Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the... more Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the R...
Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large numb... more Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14th century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, i...
In ancient DNA research, the degraded nature of the samples generally results in poor yields of h... more In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits – have different characteristics that may influence the capture efficiency, specificity, and reproducibility. Here, we compared their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum of 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens, and RNA baits usually perform better than DNA baits.Method summaryWe compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity, and reproducibility for ancient and modern Mycobacterium leprae ...
Das Graberfeld von Wittmar umfasst 51 Graber unterschiedlicher Ausrichtung, differenzierter Korpe... more Das Graberfeld von Wittmar umfasst 51 Graber unterschiedlicher Ausrichtung, differenzierter Korperhaltung der Toten und Bandkeramischer, Stichbandkeramischer als auch Rossener Inventare. Die genetische Analyse von 34 Individuen erbrachte fur sechs der Rossener Bestattungen die Bestimmung der Haplogruppe. Im Ergebnis konnten die Haplogruppen H, HV0, U5 und K festgestellt werden und deutet sich eine Kontinuitat in der mutterlichen Linie der Bestatteten an. Zudem findet sich mit der Haplogruppe U5 ein Indiz fur Kontakte zu mesolithisch wirtschaftenden Gruppen.
Rye (Secale cereale ssp. cereale L.) is a secondary domesticate, considered to have originated as... more Rye (Secale cereale ssp. cereale L.) is a secondary domesticate, considered to have originated as a weed in wheat fields and to have developed traits of domestication by evolving similar physiological and morphological characteristics to those of wheat. Although it migrated into Europe as a weed possessing domestication traits, it became one of the most significant crops grown in large parts of Europe from the medieval period onward. Within the modern borders of Germany, rye was grown using at least two divergent cultivation practices: eternal rye monoculture and three-field rotation. The straw of rye was used to produce Wellerhölzer, which are construction components in traditional half-timbered houses that have enabled a desiccated preservation of the plant remains. In order to assess the impact of cultivation practices, local environmental conditions and genetic variation on the genetic diversification of rye, we seek to integrate well-established archaeobotanical methods with aD...
The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important... more The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections.
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity an... more The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
The history of humankind is marked by the constant adoption of new dietary habits affecting human... more The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as My... more Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branch...
Farming was first introduced to southeastern Europe in the mid-7thmillennium BCE – brought by mig... more Farming was first introduced to southeastern Europe in the mid-7thmillennium 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...
ZusammenfassungDas Galeriegrab von Niedertiefenbach stellt einen besonderen Befund der späten War... more ZusammenfassungDas Galeriegrab von Niedertiefenbach stellt einen besonderen Befund der späten Wartberggruppe im Neolithikum der Deutschen Mittelgebirgsschwelle dar; nur hier findet sich ein in zehn Straten geborgenes Bestattungskollektiv von mindestens 177 Individuen. Eine umfangreiche Serie von Radiokarbondatierungen belegt ein wesentlich höheres Alter des Grabes als bisher publiziert und erlaubt die Modellierung einer Bestattungssequenz zwischen 3.350 und 2.900 cal BC. Eine neue paläopathologische Untersuchung, vorerst nur an den Schädeln vorgenommen, zeigt einen hohen Krankenstand mit zahlreichen entzündlichen Prozessen. Mit einer verheilten Trepanation bei einem Kind wird aber zugleich auch ein besonderes Wissen im Bereich der medizinischen Versorgung deutlich. Erste Analysen zur aDNA mittels Hochfrequenzsequenzierung (HTS) belegen die Anwesenheit mitochondrialer DNA mit den Haplogruppen U5 und X2. Der erstmalige Einsatz eines CAD/CAM-Computersystems (CEREC) bietet eine detailli...
Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the... more Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the R...
Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large numb... more Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14th century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, i...
In ancient DNA research, the degraded nature of the samples generally results in poor yields of h... more In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits – have different characteristics that may influence the capture efficiency, specificity, and reproducibility. Here, we compared their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum of 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens, and RNA baits usually perform better than DNA baits.Method summaryWe compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity, and reproducibility for ancient and modern Mycobacterium leprae ...
Das Graberfeld von Wittmar umfasst 51 Graber unterschiedlicher Ausrichtung, differenzierter Korpe... more Das Graberfeld von Wittmar umfasst 51 Graber unterschiedlicher Ausrichtung, differenzierter Korperhaltung der Toten und Bandkeramischer, Stichbandkeramischer als auch Rossener Inventare. Die genetische Analyse von 34 Individuen erbrachte fur sechs der Rossener Bestattungen die Bestimmung der Haplogruppe. Im Ergebnis konnten die Haplogruppen H, HV0, U5 und K festgestellt werden und deutet sich eine Kontinuitat in der mutterlichen Linie der Bestatteten an. Zudem findet sich mit der Haplogruppe U5 ein Indiz fur Kontakte zu mesolithisch wirtschaftenden Gruppen.
Rye (Secale cereale ssp. cereale L.) is a secondary domesticate, considered to have originated as... more Rye (Secale cereale ssp. cereale L.) is a secondary domesticate, considered to have originated as a weed in wheat fields and to have developed traits of domestication by evolving similar physiological and morphological characteristics to those of wheat. Although it migrated into Europe as a weed possessing domestication traits, it became one of the most significant crops grown in large parts of Europe from the medieval period onward. Within the modern borders of Germany, rye was grown using at least two divergent cultivation practices: eternal rye monoculture and three-field rotation. The straw of rye was used to produce Wellerhölzer, which are construction components in traditional half-timbered houses that have enabled a desiccated preservation of the plant remains. In order to assess the impact of cultivation practices, local environmental conditions and genetic variation on the genetic diversification of rye, we seek to integrate well-established archaeobotanical methods with aD...
The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important... more The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections.
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity an... more The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
The history of humankind is marked by the constant adoption of new dietary habits affecting human... more The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as My... more Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branch...
Farming was first introduced to southeastern Europe in the mid-7thmillennium BCE – brought by mig... more Farming was first introduced to southeastern Europe in the mid-7thmillennium 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...
ZusammenfassungDas Galeriegrab von Niedertiefenbach stellt einen besonderen Befund der späten War... more ZusammenfassungDas Galeriegrab von Niedertiefenbach stellt einen besonderen Befund der späten Wartberggruppe im Neolithikum der Deutschen Mittelgebirgsschwelle dar; nur hier findet sich ein in zehn Straten geborgenes Bestattungskollektiv von mindestens 177 Individuen. Eine umfangreiche Serie von Radiokarbondatierungen belegt ein wesentlich höheres Alter des Grabes als bisher publiziert und erlaubt die Modellierung einer Bestattungssequenz zwischen 3.350 und 2.900 cal BC. Eine neue paläopathologische Untersuchung, vorerst nur an den Schädeln vorgenommen, zeigt einen hohen Krankenstand mit zahlreichen entzündlichen Prozessen. Mit einer verheilten Trepanation bei einem Kind wird aber zugleich auch ein besonderes Wissen im Bereich der medizinischen Versorgung deutlich. Erste Analysen zur aDNA mittels Hochfrequenzsequenzierung (HTS) belegen die Anwesenheit mitochondrialer DNA mit den Haplogruppen U5 und X2. Der erstmalige Einsatz eines CAD/CAM-Computersystems (CEREC) bietet eine detailli...
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Papers by B. Krause-kyora