Ancient Human Migrations Research Articles

Using climate to model ancient human migration.

Modeling fills gaps in the fossil record of early hominin movement from Africa.

Paleolithic cultures and ancient human migrations in Mongolia

Paleolithic cultures and ancient human migrations in Mongolia

Genomic evidence for ancient human migration routes along South America's Atlantic coast.

An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.

Bioarchaeological evidence for ancient human diet and migration at Epidamnus/Dyrrachion and Apollonia in Illyria, Albania

Bioarchaeological evidence for ancient human diet and migration at Epidamnus/Dyrrachion and Apollonia in Illyria, Albania

Not a bathtub: A consideration of sea-level physics for archaeological models of human migration

Accurately reconstructing past sea level is key to simulating potential migration pathways of ancient hominins, including early Homo sapiens. Models of ancient human migration events commonly construct estimates of paleoenvironments using the “bathtub” model, in which sea level is assumed to rise and fall according to a “eustatic” (global average) value over time. However, large uncertainties exist on past ice sheet sizes and shapes, particularly prior to the Last Glacial Maximum (LGM), ∼26,000 years ago. Moreover, regional sea level varies significantly due to the effects of glacial isostatic adjustment (GIA). That process includes Earth's gravitational, deformational, and rotational response to changing surface (ice plus ocean) loads across the ice age. Here, we offer an updated account of the physics of GIA-induced sea-level change and consider the impacts of these effects, together with a newly published ice sheet history, on sea-level changes across the last glacial cycle. As illustrations, we highlight the significance of these issues for studies of ancient human migration from Sunda to Sahul and for the timing of the final, post-LGM flooding of the Strait of Dover. These examples demonstrate the importance of incorporating updated ice sheet histories and accurate sea-level physics into archaeological research.

Did increased flooding during the African Humid Period force migration of modern humans from the Nile Valley?

During the Quaternary period, the eastern Sahara's hydroclimate oscillated between wet and dry intervals. These oscillations caused drastic changes in precipitation rates, often associated with ancient human migrations. In particular, significant migration of riparian populations from the Nile Valley to the west and northwestward of the Sahara occurred during the African Humid Period (AHP), an episode of increased monsoons, which characterized North Africa in response to increasing insolation. Several fossil rivers, now preserved as ridges throughout southern Egypt due to their floodplains' deflation, contain archeological artifacts and thus represent a potentially important record of fluvial activity during this episode of past human dynamics and environmental change. Here we present 14C and Optically Stimulated Luminescence (OSL) ages of sediments preserved in these palaeorivers, which cluster within the AHP and are thus consistent with increased fluvial activity during this distinct humid period. Palaeohydraulic reconstructions based on grain size, channel geometry, and drainage area suggest typical precipitation intensities of 55–80 mm/h during sediment transport events. Given previous annual rainfall estimates, these hydrologic conditions may have lasted, or occurred, during the AHP up to 3–4 times more frequently than before and after this period. Such intense fluvial activity is consistent with monsoon intensification and may have rendered the area inhospitable for human settlements, congruent with population migration out of the Nile Valley during the AHP. These findings highlight links between past human ecodynamics and environmental signals, providing a concrete narrative of human population response to warming with potential echo in the current situation.

A signature of Neanderthal introgression on molecular mechanisms of environmental responses.

Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.

Archaeoparasitology — a new source of reconstruction of migrations of ancient populations: opportunities, results, and prospects

The resilience of intestinal parasite ova to harsh environmental conditions and possibility of identification of many of them down to genus/species with the aid of conventional visual light microscopy make parasites an im-portant source of information on different aspects of life of ancient populations. Of special interest is the study of the phenomenon of parasitoidism aimed at reconstruction of ancient human migrations. Ectoparasites (the head louse) and a range of intestinal parasites of such groups as the helminths, tapeworms, and trematodes can be used as a marker of contacts and/or migration of people. Finding helminth ova in ancient samples collected in territories outside the endemic pockets can be direct evidence of contacts and/or migrations of the ancient popu-lation. An example of reconstruction of such migrations is given by, for instance, finding ova of the ascarids and whipworm on the territories of the Far North, mountainous Altai, deserts of the Central Asia etc. A remarkable example of migrations, according to the archaeoparasitology data, is the use of the helminths as a marker of an-cient human migrations, with the example of population of the American continent. It is noteworthy that almost a century old archaeoparasitology data find confirmation in the results of modern paleogenetic studies. In the recent decades, there have been review publications concerned with the finds of ova of various parasitic organisms in archaeological sites, many of which consolidated archaeoparasitology materials dealing with specific intestinal parasites, the impact of the parasites on the human evolution and their (viz., parasites and human) coevolution, and spread of the parasitic diseases as a result of climate changes both in ancient and modern times. All the works, without exception, emphasize the importance of archaeoparasitology data for the deeper understanding of these processes. However, although the first works on the reconstruction of migrations from parasitological data were published back in the beginning of the last century, the research works substantiating this approach and demonstrating its viability appeared only early in this century and elucidated biological pre-requisites for the re-construction of migrations. Therefore, new broad consolidation of the materials on the reconstruction of migrations from the data of archaeoparasitology is motivated not only by the need of reconsideration of already existing and new data, but also by the need of examination and verification of the archaeoparasitology facts in the context of the genetic data, archaeology, anthropology etc.

Molecular epidemiology of leprosy: An update.

Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology of leprosy bacilli through genomic approaches, the exact mechanisms of transmission is still unclear and the factors underlying pathological variation of the disease in different patients remain as major gaps in our knowledge about leprosy. Despite these difficulties, the last two decades have seen the development of genotyping procedures based on PCR-sequencing of target loci as well as by the genome-wide analysis of an increasing number of geographically diverse isolates of leprosy bacilli. This has provided a foundation for molecular epidemiology studies that are bringing a better understanding of strain evolution associated with ancient human migrations, and phylogeographical insights about the spread of disease globally. This review discusses the advantages and drawbacks of the main tools available for molecular epidemiological investigations of leprosy and summarizes various methods ranging from PCR-based genotyping to genome-typing techniques. We also describe their main applications in analyzing the short-range and long-range transmission of the disease. Finally, we summarise the current gaps and challenges that remain in the field of molecular epidemiology of leprosy.

Excavating new facts from ancient Hepatitis B virus sequences

Recently, two independent studies discovered 15 ancient Hepatitis B virus (aHBV) sequences, of which 7 dated back to the Neolithic age (NA) and the Bronze Age (BA). In the present research, all the available aHBV sequences were collectively re-analysed with reference to extant HBV diversity to understand the role of these aHBV genotypes in evolution of extant HBV genetic diversity. Several intergenotype recombination events were documented, which corroborated well with population admixture and ancient human migration. Present analyses suggested replacement of HBV genotype associated with early Neolithic European farming cultures by the migrating steppe people, during Bronze Age Steppe migration. Additionally, detailed analyses of recombinations revealed evolution of a number of extant genotypes and suggested their possible site of origin. Through this manuscript, novel and important findings of the analyses are communicated.

Phylogenetic dating analysis of HTLV-1 from Chile suggests transmissions events related to ancient migrations and contemporary expansion

•Human T-cell lymphotropic virus type 1 (HTLV-1) is a globally-spread virus. It is estimated that there are about 5–10 million infected people in the world. HTLV is endemic in Chile, with higher seroprevalence among indigenous people. However, little is known about HTLV-1 genetic diversity, its introduction and dispersion in this country. To gain insights into these issues, a phylogenetic dating analysis was conducted based on Chilean and closed related long terminal repeat sequences. The time tree reconstruction showed that the introduction of HTLV-1aA occurred several times in Chile. It was hypothesized that these introductions took place at least in two different historical moments: (i) during the ancient human migrations and (ii) during/after the European colonization of South America. The present study contributes toward understanding the evolutionary history of HTLV-1 in Chile and South America.

Neandertal DNA in Africans

Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.

Human mobility in the Lop Nur region during the Han-Jin Dynasties: a multi-approach study

The Lop Nur region, as the junction of the Silk Roads, played an important role in ancient human migration between the East and the West, especially during the Han-Jin Dynasties (second century CE to fourth century CE). However, the scale and volume of human mobility in the region remain poorly understood. Here, we present a multi-approach (wood identification, strontium and oxygen isotopes of tooth enamel and historical documents) to investigate the extent of human mobility in the Lop Nur region. From a Han-Jin Dynasties cemetery, the appearance of nonlocal wood might suggest the existence of human migratory behaviors in the Lop Nur region. Furthermore, a piece of lacquerware with the possible origin of eastern China and a large-scale mural tomb likely belonged to a Kushan emigrant indicate the existence of long-distance connections across the Asia interior. Strontium and oxygen isotope data show a highly mobile population in the Lop Nur region, and the great isotopic variation suggests that these immigrants have diverse origins. In context with historical documents, we infer that the Lop Nur region was once the political, economic, and cultural meeting place of various societies, and also a communication corridor on the Silk Roads during the Han-Jin Dynasties.

Jbel Bani Rock Art: Newly-discovered Shelters along Mountain Paths suggest a Significant Link between Central Sahara and North Africa (Zagora, Southern Morocco)

Abstract The authors, with the help of a team of researchers, have discovered twelve rock shelters with inside paintings on the southern slopes of the Jbel Bani Mountains in southern Morocco. The paintings vary in subject and time period and span multiple rock art styles. Majestic creatures that once inhabited southern Morocco are depicted next to hunters, pastoralists, and warriors. The shelters and paintings cast upon their walls illustrate a transfer of culture, beliefs, technology, and ideas between people groups of the Meridional and Central Sahara and the Jbel Bani region. These discoveries were all made along a mountain path in the Bani Mountains known as Foum Laachar and may help trace ancient human migration routes.

Peopling of India: Ancient DNA perspectives

To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent.

Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes.

The entry point and timing of ancient human migration into continental Sahul (the combined landmass of Australia, New Guinea, and Tasmania) are subject to debate. Unique strains of hepatitis B virus (HBV) are endemic among modern-day Australian Aboriginals (HBV/C4) and Indigenous Melanesians (HBV/C3). We postulated that HBV genomes could be used to infer human population movements because the main HBV transmission route in endemic populations is via mother-to-child for genotypes B and C infections. Phylogenetic and phylogeographic analyses of HBV genomes inferred the origin of HBV/C4 to be >59 thousand years ago (ka) (95% HPD: 34-85 ka), and most likely to have occurred on theSunda Shelf (southeast extension of the continental shelf of Southeast Asia). Our analysis further suggested an age of >51 ka (95% Highest Posterior Density (HPD): 36-67 ka) for the most recent common ancestor of HBV/C4 in Australia, correlating with the arrival time of anatomically modern humans into Australia, with the entry point suggested along a southern route via Timor. While we also inferred the origin of HBC/C3 to be on the Sunda Shelf, our analyses suggested that it was carried into Melanesia by Indigenous Melanesians who migrated through New Guinea north of the highlands. These findings reveal that HBV genomes can be used to infer ancient human population movements.

Tuberculosis and leprosy associated with historical human population movements in Europe and beyond – an overview based on mycobacterial ancient DNA

Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations.Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes.Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification.Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th–14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples.Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.

“Sea Peoples” Up-to-Date: New Research on Transformations in the Eastern Mediterranean in the 13th–11th Centuries BCE

“Sea Peoples” Up-to-Date: New Research on Transformations in the Eastern Mediterranean in the 13th–11th Centuries BCE

Evolutionary history and biogeography of Mandragora L. (Solanaceae)

Mandragora L. (Solanaceae) is the only genus of the tribe Mandragoreae, one of the two tribes of the cosmopolitan nightshade family, which occur exclusively in Eurasia and northern Africa. The genus occurs discontinuously in the Mediterranean region, Turanian region, and on the Tibetan Plateau, representing a classical disjunction pattern in the biogeography of the Old World flora. In this study, we reconstructed the genus phylogeny using AFLP, eight plastid DNA regions and one nuclear (ITS) gene, and evaluated the taxonomic value of quantitative traits time to flowering, fruit and seed size. We also analyzed the evolutionary history of the genus based on a phylogenetic framework and dating inferred from a combined data set of seven plastid regions with one fossil calibration point. Our data suggest that Mandragora originated in the Eocene, apparently along the Tethyan coast in broadleaf deciduous mesophytic forests that covered most of the Mediterranean region at that time. The Mediterranean-Turanian clade diverged from the Tibetan Plateau clade about 20.5 million years ago (Ma) as a result of the plateau uplift which probably was enhanced by aridification in the interior of Eurasia. A second split within the genus occurred about 11.1 Ma and resulted in Western Mediterranean and Near East-Turanian clades. Mandragora turcomanica was found to have very closely related evolutionary history with plants from the Near East indicating a possible ancient human assisted migration from Israel to Persia in historic times. In the Tibetan Plateau area, the morphologically distinctive M. chinghaiensis is nested within the M. caulescens clade indicating a very recent diversification within this lineage.

Phylodynamics of Merkel-cell polyomavirus and human polyomavirus 6: A long-term history with humans

New human polyomaviruses have been described in the last years, including the Merkel-cell polyomavirus (MCPyV; Human polyomavirus 5) and the Human polyomavirus 6 (HPyV6). Although their infection is usually asymptomatic, in immunocompromised host can cause life-threatening pathologies, such as the Merkel cell carcinoma, an aggressive skin neoplasia associated to the MCPyV. Despite being prevalent viruses in population, epidemiological data from South America are scarce, as well as the characterization of the viral types circulating and their origin. The aims of this work were to describe MCPyV and HPyV6 from environmental samples with different geographical origin and to analyze their phylogenetic and evolutionary histories, particularly for MCPyV.Partial and complete genome sequences were obtained from sewage samples from Argentina, Uruguay and Spain. A total number of 87 sequences were obtained for MCPyV and 33 for HPyV6. Phylogenetic analysis showed that MCPyV sequences distributed according to their geographic origin in Europe/North America, Africa, Asia, South America and Oceania groups, suggesting that viral diversification might have followed human migrations across the globe. In particular, viruses from Argentina associated with Europe/North America and South America genotypes, whereas those from Uruguay and Spain also grouped with Africa genotype, reflecting the origin of the current population in each country, which could arrive not only during ancient human migration but also during recent migratory events. In addition, the South American group presented a high level of clusterization, showing internal clusters that could be related to specific locations, such as French Guiana and Brazil or the Southern region into South America, such as Argentina and Uruguay, suggesting a long term evolutionary process in the region.Additionally, in this work, we carried out the first analysis about the evolutionary history of MCPyV trough the integration of phylogenetic, epidemiological and historical data. Since a strong association is observed between the phylogenetic relationships and the origin of the sampled population, this analysis was based on the hypothesis of co-divergence between the virus and human populations. This analysis resulted in a substitution rate of 5.1 × 10−8 s/s/y (∼5.1% of divergence per million years) for the complete genome of MCPyV, which is in the range of those estimated for other double-stranded DNA viruses.Regarding HPyV6, a South American group with clusterization was observed (sequences from Uruguay). Meanwhile, sequences from Argentina grouped with European ones (France and Spain) and remained separated from those isolated in China, USA or Australia.The analysis of viruses from the environment allowed us to deep characterize prevalent infections in different geographic regions, reveling that viruses circulating in each population reflected its origin and that there are specific lineages associated with South America.