Biology subjects

Callan, K.

Publications and source records attributed to Callan, K..

17 recordsLinked to original sources

bioRxiv2026

Collided ribosomes are rescued by the endonuclease Rae1 and trans-translation

Ribosome stalling is a major problem in all domains of life. When a ribosome stalls, trailing ribosomes may catch up to and collide with the stalled ribosome, depleting protein synthesis capacity. Here, we describe a novel pathway used by Gram-positive bacteria to rescue ribosome collisions. We used the ATPase defective ABCF protein YdiF(EQ2) to induce ribosome stalling and collisions in Bacillus subtilis. Ribosome profiling (Ribo-seq) of YdiF(EQ2)-expressing cells revealed that collided ribosomes are enriched for tmRNA, a functional RNA involved in trans-translation. We confirmed that tmRNA tagging activity is globally increased upon expression of any ATPase defective ABCF as well as in cells treated with the collision-inducing antibiotic erythromycin, suggesting this is a generalizable mechanism to rescue stalled and collided ribosomes. The global increase in tmRNA tagging that occurred in response to both erythromycin and YdiF(EQ2) induced collisions was dependent on the Rae1 endonuclease. Loss of trans-translation in cells experiencing widespread ribosome collisions leads to a severe fitness defect, consistent with the importance of this pathway in rescuing ribosomes stalled on truncated mRNAs that result from ribosome collisions. Altogether, our work supports a model in which Rae1 cleaves mRNA on collided ribosomes, thereby generating a truncated mRNA substrate for trans-translation and leading to rescue and recycling of the collided ribosomes. We term this mechanism Collision-Associated Rae1-induced trans-Translation (CART). CART broadens the repertoire of tools that bacteria use to manage ribosome collisions.

microbiology↗

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

Ancient DNA reveals matrilineal organisation and recurrent unions between dominant matrilines in Iron Age Britain

Kinship practices underpin all traditional societies, forming the basis for socially sanctioned reproductive unions, residence patterns and the inheritance of rights and property1,2. Although the relationship between biological relatedness and kinship is not always straightforward, ancient DNA studies are increasingly used to examine the extent to which biological relatedness underpinned social constructs of kinship in prehistoric societies3-6. Here, we report the analysis of genome-wide data for 534 individuals from the Arras Culture of Middle Iron Age northeast England (including 390 from Wetwang Slack, 100 from Pocklington, and 29 from Melton), finding evidence for communities with kinship systems structured along matrilineal lines. At Wetwang Slack, we reconstruct a 13-generation pedigree comprising 195 individuals structured around female-line connections: matrilineal transmissions greatly outnumbered patrilineal ones and male reproductive partners were largely absent from the cemetery, plausibly because they were buried in their own natal communities. Furthermore, the three main sites with robust sample sizes were characterised by non-overlapping dominant mitochondrial haplogroups, implying a maternal clan-based structure. Reproductive unions at Wetwang Slack suggest a recurrent alliance between two dominant maternal descent groups, with members of each group never reproducing with members of their own maternal lineage. Meanwhile, three individuals from lavishly furnished chariot burials at Wetwang Slack were close maternal relatives belonging to a lineage with consecutive generations of close kin unions, a pattern largely absent among other individuals at the site. These results indicate highly distinctive social practices among an elite group embedded in the wider kinship network of the Arras community.

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

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↗

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↗

bioRxiv2024

RqcH supports survival in the absence of non-stop ribosome rescue factors

Ribosomes frequently translate truncated or damaged mRNAs due to the extremely short half-life of mRNAs in bacteria. When ribosomes translate mRNA that lacks a stop codon (non-stop mRNA), specialized pathways are required to rescue the ribosome from the 3 end of the mRNA. The most highly conserved non-stop rescue pathway is trans-translation, which is found in greater than 95% of bacterial genomes. In all Proteobacteria that have been studied, the alternative non-stop ribosome rescue factors, ArfA and ArfB, are essential in the absence of trans-translation. Here, we investigate the interaction between non-stop rescue pathways and RqcH, a ribosome quality control factor that is broadly conserved outside of Proteobacteria. RqcH does not act directly on non-stop ribosomes but adds a degron tag to stalled peptides that obstruct the large ribosomal subunit, which allows the stalled peptide to be cleared from the ribosome by peptidyl-tRNA hydrolase (PTH). We show that Bacillus subtilis can survive without trans-translation and BrfA (Bacillus ArfA homolog), due to the presence of RqcH. We also show that expression of RqcH and its helper protein RqcP rescues the synthetic lethality of {Delta}ssrA{Delta}arfA in Escherichia coli. These results suggest that non-stop ribosome complexes can be disassembled and then cleared because of the tagging activity of RqcH, and that this process is essential in the absence of non-stop ribosome rescue pathways. Moreover, we surveyed the conservation of ribosome rescue pathways in >14,000 bacterial genomes. Our analysis reveals a broad distribution of non-stop rescue pathways, especially trans-translation and RqcH, and a strong co-occurrence between the ribosome splitting factor MutS2 and RqcH. Altogether, our results support a role for RqcH in non-stop ribosome rescue and provide a broad survey of ribosome rescue pathways in diverse bacterial species. ImportanceRibosome stalling on damaged mRNA is a major problem in bacteria. It is estimated that 2-4% of all translation reactions terminate with the ribosome stalled on a damaged mRNA lacking a stop codon. Mechanisms that rescue these ribosomes, such as trans-translation, are often essential for viability. We investigated the functional overlap between RqcH and the non-stop ribosome rescue systems (ArfA and trans-translation) that are present in both E. coli and B. subtilis. Since these two species are extremely distant relatives, our work is likely to have wider implications for understanding ribosome rescue in bacteria. Furthermore, we used a bioinformatics approach to examine the conservation and overlap of various ribosome rescue systems in >14,000 species throughout the bacterial domain. These results provide key insights into ribosome rescue in diverse phyla.

microbiology↗

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↗

bioRxiv2023

Social and genetic diversity in first farmers of central Europe

The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of central Europe, settling fertile regions from Ukraine to France during the second half of the 6th millennium BCE. The LBK had a high degree of material culture uniformity, albeit with regional differences in settlement patterns, subsistence, and mortuary practices. To date, ancient DNA data from LBK individuals have been generated for a limited number of locations and often in small sample sizes, making it challenging to study variation within and across sites. We report genome-wide data for 178 LBK individuals, from the Alfold Linearbankeramik Culture (ALPC) eastern LBK site of Polgar-Ferenci-hat in Hungary, the western LBK site of Nitra in Slovakia, and the enclosed western LBK settlement and massacre site of Schletz in Austria, as well as 42 LBK individuals from 18 other sites. We also report genome-wide data for 28 Early Neolithic Koros and Star[c]evo individuals from 13 sites, viewed as the predecessors of the LBK. We observe a higher percentage of western hunter-gatherer (WHG) admixture among individuals in the eastern LBK than in the far more widely distributed western LBK, showing that these two archaeologically distinct cultures also had different genetic trajectories. Most WHG-farmer mixture occurred just before the dawn of the LBK culture and there is no evidence that the WHG ancestry came systematically more from males or females. However, we do find strong genetic evidence for patrilocality among the LBK, extending previous findings based on isotopic analysis, with more genetic structure across sites on the male than on the female line, and a higher rate of within-site relatives for males. At Schletz we detect almost no first-degree relatives despite reporting data from almost every skeleton present at the site, showing that this massacre involved people from a large population, not a small community.

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↗

bioRxiv2021

Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples

The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against "barbarian" tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between [~]250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of todays Balkan people.

evolutionary biology↗

bioRxiv2021

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Nubia has been a corridor for the movement of goods, culture, and people between sub-Saharan Africa, Egypt, and West Eurasia since prehistory, but little is known about the genetic landscape of the region prior to the influence of the Islamic migrations that began in the late 1st millennium CE. We report genome-wide data for 66 individuals from the site of Kulubnarti ([~]650-1000 CE), increasing the number of ancient individuals with genome-level data from the Nile Valley from three to 69. Our results shed light on the genetic ancestry of a Christian Period group and help to address a long-standing question about the relationships among people buried in two neighboring cemeteries who show skeletal evidence of differences in morbidity and mortality that are broadly suggestive of differences in social status. We find that the Kulubnarti Nubians were admixed with [~]43% Nilotic-related ancestry on average (individual proportions varied between [~]36-54%) and the remaining ancestry reflecting a West Eurasian-related gene pool likely introduced into Nubia through Egypt, but ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The admixed ancestry at Kulubnarti reflects interactions between genetically-distinct people in northeast Africa spanning almost a millennium, with West Eurasian ancestry disproportionately associated with females, highlighting the impact of female mobility in this region. We find no significant differences in ancestry among individuals from the two plausibly socially-stratified cemeteries at Kulubnarti, supporting hypotheses that the groups may have been socially divided but were not genetically distinct. We identify seven pairs of inter-cemetery relatives as close as second-degree, suggesting that any social divisions at Kulubnarti did not prevent mixing between groups. Present-day Nubians are not directly descended from the Christian Period people from Kulubnarti without additional admixture, attesting to the dynamic history of interaction that continues to shape the cultural and genetic landscape of Nubia.

genomics↗

bioRxiv2020

A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Ancient DNA sampling methods--although optimized for efficient DNA extraction--are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

evolutionary biology↗

bioRxiv2020

A genetic history of the pre-contact Caribbean

Humans settled the Caribbean ~6,000 years ago, with intensified agriculture and ceramic use marking a shift from the Archaic Age to the Ceramic Age ~2,500 years ago. To shed new light on the history of Caribbean people, we report genome-wide data from 184 individuals predating European contact from The Bahamas, Cuba, Hispaniola, Puerto Rico, Curacao, and northwestern Venezuela. A largely homogeneous ceramic-using population most likely originating in northeastern South America and related to present-day Arawak-speaking groups moved throughout the Caribbean at least 1,800 years ago, spreading ancestry that is still detected in parts of the region today. These people eventually almost entirely replaced Archaic-related lineages in Hispaniola but not in northwestern Cuba, where unadmixed Archaic-related ancestry persisted into the last millennium. We document high mobility and inter-island connectivity throughout the Ceramic Age as reflected in relatives buried ~75 kilometers apart in Hispaniola and low genetic differentiation across many Caribbean islands, albeit with subtle population structure distinguishing the Bahamian islands we studied from the rest of the Caribbean and from each other, and long-term population continuity in southeastern coastal Hispaniola differentiating this region from the rest of the island. Ceramic-associated people avoided close kin unions despite limited mate pools reflecting low effective population sizes (2Ne=1000-2000) even at sites on the large Caribbean islands. While census population sizes can be an order of magnitude larger than effective population sizes, pan-Caribbean population size estimates of hundreds of thousands are likely too large. Transitions in pottery styles show no evidence of being driven by waves of migration of new people from mainland South America; instead, they more likely reflect the spread of ideas and people within an interconnected Caribbean world.

genetics↗

bioRxiv2020

The Genomic Formation of Human Populations in East Asia

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to [~]3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

genomics↗

bioRxiv2019

Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

genomics↗