Biology subjects

Rohland, N.

Publications and source records attributed to Rohland, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Hybrid Drosophila genomes rapidly purge minority ancestry but repeatedly retain selected regions

Hybridization is increasingly recognized as a widespread evolutionary process across animals, plants, and fungi, and plays a key role in driving speciation, shaping genetic diversity, and facilitating adaptation. Initial hybrid genomes are rarely observed empirically, making it challenging to observe in real time how competing forces like purifying selection and adaptive introgression interact to shape post-hybridization genomes. Here, we use replicated experimental hybrid populations between Drosophila simulans and D. sechellia to track directly genome-wide evolutionary dynamics across approximately 45 generations post-hybridization. We show that hybrid populations with primarily D. simulans ancestry rapidly recover wild-type levels of fertility and fecundity, whereas populations carrying predominantly D. sechellia ancestry experience persistent fitness reductions and frequent extinction. Genome-wide ancestry trajectories show pervasive purifying selection against minority-ancestry alleles, leading to rapid regression toward majority ancestry across the genome, with stronger purging on the X chromosome than autosomes. Following the initial purging, neutral minority ancestry stabilized at low frequencies across the genome. In striking contrast, we observe repeated increases in D. sechellia ancestry on chromosome 4 and multiple regions on chromosome 3R within D. simulans-majority populations, providing evidence for adaptive introgression. High-density sequencing revealed that these regions were repeatedly retained across independently evolving populations despite near-complete genome-wide purging. Simulations support a model in which recombination rapidly uncouples beneficial introgressed alleles from linked incompatibility-associated alleles during the initial generations, allowing positive selection to act. Our temporal allele-frequency analyses suggest that hybrid genome stabilization of the introgressed regions is highly repeatable but not identical, yielding parallel outcomes across replicate populations. We establish a tractable experimental framework to directly observe how hybrid genomes reorganize in real time, and demonstrate how purifying selection, positive selection, recombination, and stochastic processes interact to restructure hybrid genomes shortly after admixture.

genetics↗

bioRxiv2026

The south Congo Basin was critical to Bantu settlement of south central Africa

South central Africa, between the Congo Basin, the Great Lakes, and southern Africa, has long served as a corridor for human movement. Yet, it remains unclear whether there is genetic continuity between pre-Iron Age foragers and later Bantu-associated populations and whether the settlement of this region reflects multiple Bantu-associated migrations rather than the simpler serial founder model suggested by existing genomic data. To do so, we generated genome-wide ancient DNA from 71 Iron Age and historical individuals from present-day Zambia and Malawi, and analyzed these genomes alongside published data from present-day Africans. One late Iron Age individual (16th-17th century) from Kalala Island in the Kafue River, Zambia, carries 40% non Bantu related ancestry that closely matches local Later Stone Age foragers. Admixture for this individual is estimated to be 850 years ago, several centuries earlier than reported for present day BaTwa from the same region. Focusing on the Bantu-related ancestry, haplotype-based analyses identify two main clusters among Iron Age, historical, and present-day south central Bantu groups associated with different Bantu-related migrations. These results reveal a layered history in which at least two Bantu expansions radiated from the southern Congo Basin, with south central Africa acting both as a crossroads of these movements and as a staging area for the subsequent southward expansion toward southern Africa.

evolutionary biology↗

bioRxiv2026

The Pan-European Impact of the Balkan Hunter-Gatherers

During the Last Glacial Maximum (LGM) 26-19 thousand years ago (kya), Europe had three principal refugia not covered by ice: the Iberian, Italian, and Balkan peninsulas1,2. While the Iberian and Italian refugia have been studied with ancient DNA3-7, the legacy of the Balkan refugium has remained a mystery due to a lack of genetic data 30-12 kya. We present genome-wide data from nine newly reported individuals: three Epipaleolithic from Romania, one Epipaleolithic from Bosnia and Herzegovina, three Mesolithic from Greece, one Epipaleolithic from Southern Italy, and one Mesolithic from Sardinia. We find that the Epipaleolithic individuals from Romania and the Mesolithic individual from mainland Greece were from a previously unsampled population that was the primary source for later European hunter-gatherers. Westward expansion of Balkan Epipaleolithic people into the Italian Peninsula and mixture with a minority contribution from pre-LGM Italians, produced a population that then spread further west to become the primary ancestry of west-ern European Mesolithic people. Northeastward expansion, bypassing Italy, contributed the European ancestry source of Scandinavian and Eastern European hunter-gatherers. Southeastward expansion to the Aegean led to Anatolian-European mixtures before the spread of farming.

genetics↗

bioRxiv2026

Buried in two places: Lineages from elite Maya tombs also found in distant caves

Classic Maya societies (250-900 CE) carved out urban centers in the rainforest reaching population heights and political complexity previously unknown in the Mesoamerican tropics. Kinship was a central feature of the social fabric, and rulership was legitimized through claims of direct descent from mythical ancestors. Mortuary practices kept the dead close to the living, and ancestor veneration sometimes produced complex deposits of disarticulated remains that are difficult to identify and whose biological relationships to one another cannot be understood without genetic data. We screened 487 human tooth and bone samples and successfully generated genome-wide data for 430 of them. Of these, 341 samples representing 107 distinct individuals were recovered from both elite and non-elite tombs in a Classic period kingdom (250-900) CE in the rugged Maya Mountains of Belize. Remarkably, 24 of these individuals have skeletal elements in both an elite tomb and in a ritual tooth cache in a distant cave located 26.5km away on the other side of the Maya Mountains. These results indicate that elite lineages created ancestors from their deceased relatives in geographically expansive ways and highlights the importance of caves in the belief system of Classic Maya elites.

genetics↗

bioRxiv2026

First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America

The population history of the Caribbeans first inhabitants has been challenging to reconstruct because few human remains are known from the regions earliest occupation which began around 6,000 years ago in Hispaniola, Cuba, and Puerto Rico. We generated genome-wide data from 19 individuals from Hispaniolas Samana Peninsula and focused on four who lived during the earliest pre-Ceramic "Lithic Age". Extending the Caribbean genetic record by more than a millennium to [~]4,400 calBP, we show that pre-Ceramic Age populations across Hispaniola and Cuba derive from a single ancestry source and document long-term genetic continuity across islands, with some local genetic structure within Hispaniola. Pre-Ceramic Age Caribbean ancestry shares most drift with populations from Central America and northern South America, although no sampled mainland group provides an adequate proxy. We infer very small effective community sizes, consistent with locally structured mating pools and little evidence of close-kin mating. These findings extend our understanding of Caribbean population history into its earliest phase. TeaserEarly Caribbean people shared ancestry across islands and lived in small, locally structured communities.

genetics↗

bioRxiv2026

Convergent natural selection at both ends of Eurasia during parallel radical lifestyle shifts in the last ten millennia

Ancient DNA-based studies of natural selection have focused on West Eurasia due to the availability of large sample sizes, but rich insights are expected to come from comparative studies that can reveal which patterns are shared and which region-specific. We test around seven million variants for selection in 1,862 ancient East Eurasians (867 with new data) distributed over the last ten millennia. Using a generalized linear mixed model to control for population structure, we identify 40 genome-wide significant signals of selection, which have a particularly strong impact on immune and cardiometabolic traits just as in West Eurasia. East and West Eurasia show highly correlated signals of adaptation both for individual alleles and for complex traits, showing how these geographically separate groups experienced convergent evolution in response to parallel transitions to food producing economies and the accompanying lifestyle changes. An exception is the genetic determinants of light skin color: West Eurasians depigmented in the last 10,000 years, but most skin lightening in East Asians arose prior to the Holocene.

evolutionary biology↗

bioRxiv2026

Subsistence transition preceded population turnover in the eastern Colombian Andes

Northwest South America was a pivotal region for human dispersals and cultural exchange during the Holocene. The Altiplano Cundiboyacense, a high-altitude plateau in the Eastern Cordillera of the Northern Andes of Colombia, preserves one of the most continuous archaeological sequences in the Americas, spanning from late Pleistocene hunter-gatherer groups to final late Holocene Muisca chiefdoms. Increasing the regional ancient DNA sample size 11-fold, we report genome-wide data from 209 individuals who lived over a period of more than 7000 years. This includes hunter-gatherers from the early-middle (10,000-7000 BP) and middle (7000-4000 BP) Holocene, initial late Holocene people (4000-2500 BP) who have the first isotopic evidence of C-enriched diets (attributed to maize), and populations associated with increasing sedentism and food production in the Herrera (2200-1300 BP) and Muisca (1200-500 BP) Periods. Previous work identified a major population turnover distinguishing earlier groups from Herrera-Muisca Period populations, but the absence of individuals dating 6000-2000 BP in that study left unresolved whether this ancestry shift was gradual or abrupt and whether it accompanied the earliest isotopic evidence of dietary input from maize or coincided with the later emergence of Herrera culture. We show that individuals predating the Herrera Period form a lineage that persisted for over five millennia, with population structure driven by drift in small groups and no detectable external gene flow. Two individuals who lived [~]2800 years ago - one directly dated to 983-835 calBCE - exhibit genetic profiles entirely consistent with hunter-gatherer ancestry yet have isotopic values consistent with the incorporation of maize into their diets, indicating subsistence change without population replacement. The emergence of Herrera culture [~]2200 BP coincided with a sharp genetic break, reflecting the migration of people carrying ancestry diverged by up to ten millennia into the Sabana de Bogota and displacing previously established peoples. By co-analyzing ancient data with modern Native Americans, we show these later populations derived from a mixture [~]4000 years ago of groups related to Chibchan language speakers of lower Central America and ones related to present-day people at the Amazonian-Andean interface who may have lived along the Chibchan expansion route. In the Herrera and Muisca Periods, genetic substructure distinguishes people from the southern and northern Altiplano, consistent with the cultural differentiation of these regions in the archaeological record. IN BRIEFAncient DNA data from the eastern Colombian Andes reveal five millennia of population continuity during which C plants were incorporated into subsistence systems without population replacement, followed later by a major ancestry turnover involving a population with ancestry admixed between that found in Chibchan-related groups and at the Amazonian-Andean interface.

genetics↗

bioRxiv2026

Ancient genomes from Ladakh reveal 2800-year-old mixture between Tibetans and South Asians

Reconstructing population history is harder in South Asia than in many other world regions due to a paucity of ancient DNA. We report genome-wide data for ten individuals from Old Lady Spider Cave, which lies 4000 meters above sea level in the Himalayan region of Ladakh, and dates to around 1500 years before present (BP). These individuals were genetically homogeneous and had an ancestry signature rare in South Asians today: admixed in roughly 50-50% proportions between a population well-proxied by present-day North Indians, and another genetically similar to ancient Tibetans. By analyzing the typical sizes of segments of DNA inherited from each of these ancestral populations, we find that mixture of these groups began at least fifty generation before the date of the individuals, that is, by around 2800 BP. TeaserDiscovery of a previously unknown population that lived 2800-1500 years ago in the Himalayan region of Ladakh.

evolutionary biology↗

bioRxiv2025

Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups

The first phase of the ancient DNA revolution painted a broad-brush picture of European Holocene prehistory, whereby 6500-4000 BCE, farmers descending from western Anatolians mixed with local hunter-gatherers resulting in 70-100% ancestry turnover, then 3000-2500 BCE people associated with the Corded Ware complex spread steppe ancestry into north-central Europe. We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry ([~]50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a characteristic early Corded Ware Y-chromosome. The limited influx may reflect the unique ecology of the regions river-dominated landscapes, which were not amenable to wholesale adoption of the early Neolithic type of farming introduced by Linearbandkeramik, making it possible for previously established groups to thrive, and creating a persistent but permeable boundary that allowed transfer of ideas and low-level gene flow. This changed with the formation-through-mixture of Bell Beaker using populations [~]2500 BCE by fusion of local Rhine-Meuse people (9-17%) and Corded Ware associated migrants of both sexes. Their expansion from the Rhine-Meuse region then had a disruptive impact across a much wider part of northwest Europe, including Britain where its arrival was the main source of a 90-100% replacement of local Neolithic peoples.

genomics↗

bioRxiv2025

Tracing social mechanisms and interregional connections in Early Bronze Age Societies in Lower Austria

In this study, we present the results of archaeogenetic investigations of Early Bronze Age individuals from Lower Austria, specifically associated with the Un[e]tice and Unterwolbling cultural groups. Through analysing newly generated genome-wide data of 138 individuals, we explore the social structure and genetic relationships within and between these communities. Our results reveal a predominantly patrilocal society with non-strict female exogamic practices. Additionally, Identity-by-Descent (IBD) analysis detects long-distance genetic connections, emphasizing the complex network of interactions in Central Europe during this period. Despite shared social dynamics, notable genetic distinctions emerge between the Un[e]tice and Unterwolbling groups. These insights contribute to our understanding of Bronze Age population interconnections and call for a nuanced interpretation of social dynamics in this historical context.

genetics↗

bioRxiv2025

Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin

Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.

genomics↗

bioRxiv2024

Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation

We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from [~]0% to [~]20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from [~]0% to [~]8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from [~]2% to [~]9% from [~]5500 to [~]3000 years ago before dropping to [~]3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.

evolutionary biology↗

bioRxiv2024

Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians

During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.

genetics↗

bioRxiv2024

A genomic history of the North Pontic Region from the Neolithic to the Bronze Age

The north Black Sea (Pontic) Region was the nexus of the farmers of Old Europe and the foragers and pastoralists of the Eurasian steppe1,2, and the source of waves of migrants that expanded deep into Europe3-5. We report genome-wide data from 78 prehistoric North Pontic individuals to understand the genetic makeup of the people involved in these migrations and discover the reasons for their success. First, we show that native North Pontic foragers had ancestry not only from Balkan and Eastern hunter-gatherers6 but also from European farmers and, occasionally, Caucasus hunter-gatherers. More dramatic inflows ensued during the Eneolithic, when migrants from the Caucasus-Lower Volga area7 moved westward, bypassing the local foragers to mix with Trypillian farmers advancing eastward. People of the Usatove archaeological group in the Northwest Pontic were formed ca. 4500 BCE with an equal measure of ancestry from the two expanding groups. A different Caucasus-Lower Volga group, moving westward in a distinct but temporally overlapping wave, avoided the farmers altogether, and blended with the foragers instead to form the people of the Serednii Stih archaeological complex7. A third wave of expansion occurred when Yamna descendants of the Serednii Stih forming ca. 4000 BCE expanded during the Early Bronze Age (3300 BCE). The temporal gap between Serednii Stih and the Yamna expansion is bridged by a genetically Yamna individual from Mykhailivka in Ukraine (3635-3383 BCE), a site of uninterrupted archaeological continuity across the Eneolithic-Bronze Age transition, and the likely epicenter of Yamna formation. Each of these three waves propagated distinctive ancestries while also incorporating outsiders during its advance, a flexible strategy forged in the North Pontic region that may explain its peoples outsized success in spreading their genes and culture across Eurasia3-5,8-10.

genetics↗

bioRxiv2022

The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast

The peoples of the Swahili coast of eastern Africa established a literate urban culture by the second millennium CE. They traded across eastern Africa and the Indian Ocean and were among the first sub-Saharan practitioners of Islam. An open question has been the extent to which these early interactions between Africans and non-Africans were accompanied by genetic admixture. We report genome-wide ancient DNA from 80 individuals in five medieval and early modern (1300-1800 CE) coastal towns, as well as people from an inland town postdating 1650 CE. Over half of the ancestry of most coastal individuals came from African ancestors; these African ancestors were primarily female. A slightly smaller proportion of ancestry was from Asia. This Asian component was approximately eighty to ninety percent from Near Eastern males and ten to twenty percent from Indian females. Peoples of African and Asian origins began to mix by around 1000 CE, a time when archaeological evidence documents changes on the coast that are often interpreted as marking the large-scale adoption of Islam. Before roughly 1500 CE, the Near Eastern ancestry detected in the individuals was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by the Swahili themselves. After this time, the sources of Near Eastern ancestry became increasingly Arabian, consistent with the archaeological and historical evidence of growing interactions between the Swahili coast and parts of southern Arabia. Subsequent interactions of Swahili coast peoples with other Asian and African groups further changed the ancestry of present-day peoples relative to the ancient individuals we sequenced, highlighting how Swahili genetic legacies can be more clearly understood with ancient DNA.

genetics↗

bioRxiv2022

Technical Report on Ancient DNA analysis of 27 African Americans from Catoctin Furnace, Maryland

Catoctin Furnace is an industrial site that functioned from 1776-1903 and was operated at least partially by an enslaved workforce until about 1850, when it shifted to paid European laborers. A cemetery including 35 graves from which the remains of 32 individuals identified with African ancestry were excavated in 1979-1980 during construction of a highway that impacted the site. Since then, the human remains have been under the stewardship of the Smithsonians National Museum of Natural History (NMNH). The goal of this report is to document the successful generation of ancient DNA from 27 individuals from the cemetery. The analysis of the Catoctin individuals is part of a long-term study dedicated to restoring knowledge of the identity, origins, and legacy of the enslaved and free African Americans who labored and were buried at Catoctin Furnace1.

genomics↗

bioRxiv2022

Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

We report genome-wide data for 33 Ashkenazi Jews (AJ), dated to the 14th century, following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ and have substantial Southern European ancestry, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried the same nearly-AJ-specific mitochondrial haplogroup and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. However, the Erfurt bottleneck was more severe, implying substructure in medieval AJ. Together, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.

genetics↗

bioRxiv2022

Three Reagents for in-Solution Enrichment of Ancient Human DNA at More than a Million SNPs

In-solution enrichment for hundreds of thousands of single nucleotide polymorphisms (SNPs) has been the source of >70% of all genome-scale ancient human DNA data published to date. This approach has made it possible to generate data for one to two orders of magnitude lower cost than random shotgun sequencing, making it economical to study ancient samples with low proportions of human DNA, and increasing the rate of conversion of sampled remains into working data thereby facilitating ethical stewardship of human remains. So far, nearly all ancient DNA data obtained using in-solution enrichment has been generated using a set of bait sequences targeting about 1.24 million SNPs (the 1240k reagent). These sequences were published in 2015, but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies made available reagents that target the same core set of SNPs along with supplementary content. Here, we test the properties of the three reagents on a common set of 27 ancient DNA libraries across a range of richness of DNA content and percentages of human molecules. All three reagents are highly effective at enriching many hundreds of thousands of SNPs. For all three reagents and a wide range of conditions, one round of enrichment produces data that is as useful as two rounds when tens of millions of sequences are read out as is typical for such experiments. In our testing, the "Twist Ancient DNA" reagent produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. Allelic bias in 1240k enrichment has made it challenging to carry out joint analysis of these data with shotgun data, creating a situation where the ancient DNA community has been publishing two important bodes of data that cannot easily be co-analyzed by population genetic methods. To address this challenge, we introduce a subset of hundreds of thousands of SNPs for which 1240k data can be effectively co-analyzed with all other major data types.

genomics↗