Biology subjects

Krause-Kyora, B.

Publications and source records attributed to Krause-Kyora, B..

9 recordsLinked to original sources

bioRxiv2024

Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants

In medieval central Europe, rye was one of the most important agricultural crops. Its properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a "secondary domesticate", i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th century from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries. HighlightsO_LIHistorical plant material covering four centuries was obtained from half-timbered houses from five locations in Germany C_LIO_LIIntegrative archaeobotanical analyses and ancient DNA sequencing provided insights into genetic diversity of rye plants from historical farmland fields. C_LIO_LISequence analyses of complete assembled chloroplast genomes reveal expectational diversity in rye populations. C_LIO_LILate domestication of rye preserved genetic diversity over centuries. The more recent intensification of rye breeding has however conferred a considerable loss of genetic diversity in this important crop. C_LI

evolutionary biology↗

bioRxiv2024

Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans

BackgroundThe hypomorphic variant rs11209026-A in the IL23R gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel disease (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe. MethodsThis study comprised 251 ancient genomes from Europe spanning over 14,000 years. In these samples, the investigation focused on admixture informed analyses and selection scans of rs11209026-A and its haplotypes. Findingsrs11209026-A was found at high frequencies in Anatolian Farmers (AF, 18%) where it was likely under weak positive selection. AF later introduced the allele into the ancient European gene-pool. Subsequent admixture caused its frequency to decrease and formed the current southwest-to-northeast allele frequency cline in Europe. The geographic distribution of rs11209026-A may influence the gradient in IBD incidence rates that are highest in northern and eastern Europe. InterpretationGiven the dramatic changes from hunting and gathering to agriculture during the Neolithic, AF might have been exposed to selective pressures from a pro-inflammatory lifestyle and diet. Therefore, the protective A-allele may have increased survival by reducing intestinal inflammation and microbiome dysbiosis. The adaptively evolved function of the variant likely contributes to the high efficacy and low side-effects of modern IL-23 neutralization therapies for chronic inflammatory diseases. This study highlights how evolutionary informed research can provide promising targets for new therapeutic strategies. FundingDeutsche Forschungsgemeinschaft (DFG German Research Foundation) under Germanys Excellence Strategy - EXC 2167 390884018 and EXC 2150 390870439.

evolutionary biology↗

bioRxiv2024

Genomic Evidence of Fisheries Induced Evolution in Eastern Baltic cod

Humans have become one of the greatest evolutionary forces, and their perturbations are expected to elicit strong evolutionary responses. Accordingly, during (size) selective overharvesting of wild populations, marked phenotypic changes have been documented, while the evolutionary basis is often unresolved. Time-series collections combined with genomic tools present unique opportunities to study how evolutionary changes are manifested at the genome-wide level. Here, we take advantage of a unique temporal dataset from the overexploited Eastern Baltic cod (Gadus morhua) population that exhibited a 48% decrease in asymptotic body length over the last 25 years. A genome-wide association study revealed pronounced peaks of outliers linked to growth performance. The contributing loci showed signals of directional selection with significantly high autocovariance in the allele frequency and excessive intersections with regions of high Fst as well as genes relevant to growth and reproduction. Moreover, pattern of directional selection for ancestral haplotype of the well-known chromosomal inversions in Atlantic cod (on linkage group 12) was observed, while the double crossover ([~]1Mb) enharbouring the vitellogenin genes within this region showed signs of drift or balancing selection. Our results demonstrate evident response of the genome over a relatively short time frame and further underscore implications for fisheries management and conservation policy regarding the adaptive potential of marine populations.

evolutionary biology↗

bioRxiv2023

Dietary 14C reservoir effects and the chronology of prehistoric burials at Sakhtysh, central European Russia

We present the first robust radiocarbon (14C) chronology for prehistoric burial activity at Sakhtysh, in European Russia, where nearly 180 inhumations attributed to Lyalovo and Volosovo pottery-using hunter-gatherer-fishers represent the largest known mortuary populations of these groups. Past attempts at 14C dating were restricted by poor preservation and limited understanding of diet and dietary 14C reservoir effects (DREs). We obtained 32 new AMS (Accelerator Mass Spectrometry) 14C dates on human petrous bones. Dietary stable isotopes ({delta}13C, {delta}15N) for all AMS-dated human samples allow us to propose a novel DRE correction model, using differences in 14C, {delta}13C and {delta}15N from bones and teeth of the same individuals to predict DREs of up to c.900 14C years. Our chronological model for 40 individuals dates Lyalovo burials to the early 5th millennium cal BC, and Volosovo burials to the mid-4th to early 3rd millennium. It reveals a previously unrecognised shift in the Volosovo subsistence economy at c.3300 cal BC, coinciding with a reorientation of trade networks, and shows that the last burial at Sakhtysh was the only one in a crouched position, which coincided with the beginning of Fatyanovo practices, the regional expression of the Yamnaya/Corded Ware expansion.

ecology↗

bioRxiv2023

Admixture as a source for HLA variation in Neolithic European farming communities

The northern European Neolithic is characterized by two major demographic events: immigration of early farmers (EF) from Anatolia (5500 BCE) and their admixture (from [~]4200 BCE) with western hunter-gatherers (WHG) forming late farmers (LF). The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. Here, we conducted population and immunogenetic analyses on 83 individuals from six EF and LF sites located in present-day Germany. We observed significant shifts in HLA allele frequencies from EF to LF. The HLA diversity increased from EF to LF, likely due to admixture with WHG. However, it was considerably lower than in modern populations. Both EF and LF exhibited a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time. We additionally noted that LF resulted from sex-biased admixture from male WHG. TEASERMore restricted HLA allele spectrum and lower diversity in Neolithic farmers than in modern populations

genetics↗

bioRxiv2019

Gene-flow from steppe individuals into Cucuteni-Trypillia associated populations indicates long-standing contacts and gradual admixture

The Cucuteni-Trypillia complex (CTC) flourished in eastern Europe for over two millennia (5100 - 2800 BCE) from the end of the Neolithic to the Early Bronze Age. Its vast distribution area encompassed modern-day eastern Romania, Moldova and western/central Ukraine. Due to a lack of existing burials throughout most of this time, only little is known about of the people associated with this complex and their genetic composition. Here, we present genome-wide data generated from the skeletal remains of four females that were excavated from two Late CTC sites in Moldova (3500 - 3100 BCE). All individuals carried a large Neolithic-derived ancestry component and were genetically more closely related to Linear Pottery than to Anatolian farmers. Three of the specimens also showed considerable amounts of steppe-related ancestry, suggesting influx into the CTC gene-pool from people affiliated with, for instance, the Ukraine Mesolithic. The latter scenario is supported by archaeological evidence. Taken together, our results confirm that the steppe component had arrived in eastern Europe farming communities maybe as early as 3500 BCE. In addition, they are in agreement with the hypothesis of ongoing contacts and gradual admixture between incoming steppe and local western populations.

genomics↗

bioRxiv2019

Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

The Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.

evolutionary biology↗

bioRxiv2018

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and went possibly extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.

evolutionary biology↗

bioRxiv2017

The Genomic History Of Southeastern Europe

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

genetics↗