We address phylogenomic and population genomic questions using whole genome sequencing data. We use the de.NBI Cloud for bioinformatics tasks such as cleaning and filtering data, as well as for analyses using different software. The excellent support and powerful machines are extremely helpful. Project summary: climate change is one of the major threats to biodiversity, yet there is still much uncertainty surrounding how plants can adapt to and survive in rapidly changing habitats. In this study, we propose investigating key evolutionary processes in plants that are relevant in this context. First, we will assess the importance of two poorly understood processes: homoploid hybridisation and immediate introgression. We will do this by linking them to ecological innovations and selective signals. To do so, we will construct phylogenetic networks and apply tests such as invariant-based methods and simulations. Secondly, we will infer the responses that plants can be expected to exhibit under the ongoing warming scenario by reconstructing the phylogeographical history and adaptive evolution that species underwent following the last glacial maximum. We will address these topics using the bryophyte genus Schistidium. This genus encompasses many pioneer species that are adapted to colonise bare rock surfaces, including artificial substrates such as concrete and asphalt. This ability enables these species to mitigate the effects of climate change by colonising deglaciated and desertified land. The dominance of the haploid generation in this lineage facilitates the detection of evolutionary signals and speeds up purifying selection, while the high reproductive effort favours hybridisation events. This project builds on an extensive preliminary analysis of genome sizes, as well as ecological and morphological divergence, in the proposed model system. We use high-throughput target capture and whole-genome sequencing to generate genomic data from the coding and non-coding regions of all three parts of the genome (nuclear, plastid and mitochondrial). This study will shed light on the evolutionary patterns of speciation in early land plants, as well as adaptive divergence at the intraspecific level. The results will emphasise the significance of homoploid hybridisation in plant evolution, draw attention to the under-recognised process of immediate introgression, and stimulate further research on this topic. Furthermore, the study will enhance our comprehension of the adaptive potential of pioneer species and primary producers, which are set to play a pivotal role in mitigating the effects of climate change.
