held in Mendoza, Argentina in November 2025
For the course taught in July 2024 at IKIAM University in Tena, Ecuador, see the folder 2024.
This course is taught by Karin Näsvall, Nicol Rueda, Fernando Seixas, and Joana Meier from the Wellcome Sanger Institute and by Melisa Olave (CONICET, Argentina). Some of the course material is based on the speciation genomics course by Joana Meier and Mark Ravinet.
The course website showing logistics and useful information about Mendoza is here.
Day 0:
- Slides basic introduction to unix and the command line
- Exercise on how to use the command line
- Exercise on more use of the command line
- Exercise for more advanced users (awk, variables, arrays, writing a bash script)
Day 1:
- Slides introducing biodiversity genomics and sequencing technologies
- Slides introducing the structure of Illumina reads and fastq files
- Exercise on exploring Illumina reads and visualising the quality with fastqc which uses these input files
- Slides on interpreting fastqc output of RAD data
- Exercise on filtering and trimming reads
- Slides on assembling reference genomes
Day 2:
- Slides on aligning reads to a reference genome
- Exercise on aligning reads to a reference genome
- Slides on calling variants and genotypes
- Exercise on calling variants and genotypes
Day 3:
- Excercise on filtering vcf files
- Slides on population structure visualisation with PCA (principal components analysis)
- Excercise on running a PCA
- Slides on Phylogenomics: gene trees, species trees and networks
- Excercise on phylogenomic networks with gene trees
Day 4:
- Exercise on phylogenomics using SNPs
- Slides on inferring hybridisation
- Exercise on computing D statistics with Dsuite
- Slides on genome scans
- Exercise on genome scans
Day 5:
- slides on detecting selection at long time-scales
- exercise on detecting selection at long time-scales
- slides on large-scale sequencing initiatives
- slides on comparative genomics
- exercise on genome synteny
Advanced materials:
- Statistical phasing Exercise
- Extended haplotype statistics Exercise
- Identifying genes at selection peaks Exercise
Physalia courses offers lots of great courses on genomics, bioinformatics, and related fields. The Speciation Genomics course was a course taught via Physalia.
https://speciationgenomics.github.io/ contains many more tutorials, including topics not covered here, such as demographic modeling, haplotype-based tests for selection, advanced unix and R tutorials, simulating data with SliM, etc.
Workshop website contains many useful tutorials that are quite advanced, including machine learning and pangenomics.
28 October - 1 November 2024: Online, free conference on biodiversity genomics across all time zones: https://www.biodiversitygenomicsconference.org
If you have short-read data for only a subset of the genome because you used a reduced-representation technique (e.g. RAD or UCE), most of the tutorial will still be relevant. For RAD or UCE data you do not necessarily need a reference genome, unless you want to run the genome scans for finding regions with high differentiation or introgression. If you have RAD (restriction-enzyme associated DNA) data, you can either follow the steps in our tutorial with mapping reads to a reference genome or if you do not have a reference genome, you can do a de novo assembly, i.e. make your own reference for just the RAD loci. The most widely used tool for RAD data analysis is STACKS or if you have a phylogenetic dataset with many species, we can recommend ipyrad. If you are working with polyploids, check out polyRAD. If you have UCE (ultra-conserved elements) data, have a look at this website for guidance.
- Introduction to the Unix Command Line Dowling, et al., 2019
- Unix and Perl Primer for Biologists Bradnam, et al 2016
- How genomics can help biodiversity conservation Theissinger et al. 2023
- Genomics and the origin of species Seehausen et al. 2015
- Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation van der Heijden et al. 2024
- Genomic evidence reveals three W-autosome fusions in Heliconius butterflies Rueda et al. 2024
- Arima-HiC Mapping Pipeline Arima Genomics
- Tutorial on ASTRAL Mirarab, et al
- DensiTree Manual: Making sense of sets of trees Bouckaert, et_al 2014
- Local PCA Shows How the Effect of Population Structure Differs Along the Genome Li, et al., 2019
- The Sequence Alignment/Map format and SAMtools Li, et al., 2019
- Dsuite - Fast D-statistics and related admixture evidence from VCF files Malinsky, et al., 2020
- Sequence Alignment Map Format Specification SAM BAM group
- Quality Scores for Next-Generation Sequencing Illumina
- Accurate, scalable and integrative haplotype estimation (SHAPEIT4) Delaneau, et al., 2019
- WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads Patterson, et al., 2015
- Modern technologies and algorithms for scaffolding assembled genomes Ghurye, et al., 2019
- BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes Manni, et al., 2021
- OrthoFinder and recap on orthologs and paralogs github.com/davidemms/OrthoFinder
- IQtree manual iqtree.org
- Phylogenomics and the reconstruction of the tree of life Delsuc, et al., 2005
- Phylogenetic tree building in the genomic age Kapli, et al., 2020
- Genetic Terminology Elston, et al 2012
- Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths Kawahara, et al 2019
- A method for genome-wide genealogy estimation for thousands of samples Speidel, et al., 2019
- What does Drosophila genetics tell us about speciation? Mallet, J., 2006
- Defining the speciation continuum. Stankowski, et al., 2021
- Phylogenomic approaches to detecting and characterizing introgression Hibbins, et al., 2022
- Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci Martin, et al., 2015
- The genetic consequences of hybridization Moran, et al., 2021
- How reticulated are species? Mallet, et al., 2015
- Chromosomal rearrangements and speciation. Rieseberg, et al., 2021
- Chromosome evolution Ingo Schubert, 2019
- The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution Lucek, et al., 2023
- Next-Generation Sequencing Technology: Current Trends and Advancements Satam, et al., 2023
- Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography Van Belleghem, et al., 2017
- Complex modular architecture around a simple toolkit of wing pattern genes Van Belleghem, 2018