Biology subjects

Ebert, D.

Publications and source records attributed to Ebert, D..

31 records · Page 2Linked to original sources

bioRxiv2022

Structural and functional analysis of natural capsid variants reveals sialic-acid independent entry of BK polyomavirus

BK Polyomavirus (BKPyV) is an opportunistic pathogen that causes nephropathy in kidney transplant recipients. The BKPyV major capsid protein, VP1, engages gangliosides, lipid-linked sialylated glycans at the cell surface, to gain entry into cells. Here, we characterise the influence of VP1 mutations observed in patients with persistent post-transplant BKPyV replication on ganglioside binding, VP1 protein structure, and the tropism of the virus in two renal cell lines: 293TT and immortalised renal tubular epithelial (RS) cells. Infectious entry of single mutants E73Q, E73A and the triple mutant A72V-E73Q-E82Q (VQQ) remained sialic acid-dependent. These three variants acquired binding to a-series gangliosides, including GD1a, although only E73Q was able to infect GD1a-supplemented LNCaP or GM95 cells. Crystal structures of the three mutants showed a clear shift of the BC2 loop in mutants E73A and VQQ that correlated with the inability of these VP1 variants to infect ganglioside complemented cells. On the other hand, the double mutant K69N-E82Q lost the ability to bind sialic acid, with the K69N mutation leading to a steric clash which precludes sialic acid binding. Nevertheless, this mutant retained significant infectivity in 293TT cells that was not dependent on heparan sulphate proteoglycans, implying that an unknown sialic acid-independent entry receptor for BKPyV exists.

microbiology↗

bioRxiv2022

Genetic drift shapes the evolution of a highly dynamic metapopulation

The dynamics of extinction and (re)colonization in habitat patches are common features of metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared to the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in more isolated, younger subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that the evolutionary process is largely driven by genetic drift.

evolutionary biology↗

bioRxiv2022

Population genetic analysis reveals the role of natural selection and phylogeography on genome-wide diversity in an extremely compact and reduced microsporidian genome

The determinants of variation in a species genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from ten populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We found patterns of more efficient purifying selection in O. colligata relative to other microsporidia sharing the same host, which likely allowed this parasite to maintain its very compact genome. We also identified regions under potential selection related to coevolution including the ribosomal protein L24, a leucyl-tRNA synthetase, and a putative ABC-like lipid transport protein. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite. Author summaryMicrosporidia are intracellular parasites that infect vertebrates, invertebrates, and even unicellular organisms. Due to their high variation in many aspects of life history and genomics, microsporidia have become a model clade for understanding evolutionary processes related to intracellular parasitism. However, the evolution of extreme genomic architectures in microsporidia and the coevolution with their hosts is still under-surveyed, especially given their role in human disease. Here, we study past and present evolutionary dynamics in a microsporidian species with one of the smallest known eukaryotic genomes, O. colligata. Close relatives of O. colligata cause death and disease in humans and agriculturally important animals. We show that purifying selection helped maintaining its reduced, compact genome and corroborate hypotheses about the evolution of different genome sizes in microsporidia. Importantly, we utilize the highly resolved phylogeny of its host to estimate the parasites mutation rate. This methodology allowed us to establish the first mutation rate estimate for a microsporidium, an estimate which is within the range of mutation rates estimated for phylogenetically related, non-parasitic fungi. Our study exemplifies how the combined knowledge about a species biology, ecology, and genomic diversity helps to resolve its evolutionary dynamics, in particular when phylogenomic information can be brought to bear for both host and parasite.

evolutionary biology↗

bioRxiv2022

A genomic analysis of parasite-mediated population differentiation in a metapopulation

Understanding the genetics of host adaptation is a powerful approach to study host - parasite interactions. Hosts are often assumed to have a simple genetic architecture underlying resistance. However, in natural populations the genetics are rarely known and the link between host adaptation and evolutionary models cannot be easily established. To shed light on the genetic basis of host evolution in the presence and absence of parasites we studied a highly dynamic rockpool metapopulation of the planktonic crustacean Daphnia magna and its microsporidian parasite Hamiltosporidium tvaerminnensis. We examined genome-wide allele frequencies estimated from pooled Illumina sequencing (Pool-seq) of 12 subpopulations of a metapopulation. Subpopulations that had evolved for several years with the parasite were contrasted to uninfected subpopulations, with the aim to find genomic sites of diversifying selection. Consistent with earlier attempts to find resistance genes in this system, we observe many minor-effect outliers, suggesting that the response of the host to this parasite is based on a quantitative-trait architecture. We found 34 outliers across 11 genomic regions that indicate increased differentiation between population groups as well as signs of positive selection. Some of these regions contain immune-related genes, of which four are likely involved in immune downregulation. Our findings show that in the presence of the microsporidium parasite, hosts evolve in a complex polygenic way, driving population differentiation in the metapopulation under study. Such evolutionary differentiation is a powerful mechanism to maintain genetic diversity in spatially structured populations.

evolutionary biology↗

bioRxiv2021

Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution

Analyzing variation in a species genomic diversity can provide insights into its historical demography, biogeography and population structure, and thus, its ecology and evolution. Although such studies are rarely undertaken for parasites, they can be highly revealing because of the parasites coevolutionary relationships with hosts. Modes of reproduction and transmission are thought to be strong determinants of genomic diversity for parasites and vary widely among microsporidia (fungal-related intracellular parasites), which are known to have high intraspecific genetic diversity and interspecific variation in genome architecture. Here we explore genomic variation in the microsporidium Hamiltosporidium, a parasite of the freshwater crustacean Daphnia magna, looking especially at which factors contribute to nucleotide variation. Genomic samples from 18 Eurasian populations and a new, long-read based reference genome were used to determine the roles that reproduction mode, transmission mode and geography play in determining population structure and demographic history. We demonstrate two main H. tvaerminnensis lineages and a pattern of isolation-by-distance, but note an absence of congruence between these two parasite lineages and the two Eurasian host lineages. We suggest a comparatively recent parasite spread through Northern Eurasian host populations after a change from vertical to mixed-mode transmission and the loss of sexual reproduction. While gaining knowledge about the ecology and evolution of this focal parasite, we also identify common features that shape variation in genomic diversity for many parasites, e.g., distinct modes of reproduction and the intertwining of host-parasite demographies.

evolutionary biology↗

bioRxiv2021

Sex differences in the strength of selection under facultative sex

Facultative sex, the ability to reproduce both sexually and asexually, is widespread across the tree of life. In anisogamous species, the frequency of sex modulates selection on traits with sex-specific expression. Current theory on conditional gene expression posits that the strength of selection on loci only expressed by a subset of individuals, and/or in a subset of environments, is proportional to the frequency of expressers in the population. We show here that this assumption does not hold when the subsets in question are males or females (because of the Fisher condition) and is most important in facultatively sexual populations. In this case, the proportion of sexually produced offspring is not determined by male frequency (sex ratio), but on relative female investment in sexual versus asexual reproduction. This breaks the link between the frequency of expressers and selection for loci with sex-specific expression. However, certain conditions can re-establish this link, for example male traits that predict mating success better under strong male-male competition, and sex ratio affecting the relative fecundity of sexual versus asexual females. Our work highlights the importance of the Fisher condition for understanding the efficiency of selection and has implications for differences in the genetic load among sexes.

evolutionary biology↗

bioRxiv2021

Genetic slippage after sex maintains diversity for parasite resistance in a natural host population

Although parasite-mediated selection is thought to be a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored a large population of the planktonic crustacean Daphnia magna over eight years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed a cyclical pattern of resistance evolution: resistant phenotypes increased in frequency throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages, a phenomenon described as genetic slippage in response to sex. Collecting and hatching D. magna resting stages across multiple seasons showed that largely resistant host populations can produce susceptible offspring through recombination. Resting stages produced throughout the planktonic season accurately represent the hatching population cohort of the following spring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with these findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction has the potential to maintain genetic diversity of host resistance.

evolutionary biology↗

bioRxiv2020

A two-locus system with strong epistasis underlies rapid parasite-mediated evolution of host resistance

Parasites are a major evolutionary force, driving adaptive responses in host populations. Although the link between phenotypic response to parasite-mediated natural selection and the underlying genetic architecture often remains obscure, this link is crucial for understanding the evolution of resistance and predicting associated allele frequency changes in the population. To close this gap, we monitored the response to selection during epidemics of a virulent bacterial pathogen, Pasteuria ramosa, in a natural host population of Daphnia magna. Across two epidemics, we observed a strong increase in the proportion of resistant phenotypes as the epidemics progressed. Field and laboratory experiments confirmed that this increase in resistance was caused by selection from the local parasite. Using a genome wide association study (GWAS), we obtained a genetic model in which two genomic regions with dominance and epistasis control resistance polymorphism in the host. We verified this model by selfing host genotypes with different resistance phenotypes and scoring their F1 for segregation of resistance and associated genetic markers. Applying the model to the dynamics of the field population revealed moderate changes in allele frequencies at the two resistance loci relative to the profound changes observed at the phenotypic level. This apparent discrepancy is explained by strong epistasis and dominance at the two resistance loci, which reduces the effect of selection on alleles at both loci. Such epistatic effects with strong fitness consequences in host-parasite coevolution are believed to be crucial in the Red Queen model for the evolution of genetic recombination.

evolutionary biology↗

bioRxiv2020

Estimation of the propensity for sexual selection in a cyclical parthenogen

Cyclical parthenogenesis is a widespread reproductive strategy in which organisms go through one or multiple rounds of clonal reproduction before sexual reproduction. Because sexual reproduction is typically less common than parthenogenesis in populations of the planktonic cladoceran Daphnia magna, it is not frequently studied. Here we examine the sexual process of D. magna and its relation to sexual selection in Daphnia rockpool populations by observing natural mating in these shallow habitats where sex generally occurs throughout the summer. Although microsatellite markers were found to reveal no evidence of disassortative mating or, thus, of inbreeding avoidance, body length and infection status did reveal assortative mating, suggesting sexual selection to act. When two males mated with a single female, the larger male was observed to remain longer, possibly giving it an advantage in sperm competition. Indirect evidence points at the brood pouch as the likely site of fertilization and thus, sperm competition. Sperm length was as variable within ejaculates as it was among males from different populations. Our data provide firm evidence that sexual selection is present in this species, most likely manifesting itself through a combination of female choice and male-male competition.

evolutionary biology↗

bioRxiv2020

Evolution of sperm morphology in Daphnia

AO_SCPLOWBSTRACTC_SCPLOWSperm is the most fundamental male reproductive feature. It serves the fertilization of eggs and evolves under sexual selection. Two components of sperm are of particular interest, their number and their morphology. Mode of fertilization is believed to be a key determinant of sperm length across the animal kingdom. External fertilization, unlike internal, favors small and numerous sperm, since sperm density is thinned out in the environment. Here, we study the evolution of sperm morphology in the genus Daphnia, where fertilization occurs in a receptacle, the brood pouch, where sperm can constantly be flushed out by a water current. Based on microscopic observations of sperm morphologies mapped on a phylogeny with 15 Daphnia and 2 outgroup species, we found that despite the internal fertilization mode, Daphnia have among the smallest sperm recorded, as would be expected with external fertilization. Despite being all relatively small compared to other arthropods, sperm length diverged at least twice, once within each of the Daphnia subgenera Ctenodaphnia and Daphnia. Furthermore, species in the latter subgenus also lost the ability of cell compaction by extracellular encapsulation and have very polymorphic sperm with long, and often numerous, filopodia. We discuss the different strategies that Daphnia evolved to achieve fertilization success in the females brood pouch.

evolutionary biology↗

bioRxiv2019

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and are often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species and have rarely been compared across genotypes and populations and intraspecific differences in overall microsatellite content have rarely been explored. To investigate the accumulation of microsatellite DNA over long-and short-time periods, we quantified the abundance and genome-wide mutation rates in whole-genome sequences of 47 mutation accumulation (MA) lines and 12 non-MA lines derived from six different genotypes of the crustacean Daphnia magna collected from three populations (Finland, Germany, and Israel). Each genotype possessed a distinctive microsatellite profile and clustered according to their population of origin. During the period of mutation accumulation, we observed very high microsatellite mutation rates (a net change of -0.19 to 0.33 per copy per generation), which surpass rates reported from a closely-related congener, D. pulex, by an order of magnitude. Rates vary between microsatellite motifs and among genotypes, with those starting with high microsatellite content exhibiting greater losses and those with low microsatellite content exhibiting greater gains. Our results show that microsatellite mutation rates depend both on characteristics of the microsatellites and the genomic background. These context-dependent mutation dynamics may, in conjunction with other evolutionary forces that may differ among populations, explain the differential accumulation of repeat content in the genome over long time periods.

genomics↗

bioRxiv2018

Rearing temperature and fatty acid supplementation jointly affect membrane fluidity and heat tolerance in Daphnia

The homeoviscous adaptation hypothesis states that the relative abundance of polyunsaturated fatty acids (PUFA) decreases in the membrane phospholipids of ectothermic organisms at higher temperatures to maintain vital membrane properties. We hypothesized that the well-documented reduced heat tolerance of cold-reared Daphnia is due to the accumulation of PUFA in their body tissues and that heat-reared Daphnia contain reduced amounts of PUFA even when receiving a high dietary supply of PUFA. In Daphnia reared at 15{degrees}C, supplementation of a PUFA-deficient food with the long-chain PUFA eicosapentaenoic acid (EPA) resulted in an increase in the relative abundance of EPA in body tissues and a decrease in heat tolerance. However, the same was observed in Daphnia reared at 25{degrees}C, indicating that the ability of heat-acclimated Daphnia to adjust EPA body concentrations is limited when exposed to high dietary EPA concentrations. Daphnia reared at 25{degrees}C showed the lowest change in membrane fluidity, measured as fluorescence polarization. For Daphnia reared at three different temperatures, thermal tolerance (time to immobility at a lethally high temperature) and increasing dietary EPA concentrations correlated with fluorescence polarization and the degree of fatty acid unsaturation. Overall, our results support the homeoviscous adaptation hypothesis by showing that cold-reared Daphnia, which accumulate PUFA within their tissues, are more susceptible to heat than hot-reared Daphnia, which contain less PUFA.

ecology↗

bioRxiv2018

Environmental sources of bacteria and genetic variation in behavior influence host-associated microbiota

In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animals microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic, but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We find that the bacterial composition of the environment and genotype-specific browsing intensity together influence the diversity and composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that individual behavior can mediate genotype-by-environment interaction effects on microbiome composition.\n\nSummary statementGenetic differences in Daphnia behavior contribute to the amount of environmental bacteria present in their microbiome

evolutionary biology↗