Denisovan Phalanx Morphology Closer to Modern Humans than to Neanderthals

Australia: The Land Where Time Began

Denisovan Phalanx Morphology Closer to Modern Humans than to Neanderthals

In 2010 it was revealed by a fully sequenced high quality genome that a human population existed in Asia, the Denisovans, related to, and contemporaneous with Neanderthals. There are only 5 skeletal remains that are known from the Denisovans, mostly molars; the proximal fragment of a 5^th finger phalanx was used to generate a genome, however, was not complete enough to yield useful morphological information. In this paper Bennett et al. demonstrate by ancient DNA analysis that a distal fragment of a 5^th finger phalanx from Denisova Cave is the larger missing part of this phalanx. It was shown by their morphometric analysis that its dimensions and shape are within the variability of Homo sapiens and distinct from the 5^th finger phalanges of Neanderthals. It therefore differs from the molars of Denisovans which display archaic characteristics that are not present in modern humans; the only Denisovan postcranial bone identified to date that is morphologically informative is suggested in this paper to be plesiomorphic and shared between Denisovans and modern humans.

A small fragment of a finger phalanx was recovered from the Denisova Cave (Denisova 3) in southern Siberia in 2010 yielded a mitochondrial and a draft genomic sequence that changed the view of the evolution of the Late Pleistocene hominin lineages in Eurasia (Krause et al., 2010; Reich et al., 2010), it revealed a human population that was previously unknown. A divergence date was yielded by phylogenetic analysis of the Denisova 3 mitogenome for the ancestors of anatomically modern humans (AMH) and Neanderthals of about 1 Ma (1.3 to 0.7 Ma) (Krause et al., 2010; Meyer et al., 2014; Posth et al., 2017), i.e., much earlier than the mitogenomes from Neanderthals from the Late Pleistocene that diverged about 500 ka [690 to 350 ka; (Posth et al., 2017)]. However, it was suggested by the nuclear genome that there was a much more recent common ancestor between European Neanderthals (Vindija) and Denisovans dating to about 400 ka [440-390 ka; (Prüfer et al., 2017)] which characterised the Denisovans as a sister group to Neanderthals (Meyer et al., 2014; Prüfer et al., 2017; Mafessoni & Prüfer, 2017; Prüfer et al., 2014; Rogers, Bohlender & Huff, 2017). Traces of an archaic human that was even older have been identified in the nuclear genome of Denisova 3 (Prüfer et al., 2014), and a mitochondrial sequence related to that of Denisova 3 has been found in a specimen dating to about 400 ka from Sima de los Huesos (Spain), that had a nuclear genome that was more closely related to Neanderthals than to Denisovans (Meyer et al., 2014; Meyer et al., 2016). These data together suggest that the Denisovan mitogenome was either replaced with that of an even more archaic human following an admixture event or represents the mitogenome of the common ancestors of Neanderthals and Denisovans prior to its replacement in the lineage of Neanderthals from the Late Pleistocene (Reich et al., 2010; Meyer et al., 2014; Posth et al., 2017; Meyer et al., 2016; Meyer et al., 2012). Bennett et al. suggest that either the mitogenome of the late Neanderthals could result from an introgression (i.e. replacement of the mitogenome after admixture) from early anatomically modern humans (AMHs) after the separation of AMH and Neanderthal populations, as has been proposed in a study (Posth et al., 2017), or could be the result of incomplete lineage sorting given the uncertainties in the methods used to estimate the dates and the wide confidence intervals of the dates that were proposed. Also, the comparison of the Denisova 3 nuclear genome with the genomic sequence of a Neanderthal from the Denisova Cave that was about 100,000 years old revealed that gene flow had also been experienced from a Neanderthal population (Prüfer et al., 2014). A bone fragment from the Denisova Cave has recently been found, through genomic analysis, to belong to a female individual that was the F1 hybrid of a Neanderthal mother and a Denisovan father (Slon et al., 2018). Her maternal Neanderthal contribution is related more closely to the genome of the European Neanderthal from Vindija (Prüfer et al., 207) that dated to 40 ka than to the Neanderthal from the Denisova Cave that dated to about 100 ka. Also, it appears the paternal Denisovan genome of the hybrid bears traces of an ancient Neanderthal admixture (Slon et al., 2018). It is indicated by these data that gene flow between Neanderthals and Denisovans was not a rare occurrence.

Denisovans are indicated by molecular dating methods, based on mitochondrial sequences, to have inhabited the Altai region for more than 10s of thousands of years (Sawyer et al., 2015; Slon et al., 2017). The mitochondrial diversity of Denisovans in higher than that of Neanderthals that spanned from Spain to the Caucuses, in spite of the fact that all Denisovan mitochondrial sequences were found in the same archaeological site, Denisova Cave (Sawyer et al., 2015). As was inferred by the high-coverage Denisovan 3 genome, the Altai Denisovan population is characterised by low nuclear diversity, which is consistent with a prolonged small size of the population (Meyer et al., 2012). It appears that Neanderthal populations were also small, as assessed through the Altai and the Vindija genomes (Prüfer et al., 2017; Prüfer et al., 2014). It has been proposed on the basis of the modelling that the overall nuclear diversity of the individual local populations, the overall nuclear diversity of the Neanderthal metapopulation was higher (Rogers, Bohlender & Huff, 2017), though this point is still being discussed as it varies with the method of modelling (Mafessoni & Prüfer, 2017; Rogers, Bohlender & Huff, 2017). The extent of diversity of the Denisovan metapopulation has yet to be gnomically characterised from beyond the Denisova cave, though it is suggested by the presence of Denisovan ancestry in modern human genomes that there were at least 2 distinct Denisovan populations (Browning et al., 2018). When the genomic sequence of Denisova 3 is compared with genomes from modern human populations in Southeast Asia, above all the Melanesians, but also mainland Asia, it is revealed that there was interbreeding between Denisovans and early AMH ancestral to the human population of the present (Browning et al., 2018; Abi-Rached et al., 2011; Racimo, Mametto & Huerta-Sánchez, 2017; Vemot, 2018).

It appears that the Denisovan ancestry in Melanesians originated from a Denisovan population that was distantly related to that of Denisova 3 specimen, and a similar ancestry can also be found in East Asia, particularly in Chinese and Japanese (Browning et al., 2018). A second Denisovan introgression from a Denisovan population in East Asians that is more closely related to the Denisova 3 specimen was also detected (Browning et al., 2018). The introgression proved to be adaptive in some cases, e.g., in Tibetans (Huerta-Sánchez et al., 2014) and Inuits (Racimo et al., 2017).

The distribution and diversity of Denisova DNA in human populations of the present suggests that Denisovans were widely distributed throughout Asia at some time in the past (Browning et al., 2018; Vemot, 2018). This evidence contrasts with the scarcity of unambiguously identified remains and of characteristic morphological features that were associated with the remains. The mandible from Xiahe on the Tibetan Plateau and 3 teeth from Denisova Cave (Reich et al., 2010; Sawyer et al., 2015; Slon et al., 2017; Chen et al., 2019) provide the little morphological information that is available. A deciduous molar (Denisova 2) and 2 large sized permanent molars (Denisova 4 and 8), have provided Denisovan mitochondrial genome sequences and low amounts of nuclear DNA, while the mandible has been identified as Denisovan based on proteomic information (Chen et al., 2019). The Xiahe mandible has a morphology that is similar to that of specimens such as the Lantian and Zhoukoudian from China dating to the Middle Pleistocene, with features of the dental arcade shape that separate it from Homo erectus (Chen et al., 2019). It has some traits that are reminiscent of Neanderthals, though it lacks other specifically Neanderthal features (Chen et al., 2019). Therefore, the rare Denisovan human remains that have been identified to date show affinity to hominins from the Middle Pleistocene (Reich et al., 2010; Sawyer et al., 2015; Slon et al., 2017), in particular to those from China (Chen et al., 2019) and to the Neanderthal lineage, though to a lesser extent (Sawyer et al., 2012). The permanent molars that were recovered from Denisova Cave exhibit complex occlusal morphology (Krause et al., 2010; Sawyer et al., 2015; Slon et al., 2017). It remains to be seen whether these peculiar characteristics of the molars result from introgression from a more archaic population from Eurasia, though it cannot be excluded as such a low level introgression has been identified in the Denisova 3 genome (Prüfer et al., 2014).

Identificati0on of Denisovan post cranial remains relies at present only on genomic data, as these remains of Denisovans exhibiting diagnostic features have not yet been reported, in spite of the importance of the Denisovan population for the study of human evolution. For the identification of Denisovan remains, and for the ability to characterise better Denisovan population genomic diversity, progress in the identification of Denisovan skeletal remains would be instrumental. In this paper Bennett et al. report the morphometric analysis of a phalanx fragment that they show through its mitochondrial sequence to be the larger distal part of the original Denisova 3 phalanx, the genome of which was published in 2010 and 2012 (Krause et al., 2010; Reich et al., 2010; Meyer et al., 2012). The phalanx was cut into 2 parts in 2009. Prior to the cutting the Russian scientific team took pictures of the phalanx; however, they have been lost. The smaller proximal part of the bone was sent to the Max Planck Institute (MPI) for Evolutionary Anthropology in Leipzig, Germany, and sampling for palaeogenomic analysis was performed. In 2010, the larger distal part was sent to the University of Berkeley, CA, USA, from there to the “Institut Jacques Monod” (IJM) in Paris, France, where it was measured and photographed and genetically analysed. In 2011 it was returned to the University of Berkeley.

This analysis of both parts of the phalanx represents the first morphological study of non-dental remains of this mysterious population that inhabited Asia for 100s of thousands of years and has occasionally interbred with Neanderthals as well as possibly with Eurasian humans that were more archaic, and continues to endure in genomes of some human populations of the present.

Summary

The Denisova 3 DP5 (5^th distal fragment) is indicated by the evidence from the distal and proximal fragments to be from an adolescent. It was shown by nuclear DNA analysis that this individual was a female, which allowed the narrowing of the age at death to about 13.5 years based on the standards from extant humans and assuming that the Denisovans had a fairly similar development. It is possible to tentatively identify both digit and side for Denisova 3, if it is accepted that the phalanx is close to the mature state, then it is possible to identify tentatively both digit and side for Denisova 3. If the diversity of modern humans is considered, the estimated maximum length of Denisova 3 falls best within the variability of the DP5s (Scheuer & Black, 2000). Also the asymmetry of the ungual tuberosity and the curvature of the shaft in the dorsal view indicate that it is indicated that it is likely the DP5 is from the right side [(Case & Heilman, 2006); I. Crevecoeur, personal conversation].

Morphometric comparison

Bennett et al. performed morphometric analyses of the DP5 of Denisova 3 based on the measurements that were made on the original specimen and the virtual reconstruction of the maximum length. They compared these measurement with data from published and unpublished DPs of Neanderthals, AMH from the Pleistocene, and 3 samples of recent AMH from France and Belgium dated from the Neolithic to the Middle Ages, using univariate and multivariate analyses. The comparison sample includes 1 AMH and 1 Neanderthal specimen in which the proximal epiphyses were in the process of fusing.

All dimensions of Denisova 3 fall within the range of variation of modern human DP5s, with the possible exception of the proximal breadth. With regard to the measurements of the articular surface, the dimensions of the proximal extremity fall within the lower part of the variation of the modern human DP5 and outside that of the Neanderthals. Bennett et al. suggest that this may be related to the state of preservation of the proximal extremity and, probably also, to its state of fusion. Though the midshaft height of the diaphysis and the distal height of the apical tuft are close to the mean of modern humans, the remaining measurements fall within the lower range of variation, which indicates that the Denisova 3 phalanx is gracile. Nevertheless, the fact that an adolescent female is being dealt with must be taken into consideration with regard to the potential size and gracility.

Bennett et al. performed a multivariate analysis using size-adjusted dimensions to allow a comparison of the DPs based on shape instead of size. Along the first 2 principal components the projections are given in the 2 following bivariate plots. More than 50% of the total variation is represented by the first 2 principal components. There is a clear distinction that is visible between the Neanderthal and the modern human samples, with Denisova 3 positioned in the lower right quadrant within modern human variation. The DP5 of the Denisova differs from that of the Neanderthals in that the former combines a narrow apical tuft (distal breadth) with a thicker DP, as expressed by the correlation circle, particularly at the midshaft and the proximal end (midshaft height and proximal height).

It has been usual to describe Neanderthal DPs as notably different from modern humans because of the length, shape and dimensions of their tufts (e.g., Musgrave, 1971; Trinkaus, 1983). Compared with modern humans the DPs of Neanderthals are proportionately longer with wider extremities, which give the impression of flattening of the bone (Niewoehner, 2006). According to Bennett et al., among the Neanderthals this conformation of the apical tuft appears to be related to functional rather than to cold climate adaptations (Mittra et al., 2007).

The analysis of Bennett et al. confirms these characteristics; though there are additional observations that can be made regarding DP5s. This difference bertween the 5^th and the other phalanges, that is not visible in the modern human sample, is due to the specific morphology of the Neanderthal DP5 compared with other digits, driven by the shape of the shape of the midshaft as well as the apical tuft, both of which are narrower than the remaining digits. On the contrary, when the size factor is not taken into account, DP5s of AMH scatter within variability of the other DPs

The Neanderthal and Denisovan nuclear genomes are closer to each other than to modern humans, and it has been estimated that the time of the split between Neanderthals and Denisovans is about 410 ka (Prüfer et al., 2017), while the population split time between these archaic humans and the ancestors of AMH is about 580 ka (Prüfer et al., 2017; Prüfer et al., 2014; Meyer et al., 2012). The Denisova 3 DP5 does not exhibit any of the features that are exhibited in Neanderthals, in spite of Denisovans and Neanderthals being sister groups. The morphology of the Denisova 3 DP5 is not distinguishable from that of modern humans and is located within the variation of modern humans, which Bennett et al. suggest is likely to represent the plesiomorphic morphology of nonpollical DPs within the genus Homo which is seen in both the Olduvai hominin OH 7 and the Dmanisi hominins (Susman & Creel, 1979; Lordkipanidze et al., 2007). The Neanderthal specific characters of the phalanx evolved after the divergence of the Denisovans and the Neanderthals. The Neanderthal from Moula-Guercy, one of the earliest members of the Neanderthal lineage from the sample of Bennett et al. dating to about 100 ka, is the only Neanderthal DP5 that falls within the middle of modern human variation (Defleur et al., 1999). This observation raises the possibility that the derived properties of the Neanderthal phalanx occurred rather late during evolution of the Neanderthals. The similarity that is observed between the Denisovan phalanx and those of AMHs contrasts with the morphology of the molars of the Denisovan individuals which are closer, morphologically, to more archaic humans from the Middle Pleistocene to the Late Pleistocene (Reich et al., 2010; Sawyer et al., 2015; Slon et al., 2017).

Conclusions

According to Bennett et al. they could link genetically the distal part of a DP5 from the Denisova Cave in Siberia to the Denisovan 3 phalanx fragment, which was identified by genome as being a representative of a population that was related more closely Neanderthals than to modern humans. Morphometric analysis that was based on high resolution pictures, linear measurements, and the comparison with the DP5s of Neanderthals as well as Pleistocene and recent modern humans shows that it is within the range of variation of the dimensions of the DP5s of modern humans and distinct from that of Neanderthals. Bennett et al., proposed that this represents the plesiomorphic morphology within the genus Homo (Lordkipanidze et al., 2007), which is consistent with the morphology of early Homo DPs (Susman & Creel, 1979), and that the derived morphology of the Neanderthal phalanx evolved following their split from the ancestors of the young woman from Denisova Cave. They suggest that this calls for caution when identifying potential Denisovan postcranial skeletal remains beyond Denisova, as their morphology might be ambiguous or more similar to modern human than to Neanderthals.

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