held for the first time at Ikiam, in Tena, Ecuador in July 2024
This course taught by Karin Näsvall, Nicol Rueda and Joana Meier from the Wellcome Sanger Institute is an adapted version of the speciation genomics course by Mark Ravinet and Joana Meier. Here you will find all relevant course materials for the biodiversity genomics course, including all files we used during the course in case you want to redo anything at home.
Day 1:
- Slides introducing biodiversity genomics and sequencing technologies
- Slides summarising the steps from getting raw Illumina reads, filtering, aligning them to a reference and calling variants and genotypes
- Slides introducing the structure of Illumina reads and fastq files
- Slides on logging on to the Amazon server by Carlo Pecoraro from Physalia Courses
- Exercise on exploring Illumina reads and visualising the quality with fastqc which uses these input files
- Slides on interpreting fastqc output of RAD data
Day 2:
- Exercise on filtering Illumina reads with fastp which uses these input files
- Slides on aligning reads to a reference genome
- Exercise to align Illumina paired-end reads to a reference genome with bwa-mem2
- Slides about variant and genotype calling
Day 3:
- Exercise on variant and genotype calling with bcftools.
- Exercise on filtering vcf files.
- Slides introducing ithomiini butterflies and PCA
- Exercise on PCA.
- Exercise on making phylogenies with iqtree.
Day 4:
- Slides on identifying introgression with D statistics
- Exercise on Dstatistics to infer introgression using Dsuite
- Slides on genome scans to locate genomic regions under selection and introgression
- Exercise on genome scans
Day 5:
- Slides on comparative genomics
- Exercise on macrosynteny
- Slides on phylogenomics with BUSCO genes
- Exercise on phylogenomics with BUSCO genes
- Slides summarising the course and giving some suggestions for further learning
Free to attend, fully online tutorials about genome assembly, curation and annotation, comparative genomics and more. The next session will be in October and all tutorials of last year are available on Youtube/GitPod: https://thebgacademy.org
28 October - 1 November: Online, free conference on biodiversity genomics across all time zones: https://www.biodiversitygenomicsconference.org
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.
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. 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