Supplementary Fig. 7). Subsequently, a steep population expansion appears to have occurred before the Neanderthal extinction, in accordance with the reported analyses of chromosome 21 of the Vindija late Neanderthal14  |
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Post by Admin on Jul 15, 2017 19:56:48 GMT
 Table 1: Divergence times and molecular ages estimated in BEAST. Molecular dating analyses To estimate the molecular age of HST and other undated Neanderthal mtDNAs as well as the temporal range of MRCAs (TMRCAs) on the mtDNA tree, we performed a Bayesian dating analysis as implemented in BEAST v.1.8.1 (ref. 33). A multiple genome alignment of the coding region from 54 modern humans, 18 Neanderthals and 1 Denisovan mtDNA were tested for a strict and uncorrelated lognormal relaxed clock under both a constant size and a Bayesian skyline tree prior (see Methods section). As reported above, a fixed mutation rate was selected for the coding region10 with the addition of eight dated Neanderthal mtDNAs as time anchors on the Neanderthal branch (Supplementary Table 6). The four model combinations were compared by stepping-stone and path sampling (PS) methods34. This analysis indicated that a skyline model associated with a strict rate variation among branches is the model that most adequately fits the data (Supplementary Table 7). In Table 1 we report the TMRCAs between Neanderthal and modern human mtDNAs and among modern human mtDNAs itself, which largely overlap with previously published studies10,11. We further estimate the divergence time between HST and all other Neanderthals to ∼270 ka (95% HPD 316–219 ka), while the TMRCA for the Altai branch was inferred to be ∼160 ka (95% HPD 199–125 ka). Based on phylogenetic branch shortening, we then molecularly dated 10 Neanderthal sequences that had not been radiocarbon dated previously or were considered beyond the radiocarbon dating detection limit (Table 1). The two oldest mtDNAs were HST with an age of 124 ka (95% HPD 183–62 ka) and Altai Neanderthal with an age of 130 ka (95% HPD 172–88 ka). Notably, the mean value for the latter individual largely overlaps with the inferred age of 136–129 ka from its high coverage nuclear genome analyses, when applying recent estimates of the human mutation rate5.  Exploration of putative Neanderthal mtDNA replacements The probability that the initial Denisovan-like Neanderthal mtDNA present in Eurasia was totally displaced by an incoming lineage8 is dependent not only on the admixture rate but also on the size of the introgressing population compared to the local one (Supplementary Fig. 8). When considering the effective population size history estimated with the Bayesian skyline method (Supplementary Fig. 7), the probability that all Neanderthal mtDNA originated from an introgression event is almost directly proportional to the admixture rate (Supplementary Fig. 9 and Supplementary Note 5). Moreover, assuming that a complete mtDNA replacement took place, we estimated under neutrality35 (see Methods section) the mean time period necessary for such a lineage to reach fixation given a mtDNA introgressing fraction below 20% and initial effective population size (Ne) up to 10,000 units (Supplementary Table 8). We molecularly dated the split of the HST lineage from other Neanderthal mtDNAs to ∼270 ka (Table 1) that represents the minimum time available for the Late Pleistocene branch to replace the pre-existing Denisovan-like mtDNA. From our calculations, if Ne was <5,000 units, a mean temporal interval of 300 ka is sufficient for an incoming mtDNA lineage below 0.1% in frequency to drift up to fixation. Within the Late Pleistocene mtDNA clade, we explored if the HST mtDNA branch might have survived long after the estimated molecular age of the HST femur. All complete Neanderthal mtDNAs were combined with sequences from published hypervariable regions (HVRI) of four additional Neanderthal individuals. We identified the Valdegoba sequence (JQ670672) sharing three derived mutations with HST and falling on the same branch in a HVRI tree (Supplementary Fig. 10 and Methods section). This specimen was found on the Iberian Peninsula and dates to 48,400±3,300 14C years BP36. Although a complete mtDNA would be necessary to measure the total mtDNA distance between HST and Valdegoba, this finding might suggest that the HST branch was found during the Late Pleistocene as far as western Europe. Based on the geographical and temporal distributions of HVRI sequences, it was proposed that the Neanderthal population in western Europe underwent a demographic turnover followed by a subsequent recolonization36. Under that scenario, the HST lineage would have been largely replaced towards the end of the Neanderthal temporal range by mtDNAs descendants on the Altai branch. |
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