Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

Ancient genomes reveal insights into ritual life at Chichén Itzá

The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

Ancient Plasmodium genomes shed light on the history of human malaria

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.

Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry

The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.

Effects and considerations of multiplexing ForenSeq Kintelligence libraries with a negative control

The negative template control or negative amplification control has been an essential component of the forensic DNA analysis workflow that helps monitor contamination. As such, the inclusion of a negative control in forensic DNA analysis has been a requirement for all laboratories audited under the FBI's Quality Assurance Standards. As massively parallel sequencing (MPS) becomes more conventional in forensic laboratories, considerations for the inclusion of a negative control in every sequencing run can be evaluated. Although the inclusion of a negative control in library preparation and the first sequencing run has a practical function, there is less utility for its inclusion in all subsequent sequencing runs for that library preparation. Although this is universal to all MPS assays, it is most relevant for an assay that has a low sample multiplexing capacity, such as the ForenSeq Kintelligence Kit (Qiagen/Verogen, Inc.). The ForenSeq Kintelligence Kit is an investigative genetic genealogy (IGG) sequencing-based assay that targets 10,230 forensically relevant single-nucleotide polymorphisms. The manufacturer recommends multiplexing 3 libraries per sequencing run, which includes controls. The purpose of this study was to investigate the effect of the inclusion of a negative control in every Kintelligence sequencing run. We observed that the library generated from a negative amplification control will take 7%-14% of the run output. The loss of sequencing space taken by a negative control decreased the available output for DNA-containing samples, leading in some cases to allele or locus dropout and accompanying higher numbers of sixth to seventh order unknown associations in GEDmatch PRO.

Network of large pedigrees reveals social practices of Avar communities

From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.

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.

Ancient genome of the Chinese Emperor Wu of Northern Zhou

Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.1,2 Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.

The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany

Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

Detection of chromosomal aneuploidy in ancient genomes

Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

An individual with Sarmatian-related ancestry in Roman Britain

In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.1,2,3 In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.4,5 Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.

Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland

Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.

A genetic history of the Balkans from Roman frontier to Slavic migrations

The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.

Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics

Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.

Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia

As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.1,2 To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries3,4,5 at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site6 and analyzed them alongside data from over 550 penecontemporaneous individuals.7,8,9,10,11,12,13,14,15,16,17,18,19 The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial customs and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artifacts and genetic ancestry among 5th century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.

Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics

The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.

The genetic legacy of African Americans from Catoctin Furnace

Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.

Early contact between late farming and pastoralist societies in southeastern Europe

Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000-6000 BC (refs. 1-3) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 BC (refs. 4,5). The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication6-9. However, what happened between the demise of the Copper Age settlements around 4250 BC and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500 BC on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300 BC.

Insights into the genetic histories and lifeways of Machu Picchu's occupants

Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.

Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts

This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.

Yersinia pestis genomes reveal plague in Britain 4000 years ago

Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Eurasia between 5000 and 2500 years before present (BP). One of these, termed the 'LNBA lineage' (Late Neolithic and Bronze Age), has been suggested to have spread into Europe with human groups expanding from the Eurasian steppe. Here, we show that the LNBA plague was spread to Europe's northwestern periphery by sequencing three Yersinia pestis genomes from Britain, all dating to ~4000 cal BP. Two individuals were from an unusual mass burial context in Charterhouse Warren, Somerset, and one individual was from a single burial under a ring cairn monument in Levens, Cumbria. To our knowledge, this represents the earliest evidence of LNBA plague in Britain documented to date. All three British Yersinia pestis genomes belong to a sublineage previously observed in Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Eastern Asia ~3200 cal BP. While the severity of the disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.

Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic

Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.

Ancient human DNA recovered from a Palaeolithic pendant

Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals¹ who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited^2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.

Genetic population structure of the Xiongnu Empire at imperial and local scales

The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.

Density separation of petrous bone powders for optimized ancient DNA yields

Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30 to 2.35 g/cm3 and 2.35 to 2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm3 intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.

Overflow Control for Sustainable Development by Superwetting Surface with Biomimetic Structure

Liquid flowing around a solid edge, i.e., overflow, is a commonly observed flow behavior. Recent research into surface wetting properties and microstructure-controlled overflow behavior has attracted much attention. Achieving controllable macroscale liquid dynamics by manipulating the micro-nanoscale liquid overflow has stimulated diverse scientific interest and fostered widespread use in practical applications. In this review, we outline the evolution of overflow and present a critical survey of the mechanism of surface wetting properties and microstructure-controlled liquid overflow in multilength scales ranging from centimeter to micro and even nanoscale. We summarize the latest progress in utilizing the mechanisms to manipulate liquid overflow and achieve macroscale liquid dynamics and in emerging applications to manipulate overflow for sustainable development in various fields, along with challenges and perspectives.

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia

The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.

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

We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14^th century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ 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. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14^th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.

The mitochondrial genome of the red icefish (Channichthys rugosus) casts doubt on its species status

Antarctic notothenioid fishes are recognised as one of the rare examples of adaptive radiation in the marine system. Withstanding the freezing temperatures of Antarctic waters, these fishes have diversified into over 100 species within no more than 10–20 million years. However, the exact species richness of the radiation remains contested. In the genus Channichthys, between one and nine species are recognised by different authors. To resolve the number of Channichthys species, genetic information would be highly valuable; however, so far, only sequences of a single species, C. rhinoceratus, are available. Here, we present the nearly complete sequence of the mitochondrial genome of C. rugosus, obtained from a formalin-fixed museum specimen sampled in 1974. This sequence differs from the mitochondrial genome of C. rhinoceratus in no more than 27 positions, suggesting that the two species may be synonymous.

Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal

The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in New Zealand (NZ), including their relationship to the Australian grayling, is poorly understood. The NZ grayling (Prototroctes oxyrhynchus) is the only known fish in NZ to have gone extinct since human arrival there. Despite its historical abundance, only 23 wet and dried, formalin-fixed specimens exist in museums. We used high-throughput DNA sequencing to generate mitogenomes from formalin-fixed P. oxyrhynchus specimens, and analysed these in a temporal phylogenetic framework of retropinnids and osmerids. We recovered a strong sister-relationship between NZ and Australian grayling (P. mareana), with a common ancestor ~13.8 Mya [95% highest posterior density (HPD): 6.1–23.2 Mya], after the height of Oligocene marine inundation in NZ. Our temporal phylogenetic analysis suggests a single marine dispersal between NZ and Australia, although the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible extinction drivers of the NZ grayling, informs discussion regarding reintroduction of Prototroctes to NZ and highlights how advances in palaeogenetics can be used to test evolutionary hypotheses in fish, which, until relatively recently, have been comparatively neglected in ancient-DNA research.

The genetic history of the Southern Arc: A bridge between West Asia and Europe

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel

Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.

Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete

During the late 3^rd millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.^1-4 However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.⁵ The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,^5-8 circulated across Eurasia at least from the onset of the 3^rd millennium BCE,^9-13 but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y.pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.

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

Previous research indicates that human genetic diversity 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. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. 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.

The source of the Black Death in fourteenth-century central Eurasia

The origin of the medieval Black Death pandemic (ad 1346–1353) has been a topic of continuous investigation because of the pandemic’s extensive demographic impact and long-lasting consequences^1,2. Until now, the most debated archaeological evidence potentially associated with the pandemic’s initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan^1,3–9. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338–1339 state ‘pestilence’ as the cause of death for the buried individuals⁹. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic’s emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry.

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.

Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites

The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.

South-to-north migration preceded the advent of intensive farming in the Maya region

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.

Ancient DNA and deep population structure in sub-Saharan African foragers

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa^1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations^3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.

Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing

Background

Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workflows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input flexibility (1 ng-1 μg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits.

Results

We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits’ fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection.

Conclusions

The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quantabio are good alternatives to the tagmentation based Nextera DNA flex kit from Illumina, offering reproducible results using flexible DNA inputs, quick workflows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08316-y.

Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy

The Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.

Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.

Predicting Physical Appearance from DNA Data-Towards Genomic Solutions

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.

Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments.

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.