23301b
Seminar
WiSe 17/18: S Molecular Phylogenetics
Thomas Borsch
Hinweise für Studierende
Please bring your laptop.
Zusätliche Modulinfos: www.bcp.fu-berlin.de/studium-lehre/studiengaenge/biologie/master_bio/zerstueckelte-Ordnung/Modulvarianten-Master-Biologie/Vertiefte-Biodiv-Evo-Oeko/Molecular_Phylogenetics.pdf Schließen
Zusätliche Modulinfos: www.bcp.fu-berlin.de/studium-lehre/studiengaenge/biologie/master_bio/zerstueckelte-Ordnung/Modulvarianten-Master-Biologie/Vertiefte-Biodiv-Evo-Oeko/Molecular_Phylogenetics.pdf Schließen
Zusätzl. Angaben / Voraussetzungen
Compulsory pre-course meeting on Mo 04.12.2017, 11:00, Kleiner Hörsaal BGBM (Königin-Luise-Straße 6-8). Please bring your laptop.
Kommentar
Inhalte:
The course will use selected groups of flowering plants as exemplars to reconstruct phylogenetic trees based on DNA sequence data. It starts with the collection and documentation of plant material (living collection and herbarium of the BGBM) and the isolation of genomic DNA. Subsequently, laboratory steps including PCR amplification and sequencing will be carried out. The primary data (such as pherograms) will be analyzed, assembled and processed into a matrix of sequence characters. Data matrices will then be analyzed with a spectrum of methods and computer programs to reconstruct phylogenetic trees, The trees will be digitally visualized and discussed in relation to the knowledge gained on the respective study group. The course employs a mini-project approach with which participants can, to a large extend, generate and analyze their own data.
The lecture and seminar part will address the theory of phylogenetics (cladistics), homology and definition of characters comparing DNA and morphology, sources of molecular characters from the different genomic compartments (plastid, mitochondrial, nuclear), study design, multiple sequence alignment, models of sequence evolution, phylogenetic tree reconstruction using parsimony, Maximum Likelihood and Bayesian Interference, evaluation of node confidence, the use of phylogenetic trees to understand character and trait evolution and to inform classification, as well as current trends in molecular phylogenetics and our understanding of the evolutionary diversification of plants. While the course works with plants, the basic concepts and methods are also applicable to other groups of organisms.
Qualifikationsziele:
Understanding phylogenetic relationships is of fundamental importance in biology. Today phylogenetic hypotheses open up a wide field of further questions such as character and trait evolution, tempo and mode of species diversification, taxonomic classification, and historical biogeography. This course provides an introduction to phylogenetic theory and methods for generating molecular phylogenetic trees.
After the course, the students should (1) be familiar with the basic concepts of phylogenetics and be able to critically reflect on the phylogenetic aspects in relevant biological literature; and should (2) know protocols and methods (wet lab and bioinformatics analysis) that are widely applied in phylogeny reconstruction.
The student will learn methods and protocols, from material collection to sequence generation, by implementing them in the lab. Furthermore, students will acquire knowledge on how to analyze sequence data with the goal of reconstructing phylogenetic trees, and get familiar with the most important computer programs. Schließen
The course will use selected groups of flowering plants as exemplars to reconstruct phylogenetic trees based on DNA sequence data. It starts with the collection and documentation of plant material (living collection and herbarium of the BGBM) and the isolation of genomic DNA. Subsequently, laboratory steps including PCR amplification and sequencing will be carried out. The primary data (such as pherograms) will be analyzed, assembled and processed into a matrix of sequence characters. Data matrices will then be analyzed with a spectrum of methods and computer programs to reconstruct phylogenetic trees, The trees will be digitally visualized and discussed in relation to the knowledge gained on the respective study group. The course employs a mini-project approach with which participants can, to a large extend, generate and analyze their own data.
The lecture and seminar part will address the theory of phylogenetics (cladistics), homology and definition of characters comparing DNA and morphology, sources of molecular characters from the different genomic compartments (plastid, mitochondrial, nuclear), study design, multiple sequence alignment, models of sequence evolution, phylogenetic tree reconstruction using parsimony, Maximum Likelihood and Bayesian Interference, evaluation of node confidence, the use of phylogenetic trees to understand character and trait evolution and to inform classification, as well as current trends in molecular phylogenetics and our understanding of the evolutionary diversification of plants. While the course works with plants, the basic concepts and methods are also applicable to other groups of organisms.
Qualifikationsziele:
Understanding phylogenetic relationships is of fundamental importance in biology. Today phylogenetic hypotheses open up a wide field of further questions such as character and trait evolution, tempo and mode of species diversification, taxonomic classification, and historical biogeography. This course provides an introduction to phylogenetic theory and methods for generating molecular phylogenetic trees.
After the course, the students should (1) be familiar with the basic concepts of phylogenetics and be able to critically reflect on the phylogenetic aspects in relevant biological literature; and should (2) know protocols and methods (wet lab and bioinformatics analysis) that are widely applied in phylogeny reconstruction.
The student will learn methods and protocols, from material collection to sequence generation, by implementing them in the lab. Furthermore, students will acquire knowledge on how to analyze sequence data with the goal of reconstructing phylogenetic trees, and get familiar with the most important computer programs. Schließen
Literaturhinweise
V. Knoop & K. Müller (2009): Gene und Stammbäume – Ein Handbuch zur molekularen Phylogenetik. 2.Aufl. Spektrum Akademischer Verlag [ebook available through Primo/Springer: https://link.springer.com/book/10.1007/978-3-8274-2230-9/page/1] Schließen