Biology subjects

Kapopoulou, A.

Publications and source records attributed to Kapopoulou, A..

8 recordsLinked to original sources

bioRxiv2025

Pervasive Intraspecific Genetic Local Adaptation Within the Natural Gut Microbiome

Gut microbial communities are shaped by the physicochemical gradients and compartmentalization along the gastrointestinal tract. Whether spatially variable selection is strong enough to promote lasting genetic divergence within microbial species subject to migration and clonal expansion remains unclear. We performed a metagenomic population-genetic analysis of roe deer microbiota across metabolically and structurally distinct gut compartments. Remarkably, 10 of 20 prevalent bacterial species exhibited clear signatures of genetic local adaptation, despite the homogenizing effects of frequent migration. Nutrient availability and environmental stability emerged as primary drivers of selection, with horizontal gene transfer as a key mechanism enabling local adaptation. Our findings demonstrate that a comprehensive understanding of ecological and evolutionary dynamics in the gut necessitates considering fine-scale genetic variation within species.

evolutionary biology↗

bioRxiv2025

Extended-spectrum beta-lactamase (ESBL)-producing E. coli in livestock and free-roaming wildlife: a combined phenotyping whole-genome sequencing One Health approach

Antimicrobial resistance (AMR) in Enterobacterales, particularly extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec), poses a significant public health concern. Widespread antimicrobial use exerts selection pressure, driving the persistence and spread of resistant bacteria in diverse environments. While ESBL-Ec is well-documented in clinical and agricultural settings, its presence in reservoirs remains poorly understood. This study assessed the prevalence, AMR profiles, and genetic diversity of ESBL-Ec in Swiss dairy cattle and wildlife. Between 2021 and 2023, 775 samples were analysed, including rectal swab samples from dairy cows (n=475), and fecal or cloacal swab samples and wildlife (n=300). ESBL-Ec was detected in 0.6% of dairy cattle and 3.7% of wildlife. Whole-genome sequencing of 54 ESBL-Ec isolates identified 28 sequence types with no overlap between livestock and wildlife, suggesting distinct evolutionary trajectories. Phenotypic testing revealed resistance beyond beta-lactams, notably against aminoglycosides, tetracyclines, and sulfonamides, whereas all isolates remained susceptible to tigecycline and meropenem. Multidrug resistance was prevalent (89%), with blaCTX-TEM1 (in dairy cattle), blaCTX-M55 and blaTEM-176 (in red foxes) widely distributed across Switzerland. Clonal plasmids (IncFIB, IncX1) were detected across hosts and some individuals harbored multiple ESBL-Ec strains. Despite their low prevalence, spatial clustering indicated local persistence in both livestock and wildlife, highlighting potential transmission. The observed presence of clinically relevant ESBL-Ec in wildlife highlights the need for a One Health approach to tackle the dangers of AMR. Our findings contribute to AMR surveillance by providing baseline data on ESBL-Ec reservoirs and informing the design of strategies to mitigate its environmental spread.

molecular biology↗

bioRxiv2024

Comparative and population genomics analyses of the regulatory Transcription Factor (TF)-DNA interaction

Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype to phenotype transitions. On the molecular level, these genotype to phenotype transitions are shaped by the regulatory sequences (RSs). In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific RS classes involved in the regulatory transcription factor (TF)-DNA interactions. These interactions consist of two motifs, namely: TF-binding domains (TF-BDs) and TF-binding sites (TF-BSs). Using publicly available annotation data, we constructed the species-specific lists of the TF-BD and TF-BS regions. We also constructed a non-synonymous equivalent class for the TF-BS regions for making comparative analyses across the coding and non-coding regions. On applying some of the commonly used summary statistics, we found a consistent signal of purifying selection acting on TF-BDs, consistent with their functional importance. Interestingly, we also observed that non-coding TF-BS regions showed similar levels of constraint to that of coding regions for populations with large Ne. Concerning positive selection, we showed that the regulatory motifs of large Ne species are, overall, subject to an increased intensity of positive selection. We found an overall positive correlation between the intensity of purifying and positive selection and the species-specific Ne, which is expected under drift-selection equilibrium. Finally, we contrasted the signal of positive selection in H. sapiens and D. melanogaster (outcrossing species) with A. thaliana (selfing species) and noted that selfing plays a key role in influencing the action of positive selection.

evolutionary biology↗

bioRxiv2022

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

Recirculating aquaculture systems (RAS) heavily depend on microbial communities to maintain water quality. These communities therefore influence the growth, development, and welfare of farmed fish. With the increasing socio-economic role of fish farming e.g. regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective. However, the data situation regarding the composition of microbial communities within RAS is patchy. Since this is partly ascribed to method choices, there clearly is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems. Here, we compare the performance of 16S amplicon sequencing, Pac-Bio long-read amplicon sequencing, and amplification-free shotgun metagenomics in the characterization of microbial communities in two commercial-size RAS fish farms. We show that, even though primer choice affects read quality, diversity, and assigned taxa, distinct primer pairs uncover similar spatio-temporal patterns between sample types, farms, and time points. We find that long-read amplicons underperform regarding quantitative resolution of spatio-temporal patterns, but allow for species-level identification of functional services and pathogens. Finally, shotgun metagenomics data identified fungi, viruses, and bacteriophages, opening avenues for an exploration of natural approaches regarding antipathogenic treatments. Overall, the datasets agreed on major prokaryotic players. In conclusion, different sequencing approaches yield overlapping and highly complementary results, with each contributing data no other approach could. Such a tiered approach therefore constitutes a practical and cost-effective strategy for obtaining the maximum amount of information on aquaculture microbial communities. These data could lead to better farm management practices and at the same time inform basic research on community evolution dynamics.

microbiology↗

bioRxiv2020

The mixed genetic origin of the first farmers of Europe

The precise genetic origins of the first Neolithic farming populations, as well as the processes and the timing of their differentiation, remain largely unknown. Based on demogenomic modeling of high-quality ancient genomes, we show that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Near Eastern population with a strongly bottlenecked Western hunter-gatherer population after the Last Glacial Maximum. Moreover, the population branch leading to the first farmers of Europe and Anatolia is characterized by a 2,500-year period of extreme genetic drift during its westward range expansion. Based on these findings, we derive a spatially explicit model of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene. One-Sentence SummaryEarly European farmers emerged from multiple post LGM mixtures and experienced extreme drift during their westward expansion.

evolutionary biology↗

bioRxiv2018

Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel

The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies.

genomics↗

bioRxiv2018

The demographic history of African Drosophila melanogaster

As one of the most commonly utilized organisms in the study of local adaptation, an accurate characterization of the demographic history of Drosophila melanogaster remains as an important research question. This owes both to the inherent interest in characterizing the population history of this model organism, as well as to the well-established importance of an accurate null demographic model for increasing power and decreasing false positive rates in genomic scans for positive selection. While considerable attention has been afforded to this issue in non-African populations, less is known about the demographic history of African populations, including from the ancestral range of the species. While qualitative predictions and hypotheses have previously been forwarded, we here present a quantitative model fitting of the population history characterizing both the ancestral Zambian population range as well as the subsequently colonized west African populations, which themselves served as the source of multiple non-African colonization events. These parameter estimates thus represent an important null model for future investigations in to African and non-African D. melanogaster populations alike.

evolutionary biology↗

bioRxiv2018

Early split between African and European populations of Drosophila melanogaster

Natural populations of the fruit fly Drosophila melanogaster have been used extensively as a model system to investigate the effect of neutral and selective processes on genetic variation. The species expanded outside its Afrotropical ancestral range during the last glacial period and numerous studies have focused on identifying molecular adaptations associated with the colonization of northern habitats. The sequencing of many genomes from African and non-African natural populations has facilitated the analysis of the interplay between adaptive and demographic processes. However, most of the non-African sequenced material has been sampled from American and Australian populations that have been introduced within the last hundred years following recent human dispersal and are also affected by recent genetic admixture with African populations. Northern European populations, at the contrary, are expected to be older and less affected by complex admixture patterns and are therefore more appropriate to investigate neutral and adaptive processes. Here we present a new dataset consisting of 14 fully sequenced haploid genomes sampled from a natural population in Ume[a], Sweden. We co-analyzed this new data with an African population to compare the likelihood of several competing demographic scenarios for European and African populations. We show that allowing for gene flow between populations in neutral demographic models leads to a significantly better fit to the data and strongly affects estimates of the divergence time and of the size of the bottleneck in the European population. Our results indicate that the time of divergence between cosmopolitan and ancestral populations is 30,000 years older than reported by previous studies.

evolutionary biology↗