Biology subjects

Elsner, D.

Publications and source records attributed to Elsner, D..

3 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↗

bioRxiv2023

High-quality long-read genome assemblies reveal evolutionary patterns of transposable elements and DNA methylation in termites

Arms races between parasites and hosts are key drivers of evolution. Selfishly replicating transposable elements (TEs) are thought to follow similar dynamics, but strong evidence is missing. We tested this in termites, social insects in which TEs have been linked to ageing. Sequencing genomes and profiling DNA methylation across the termite phylogeny revealed corresponding phylogenetic signals in TEs and TE methylation, indicative of selection. TE methylation reduces TE success, as both TE abundance and spreading efficiency decrease with increasing methylation. TEs also become less harmful with TE age: evolutionarily older TEs spread less, insert less into exons, and erode into short remnants. Correspondingly, defence through methylation is strongest against young TEs. Yet, as in typical host-parasite arms races, some TEs persist, implying resistance or recurrent invasions. Our results reveal arms races between TEs and DNA methylation, positioning TEs as drivers of genome evolution similar to symbionts in organismic evolution.

evolutionary biology↗

bioRxiv2022

Resource sharing leads to the emergence of division of labour

Division of labour occurs in a broad range of organisms. Yet, how division of labour can emerge in the absence of pre-existing interindividual differences is poorly understood. Using a simple but realistic model, we show that in a group of initially identical individuals, division of labour emerges spontaneously if returning foragers share part of their resources with other group members. In the absence of resource sharing, individuals follow an activity schedule of alternating between foraging and other tasks. If non-foraging individuals are fed by other individuals, their alternating activity schedule becomes interrupted, leading to task specialisation and the emergence of division of labour. Furthermore, nutritional differences between individuals reinforce division of labour. Such differences can be caused by increased metabolic rates during foraging or by dominance interactions during resource sharing. Our model proposes a plausible mechanism for the self-organised emergence of division of labour in animal groups of initially identical individuals. This mechanism could also play a role for the emergence of division of labour during the major evolutionary transitions to eusociality and multicellularity.

evolutionary biology↗