Monday – Classes from 2 to 8 pm Berlin time

 

Lecture 1: Introduction to Phylogenomics

- Sequencing technology
- Case studies
- Basic phylogenetics concepts: alignment, substitution models, inference methods

Lab 1: Alignment and Phylogenetic Inference

- Alignment with MAFFT
- Alignment visualization with AliView
- Selection of substitution models with jModelTest
- Maximum-likelihood phylogenetic inference with RAxML
- Tree visualization with FigTree

Lab 2: Bayesian Phylogenetics

- Bayesian phylogenetic inference with BEAST2
- Bayesian selection of substitution models with bModelTest

 

 

 

Tuesday – Classes from 2 to 8 pm Berlin time

 

 Lecture 2: Macroevolutionary Phylogenomics

- Ortholog identification
- Criteria of suitable phylogenetic markers
- Molecular clocks

Lab 3: Ortholog Identification

- Ortholog identification with BLAST
- Target-restricted assembly with aTRAM

Lab 4: Divergence-time Estimation

- Node dating with BEAST2
- Time-calibration with CladeAge
- The fossilized birth-death process in BEAST2

 

 

 

Wednesday – Classes from 2 to 8 pm Berlin time

 

 Lecture 3: The Coalescent and its Implications

- Incomplete lineage sorting
- Gene tree heterogeneity
- Concatenation versus the multi-species coalescent

Lab 5: Gene-tree / Species-tree Approaches

- Maximum-likelihood species-tree inference with ASTRAL
- Bayesian species-tree inference with StarBEAST2

Lab 6: Species-tree Inference based on SNP Data

- Bayesian species-tree inference with SNAPP
- Divergence-time estimation with SNAPP

 

 

Thursday – Classes from 2 to 8 pm Berlin time

 

Lecture 4: Introgression

- Adaptive introgression and diversification
- Species networks
- Identification of introgression using allele frequencies
- Tree-based tests for introgression

Lab 7: Identifying Introgression

- Introgression tests based on D-statistics
- Introgression tests based on gene-tree topologies
- Introgression tests based on gene-tree divergence times

Lab 8: Species Networks

- Analysing introgression with the SpeciesNetworks package for BEAST2

 

 

 

 Friday – Classes from 2 to 8 pm Berlin time

 

Lecture 5: Genome-scan Phylogenetics

- Mapping to reference genomes
- Filtering approaches to exclude paralogs
- Phasing
- Detection of recombination breakpoints
- Hidden-Markov models
- Sliding-window analyses

Lab 9: Whole-genome Alignments

- Mapping reads with BWA
- Filtering with VCFTOOLS and PLINK
- Phasing with SHAPEIT
- Detecting recombination breakpoints with SAGUARO

Lab 10: Gene-tree Variation across the Genome

- Analysing gene-tree variation across the genome with TWISST