ORCID Profile
0000-0002-4204-5018
Current Organisations
University of Adelaide
,
Max Planck Institute for Evolutionary Anthropology
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Publications
Bronze Age Northern Eurasian Genetics in the Context of Development of Metallurgy and Siberian Ancestry
Publisher: Cold Spring Harbor Laboratory
Date: 10-2023
Ten millennia of hepatitis B virus evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-10-2021
Abstract: Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that erged about 20,000 years ago. —LMZ
A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics
Publisher: Elsevier BV
Date: 08-2022
DCATS: differential composition analysis for complex single-cell experimental designs
Publisher: Cold Spring Harbor Laboratory
Date: 23-03-2022
DOI: 10.1101/2022.03.21.485232
Abstract: Differential composition analysis – the identification of cell types that have statistically significantly change in abundance between multiple experimental conditions – is one of the most common tasks in single cell omic data analysis. However, it remains challenging to perform differential composition analysis in the presence of complex experimental designs and uncertainty in cell type assignment. Here, we introduce a statistical model and an open source R package, DCATS, for differential composition analysis based on a beta-binomial regression framework that addresses these challenges. Our empirical evaluation shows that DCATS consistently maintain high sensitively and specificity compared to state-of-the-art methods.
Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-2016
Abstract: Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes.
Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers
Publisher: American Association for the Advancement of Science (AAAS)
Date: 29-05-2020
Abstract: Shedding light on first encounters between late hunter-gatherers and early farmers in western Europe.
A Woman with a Sword? – Weapon Grave at Suontaka Vesitorninmäki, Finland
Publisher: Cambridge University Press (CUP)
Date: 15-07-2021
DOI: 10.1017/EAA.2021.30
Abstract: In 1968, a weapon grave with brooches was found at Suontaka Vesitorninmäki, Hattula, Finland. Since then, the grave has been interpreted as evidence of powerful women, even female warriors and leaders in early medieval Finland. Others have denied the possibility of a woman buried with a sword and tried to explain it as a double burial. We present the first modern analysis of the grave, including an examination of its context, a soil s le analysis for microremains, and an aDNA analysis. Based on these analyses, we suggest a new interpretation: the Suontaka grave possibly belonged to an in idual with sex-chromosomal aneuploidy XXY. The overall context of the grave indicates that it was a respected person whose gender identity may well have been non-binary.
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact
Publisher: MDPI AG
Date: 24-06-2021
Abstract: The tropical archipelago of Wallacea contains thousands of in idual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been h ered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new s les from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.
Unsupervized Quantification of Demographic Structure for Single-copy Alignments
Publisher: Cold Spring Harbor Laboratory
Date: 04-06-2018
DOI: 10.1101/338442
Abstract: Single-copy sequence alignments have been a valuable source of information for genetic studies their lack of recombination makes phylogenetic analyses tractable [1]. Specifically, mitochondrial DNA will continue to play an important role in genetic studies due to its high mutation rate and high copy per cell count of the molecule [2]. In this paper we develop a new method for the analysis of single-copy sequence data that simultaneously considers the relationships between sequenced in iduals and positions of interest in the genome. We then show that tests for relationships between genetic information and qualitative and quantitative characteristics can be calculated. We motivate the use of our method with ex les from empirical data.
Extensive pedigrees reveal the social organization of a Neolithic community
Publisher: Springer Science and Business Media LLC
Date: 26-07-2023
DOI: 10.1038/S41586-023-06350-8
Abstract: Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations 1–4 . However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between in iduals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 in iduals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic around 4850–4500 bc . We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of in iduals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality 5 . Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.
Early cave art and ancient DNA record the origin of European bison
Publisher: Springer Science and Business Media LLC
Date: 18-10-2016
DOI: 10.1038/NCOMMS13158
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus ) before the Holocene ( .7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison ( Bison priscus ) and ancestors of modern cattle (aurochs, Bos primigenius ) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe
Publisher: Cold Spring Harbor Laboratory
Date: 19-02-2021
DOI: 10.1101/2021.02.19.431761
Abstract: 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.
Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers
Publisher: Springer Science and Business Media LLC
Date: 03-2023
DOI: 10.1038/S41586-023-05726-0
Abstract: Modern humans have populated Europe for more than 45,000 years 1,2 . 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 period 3 . Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 in iduals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in in iduals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe 4 , but resembles that of preceding in iduals 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.
Early contact between late farming and pastoralist societies in southeastern Europe
Publisher: Springer Science and Business Media LLC
Date: 19-07-2023
DOI: 10.1038/S41586-023-06334-8
Abstract: 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 domestication 6–9 . 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 in iduals 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 .
Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily
Publisher: Elsevier BV
Date: 05-2022
Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites
Publisher: Elsevier BV
Date: 04-2022
Dynamic changes in genomic and social structures in third millennium BCE central Europe
Publisher: American Association for the Advancement of Science (AAAS)
Date: 27-08-2021
Abstract: Archaeogenetic time transect in Europe unravels genetic and social changes before and after the arrival of “steppe” ancestry.
A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum
Publisher: Springer Science and Business Media LLC
Date: 03-2023
DOI: 10.1038/S41559-023-01987-0
Abstract: Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of in iduals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European in iduals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated in idual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr bp . The Malalmuerzo in idual carried genetic ancestry that directly connects earlier Aurignacian-associated in iduals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where in iduals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, in iduals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with in iduals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age in iduals from southern Iberia.
A systematic investigation of human DNA preservation in medieval skeletons
Publisher: Springer Science and Business Media LLC
Date: 26-10-2020
DOI: 10.1038/S41598-020-75163-W
Abstract: Ancient DNA (aDNA) analyses necessitate the destructive s ling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, 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. However, destructive s ling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. 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 s ling 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.
Author Correction: Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers
Publisher: Springer Science and Business Media LLC
Date: 22-03-2023
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNAde novoassembly
Publisher: Cold Spring Harbor Laboratory
Date: 24-03-2021
DOI: 10.1101/2021.03.24.436838
Abstract: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional ersity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern s les, ancient s les are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient s les is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient s les and sequences. However, existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both simulated, and empirical aDNA data from archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, PyDamage opens up new doors to explore functional ersity in ancient metagenomic datasets.
Ancient human genomes reveal a hidden history of strong selection in Eurasia
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2020
DOI: 10.1101/2020.04.01.021006
Abstract: The role of natural selection in shaping biological ersity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied upon genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between erged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has likely been underappreciated in the evolutionary history of humans and suggests that our current understanding of the tempo and mode of selection in natural populations may be quite inaccurate.
Author Correction: Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland
Publisher: Springer Science and Business Media LLC
Date: 16-09-2020
DOI: 10.1038/S41467-020-18561-Y
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Admixture has obscured signals of historical hard sweeps in humans
Publisher: Springer Science and Business Media LLC
Date: 31-10-2022
DOI: 10.1038/S41559-022-01914-9
Abstract: The role of natural selection in shaping biological ersity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between erged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland
Publisher: Springer Science and Business Media LLC
Date: 20-04-2020
DOI: 10.1038/S41467-020-15560-X
Abstract: Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860–2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.
Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites
Publisher: Proceedings of the National Academy of Sciences
Date: 21-04-2022
Abstract: By integrating genomic and archaeological data, we provide new insights into the Neolithic French monumental site of Fleury-sur-Orne in Normandy, where a group of selected in iduals was buried in impressively long monuments. The earliest in iduals buried at Fleury-sur-Orne match the expected western European Neolithic genetic ersity, while three in iduals, designated as genetic outliers, were buried after 4,000 calibrated BCE. We hypothesize that different, unrelated families or clans used the site over several centuries. Thirteen of 14 of the analyzed in iduals were male, indicating an overarching patrilineal system. However, one exception, a female buried with a symbolically male artifact, suggests that the embodiment of the male gender in death was required to access burial at the monumental structures.
Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus
Publisher: Elsevier BV
Date: 05-2020
Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies
Publisher: Public Library of Science (PLoS)
Date: 19-05-2015
Kinship practices in the early state El Argar society from Bronze Age Iberia
Publisher: Springer Science and Business Media LLC
Date: 27-12-2022
DOI: 10.1038/S41598-022-25975-9
Abstract: The Early Bronze Age in Europe is characterized by social and genetic transformations, starting in the early 3rd millennium BCE. New settlement and funerary structures, artifacts and techniques indicate times of change with increasing economic asymmetries and political hierarchization. Technological advances in metallurgy also played an important role, facilitating trade and exchange networks, which became tangible in higher levels of mobility and connectedness. Archeogenetic studies have revealed a substantial transformation of the genetic ancestry around this time, ultimately linked to the expansion of steppe- and forest steppe pastoralists from Eastern Europe. Evidence for emerging infectious diseases such as Yersinia pestis adds further complexity to these tumultuous and transformative times. The El Argar complex in southern Iberia marks the genetic turnover in southwestern Europe ~ 2200 BCE that accompanies profound changes in the socio-economic structure of the region. To answer the question of who was buried in the emblematic double burials of the El Argar site La Almoloya, we integrated results from biological relatedness analyses and archaeological funerary contexts and refined radiocarbon-based chronologies from 68 in iduals. We find that the El Argar society was virilocally and patrilineally organized and practiced reciprocal female exogamy, supported by pedigrees that extend up to five generations along the paternal line. Synchronously dated adult males and females from double tombs were found to be unrelated mating partners, whereby the incoming females reflect socio-political alliances among El Argar groups. In three cases these unions had common offspring, while paternal half-siblings also indicate serial monogamy or polygyny.
Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia
Publisher: Springer Science and Business Media LLC
Date: 08-03-2017
DOI: 10.1038/NATURE21416
Abstract: Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka) however, little is known about the processes underlying the enormous linguistic and phenotypic ersity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair s les, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.
BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data
Publisher: Cold Spring Harbor Laboratory
Date: 18-04-2023
DOI: 10.1101/2023.04.17.537144
Abstract: Robust and reliable estimates of how in iduals 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 in iduals, 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 in idual, 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 0.04 X 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.
Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia
Publisher: American Association for the Advancement of Science (AAAS)
Date: 19-11-2021
Abstract: Ancient human DNA from southern Iberia reveals social and genomic changes during the emergence of the Bronze Age in Europe.
Population Genetics and Signatures of Selection in Early Neolithic European Farmers
Publisher: Oxford University Press (OUP)
Date: 17-05-2022
Abstract: Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 in iduals) in Central Germany. Population genetic analyses show that the DER in iduals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 in iduals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.
Related Organisations
Max Planck Institute For The Science Of Human History
Location: Germany
Related Funding Activities
No related grants have been discovered for Adam Rohrlach.