Biology subjects

Haak, W.

Publications and source records attributed to Haak, W..

18 recordsLinked to original sources

bioRxiv2025

Detecting and Quantifying Networks of Biological Kinship via Exponential Family Random Graph Models

Genetic relatedness between ancient humans can help to identify close and distant connections between groups and populations, uncovering signatures of demographic histories such as identifying mating networks or long-range migration. Critical to researchers are the characteristics that connected individuals, or groups of individuals, share, and how these characteristics interact and are correlated. Here we use Exponential Random Graph models as a method to explore demographic and contextual parameters that may help to explain the significant drivers of the topology of mating networks, as well as to quantify their effects. We show through simulations that model selection and coefficient estimators facilitate the exploration of such networks, and apply the method to individuals from a collection of Avar-associated cemeteries from the Carpathian Basin dating to the 6th to the 9th centuries CE.

bioinformatics↗

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↗

bioRxiv2024

The Genetic History of the South Caucasus from the Bronze to the Early Middle Ages: 5000 years of genetic continuity despite high mobility

Archaeological and archaeogenetic studies have highlighted the pivotal role of the Caucasus region throughout prehistory, serving as a central hub for cultural, technological, and linguistic innovations. However, despite its dynamic history, the critical area between the Greater and Lesser Caucasus mountain ranges, mainly corresponding to modern-day Georgia, has received limited attention. Here, we generated an ancient DNA time transect consisting of 219 individuals with genome-wide data from 47 sites in this region, supplemented by 97 new radiocarbon dates. Spanning from the Early Bronze Age 5000 years ago to the so-called Migration Period that followed the fall of the Western Roman Empire, we document a largely persisting local gene pool that continuously assimilated migrants from Anatolia/Levant and the populations of the adjacent Eurasian steppe. More specifically, we observe these admixture events as early as the Middle Bronze Age. Starting with Late Antiquity (late first century AD), we also detect an increasing number of individuals with more southern ancestry, more frequently associated with urban centers - landmarks of the early Christianization in eastern Georgia. Finally, in the Early Medieval Period starting 400 AD, we observe genetic outlier individuals with ancestry from the Central Eurasian steppe, with artificial cranial deformations (ACD) in several cases. At the same time, we reveal that many individuals with ACD descended from native South Caucasus groups, indicating that the local population likely adopted this cultural practice.

genetics↗

bioRxiv2024

Poseidon - A framework for archaeogenetic human genotype data management

1The study of ancient human genomes, archaeo- or palaeogenetics, has accelerated in the last ten years, with now thousands of new ancient genomes being released each year. Operating at the interface of genetics, anthro-pology and archaeology, this data includes features from all three fields, including rich meta- and context-data, for example regarding spatiotemporal provenience. While archives and standards for genetic sequencing data al-ready exist, no such infrastructure exists for combined genetic and meta-data that could ensure FAIR principles across the field. Here, we present Poseidon, a framework for open and FAIR data handling in archaeogenetics, including a specified package format, software tools, and public, community-maintained online archives. Poseidon emphasises human- and machine-readable data storage, the development of convenient and interoperable command line software, and a high degree of source granularity to elevate the original data publication to the main unit of long-term curation.

genetics↗

bioRxiv2023

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 individuals associated with BA metallurgical production, specifically the Seima-Turbino (ST) phenomenon ([~]2,200-1,900 BCE) associated with elaborate metal objects found across Northern Eurasia. The genetic profiles of nine ST-associated individuals vary widely ranging between ancestries maximized in individuals from the Eastern Siberian Late Neolithic/BA, and those of the Western Steppe Middle Late BA. The genetic heterogeneity observed is consistent with the current understanding of the ST metallurgical network as a transcultural phenomenon. The new data also shed light on the temporal and spatial range of an ancient Siberian genetic ancestry component, which is shared across many Uralic-speaking populations, and which we explore further via demographic modeling using additional genome-wide (2 individuals) and whole genome data (5 individuals, including a [~]30x genome) from northwestern Russia.

genetics↗

bioRxiv2023

BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data

Robust and reliable estimates of how individuals are biologically related to each other are a key source of information when reconstructing pedigrees. In combination with contextual data, reconstructed pedigrees can be used to infer possible kinship practices in prehistoric populations. However, standard methods to estimate biological relatedness from genome sequence data cannot be applied to low coverage sequence data, such as are common in ancient DNA (aDNA) studies. Critically, a statistically robust method for assessing and quantifying the confidence of a classification of a specific degree of relatedness for a pair of individuals, using low coverage genome data, is lacking. In this paper we present the R-package BREADR (Biological RElatedness from Ancient DNA in R), which leverages the so-called pairwise mismatch rate, calculated on optimally-thinned genome-wide pseudo-haploid sequence data, to estimate genetic relatedness up to the second degree, assuming an underlying binomial distribution. BREADR also returns a posterior probability for each degree of relatedness, from identical twins/same individual, first-degree, second-degree or "unrelated" pairs, allowing researchers to quantify and report the uncertainty, even for particularly low-coverage data. We show that this method accurately recovers degrees of relatedness for sequence data with coverage as low as 0.04X using simulated data, and then compare the performance of BREADR on empirical data from Bronze Age Iberian human sequence data. The BREADR package is designed for pseudo-haploid genotype data, common in aDNA studies.

bioinformatics↗

bioRxiv2023

Socio-cultural practices affect sexual dimorphism in stature in Early Neolithic Europe

AbstractThe rules and structure of human culture impact health and disease as much as genetics or the natural environment. To study the origin and evolution of these patterns, we take a multidisciplinary approach combining ancient DNA, skeletal metrics, paleopathology, and stable isotopes. Our analysis focuses on cultural, environmental, and genetic contributions to variation in stature in four populations of Early Neolithic Europe. In Central Europe, low female stature is likely due to male preference in resource allocation under conditions of stress. In contrast, shorter male stature in Mediterranean populations may reflect a lack of preference. Our analysis suggests that biological consequences of sex-specific inequities can be linked to culture as early as 7000 years before present. Understanding these patterns is key to interpreting the evolution of genetic and socio-cultural determinants of health, and our results show that culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.

genetics↗

bioRxiv2021

Predicting skeletal stature using ancient DNA

ObjectivesAncient DNA provides an opportunity to separate the genetic and environmental bases of complex traits by allowing direct estimation of genetic values in ancient individuals. Here, we test whether genetic scores for height in ancient individuals are predictive of their actual height, as inferred from skeletal remains. We estimate the contributions of genetic and environmental variables to observed phenotypic variation as a first step towards quantifying individual sources of morphological variation. Materials and MethodsWe collected stature estimates and femur lengths from West Eurasian skeletal remains with published genome-wide ancient DNA data (n=167, dating from 33,000-850 BP). We also recorded genetic sex, genetic ancestry, date and paleoclimate data for each individual, and{delta} 13C and{delta} 15N stable isotope values where available (n=67). ResultsA polygenic score (PRS) for height predicts 6.8% of the variance in femur length in our data (n=117, SD=0.0068%, p<0.001), controlling for sex, ancestry, and date. This is consistent with the predictive power of height PRS in present-day populations and the low coverage of ancient samples. Comparatively, sex explains about 15% of the variance in femur length in our sample. Environmental effects also likely play a role in variation, independent of genetics, though with considerable uncertainty (longitude: R2=0.0317, SD=0.009, p=0.019). DiscussionPolygenic scores explain a small but significant proportion of the variance in height in ancient individuals, though not enough to make useful predictions of individual phenotypes. However, environmental variables also contribute to phenotypic outcomes and understanding their interaction with direct genetic predictions will provide a framework with which to model how plasticity and genetic changes ultimately combine to drive adaptation and evolution.

evolutionary biology↗

bioRxiv2021

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

genetics↗

bioRxiv2020

A systematic investigation of human DNA preservation in medieval skeletons

Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently the dense inner portion of the petrous pyramid, the location of the skull that houses the inner ear, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. Destructive sampling of the petrous pyramid, assuming its recovery, is often not recommended for highly valued specimens. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.

molecular biology↗

bioRxiv2020

A dynamic 6,000-year genetic history of Eurasia's Eastern Steppe

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the regions population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

genomics↗

bioRxiv2020

Genomic and dietary transitions during the Mesolithic and Early Neolithic in Sicily

Southern Italy is a key region for understanding the agricultural transition in the Mediterranean due to its central position. We present a genomic transect for 19 prehistoric Sicilians that covers the Early Mesolithic to Early Neolithic period. We find that the Early Mesolithic hunter-gatherers (HGs) are a highly drifted sister lineage to Early Holocene western European HGs, whereas a quarter of the Late Mesolithic HGs ancestry is related to HGs from eastern Europe and the Near East. This indicates substantial gene flow from (south-)eastern Europe between the Early and Late Mesolithic. The Early Neolithic farmers are genetically most similar to those from the Balkan and Greece, and carry only a maximum of [~]7% ancestry from Sicilian Mesolithic HGs. Ancestry changes match changes in dietary profile and material culture, except for two individuals who may provide tentative initial evidence that HGs adopted elements of farming in Sicily. One-sentence summaryGenome-wide and isotopic data from prehistoric Sicilians reveal a pre-farming connection to (south-) eastern Europe, and tentative initial evidence that hunter-gatherers adopted some Neolithic aspects prior to near-total replacement by early farmers.

genetics↗

bioRxiv2019

Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective

Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies - Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinias Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the \"Steppe\" ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia.

genetics↗

bioRxiv2018

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity ([~]80-90%) between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

genetics↗

bioRxiv2018

Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

European history has been shaped by migrations of people, and their subsequent admixture. Recently, evidence from ancient DNA has brought new insights into migration events that could be linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known so far about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and Northwest Russia. We show that the specific genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago. This ancestry was subsequently admixed into many modern populations in the region, in particular populations speaking Uralic languages today. In addition, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age than today, which adds to historical and linguistic evidence for the population history of Finland.

genomics↗

bioRxiv2017

The Genomic History Of Southeastern Europe

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europes population.

genetics↗

bioRxiv2017

The Genetic History of Northern Europe

Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from [~]7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adoption of bronze metallurgy. We show that Scandinavia was settled after the retreat of the glacial ice sheets from a southern and a northern route, and that the first Scandinavian Neolithic farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Western European Mesolithic hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers until around 2,900 calBCE when the arrival of steppe pastoralists introduced a major shift in economy and established wide-reaching networks of contact within the Corded Ware Complex.

genetics↗

bioRxiv2016

The Stone Age Plague: 1000 years of Persistence in Eurasia

Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis caused some form of disease in humans prior to the first historically documented pandemic. Here, we present six new Y. pestis genomes spanning from the European Late Neolithic to the Bronze Age (LNBA) dating from 4,800 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe people, persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in parallel with subsequent human population movements.

evolutionary biology↗