The aim of this course is to understand the main concepts and methodologies in phylogenomics and comparative genomics. It provides a rigorous training on the use of phylogenetic methods to infer evolutionary history and diversification mechanisms using high-throughput sequencing data. Furthermore, showcases the main comparative approaches to ascertain the evolution of genes and complete genomes, covering genome wide analyses of gene gains, losses, duplications and gene order conservation. The course places special emphasis on developing practical experience in state-of-the-art software through case studies grounded in current and future applications of phylogenomics and comparative genomics.
Teachers
Person in charge
Jesús Lozano Fernández (
)
Others
Miguel Angel Arnedo Lombarte (
)
Weekly hours
Theory
2
Problems
2
Laboratory
0
Guided learning
0
Autonomous learning
6
Objectives
Inferring phylogenies using genome-scale data
Related competences:
K1,
K2,
K7,
S2,
S3,
Acquisition of the specific knowledge of statistical inference and modelling in phylogenetics
Related competences:
K2,
K3,
S1,
S3,
S7,
S8,
C4,
Use comparative genomics tools for solving biological problems
Related competences:
K1,
S2,
S3,
S5,
C2,
C3,
C4,
Contents
Genes and their functions
Origin of genes, duplication, losses and evolution. Gene structure and expression. Relationships between sequence, structure, and function and their evolution. Homology based functional inference. Protein domains and domain shuffling.
Phylogenetic analyses
Conceptual framework. Parsimony. Maximum Likelihood. Bayesian. Nodal support. Species and gene family tree reconstruction. Inference of gene duplication and other evolutionary events.
Comparative sequence analyses
Homology, Paralogy and Orthology. Methods for predicting orthology and paralogy: clustering-based and phylogeny-based. Gene families. Gene duplication, neo- and sub-functionalization. Gene family expansions and contractions. Adaptation and genome evolution.
Phylogenomics
Genome-wide phylogenetic analysis (phylome). Species tree reconstruction. Gene tree vs species tree. Non-vertical processes of evolution, horizontal gene transfer. Whole genome duplication. Timetrees and ancestral-state reconstruction
Modelling molecular substitutions
Model selection. Topological evaluation and incongruence. Inference in practice
Genome comparisons
Genome alignments and detection of conserved regions. Recent availability of chromosome-scale genomes and annotations thanks to global efforts (EBP, ERGA, CBP,...). Conserved motif discovery. Genome re-arrangements. Synteny analysis. Prediction of function from conserved gene order. Presence absence patterns. Convergent evolution. Gene tree comparison. Co-evolution between genes.
Gene expression and functional analyses
Genomics-based methods to assess gene expression. genome-wide functional annotation. Long-non-coding RNAs. Efforts in model and non-model species. Diversity of life and the tree of life. Variation of genome size and organization. Extreme genome expansions and reductions.
Lectures will be mainly of expository type. There will be also practical sessions using a wide range of phylogenetics and comparative genomics softwares, a small research project developed in group, and a group seminar covering a recent comparative genomics publication.
Evaluation methodology
Laboratory practices and seminars are mandatory. The course assessment is as follows:
60% consists of a 2 partial theoretico-practical exams taken at mid term (20%) and final term (40%).
15% corresponds to regular individual practical assignments
15% corresponds to a research project done in teams
10% corresponds to a seminar presentation in teams
Recuperation Information
Only the students that after the evaluation have a grade equal or greater than 3,5 can perform the re-evaluation exam. The re-evaluation exam will substitute the theoretico-practical part (60%).
Bibliography
Basic:
Reading the story in DNA : a beginner's guide to molecular evolution -
Lindell Bromham,
Oxford ; New York : Oxford University Press, 2008, 2008. ISBN: 9780199290918