Faculty of Science, Charles University

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR.

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

The first species-level phylogeny of the Sabulina verna group is presented. Genetic clusters are congruent with geography and mostly supported by morphological traits. Metalliferous and serpentine soils were colonized multiple times independently.

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored.

Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events.

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.