Biology subjects

McColl, H.

Publications and source records attributed to McColl, H..

9 recordsLinked to original sources

bioRxiv2026

Migrations facilitated the cultural diffusion of megaliths in Neolithic Europe

Around 6700 BP (years before present), Neolithic Europe saw the emergence of megalithic monuments in northern France, followed by a rapid spread to the rest of the continent1. However, whether this was driven by the transmission of ideas (cultural diffusion) or the movement of people remains debated. To test whether this spread coincided with population movements, we reconstructed the population history of the European Neolithic ([~]6500-4800 BP) by analysing genomic data from 2963 ancient individuals, including 46 unpublished genomes from megalithic and related contexts. To assess the alternative scenario whereby megaliths spread through contact networks, as expected under cultural diffusion, we integrated archaeological evidence with radiocarbon chronologies to reconstruct past trading networks. We identify northern France, where megaliths first emerged, as a zone of genetic admixture and cultural influence from the two major early Neolithic divisions: the Cardial of the Western Mediterranean and the Linear Pottery traditions of central Europe. From this admixed population, we uncover several migrations associated with the formation of the Funnel Beaker Culture in north-central Europe and the neolithisation of Scandinavia and the British Isles. We find that megaliths were spread exclusively within regions impacted by Cardial-related genetic ancestry, but only in the British Isles and Ireland did their emergence coincide with the time of the migration. The temporal delay between the migrations and the spread of megaliths elsewhere reveals that neither population movements nor cultural diffusion alone fully explains the geospatial distribution of the megalithic tradition. Rather, megaliths diffused across different Neolithic groups whose long-distance trade networks formed in the wake of earlier population movements. Our findings highlight the need to move beyond simplistic interpretations that present migrations or cultural diffusion as isolated events bringing technological and cultural innovations.

evolutionary biology↗

bioRxiv2025

ybyra: Y-chromosome haplogroup calling using a tree-based scoring method

We present ybyra, a Snakemake workflow for automated Y-chromosome haplogroup assignment using a tree-based scoring method with robust and transparent heuristics. The pipeline supports both human reference genome builds 37 and 38, makes use of three different well-curated Y-SNP tree topologies and features an optional ancient DNA damage filter to accommodate low-coverage degraded samples. ybyra produces reproducible, scalable haplogroup calls with detailed scoring outputs to facilitate quality assessment and reporting. We further showcase its versatility by applying it to horse Y-chromosome data, highlighting its applicability beyond humans. Availabilityybyra is published under the MIT license and freely available at github.com/tpinotti/ybyra.

bioinformatics↗

bioRxiv2025

Tracing the Spread of Celtic Languages using Ancient Genomics

Celtic languages, including Irish, Scottish Gaelic, Welsh and Breton, are today restricted to the Northern European Atlantic seaboard. However, between three and two thousand years before present (BP), Celtic was widely spoken across most of Europe before being largely replaced by Germanic, Latin or Slavic1-4. Despite this rich history, how Celtic spread across the European continent remains contentious5. The debate is currently focused around three main models based on historical linguistics and archaeology: (1) a Late Bronze Age/Early Iron Age spread from Central Europe associated with the Hallstatt and La Tene Cultures6-9; (2) a Late Neolithic/Early Bronze Age spread along the Atlantic seaboard linked to the Bell Beaker Culture10-13; and (3) a Bronze Age spread from France, Iberia or Northern Italy14-16. Previous genomic investigations are centred around the arrival of Celtic to specific regions: Britain17, Iberia18 and Southwestern Germany19. Here, we utilise new genomic data from Bronze and Iron Age Europe to test how the population histories align with the three models of prehistoric spread of the Celtic languages. In line with the theory that Celtic spread from Central Europe during the Late Bronze Age to Early Iron Age, we find Urnfield-related ancestry - specifically linked to the Knoviz subgroup to have formed between 4 and 3.2 kyr BP, and subsequently expanded across much of Western Europe between 3.2 and 2.8 kyr BP. This ancestry further persisted into the Hallstatt Culture of France, Germany and Austria, impacting Britain by 2.8 kyr BP and Iberia by 2.5 kyr BP. Our findings thus agree with the model of Central European spread of the Celtic languages through consecutive expansions of the Urnfield, Hallstatt and La Tene Cultures rather than the competing models. These results demonstrate, yet again, the power of ancient population genomics in addressing long-standing debates in historical linguistics and archaeology.

evolutionary biology↗

bioRxiv2024

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages

The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious1-5. It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age6,7. However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages8,9. To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic10,11 and Graeco-Armenian1,12,13 hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.

genetics↗

bioRxiv2024

Steppe Ancestry in western Eurasia and the spread of the Germanic Languages

Today, Germanic languages, including German, English, Frisian, Dutch and the Nordic languages, are widely spoken in northwest Europe. However, key aspects of the assumed arrival and diversification of this linguistic group remain contentious1-3. By adding 712 new ancient human genomes we find an archaeologically elusive population entering Sweden from the Baltic region by around 4000 BP. This population became widespread throughout Scandinavia by 3500 BP, matching the contemporaneous distribution of Palaeo-Germanic, the Bronze Age predecessor of Proto-Germanic4-6. These Baltic immigrants thus offer a new potential vector for the first Germanic speakers to arrive in Scandinavia, some 800 years later than traditionally assumed7-12. Following the disintegration of Proto-Germanic13-16, we find by 1650 BP a southward push from Southern Scandinavia into presumed Celtic-speaking areas, including Germany, Poland and the Netherlands. During the Migration Period (1575-1375 BP), we see this ancestry representing West Germanic Anglo-Saxons in Britain, and Langobards in southern Europe. We find a related large-scale northward migration into Denmark and South Sweden corresponding with historically attested Danes and the expansion of Old Norse. These movements have direct implications for multiple linguistic hypotheses. Our findings show the power of combining genomics with historical linguistics and archaeology in creating a unified, integrated model for the emergence, spread and diversification of a linguistic group.

genetics↗

bioRxiv2022

The Selection Landscape and Genetic Legacy of Ancient Eurasians

The Holocene (beginning [~]12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical, and mental health of present-day populations. Using a dataset of >1600 imputed ancient genomes 1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported, and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in >400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic, and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, while risk alleles for diabetes and Alzheimers disease are enriched for Western Hunter-gatherer ancestry. Our results suggest that ancient selection and migration were major contributors to the distribution of phenotypic diversity in present-day Europeans.

evolutionary biology↗

bioRxiv2022

Population Genomics of Stone Age Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. To investigate the cross-continental impacts we shotgun-sequenced 317 primarily Mesolithic and Neolithic genomes from across Northern and Western Eurasia. These were imputed alongside published data to obtain diploid genotypes from >1,600 ancient humans. Our analyses revealed a Great Divide genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers (HGs) were highly genetically differentiated east and west of this zone, and the impact of the neolithisation was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacements of HGs in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, while east of the Urals relatedness remained high until [~]4,000 BP, consistent with persistence of localised HG groups. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive but we demonstrate that HGs from the Middle Don region contributed ancestry to them. Yamnaya-groups later admixed with individuals associated with the Globular Amphora Culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a Neolithic steppe cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

evolutionary biology↗

bioRxiv2018

The population history of northeastern Siberia since the Pleistocene

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of \"Ancient North Siberians\" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and \"Ancient Paleosiberians\" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the \"Neosiberians\" from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

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↗