Archaic Hominins Research Articles

Archaic hominin introgression into modern human genomes.

Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?

An alternative scenario for the first human dispersal out of Africa

Recent paleoanthropological evidence from the early Pleistocene site of Dmanisi in Georgia has revealed that the first hominins out of Africa were more archaic than the coeval African Homo erectus. Therefore, anatomical or cultural innovations associated with the later species cannot be invoked as a cause for the first out of Africa. More evidence suggests that these archaic hominins were forest dwellers rather than savannah inhabitants. This is in agreement with their trophic role as passive scavengers. In contrast with open-dry savannah, passive scavenging is much easier and safer in forest, were carcasses can remain untouched for up two days. Moreover, forest-adapted sabertooths could have supply hominids with more carrion than modern savannah felids. Between 1.8 and 1.6 Ma a climate crisis caused a new spread of savannah and arid zones across large parts of Africa. As a consequence, early Homo populations splitted, with some populations becoming adapted to the new ecological conditions and others following woodland areas in their regression. For these last populations Southern Caucasus could have acted as a refugium area, with dominant forest conditions, still inhabited by sabertooths and with easy access to carcasses.

Adaptive archaic hominin genes

Human Evolution As they migrated out of Africa and into Europe and Asia, anatomically modern humans interbred with archaic hominins, such as Neanderthals and Denisovans. The result of this genetic introgression on the recipient populations has been of considerable interest, especially in cases of selection for specific archaic genetic variants. Hsieh et al. characterized adaptive structural variants and copy number variants that are likely targets of positive selection in Melanesians. Focusing on population-specific regions of the genome that carry duplicated genes and show an excess of amino acid replacements provides evidence for one of the mechanisms by which genetic novelty can arise and result in differentiation between human genomes. Science , this issue p. [eaax2083][1] [1]: /lookup/doi/10.1126/science.aax2083

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes.

Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.

Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.

Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.

Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia)

Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.

The repertoire of family A-peptide GPCRs in archaic hominins

Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.

A late middle pleistocene Denisovan mandible from the Tibetan Plateau

Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1–3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau7,8, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis9,10, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160 thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens. Fossil evidence indicates that Denisovans occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to this high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.

Enigmatic Cranial Superstructures among Chamorro Ancestors from the Mariana Islands: Comparative Geographic Variation and a Proposal About Their Meaning

Sublime expression of three ectocranial occipital superstructures (OSSs)—occipital torus tubercles (TOTs), retromastoid processes (PRs), and posterior supramastoid tubercles (TSPs)—is virtually restricted to Oceania, with epicenters in the Mariana Islands, Tonga, Mocha Island, and perhaps other Oceanic locales such as the West Sepik Coast of New Guinea. Enigmatic in etiology, OSSs are anatomically related to entheses for the trapezius, superior oblique (suboccipital), and sternocleidomastoid muscles, respectively. Our study focuses on Latte Period (950–250 BP) Chamorro ancestors of the Mariana Islands, contextualized with other skeletal samples from Remote Oceania, Near Oceania, and the Asian and American Pacific Rims. Frequent co-variation and pair-wise patterning of multiple markedly expressed OSSs distinguishes ancestral Chamorros from all other populations, but markedly expressed individual OSSs exhibit a broad network of pan-Pacific morphological affinities. The presence of markedly developed PRs and TSPs in archaic Javanese hominins indicates deep Southeast Asian origins for these morphs, but a Northeast Asian origin for tuberculated TOTs is suggested by their earliest presence in Late Pleistocene Okinawans and Neolithic Taiwanese. The central goal of this paper is to present and evaluate evidence that OSSs are informative of both Pacific population history and the life histories of “bone-forming” Pacific Islander and Pacific Rim individuals.

The antiquity and evolution of the neural bases of rhythmic activity.

The evolution of the anatomy and neural circuits that regulate the rhythm of speech can be traced back to the Devonian age, 400 million years ago. Epigenetic processes 100 million years later modified these circuits. Natural selection on similar genetic processes occurred during the evolution of archaic hominins and humans. The lungs and larynx-anatomy that produces the rhythmic fundamental frequency patterns of speech-have a deep evolutionary history. Neural circuits linking the cortex, basal ganglia, and other subcortical structures plan, sequence, and execute motor as well as cognitive acts. These neural circuits generate the rhythm of speech, singing, and chanting. The human form of the transcription factor FOXP2 increased synaptic connectivity and plasticity in basal ganglia circuits, enhancing motor control and cognitive and linguistic capabilities in humans as well as Neanderthals. The archeological record also suggests that Neanderthals passed spoken language. Homologous circuits existed in amphibians. In songbirds, the avian form of FOXP2 acted on similar neural circuits allowing birds to learn and produce new songs. Current studies point to natural selection on genetic events enhancing these and other neural circuits to yield fully human rhythmic speech, and motor, cognitive, and linguistic capabilities, rather than the saltation proposed by Noam Chomsky.

Using hominin introgression to trace modern human dispersals

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.

Engraved bones from the archaic hominin site of Lingjing, Henan Province

Abstract

Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.

Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.

Neuroimaging supports the representational nature of the earliest human engravings.

The earliest human graphic productions, consisting of abstract patterns engraved on a variety of media, date to the Lower and Middle Palaeolithic. They are associated with anatomically modern and archaic hominins. The nature and significance of these engravings are still under question. To address this issue, we used functional magnetic resonance imaging to compare brain activations triggered by the perception of engraved patterns dating between 540 000 and 30 000 years before the present with those elicited by the perception of scenes, objects, symbol-like characters and written words. The perception of the engravings bilaterally activated regions along the ventral route in a pattern similar to that activated by the perception of objects, suggesting that these graphic productions are processed as organized visual representations in the brain. Moreover, the perception of the engravings led to a leftward activation of the visual word form area. These results support the hypothesis that these engravings have the visual properties of meaningful representations in present-day humans, and could have served such purpose in early modern humans and archaic hominins.

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.

A statistical model for reference-free inference of archaic local ancestry.

Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.

A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1-3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau7,8, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis9,10, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

Nutrition and its role in human evolution.

Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300000years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50000-100000years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.

Comparative observations on the premolar root and pulp canal configurations of Middle Pleistocene Homo in China.

The aim of this study is to explore the root and root canal morphology of Homo fossil occupying China during the Middle Pleistocene period. Human occupation and evolutionary dynamics in East Asia during the Middle Pleistocene period is one of the most intriguing issues in paleoanthropology, with the coexistence of multiple lineages and regional morphs suggesting a complex population interaction scenario. Although premolar root and canal morphology has certain phylogenetic, taxonomic, and functional implications, its morphological diversity, possible evolutionary trend and characteristics regarding Middle Pleistocene hominins inhabiting East Asia are still insufficiently understood; where these populations fits within the Homo lineage (with respect to root and pulp canal structure) needs to be explored. Using microtomography, we directly observed and assessed the nonmetric variability of root and canal forms in maxillary and mandibular premolars of Chinese Middle Pleistocene Homo (N = 19), and compared our observed variations with Eurasian Early Pleistocene specimens from the Asia continent (N = 1) and Java (N = 2), as well as with Neanderthals (N = 28) and recent modern humans (N = 67). A total number of nine types of root-canal forms were recorded. As a whole, the Chinese Middle Pleistocene record shows an evolutionary trend toward a modern human-like condition (a reduction of root/canal number and a simplification of root surface structure). We documented primitive signals like high percentage of Tomes' root in lower premolars. A considerable occurrence of incompletely separated root branches and bifid root and canal apices, representing evolutionary transformation from multi-root to single-root condition was also noticed. The results were compared with previous publications on Early and Middle Pleistocene Homo in East Africa, North Africa, and Eurasia. This work provides new original data, incorporates the latest human fossil discoveries and suggests that analyzing the variation of premolar root structural organization, notably integrating together root/canal form and number, could possibly contribute to taxonomic and phylogenetic assessments. The mid-Middle Pleistocene populations, or "classic" Homo erectus, in our study show closer affinity to Early and Middle Pleistocene hominins in Eurasia, than to East African early Homo, which supports the suggestion that at least some of the Early Pleistocene hominin groups in Eurasia contribute to the later population; on the other hand, it is still difficult to clearly trace the evolutionary fate of those late Middle Pleistocene populations (roughly assigned as archaic Homo sapiens through a craniodental perspective). More comparable materials from the Early to Middle Pleistocene period as well as precise chronological framework is needed to further explore the evolutionary trends of archaic hominins in the Asian continent before the arrival of modern humans.