Biology subjects

Gaspar, B.

Publications and source records attributed to Gaspar, B..

4 recordsLinked to original sources

bioRxiv2023

Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. However, manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd sourcing efforts could offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. Here, we present an example of such crowd sourcing effort developed through both in-person and online courses built around a collaborative peer-reviewed teaching process that can be used as teaching reference guide for similar projects. The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs: A hidden treasure awaits discovery within non-model organisms.

evolutionary biology↗

bioRxiv2020

Intraspecific variation in land use-related functional traits in Plantago lanceolata

Background and aimsIntraspecific variation in functional traits is essential for the evolutionary success of organisms. The co-variation between trait variation and environment, as well as between different traits, can help us to understand which ecological factors drive habitat adaptation, and to what extent adaptation may be constrained by trait correlations and trade-offs. In managed grasslands, plants experience a combination of competition, recurrent biomass removal and nutrient pulses. Each of these ecological challenges requires specific plant tolerances, and populations should locally adapt if intraspecific variation exists in these traits. MethodsWe studied variation in land use-related traits in the common grassland plant Plantago lanceolata. In a common environment, we quantified the competitive ability (R*), clipping tolerance and responses to a nitrogen pulse of plants from 54 populations with different land use intensities across Germany. Key resultsWe found significant population differentiation in competitive ability but there was little evidence that trait variation was related to land use intensity. There was a positive relationship between competitive ability and clipping tolerance at the population level, indicating a genetic, and possibly functional, link between these two traits. In contrast, clipping tolerance and nitrogen responses were negatively correlated at the levels of plant individuals, indicating a physiological trade-off between plant responses to these two land-use processes. ConclusionsOur results show that there is substantial intraspecific variation in some of the key functional traits for plant success in managed grasslands, and that rapid evolution and adaptation is therefore possible in these traits.

plant biology↗

bioRxiv2020

Rapid evolution in managed grasslands: different land-use regimes are associated with contrasting phenotypes in Plantago lanceolata

Land-use intensification is a major driver of biodiversity declines, and it is known to decrease species numbers and alter community composition of managed grasslands. An open question is whether similar impacts occur within species, i.e. whether grassland management affects also the genetic diversity of plant populations and alters their genetic composition, possibly reflecting adaptation to land use. To address these questions, we sampled 61 populations of the common grassland herb Plantago lanceolata that covered a broad range of land use intensities in the German Biodiversity Exploratories, and we grew their offspring in a common environment to quantify variation in plant size, architecture, reproduction, and leaf economy. All measured traits harboured substantial heritable variation, and six out of nine traits showed population differentiation. Interestingly, several traits were significantly correlated with land use intensity, but with opposing trends for mowing versus grazing: Increased mowing intensity was associated with larger plant size and lower specific leaf area (SLA), which may reflect evolutionary responses to increased light competition and a lesser need for resource conservation in highly productive meadows. In contrast, increased grazing intensity tended to be associated with smaller plant size and higher SLA, a phenotype syndrome known from grazing lawns. Moreover, we found that land-use intensification also affected genetic diversity, again with opposing effects for mowing versus grazing: while increased mowing was associated with decreased levels of intrapopulation phenotypic variation, the opposite was true for increased grazing intensity. In summary, land use intensification has not only already caused rapid evolutionary changes in these grassland populations, it also affects their future evolutionary potential.

plant biology↗

bioRxiv2017

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Growing evidence makes a strong case that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology from dissecting developmental processes to understanding aspects of human health and disease. In ecology, recent studies have merged ecological experimental design with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress response, adaptation to habitat, or species range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, many studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism. To understand the true significance of epigenetics for plant ecology and evolution, we must combine both approaches transferring knowledge and methods from model-species research to genomes of evolutionarily divergent species, and examining responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration between molecular epigeneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

ecology↗