Who and What are the Denisovans?
Introduction
Who and what are the Denisovans and what role do they play in the evolutionary history of the genus Homo? Unlike other hominin discoveries, the Denisovans are unique for being revealed primarily through their DNA as opposed to fossilised remains. With a limited set of remains discovered to date, no morphological description currently exists for the Denisovans, and as such, a consensus on their taxonomic classification has not been reached. Conversely, the DNA evidence that has been recovered from their relatively sparse remains is extensive, and much has been discovered about their evolutionary role with regard to our own species and genus. We know they share a common ancestor with Homo sapiens and Homo neanderthalensis, being more recently diverged from the latter. Genetically distinct from both aforementioned species, at various times and across multiple geographical locations during the late Pleistocene, they were also contemporaneous with them, interbreeding and producing fertile hybrid offspring that contribute a small amount of the genetic variation in select present-day human populations. This article examines the significance of these admixture events including how they have changed our understanding of human evolution and challenged the concept and classification of ‘species’. First beginning with a brief summary of the rapid advances in the fields of genetics and genomics that has revealed them.
Next Generation Sequencing
In 2010, mitochondrial DNA extracted from a small fragment of finger (Denisova 3) recovered from the Denisovan cave in the Altai region of southern Siberia revealed a previously unknown archaic hominin population (Bennett et al., 2019). Further sequencing of the same fragment produced high-coverage data from the nuclear genome using a newly developed technique that was able to successfully exploit single strands of DNA, overcoming degradation to the double-stranded material typical of ancient DNA (aDNA) (Hawks, 2013). From the advent of the Human Genome Project in 1990, and as a result of it, advances in DNA sequencing techniques have moved forward at an exponential rate. The development of ‘next generation sequencing’ techniques, in conjunction with dramatic improvements in computational through-put and software, have seen the cost of sequencing plummet from $1,000 per megabase in 2005, down to a mere ten cents by 2012 (Shendure & Lieberman Aiden, 2012). For Palaeoanthropology, this has opened new doors into the study of aDNA, offering previously unattainable insights into the biology and phylogeny of extinct archaic hominin populations such as the Denisovans (Hawks, 2013). With now broadly accessible high-quality reference genomes of current human populations as well as extinct archaic hominins such as the Neanderthals and Denisovans, It is the comparative analysis of these ancient genomic sequences that have modified our understanding of human evolution.
Diverging Lineages
Comparison of present-day human, Denisovan and Neanderthal reference genomes suggests a more recent divergence between Denisovan and Neanderthals than either group has to Homo sapiens, thus placing the Denisovans as a sister group to Neanderthals (Reich et al., 2010). This would support the hypothesis that an ancestral population to Denisovans, Neanderthals and present-day humans, a hominin most commonly referred to as Homo heidelbergensis, left Africa and split into two distinct lineages that became the Neanderthals and Denisovans, while the population of Homo heidelbergensis that remained in Africa gave rise to Homo sapiens. Genetic evidence in support of this model can be achieved by calculating the divergence between reference genomes of Denisovans, Neanderthals and present-day humans as a fraction of change to that of present-day humans to chimpanzees (Reich et al., 2010). Assuming a divergence of 6.5 million years for Homo-Pan, the Denisovan genome diverges from the Neanderthal genome 9.84% (640,000 years ago) of the way back along that lineage, while both diverge from the present day human genome 12.38% (804,000 years ago) of the way back (Reich et al., 2010). It is important to note that reported divergence timeframes can vary considerably. This can be due to multiple calibration points that are based on evolutionary rates being constant which is not always the case. What we do know based on this divergence model and further supporting genetic evidence, is that after a significant period of reproductive isolation, these groups came into contact with each other at various times and locations and exchanged genetic material.
Admixing with Sapiens
According to Anderson & Hubricht (1938, cited in Gokcumen 2020) “Introgression (or introgressive hybridization) is gene flow from the gene pool of one distinct biological taxon (often a species) to another by hybridization.” The varying proportions and geographical dispersal of Denisovan ancestry in present-day human populations provides not only evidence of admixture events leading to introgression, but also suggest that the Denisovans were once wide ranging throughout Asia (Bennett et al., 2019). Thousands of miles from the Altai region of Siberia, the highest proportion of Denisovan DNA is found in Aboriginal Australians and Australo-Papuans (∼3 to 6%), followed by proportionally lesser amounts in the peoples of Oceania, with smaller amounts again (<1%) in the genomes of South and East Asians (Teixeira & Cooper, 2019). However, what has now become evident from further advances in the technology and methods for studying genomic signatures of Denisovan ancestry in present-day populations, is that there were at least two separate admixture events from quite distinct populations of Denisovans, one from a population closely related to that of the Denisova 3 phalanx found in the Altai region of Siberia, and the other considered distantly related to it (Browning et al., 2018). From a geographical perspective, it is the Aboriginal Australians, Australo-Papuans, and South Asians that have introgression from the distantly related population, while East Asians have introgression from both the closely related and distantly related populations (Browning et al., 2018). What we can infer from these admixture events, is that the Denisovans were wide ranging, exhibiting a degree of variability that suggests a level of demographic success over both time and space which is far beyond what has been discovered to date via their archaeological remains. Without a more detailed archaeological record, it is impossible to make inferences about the circumstances of these encounters that led to hybridization. However, the effects of the subsequent introgressed sequences into the genome of Homo sapiens may have inadvertently provided some select advantages as sapiens dispersed into new environments.
Introgressive Hybridisation
It is well understood in the fields of genetics and evolutionary biology that genetic variation is essential as it provides the ingredients for natural selection to act upon. Conceptually, the optimal level of genetic variation may best be described by the peak of a bell curve as opposed to a linear progression, where the far-left side of the curve represents insufficient variation (inbreeding), and the far right-hand side is where reproductive isolation is achieved, preceded by increasing genetic incompatibility such as sterility in offspring. While fertile offspring as a result of hybridization with Denisovans and Homo sapiens was likely unusual and subject to wide-spread purifying selection, some of these surviving hybrids acquired adaptations that may have been advantageous to early populations of Homo sapiens as they dispersed into unfamiliar environments and were faced with novel selective pressures (Gittelman et al., 2016). One such introgression is now understood to have facilitated the adaptation seen in present-day Tibetans that effects haemoglobin concentration at high altitude, enabling them to reproduce and settle in this otherwise inhospitable environment (Huerta-Sánchez et al., 2014). The evidence to support this trait being introgressed from Denisovan admixture has come about through analysis of the gene EPAS1, responsible for the physiological response to oxygen concentration. A comparative analysis of the genomic region surrounding EPAS1 between Tibetans, various present-day populations, and the aDNA of the Denisovan genome from Altai, show a matching haplotype between the Tibetans and the Denisovan genome that can only be explained by introgression from Denisovans into the ancestors of present day Tibetans (Huerta-Sánchez et al., 2014). This is just one example of adaptive introgression with other studies providing evidence for similar positively selected traits including skin pigmentation and disease immunity. While it has been accepted for some time that the evolution of the genus Homo is far from a unilinear progression, what we are now beginning to understand, is that the rapid adaptation to new environments and demographic success of Homo sapiens may have been supported to some small degree by gene flow from what some would classify as different species of the same genus.
The Problem with ‘Species’
It is impossible to address the question of whether the Denisovans are a separate species, subspecies, or population, without addressing the concept and classification of species itself. The classification of extinct taxa has traditionally relied upon morphology as the basis for taxonomic grouping into species. In the case of the Denisovans, a limited set of remains have been found (or retrospectively assigned) since the initial discovery of the Denisova 3 phalanx which include 3 molars, a long bone fragment and a parietal fragment (all from the same location in Altai), and a mandible originating from Xiahe on the Tibetan Plateau (Bennett et al., 2019). The extent of these remains has not been sufficient to achieve a taxonomic consensus based on morphology. However, the recovered DNA sequences have offered unprecedented insight into the relationship of the Denisovans to past and present hominin populations which should be viewed as complementary, and not stand-alone, to morphology (Reich et al., 2010). To further complicate matters, the morphological analysis of the Denisova 3 phalanx fragment shows that it is clearly distinct from Neanderthals, but within range of present-day human variation. This could potentially be explained by this particular morphology being plesiomorphic to the genus Homo and thus derived in Neanderthals after the more recent divergence from the Denisovans (Bennett et al., 2019). Perhaps the issue is that the word ‘species’ pre-dates Charles Darwin’s 1959 revelation to the world and carries with it the unshakable connotation of a static concept, when in fact all forms extant and extinct are transitional, and in the process of evolving.
Conclusion
The Denisovans are a biologically distinct taxa that have played a relatively recent role in the evolution of the genus Homo. The genetic evidence supports a common ancestor with Homo sapiens and Homo neanderthalensis, with a more recent divergence from the latter, followed by a significant period of reproductive isolation, providing for a quite separate evolutionary history. During this period, genetic evidence infers that the Denisovans dispersed and settled as multiple population lineages across Asia where they evolved unique adaptations to novel environments under emergent selective pressures. As a result of admixture events with Homo sapiens, some of these adaptations were passed via adaptive introgression which has facilitated some select populations of Homo sapiens adapting to these environments more rapidly than natural selection alone could allow. Although comparative analysis of present-day human genomes suggests at least two separate waves of admixture events from two relatively distinct populations of Denisovans, improved genomic sample data sets of present-day human populations are needed to provide better clarity on this. It is also important to consider that genetic analysis of present-day human populations does not have a direct bearing on the location of historical divergence events and that further fossil evidence is required to allow us to better understand the Denisovans spatial and temporal ranges. Finally, the significance of these admixture events must be kept in perspective as they do not quantify a sudden change to a multiregional model as could be suggested. Given the relatively low levels of introgression in present-day populations in contrast to the genomic similarity between non-African and African populations, a recent African origin model is still favoured.
References
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