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Morphology of the Denisovan Phalanx Closer to Modern Humans Than to Neanderthals

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Morphology of the Denisovan Phalanx Closer to Modern Humans Than to Neanderthals

E Andrew Bennett et al. Sci Adv.

Abstract

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.

Figures

Fig. 1
Fig. 1. Model of the phylogeny of Neanderthal, Denisovan, and AMH populations over the past 1,400,000 years as deduced from both nuclear (blue envelope) and mitochondrial genomes (red lines).
The vertical axis represents time in thousands of years (ka) ago. Population divergence dates estimated from genomic data and mitochondrial genome bifurcation date estimations originate from Prüfer et al. and Meyer et al., respectively (3, 5). Markers on the left indicate the means of the estimates for dates, and error bars indicate 95% confidence intervals. Gene flow events inferred from genome sequences are represented as dotted blue arrows (see text).
Fig. 2
Fig. 2. Distribution of DNA fragment lengths mapping to the Denisova mitochondrial sequence.
Fragment lengths given in 10-bp bins are shown. Median is indicated by the dotted orange line. Read pairs that did not overlap sufficiently to be merged (i.e., longer than 134 nucleotides) but that could be mapped as paired-end reads were analyzed individually, and fragments carrying Denisovan single nucleotide polymorphisms (SNPs) were kept.
Fig. 3
Fig. 3. Views of the Denisova 3 DP5.
(A) Virtual reconstruction of the Denisova 3 DP5 in dorsal view. Three fragments of the Denisova 3 DP5 are shown. Natural color: Photograph of the distal two-thirds of the phalanx; green: semiring of the dorsal surface of the proximal extremity of the diaphysis of the reconstituted image based on the μCT scan; blue: its proximal articular surface. (B) Virtual reconstruction based on the μCT scan of the Denisova 3 DP5 in palmar view. (C) Virtual reconstruction of the proximal articular fragment in distal (top) and lateral (middle) views, and the dorsopalmar μCT section of this piece at the level of the fusion (bottom). The D-P line (D, dorsal; P, palmar) represents the location of the section on the distal view and helps to orient the bone in the lateral view. The red arrows indicate the fusing zone. (D) Additional views of the distal fragment and the virtual reconstruction of the proximal part of the Denisova phalanx. 1 and 2: Lateral views of the distal fragment; 3: distal; 4: proximal; 5 and 6: lateral views of the proximal fragment. The gray surfaces on the outer border of the phalanx correspond to the forceps with which the phalanx was held while the photo was taken. Photos of the distal part of the phalanx were taken by E.-M.G., IJM, CNRS, Université de Paris, UMR 7592, Paris, France. The renderings of the μCT scans and the virtual reconstruction were performed by B.V., Department of Anthropology, University of Toronto, Toronto, Canada.
Fig. 4
Fig. 4. Measurements of the Denisovan fifth finger phalanx and comparison with those of Neanderthals and AMHs.
(A) Schematic representation of the various measurements of digital phalanges reported in Table 2 and here: ML, maximal length; PH, proximal height; PAH, proximal articular height; PB, proximal breadth; PAB, proximal articular breadth; MH, midshaft height; MB, midshaft breadth; DB, distal breadth; DH, distal height. (B) Comparison of the dorsal view of the DP5 of a Neanderthal (Krapina 206.12), a recent modern human, and the reconstructed Denisova 3. (C) Scaled Z-scores of the Denisova 3 dimensions (Den) compared to both Neanderthal (NEAND) and pooled modern human (MH) ranges of variation. Den_Neand, Den_RMH, Den_NDP5, and Den_MDP5 indicate the comparison of the values of Denisova’s DP5 with the mean and SD of each comparative group from Table 2: NEAND_DP and MH_DP, all distal phalanges; NDP5 and MDP5, DP5s only. Z-scores were scaled in a way that zero represents the mean of each range of variation, and +1/−1 represent the upper and lower 95% limits of each range of variation, respectively (see Materials and Methods). Therefore, when a value is lower than −1, it means that it falls outside the lower statistical limit (P = 0.05) of the range of variation of the comparative group in question. (D) Bivariate plot of the two first principal components of the PCA on size-adjusted measurements of the DPs. MH_DP, pooled sample of Pleistocene and recent modern human DPs; NEAND_DP, Neanderthal DPs. MH-DP5f, fusing DP5 from the modern human sample. (E) Correlation circle between the measurements of the distal phalanx and the two first principal components of the PCA on size-adjusted measurements of the DPs shown in (D). Photos of the distal part of the phalanx were taken by E.-M.G., IJM, CNRS, Université de Paris, UMR 7592, Paris, France. The renderings of the μCT scans and the virtual reconstruction were performed by B.V., Department of Anthropology, University of Toronto, Toronto, Canada. Photos of the Krapina 206.12 specimen from the Croatian Natural History Museum collections, Zagreb, Croatia, and from the recent human specimen from the collections of UMR 5199 PACEA, Université de Bordeaux, France, were taken by I.C., UMR 5199 PACEA, Université de Bordeaux, France.

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References

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