Evolutionary inference using phylogenetic trees and comparative genomics

17 outubro 2013, 09:30 • Miguel Nobre Parreira Cacho Teixeira

Introduction to the proposed problem on the reconstruction of the evolutionary history of ATR1 gene and ORF YMR279C.

Multiple alignment of the 37 amino acid sequences (using MUSCLE software). Analysis of the sequence aligment using JALVIEW and interpretation of results.

Construction of the phylogenetic tree using the tools made available by the Institute Pasteur Portal MOBYLE bioinformatics portal. Distance methods (PROTDIST and NEIGHBOR algorithms).  Maximum parsimony method (PROTPARS algorithm). Maximum likelihood method (PHYML algorithm). Comparison of the phylogenetic trees obtained using DENDROSCOPE software.

Methods of construction of phylogenetic trees. Distance methods: least squares (LS) and clustering approaches (UPGMA). Maximum likelihood.

Introduction to network visualizing software Cytoscape. Basic operations in the software, including creation of sub-networks, etc. Network based neighbourhood analysis of the evolutionary history of ATR1 gene and ORF YMR279C.

Discussion about the sequence similarity and gene neighbourhood methodologies.

This class was taught by Dr. Paulo Jorge Dias, a post-doctoral researcher at the BSRG

Gene and genomic duplications and the evolution of genomes

17 outubro 2013, 08:00 • Miguel Nobre Parreira Cacho Teixeira

The genomics revolution and comparative genomics. The phylogenetic trees of Hemiascomycetes and of the Saccharomyces sensu strictu species. Habitat, domestication and hybrids derived from Saccharomyces sensu strictu species. Yeast comparative genomics. Yeast Gene Order Browser (YGOB). Reconstruction of the evolutionary history of the S. cerevisiae genes TPO2 and TPO3. Yeast and human genomes architecture.

Gene duplication and its importance in the evolutionary process. Concepts of neofunctionalization, subfunctionalization and dosage selection. Life stages, mechanisms of retention and fate of gene pairs. Subfunctionalization of a galactose gene regulatory circuit in S. cerevisiae. Expansion of the Drug:H+ antiporter family 2 in the Hemiascomycetes. The human hemoglobin gene family.

The C-value paradox. Chromosome Mechanisms of genome size change. Genome size variation in animals and plants. “Selfish DNA”and the spread of transposable elements. “Junk DNA”and the accumulation of pseudogenes. Introns. Chromosome-level events. Polyploidy. Insertion-deletion biases.  Chromosome rearrangements: example using the physical maps of two Candida albicans strains. Phylogenetic positions of some likely polyploidy events during eukaryote evolution. The 2R hypothesis and the evolution of the Hox genes.

Phylogenomics. Gene content and gene order methods. Phylogenomic networks.

Classical Versus Hierarchical selection theory. Extrapolationism. Selection at the species level. Selection at the genome level.

This class was taught by Dr. Paulo Jorge Dias, a post-doctoral researcher at the BSRG

Evolutionary inference using phylogenetic trees and comparative genomics

16 outubro 2013, 12:30 • Miguel Nobre Parreira Cacho Teixeira

Introduction to the proposed problem on the reconstruction of the evolutionary history of ATR1 gene and ORF YMR279C.

Multiple alignment of the 37 amino acid sequences (using MUSCLE software). Analysis of the sequence aligment using JALVIEW and interpretation of results.

Construction of the phylogenetic tree using the tools made available by the Institute Pasteur Portal MOBYLE bioinformatics portal. Distance methods (PROTDIST and NEIGHBOR algorithms).  Maximum parsimony method (PROTPARS algorithm). Maximum likelihood method (PHYML algorithm). Comparison of the phylogenetic trees obtained using DENDROSCOPE software.

Methods of construction of phylogenetic trees. Distance methods: least squares (LS) and clustering approaches (UPGMA). Maximum likelihood.

Introduction to network visualizing software Cytoscape. Basic operations in the software, including creation of sub-networks, etc. Network based neighbourhood analysis of the evolutionary history of ATR1 gene and ORF YMR279C.

Discussion about the sequence similarity and gene neighbourhood methodologies.

This class was taught by Dr. Paulo Jorge Dias, a post-doctoral researcher at the BSRG

Introduction to key evolutionary concepts and to phylogenetic trees

16 outubro 2013, 11:00 • Miguel Nobre Parreira Cacho Teixeira

Basic concepts of the theory of evolution. Evolution versus Creationism. Basic concepts of population genetics. The synthesis of the theory of evolution. Gradualism versus punctuated equilibrium. The importance of fossil record. Species Concept. Modes of speciation.Mechanisms of reproductive isolation. Three schools of macrotaxonomy. Concepts of monophyly, paraphyly and polyphyly.

Introduction to phylogenetic trees. Cladograms, additive trees and ultrametric trees. Metric and additive distances. Ultrametric distances. Rooted and unrooted trees. Methods of rooting the phylogenetic tree: outgroup and molecular clock methods. How many rooted and unrroted trees are there? Empirical tree construction. Methods of tree construction. Methods of construction of phylogenetic trees. Maximum parsimony.

Concepts of homology and homoplasy of features. Parallel and convergent evolution and secondary loss of a feature. Homology among genes. Orthologs and paralogs genes. Gene trees and species trees.

The evolution of yeasts and of the human species.

This class was taught by Dr. Paulo Jorge Dias, a post-doctoral researcher at the BSRG

Computational Work1 (part2)

11 outubro 2013, 11:00 • Nuno Gonçalo Pereira Mira

Computational Work1 (part2): High-throughput genome sequencing: from a DNA sequence to a genome annotation