Biology subjects

Higham, T.

Publications and source records attributed to Higham, T..

8 recordsLinked to original sources

bioRxiv2025

Genetic admixture between East and West European Gravettian-associated populations in Western Europe before the Last Glacial Maximum

Modern humans first settled in Europe at least 45,000 years ago. However, limited genomic data from individuals dating between 45,000 and 20,000 years ago still restricts our understanding of population dynamics and admixture during the Upper Palaeolithic. Before the Last Glacial Maximum (LGM, 26.5-19 cal kya), Gravettian culture-associated populations were widespread and genetically diverse, comprising at least two distinct genetic groups, referred to as the Fournol and V[e]stonice clusters. We present genome-wide data from three Gravettian-associated individuals: two from cave sites in the Franco-Cantabrian region (Chufin and Isturitz) and one from Italy (Ostuni1b). These data reveal previously undetected gene flow linking the ancestry of 34,000-year-old individuals from Sungir (Russia) to Gravettian individuals from Western Europe, challenging the prevailing model of population continuity from the Aurignacian to the Solutrean. As osseous remains are scarce for this time period, DNA from sediments deposited by ancient humans opens a new possibility to obtain genomic data. We thus examine sedimentary DNA from Solutrean Layer 122 at El Miron Cave (Cantabria, [~]22,000 cal BP), recovering approximately 16,000 human SNPs, among the highest yields reported from a Palaeolithic context. Generating these data required over 1.15 billion sequencing reads, illustrating both the potential of sediment DNA for autosomal analysis and the technical challenges of the approach.

genomics↗

bioRxiv2024

Buca della Iena and Grotta del Capriolo: new chronological, lithic, and faunal analyses of two late Mousterian sites in Central Italy

New radiocarbon, lithic, faunal, and documentary analyses of two sites, Buca della Iena and Grotta del Capriolo, excavated in the 1970s, enhance our understanding of late Neanderthal settlement in the northwestern Italian peninsula and provide insights into their demise. Reassessment of stratigraphical and fieldwork documentation identified areas of stratigraphic reliability, supporting robust interpretations. Radiocarbon dating reveals broadly contemporaneous occupations at both sites between 50-40 ka cal BP, with Buca della Iena showing occupation from approximately 47 to 42.5 ka cal BP. Lithic analyses demonstrate the consistent application of the same chaine operatoire across both sites. Faunal analyses indicate that carnivores, particularly Crocuta spelaea, were the dominant accumulating agents in Buca della Iena, while limited preservation at Grotta del Capriolo prevents detailed taxonomic determination. However, hominin presence at both sites is evidenced by cut-marked bones. This study provides new perspectives on the Middle-to- Upper Palaeolithic transition in the northwestern Italian peninsula.

paleontology↗

bioRxiv2024

The Genetic Origin of the Indo-Europeans

The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/589597v1_ufig1.gif" ALT="Figure 1"> View larger version (91K): org.highwire.dtl.DTLVardef@127de98org.highwire.dtl.DTLVardef@87010aorg.highwire.dtl.DTLVardef@1554627org.highwire.dtl.DTLVardef@170dd63_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure:C_FLOATNO The origin of Indo-Anatolian and Indo-European languages. Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green). C_FIG

genetics↗

bioRxiv2023

A late Neanderthal reveals genetic isolation in their populations before extinction

Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations structure, mostly indicating that late European Neanderthals belonged to a single metapopulation with no significant evidence of deep population structure. Here we report the discovery of a late Neanderthal individual, nicknamed "Thorin", from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of their final technological traditions in this region [~]50-42 thousand years ago. Thorins genome reveals a deep divergence with other late Neanderthals. Thorin belonged to a population with small group size that showed no genetic introgression with other known late European Neanderthals, revealing genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the Neanderthals disappearance. One Sentence SummaryA new French Neanderthal fossil and its genome reveal complex population dynamics during the past 100,000 years.

genomics↗

bioRxiv2021

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this regions demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

genomics↗

bioRxiv2020

Denisovan ancestry and population history of early East Asians

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

evolutionary biology↗

bioRxiv2018

The genetic prehistory of the Greater Caucasus

Archaeogenetic studies have described the formation of Eurasian steppe ancestry as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4th millennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that - unlike today - the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

genomics↗

bioRxiv2018

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

evolutionary biology↗