Modern Human Adaptations Research Articles

The genetic and evolutionary determinants of COVID-19 susceptibility.

Devastating pandemics, such as that due to COVID-19, can provide strong testimony to our knowledge of the genetic and evolutionary determinants of infectious disease susceptibility and severity. One of the most remarkable aspects of such outbreaks is the stunning interindividual variability observed in the course of infection. In recent decades, enormous progress has been made in the field of the human genetics of infectious diseases, and an increasing number of human genetic factors have been reported to explain, to a great extent, the observed variability for a large number of infectious agents. However, our understanding of the cellular, molecular, and immunological mechanisms underlying such disparities between individuals and ethnic groups, remains very limited. Here, we discuss recent findings relating to human genetic predisposition to infectious disease, from an immunological or population genetic perspective, and show how these and other innovative approaches have been applied to deciphering the genetic basis of human susceptibility to COVID-19 and the severity of this disease. From an evolutionary perspective, we show how past demographic and selection events characterizing the history of our species, including admixture with archaic humans, such as Neanderthals, facilitated modern human adaptation to the threats imposed by ancient pathogens. In the context of emerging infectious diseases, these past episodes of genetic adaptation may contribute to some of the observed population differences in the outcome of SARS-CoV-2 infection and the severity of COVID-19 illness.

Famine, tea, and bread in Ireland: C282Y and modern human microevolution

AbstractThe HFE gene variant allele C282Y connected with hereditary hemochromatosis occurs at a frequency of about 10%–11% in Ireland, the highest known frequency in the modern global population. In this synthesis, we draw together an interdisciplinary literature to offer an agriculturally‐grounded, biocultural example of modern human adaptation and microevolution that addresses Ireland's comparatively high C282Y frequency. We argue that changing subsistence‐, diet‐, and nutrition‐related stressors framed under colonial governance played a role shaping the biology of Ireland's population historically, maintaining the C282Y variant. A population accustomed to challenges of poverty and difficult living conditions, the Irish fell under the influence of massive ecological stress with the fungus (Phytophthora infestans), the failed potato crops, and the Great Famine of 1845–52. From there, in the post‐Famine era, diet and nutrition altered further as the potato was exchanged for gluten‐rich wheaten bread and stewed black tea. With risks for iron deficiency anemia heightened by the cultural construction of diet and niche, an adaptive iron‐conserving advantage continued to be offered by the C282Y allele, influencing survival into the post‐Famine era. More recently, however, C282Y has been reframed as a potential risk in the context of contemporary, iron fortified diets.

The timing of human adaptation from Neanderthal introgression.

Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.

Late Pleistocene to early-Holocene rainforest foraging in Sri Lanka: Multidisciplinary analysis at Kitulgala Beli-lena

Sri Lanka has produced the earliest clear evidence for Homo sapiens fossils in South Asia and research in the region has provided important insights into modern human adaptations and cultural practices during the last ca. 45,000 years. However, in-depth multidisciplinary analyses of Late Pleistocene and Holocene sequences remain limited to just two sites, Fa Hien-lena and Batadomba-lena. Here, we present our findings from the reinvestigation of a third site, Kitulgala Beli-lena. New chronometric dating from the site confirms the presence of humans as early as ca. 45,000 cal. BP. in the island’s Wet Zone rainforest region. Our analyses of macrobotanical, molluscan, and vertebrate remains from the rockshelter show that this early human presence is associated with rainforest foraging. The Late Pleistocene deposits yielded evidence of wild breadfruit and kekuna nut extraction while the Holocene layers reveal a heavy reliance on semi-arboreal and arboreal small mammals as well as freshwater snails as a protein source. The lithic and osseous artefacts demonstrate that populations developed a sophisticated tool kit for the exploitation of their immediate landscapes. We place the rich Kitulgala Beli-lena dataset in its wider Sri Lankan context of Late Pleistocene foraging, as well as in wider discussions of our species’ adaptation to ‘extreme’ environments as it moved throughout Asia.

Humans thrived in South Africa through the Toba eruption about 74,000 years ago.

Approximately 74 thousand years ago (ka), the Toba caldera erupted in Sumatra. Since the magnitude of this eruption was first established, its effects on climate, environment and humans have been debated. Here we describe the discovery of microscopic glass shards characteristic of the Youngest Toba Tuff-ashfall from the Toba eruption-in two archaeological sites on the south coast of South Africa, a region in which there is evidence for early human behavioural complexity. An independently derived dating model supports a date of approximately 74 ka for the sediments containing the Youngest Toba Tuff glass shards. By defining the input of shards at both sites, which are located nine kilometres apart, we are able to establish a close temporal correlation between them. Our high-resolution excavation and sampling technique enable exact comparisons between the input of Youngest Toba Tuff glass shards and the evidence for human occupation. Humans in this region thrived through the Toba event and the ensuing full glacial conditions, perhaps as a combined result of the uniquely rich resource base of the region and fully evolved modern human adaptation.

The Aurignacian way of life: Contextualizing early modern human adaptation in the Carpathian Basin

The culture and dispersal of early modern humans are top priorities of many research agendas. While the debate primarily centers on genetics, dispersal trajectories and points of earliest presence, the context (climate, landscape, demography, culture) of the colonizing process is usually considered in a coarse-grained manner or even ignored. To understand the context of human dispersal and to decipher relevant push and pull factors requires the consideration of multiple environmental proxies and the research on different geographic scales. In this paper, we present the Late Quaternary Carpathian Basin as a specific context area of early modern human dispersal into Europe. The multitude of Early Upper Paleolithic sites in this region suggests that it was part of a major dispersal corridor along the Danube and its catchment area some 40,000 years ago. The Aurignacian land-use model describes the interaction of early modern humans with their environment. One important parameter is the specific distribution of archaeological sites that exemplifies their boundedness to specific eco-zones. To reconstruct the latter, paleo-environmental proxies and archaeological data are examined together in regional vector models and in a GIS based landscape archaeology approach. In the final section, we present the Carpathian Basin as an idiosyncratic habitat that mirrors the dynamics and complexity of early modern human adaptation.

Pavlov I: A large Gravettian site in space and time

The formation of the large site clusters of the Gravettian (Pavlovian) represents one of the final effects of modern human adaptation in central Europe, but chronology of the site formation processes at such sites are still little understood. Here we present new evidence from Pavlov I, a site now prepared for the construction of a museum and subjected to a large-scale preparatory excavation. Understanding the spatial organisation, microstratigraphies, and the effects of cryogenic processes on the site formation is the basic presumption for lithic analysis at a large and complex site. Obviously, these extensive sites have a longer prehistory than was previously thought. The detection of the Early Upper Palaeolithic/Gravettian boundary was related to a radical change in the lithic raw material composition. The early and evolved Gravettian industries complete previously recorded the techno/typological spectrum by additional microlithic assemblages. With this new evidence, the paper also discusses the question of Gravettian origin.

New evidence and perspectives on the Upper Paleolithic of the Central Plain in China

A rich group of archaeological materials from MIS3 to MIS2 has been discovered in recent years from Zhijidong, Zhaozhuang, Laonainaimiao, Xishi, and Lijiagou in Henan province. These records provide new perspectives on the technology and behavioral patterns in the Upper Paleolithic of the Central Plain in China. Human behavior underwent remarkable changes at the beginning of MIS 3, as seen in the long distant transport of raw material and the diversity of toolkits, as well as the enlargement of activity areas documented at Zhijidong. However, the technology of lithic reduction did not change, and a simple core-flake technology continued to be used as in the previous period. Blade and microblade assemblages appeared at the end of MIS3. A microblade technology was widely and intensively adopted in the northern part of China during the LGM and persisted until the end of Pleistocene. The change of lithic technology witnesses the development of the Upper Paleolithic and modern human adaptations during MIS3 and MIS2 in the Central Plain.

Recent developments in the study of the Upper Paleolithic of Vasco-Cantabrian Spain

This is an updated review of recent (post-2004) developments in the study of the rich Upper Paleolithic (40–10 uncal. ka) record from the Spanish “wing” of the classic Franco-Cantabrian culture area, composed of the provinces of Asturias, Cantabria, Vizcaya, Guipúzcoa and northern Navarra. Numerous new/ongoing excavations, radiometric dating assays, paleoenvironmental, artifact and faunal analyses are summarized here and their implications for understanding the Middle–Upper Paleolithic transition and the succession of anatomically modern human adaptations in this narrow, mid-latitude strip bounded to the north by the Gulf of Gascony and to the south by the Cantabrian Cordillera. Constants in this record are the balance between regionally distinctive characteristics (in terms of ecology, faunas, artifacts, subsistence and art) and the reality of connections to the Upper Paleolithic cultures of France and the rest of Iberia; the role of the region as a glacial-age refugium; the fundamental continuity of human settlement with movements between the coastal lowlands and the adjacent montane interior; the intensification of subsistence through situational specialization and overall diversification, with periods of intensive demographic and environmental stress; underlying facts of lithology and the differential availability and utilization of flints and non-flint raw materials for different types of tools; the demographically critical role of intra- and extra-regional social networks within the context of valley-defined local band territories. The review proceeds along the lines of traditionally defined cultural traditions: Aurignacian sensu lato, Gravettian, Solultrean, Magdalenian and Azilian, although it is recognized that these are archeological constructs and that there is both considerable variability within each of these concepts and a considerable degree of similarity cross-cutting all of them.

Neanderthal and Modern Human Adaptations in Climatic Context: New Fieldwork in Western Ukraine

Neanderthal and Modern Human Adaptations in Climatic Context: New Fieldwork in Western Ukraine

Seasonal Variation in Resource Abundance and Anatomically Modern Human Adaptations: The Blue Highways Project, NW Ethiopia

Seasonal Variation in Resource Abundance and Anatomically Modern Human Adaptations: The Blue Highways Project, NW Ethiopia

Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes

Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations.

Speculations about the Effects of Fire and Lava Flows on Human Evolution

Recent research argues that an association with fire, stretching back millions of years, played a central role in human evolution resulting in many modern human adaptations. Others argue that hominin evolution was driven by the roughness of topographic features that resulted from tectonic activity in the African Rift valley. I combine these hypotheses to propose that, for millions of years, active lava flows in the African Rift provided consistent but isolated sources of fire, providing very specific adaptive pressures and opportunities to small isolated groups of hominins. This allowed these groups of early hominins to develop many fire specific adaptations such as bipedalism, smaller teeth and mouths, shorter intestines, larger brains, and perhaps a host of social adaptations. By about 1.8 million years ago, Homo erectus emerged as a fire adapted species and mastered the technology necessary to make fire itself. This technology allowed them to move into the rest of the world, taking a new kind of fire with them that would change ecosystems everywhere they went. This hypothesis is supported by recent geologic work that describes a large lava flow occurring in the region of the Olduvai Gorge during the 200 000 year time period we believe Homo erectus emerged in the area.

Neandertal and Early Modern Human Behavioral Variability A Regional‐Scale Approach to Lithic Evidence for Hunting in the Levantine Mousterian

In southwestern Asia, both Neandertals and early modern humans are associated with the same Levantine Mousterian archaeological complex for tens of thousands of years. Thus, the Levantine Mousterian archaeological record offers the possibility of comparing long‐term patterns of Neandertal and early modern human adaptation. Ecological considerations suggest that Levantine Mousterian subsistence strategies varied along a continuum paralleling contrasts between Mediterranean woodland and Irano‐Tura‐nian steppe ecozones. This hypothesis is tested with evidence for the production and use of Levallois points, which breakage patterns suggest were used as spear points. Stone spear points would have been advantageous mainly in intercept hunting and disadvantageous in encounter hunting. High frequencies of Levallois points among assemblages from the steppic interior and southern Levant and low frequencies of points among assemblages from the coastal and northern Levant suggest support for this model of Levantine Mousterian behavioral variability. Lithic assemblages associated with Neandertals exhibit higher point frequencies than those associated with early modern humans. This could suggest that in the Levant the adaptation of Neandertals was different from and possibly more predatory than that of early modern humans.