Workshop on Molecular Evolution

This event covers contemporary topics in molecular evolution using bioinformatics. This course is lecture and computer-based.

Content has been carefully selected to provide participants with the background and practical skills required by modern molecular datasets. The schedule addresses the following subject areas, with each subject having one or more exercises focused on practical data analysis and interpretation skills.

• An evolutionary perspective on molecular data: sequence matching; protein sequence versus protein structure; homology, orthology and parology; mathematical, statistical, and theoretical aspects of sequence database searches; multiple alignment; information resources
• Foundations of phylogenetic analysis: theoretical, mathematical, and statistical principles; sampling properties of sequence data; Maximum likelihood theory and practice; Bayesian analysis; hypothesis testing
• Species-level phylogenomics: species trees from gene trees; species delimitation; multi locus and SNP data; empirical examples
• Deep phylogenomics: deep evolutionary relationships; lateral gene transfer; modeling approaches; topology testing; sequencing strategies
• Foundations of population genetic analysis: neutral theory; coalescence theory; maximum likelihood and Bayesian estimation of population genetic parameters; empirical examples
• Population genomics: phylogeography; molecular ecology; next-generation population genetics; signatures of natural selection; natural populations of non-model organisms
• Comparative genomics: genome content; genome structure; gene and genome evolutionary dynamics; prediction of gene function
• Molecular evolution integrated at organism and higher levels: population biology and ecology; natural selection; systematics and conservation
• Molecular evolution integrated at lower levels: biochemistry; cell biology; physiology; natural selection; relationship of genotype to phenotype

As the course progresses, participants learn how to use the following software to address questions concerning the origins, maintenance, and function of molecular variation: ASTRAL, BEAST2, BEST, BPP, FASTA, FigTree, GARLI, MIGRATE, MAFFT, MP-EST, RaxML, RevBayes, PAML, PAUP*, Phybase, ipyrad and SVD Quartets. Students will have the opportunity to work with software on their own laptops as well receive training on how to use the same programs on a high performance computer cluster.