Presentation about how to keep being updated in science, how to get relevant news and do not lose any important new article. Share your way in comments.
Faculty of Science, Charles University
R is nowadays probably the most powerful tool for statistics of all types. There are plenty of modules available for work with molecular data. Those will be introduced during the course. Previous knowledge of R is useful, but not necessary. If there is at least one participant not speaking Czech, the course will be in English.
Don’t be afraid of command line! It is friendly and powerful tool. Practically identical is command line also in Mac OS X, BSD and another UNIX-based systems, not only in Linux. Basic knowledge of Linux is not conditional. Course will be taught in Linux, but most of the point are applicable also for another UNIX systems like Mac OS X. Knowledge of Linux/UNIX is useful e.g. for working with molecular and another data. MetaCentrum is service provided by CESNET allowing access to huge computational capacity.
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in non-model organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region.
Since academic year 2015/16 is the course scheduled in SIS as MB120C16.
Since academic year 2015/16 is the course scheduled in SIS as MB120C17.
Arlequin is very popular tool for population genetics and in recent version (3.5) it has version running on Linux (arlecore
, only computational core without GUI) as well as possibility to parse output using R statistical language. Those two features are described only briefly in official manual. I faced some issues when running Arlequin on Linux and parsing output using R. I'm describing here my solutions in case someone else would hava similar needs and problems.
Phylogeographical studies of aquatic plants are relatively rare, although river corridors are amazing study system. There are many questions about dispersal within river catchment and between different river basins.
May 1 to 3 2008 I was on conferention Plant Population Biology for the coming decade (21th Annual Conference of the Plant Population Biology Section of the Ecological Society of Germany, Switzerland and Austria (GfÖ), Organized by the Department of Population Biology, Musée national d'histoire naturelle). I presented my poster about preliminary result of phylogeography of Nuphar lutea (yellow water lily) in Czechia.
In my bachelor thesis I present temporal pieces of knowledge on phytogeography, and especially molecular phylogeography of water clonal plants and possibilities of their dispersion. Plenty of questions about history, dispersal, relationship and population structure we can not answer without molecular technologies at all. Another very important components influencing dispersal of plants and animals are their ecology and physiology.