Michael Francken | Eberhard Karls Universität Tübingen (original) (raw)

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Papers by Michael Francken

Inflammatory bowel disease (IBD) is often described as a model for modern civilization diseases i... more Inflammatory bowel disease (IBD) is often described as a model for modern civilization diseases in which environmental factors trigger disease manifestation in genetically compromised individuals. Little is known about the evolutionary history of variants associated with IBD in modern Europeans. Here, we analysed 610 IBD-variants in 2445 ancient datasets from human remains spanning the last 12,000 years, including genotypes generated from 172 newly collected individuals from the European Neolithic. We found statistically significant differences in the frequencies of 97 IBD variants between Neolithic and modern populations that can be explained by the adoption of an agricultural lifestyle and behaviour and concomitant possible microbiome changes in the earliest farmers. Later admixture events and selection against pathogens largely influenced the genetic risk architecture of IBD in contemporary Europeans. A better understanding of the evolutionary history of disease variants is an im...

Scientific Reports, 2021

This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe ... more This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe and sheds new light on the use of combustion fuel sources in the 2nd millennium BCE Eastern Mediterranean. We applied Thermal Desorption/Pyrolysis–Gas Chromatography-Mass Spectrometry and Polarizing Microscopy to the dental calculus of 67 individuals and we identified clear evidence for combustion markers embedded within this calculus. In contrast to the scant evidence for combustion markers within the calculus samples from Egypt, all other individuals show the inhalation of smoke from fires burning wood identified as Pinaceae, in addition to hardwood, such as oak and olive, and/or dung. Importantly, individuals from the Palatial Period at the Mycenaean citadel of Tiryns and the Cretan harbour site of Chania also show the inhalation of fire-smoke from lignite, consistent with the chemical signature of sources in the northwestern Peloponnese and Western Crete respectively. This first evid...

Additional file 2: Table S4. Mapping results of the metagenomic analysis.

Additional file 1: Fig. S1. Number of reads mapping to Firmicutes. Fig. S2. Combined damage profi... more Additional file 1: Fig. S1. Number of reads mapping to Firmicutes. Fig. S2. Combined damage profiles of Clostridia. Fig. S3. Metagenomic composition of all samples. Fig. S4. Combined damage profiles of pathogens identified in bone samples. Fig. S5. Anthropological analysis of individual Abusir1630. Fig. S6. Phylogenetic trees of M. leprae genomes. Fig. S7. Date Randomization test for the M. leprae data set. Fig. S8. TempEst analysis for the M. leprae dataset. Fig. S9. Phylogenetic trees of Hepatitis B virus genomes. Fig. S10. Date Randomization test for the HBV data set. Fig. S11. TempEst analysis for the HBV dataset. Fig. S12. Combined damage profiles of Red Complex bacteria. Fig. S13. Combined damage profiles of oral pathogens. Table S1. Overview of the number of samples and sampled tissue. Table S2. Sample overview. Table S3. Microbial composition of the samples. Table S6. Approach to determine the genotype of Abusir1630. Table S7. HBV strains used for analysis. Table S8. Accessi...

Recent genomic data has revealed multiple interactions between Neandertals and modern humans1, bu... more Recent genomic data has revealed multiple interactions between Neandertals and modern humans1, but there is currently little genetic evidence about Neandertal behavior, diet, or disease. We shotgun sequenced ancient DNA from five Neandertal dental calculus specimens to characterize regional differences in Neandertal ecology. In Spy, Belgium, Neandertal diet was heavily meat based, and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In El Sidrón, Spain, no meat was detected, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering2,3. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota), and suggested that meat consumption contributed to significant variation between Neandertal microbiota. Evidence for self-medication was detected in an El Sidrón Neandertal with a dental abscess4, who also suffered from a chronic gastrointestinal pathogen (Enterocytozoon bieneusi)....

The cemetery of Schwetzingen (Baden-Württemberg) is with its 203 remaining graves one of the larg... more The cemetery of Schwetzingen (Baden-Württemberg) is with its 203 remaining graves one of the largest known necropolises of the early Neolithic Linear Bandceramic culture (LBK). It was located south of the mouth of the Neckar into the Rhine, at the edge of the Rhine valley. On the whole Schwetzingen shows the characteristics of the known cemeteries of this culture. The dead were mostly laid down on left side in a fl exed position in NE-SW-orientated, narrow grave pits. Approximately 50 % of the dead were buried with grave gifts such as pottery and tools out of stone, silex, bone and antler and trinket. The fi ndings in the grave, especially the ceramics' varying ornamentation, suggest a dating around 5200/5000 BC. Beside nearly 200 body burials some cremated remains and some so called empty graves were found at the cemetery. A complete anthropological analysis hasn´t been carried out but fundamental informations exist. Based on these results some preliminary statements concerning...

Objectives: Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeologi... more Objectives: Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeological evidence for human occupation at high elevation (4480 masl) during the Terminal Pleistocene (12,500 to 11,200 cal BP), Early Holocene (9500-9000 cal BP), and later periods. One of the excavated human burials (Feature 15-06), corresponding to a middle-aged female dated to ~8500 cal BP, exhibits skeletal osteoarthritic lesions previously proposed to reflect habitual loading and specialized crafting labor. Three small tools found in association with this burial are hypothesized to be associated with precise manual dexterity. Materials and Methods: Here, we tested this functional hypothesis through the application of a novel multivariate methodology for the three-dimensional analysis of muscle attachment surfaces (entheses). This original approach has been recently validated on both lifelong-documented anthropological samples as well as experimental studies in non-human laboratory sample...

Menschen mit Trisomie 21 sind nur selten in der archaologischen Graberfeldliteratur zu finden und... more Menschen mit Trisomie 21 sind nur selten in der archaologischen Graberfeldliteratur zu finden und die Zuschreibung der Chromosomenanomalie erfolgte bei der anthropologischen Untersuchung bislang ausschlieslich uber morphologische Merkmale an Schadeln. Im Zusammenhang mit der Ausstellung „Touchdown: Eine Ausstellung mit und uber Menschen mit Down-Syndrom“ der Bundeskunsthalle Bonn erfolgte 2016 weltweit erstmals eine Uberprufung von Verdachtsfallen an archaologischem Skelettmaterial auf Trisomie 21 mit einer aDNA-Analyse. Hierzu wurden zwei Individuen beprobt, bei denen aufgrund ihrer morphologischen Besonderheiten das Vorliegen dieser Chromosomenanomalie vermutet wurde. Die Untersuchung der aDNA erbrachte uberraschende Ergebnisse, beide untersuchten Skelette wiesen keine Trisomie 21 auf.

Science, 2021

Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worl... more Ancient DNA traces the history of hepatitis B 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 diverged about 20,000 years ago. —LMZ

Proceedings of the National Academy of Sciences, 2021

Significance The microbiome plays key roles in human health, but little is known about its evolut... more Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo -specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet.

Nature, Apr 8, 2017

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, b... more Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neander...

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 yea... more We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

Inflammatory bowel disease (IBD) is often described as a model for modern civilization diseases i... more Inflammatory bowel disease (IBD) is often described as a model for modern civilization diseases in which environmental factors trigger disease manifestation in genetically compromised individuals. Little is known about the evolutionary history of variants associated with IBD in modern Europeans. Here, we analysed 610 IBD-variants in 2445 ancient datasets from human remains spanning the last 12,000 years, including genotypes generated from 172 newly collected individuals from the European Neolithic. We found statistically significant differences in the frequencies of 97 IBD variants between Neolithic and modern populations that can be explained by the adoption of an agricultural lifestyle and behaviour and concomitant possible microbiome changes in the earliest farmers. Later admixture events and selection against pathogens largely influenced the genetic risk architecture of IBD in contemporary Europeans. A better understanding of the evolutionary history of disease variants is an im...

Scientific Reports, 2021

This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe ... more This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe and sheds new light on the use of combustion fuel sources in the 2nd millennium BCE Eastern Mediterranean. We applied Thermal Desorption/Pyrolysis–Gas Chromatography-Mass Spectrometry and Polarizing Microscopy to the dental calculus of 67 individuals and we identified clear evidence for combustion markers embedded within this calculus. In contrast to the scant evidence for combustion markers within the calculus samples from Egypt, all other individuals show the inhalation of smoke from fires burning wood identified as Pinaceae, in addition to hardwood, such as oak and olive, and/or dung. Importantly, individuals from the Palatial Period at the Mycenaean citadel of Tiryns and the Cretan harbour site of Chania also show the inhalation of fire-smoke from lignite, consistent with the chemical signature of sources in the northwestern Peloponnese and Western Crete respectively. This first evid...

Additional file 2: Table S4. Mapping results of the metagenomic analysis.

Additional file 1: Fig. S1. Number of reads mapping to Firmicutes. Fig. S2. Combined damage profi... more Additional file 1: Fig. S1. Number of reads mapping to Firmicutes. Fig. S2. Combined damage profiles of Clostridia. Fig. S3. Metagenomic composition of all samples. Fig. S4. Combined damage profiles of pathogens identified in bone samples. Fig. S5. Anthropological analysis of individual Abusir1630. Fig. S6. Phylogenetic trees of M. leprae genomes. Fig. S7. Date Randomization test for the M. leprae data set. Fig. S8. TempEst analysis for the M. leprae dataset. Fig. S9. Phylogenetic trees of Hepatitis B virus genomes. Fig. S10. Date Randomization test for the HBV data set. Fig. S11. TempEst analysis for the HBV dataset. Fig. S12. Combined damage profiles of Red Complex bacteria. Fig. S13. Combined damage profiles of oral pathogens. Table S1. Overview of the number of samples and sampled tissue. Table S2. Sample overview. Table S3. Microbial composition of the samples. Table S6. Approach to determine the genotype of Abusir1630. Table S7. HBV strains used for analysis. Table S8. Accessi...

Recent genomic data has revealed multiple interactions between Neandertals and modern humans1, bu... more Recent genomic data has revealed multiple interactions between Neandertals and modern humans1, but there is currently little genetic evidence about Neandertal behavior, diet, or disease. We shotgun sequenced ancient DNA from five Neandertal dental calculus specimens to characterize regional differences in Neandertal ecology. In Spy, Belgium, Neandertal diet was heavily meat based, and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In El Sidrón, Spain, no meat was detected, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering2,3. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota), and suggested that meat consumption contributed to significant variation between Neandertal microbiota. Evidence for self-medication was detected in an El Sidrón Neandertal with a dental abscess4, who also suffered from a chronic gastrointestinal pathogen (Enterocytozoon bieneusi)....

The cemetery of Schwetzingen (Baden-Württemberg) is with its 203 remaining graves one of the larg... more The cemetery of Schwetzingen (Baden-Württemberg) is with its 203 remaining graves one of the largest known necropolises of the early Neolithic Linear Bandceramic culture (LBK). It was located south of the mouth of the Neckar into the Rhine, at the edge of the Rhine valley. On the whole Schwetzingen shows the characteristics of the known cemeteries of this culture. The dead were mostly laid down on left side in a fl exed position in NE-SW-orientated, narrow grave pits. Approximately 50 % of the dead were buried with grave gifts such as pottery and tools out of stone, silex, bone and antler and trinket. The fi ndings in the grave, especially the ceramics' varying ornamentation, suggest a dating around 5200/5000 BC. Beside nearly 200 body burials some cremated remains and some so called empty graves were found at the cemetery. A complete anthropological analysis hasn´t been carried out but fundamental informations exist. Based on these results some preliminary statements concerning...

Objectives: Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeologi... more Objectives: Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeological evidence for human occupation at high elevation (4480 masl) during the Terminal Pleistocene (12,500 to 11,200 cal BP), Early Holocene (9500-9000 cal BP), and later periods. One of the excavated human burials (Feature 15-06), corresponding to a middle-aged female dated to ~8500 cal BP, exhibits skeletal osteoarthritic lesions previously proposed to reflect habitual loading and specialized crafting labor. Three small tools found in association with this burial are hypothesized to be associated with precise manual dexterity. Materials and Methods: Here, we tested this functional hypothesis through the application of a novel multivariate methodology for the three-dimensional analysis of muscle attachment surfaces (entheses). This original approach has been recently validated on both lifelong-documented anthropological samples as well as experimental studies in non-human laboratory sample...

Menschen mit Trisomie 21 sind nur selten in der archaologischen Graberfeldliteratur zu finden und... more Menschen mit Trisomie 21 sind nur selten in der archaologischen Graberfeldliteratur zu finden und die Zuschreibung der Chromosomenanomalie erfolgte bei der anthropologischen Untersuchung bislang ausschlieslich uber morphologische Merkmale an Schadeln. Im Zusammenhang mit der Ausstellung „Touchdown: Eine Ausstellung mit und uber Menschen mit Down-Syndrom“ der Bundeskunsthalle Bonn erfolgte 2016 weltweit erstmals eine Uberprufung von Verdachtsfallen an archaologischem Skelettmaterial auf Trisomie 21 mit einer aDNA-Analyse. Hierzu wurden zwei Individuen beprobt, bei denen aufgrund ihrer morphologischen Besonderheiten das Vorliegen dieser Chromosomenanomalie vermutet wurde. Die Untersuchung der aDNA erbrachte uberraschende Ergebnisse, beide untersuchten Skelette wiesen keine Trisomie 21 auf.

Science, 2021

Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worl... more Ancient DNA traces the history of hepatitis B 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 diverged about 20,000 years ago. —LMZ

Proceedings of the National Academy of Sciences, 2021

Significance The microbiome plays key roles in human health, but little is known about its evolut... more Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo -specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet.

Nature, Apr 8, 2017

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, b... more Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neander...

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 yea... more We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.