Joachim Burger's research while affiliated with Johannes Gutenberg-Universität Mainz and other places
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Publications (363)
During the transition from Late Antiquity to the Middle Ages, the Roman Empire dissolved in the West and medieval empires were founded. There has been much discussion about the role that migration played in this transition. This is especially true for the formation of the Baiuvariian tribe and the founding of this tribal dukedom, which took place f...
Genomic regions under positive selection harbour variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplot...
Lake sediment records from Holzmaar and the infilled maar of Auel (Eifel, Germany) are used to reconstruct landscape changes and megafauna abundances. Our data document a forested landscape from 60,000 to 48,000 yr b2k and a stepwise vegetation change towards a glacial desert after 26,000 yr b2k. The Eifel landscape was continuously inhabited from...
It is now widely accepted that agriculture and settled village life arrived in Europe as a cultural package, carried by people migrating from Anatolia and the Aegean Basin. The putative fisher-forager site of Lepenski Vir in Serbia has long been acknowledged as an exception to this model. Here, the Mesolithic–Neolithic transition—possibly inspired...
The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolit...
While early Neolithic populations in Europe were largely descended from early Aegean farmers, there is also evidence of episodic gene flow from local Mesolithic hunter-gatherers into early Neolithic communities. Exactly how and where this occurred is still unknown. Here we report direct evidence for admixture between the two groups at the Danube Go...
Today, it is widely accepted that agriculture and settled village life arrived in Europe as a cultural package, carried by people migrating from Anatolia and the Aegean Basin. The putative fisher-forager site of Lepenski Vir in Serbia has long been acknowledged as an exception to this model. Here, the Mesolithic-Neolithic transition - possibly insp...
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asia...
Twenty-four palaeogenomes from Mokrin, a major Early Bronze Age necropolis in southeastern Europe, were sequenced to analyse kinship between individuals and to better understand prehistoric social organization. 15 investigated individuals were involved in genetic relationships of varying degrees. The Mokrin sample resembles a genetically unstructur...
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the...
While the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were seque...
Lactase persistence (LP), the continued expression of lactase into adulthood, is the most strongly selected single gene trait over the last 10,000 years in multiple human populations. It has been posited that the primary allele causing LP among Eurasians, rs4988235-A [1], only rose to appreciable frequencies during the Bronze and Iron Ages [2, 3],...
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to...
Twenty-four ancient genomes with an average sequencing coverage of 0.85 were produced from the Mokrin necropolis, an Early Bronze Age (2,100-1,800 BC) Maros culture site in Serbia, to provide unambiguous identification of biological sex, population structure, and genetic kinship between individuals. Of the 24 investigated individuals, 15 were invol...
Archaeological evidence indicates that pig domestication had
begun by ∼10,500 y before the present (BP) in the Near East,
and mitochondrial DNA (mtDNA) suggests that pigs arrived in
Europe alongside farmers ∼8,500 y BP. A few thousand years after
the introduction of Near Eastern pigs into Europe, however, their
characteristic mtDNA signature disapp...
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disapp...
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disapp...
Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals
regional variation that has since been obscured by admixture in modern populations.
Comparisons of genomes of early domestic cattle to their aurochs progenitors identify
diverse origins with separate introgressions of wild stock. A later region-wide Bronze
Age shift...
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to...
Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift...
There is a long lasting debate on the nature of the neolithisation process in the northern European lowlands and in southern Scandinavia. Early evidence of domesticates and crop cultivation indicate a transition to farming in this area during the late 5th millennium cal BC. However, there is limited information how this process took place and to wh...
How humans got their goats
Little is known regarding the location and mode of the early domestication of animals such as goats for husbandry. To investigate the history of the goat, Daly et al. sequenced mitochondrial and nuclear sequences from ancient specimens ranging from hundreds to thousands of years in age. Multiple wild populations contribut...
Eine Reevaluation artifiziell deformierter Schädel des Frühen Mittelalters aus Bayern Im Rahmen eines Projektes wurden 122 Individuen aus altbayerischen Gräberfeldern einer umfassenden Reevaluation unterzogen. Unter diesen befanden sich auch 26 Individuen, denen aufgrund visueller Begutachtung ein artifiziell deformierter Schädel und damit eine mög...
Significance
Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany...
http://rdcu.be/ydIL
Link to the full text!!
Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1, 2, 3, 4, 5, 6, 7, 8 who received a limited amount of admixture from resident hunter-gatherers3, 4, 5, 9. Many open questions remain, however, about the spatial and temporal dynamics of popula...
Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highes...
X-chromosome contamination estimated with ANGSD (Korneliussen et al. 2014) and based on a previously published method (Rasmussen et al. 2011).
(XLSX)
Ancient DNA analysis.
(DOCX)
mtDNA lineages and contamination estimates based on mismatches at haplotype defining sites.
(XLSX)
X-chromosome contamination based on the number of mismatches at X-chromosome SNPs and adjacent sites.
(XLSX)
List of ancient samples selected for genotype imputation.
(XLSX)
Map and geographical locations of the archaeological locations of the samples sequenced in the present study.
(TIF)
D-statistics in the form of D(Mbuti, X; Y, Z) to test admixture between ancient populations.
(XLSX)
Estimation of imputation accuracy on chromosome 21.
Comparison of variant calls obtained for BR2, NE1, Loschbour and Stuttgart at full coverage with genotypes from the same 4 individuals downsampled to 2x and subsequently imputed. Accuracy in (A) all 3 types of genotypes; (B) homozygous reference; (C) heterozygous and (D) homozygous alternate.
(TIF...
Proportion of correctly imputed genotypes grouped by minor allele frequency bins of 0.005.
In this analysis, imputed genotypes were filtered by post imputation genotype probability ⋝ 0.99.
(TIF)
Selected D-statistics associated with Portuguese Neolithic and Bronze samples.
(XLSX)
Affinity of imputed calls from five high coverage ancient samples to reference panel populations, relative to diploid calls, for a series of MAF filters.
Results are shown for both all sites and just transversions in on left hand and right hand panels respectively. Top panels display world MAF filters of 25% and 5%. Bottom panels display European M...
Affinity of imputed calls to reference panel populations, relative to pseudo-haploid and diploid calls, for five high coverage ancient samples.
Results are shown for both all sites and just transversions in two separate panels. A world minor allele frequency of 25% has been applied. 1000 Genomes population and superpopulation names are noted along...
Coancestry matrix obtained with CHROMOPAINTER for the analysis of a dataset including 67 ancient samples and modern Eurasian genomes.
(XLSX)
Geographical and PC genetic coordinates for the Western_HG2 cluster.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE AegeanEN_HungarianLBK cluster.
(TIF)
Geographical and PC genetic coordinates for the Western_HG1 cluster.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE HungarianMLN_SpainCardialEN cluster.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE Russia_LBA cluster.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE cluster Caucasus Hunter-gatherers.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE Yamnaya_Afanasievo cluster.
(TIF)
Comparison between (A) unlinked and (B) linked CHROMOPAINTER/fineSTRUCTURE analyses.
The unlinked analysis is only able to identify 10 populations, 9 less than when incorporating the linkage model.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE Hungary_BA cluster.
(TIF)
Geographical and PC genetic coordinates for the fineSTRUCTURE Portugal_BA cluster.
(TIF)
Bar plots illustrating polygenic risk scores across time, estimated for each one of the ancient population clusters.
The traits chosen were: A) Height; B) Pigmentation; C) BMI and D) T2D. Polygenic scores were centered at the mean for the dataset. As in Fig 1 in the main text, each cluster is represented with a different colour.
(TIF)
fineSTRUCTURE tree comparison between each one of the imputed and non-imputed samples (BR2, Loschbour and LBK).
The position of aDNA samples (shown in red) is very similar in both analyses.
(TIF)
CHROMOPAINTER haplotype donation vectors between each one of the imputed and non-imputed samples.
(A) Correlation between imputed and non-imputed median haplotype donation from sample BR2 (1), Loschbour (2) and LBK (3). (B) Normal Quantile-Quantile plots and outlier detection (labelled populations). Coloured dots show populations present (red) or a...
Polygenic risk scores estimated for height using genomewide summary statistics from the Wood 2014 dataset.
(A) p = 0 (B) p<0.001. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis.
(TIF)
Polygenic risk scores estimated for T2D using genomewide summary statistics.
A) p = 0 B) p<0.001. SNPs with posterior genotype probability of less than 0.99 were excluded from analysis.
(TIF)
Height map and PCA.
Red—increased genetic height scores, black—decreased genetic height. Broadly, hunter-gatherers and populations from Copper age and after present highest proportion of height increasing associated variants followed by Neolithic farmers.
(TIF)
Polygenic scores for pigmentation.
SNPs with posterior genotype probability of less than 0.99 were excluded from analysis.
(TIF)
Extended haplotype homozygosity (EHH) in regions under selection.
Panels on the left represent the decay of EHH, or the probability of homozygosity at a certain base across 2 randomly chosen chromosomes in a population. Plots on the right represent existing haplotypes in a population, with the lower portion of the graph depicting haplotypes with th...
Comparison of ancient samples with other ancient and modern datasets using genotype data.
(DOCX)
Author summary
Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, t...
Extended haplotype homozygosity analysis.
(DOCX)
Archaeological information.
(DOCX)
Sex determination using Ry_compute.
(TIF)
Exploring ancient Iberian affinities through F- and D-statistics.
(DOCX)
Principal component analysis of 604 modern West Eurasians onto which variation from 224 ancient genomes has been projected.
The analysis is based on approximately 600,000 SNP positions. Moderns samples from the Human Origins dataset are represented in greyscale, with the exception of modern Iberians shown in green. Ancient samples are coloured by t...
Analysis of polygenic traits.
(DOCX)
Geographical and PC genetic coordinates for the fineSTRUCTURE Russia_LBA_IA cluster.
(TIF)
Y-chromosome lineages determined in the ancient Portuguese samples.
(XLSX)
Imputation of missing genotypes in ancient samples.
(DOCX)
Coancestry matrix obtained with CHROMOPAINTER for the analysis including 67 ancient samples.
(XLSX)
CHROMOPAINTER and fineSTRUCTURE analyses.
(DOCX)
List of ancient individuals used in the F4 ratio test.
This table contains the individuals which were used to estimate the approximate percentage ancestry in modern populations of five ancestral groups who have contributed to western Eurasian variation, using an F4 ratio test (Patterson 2012).
(XLSX)
Affinity of imputed calls from five high coverage ancient samples to reference panel populations, relative to diploid calls, for the final set of SNPs used in downstream analyses. 1000 Genomes population and superpopulation names are noted along the X axis.
(TIF)
Post-mortem misincorporations in ancient samples.
(TIF)
Affinity of pseudo-haploid calls to reference panel populations, relative to diploid calls, for five high coverage ancient samples.
Results are shown for world MAF filters of 25% and 5%. Only transversion SNPs are considered. 1000 Genomes population and superpopulation names are noted along the X axis.
(TIF)