Date & time: June 20-21 2022 (09:00-15:00)

Location: German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103, Leipzig. Room: Beehive (Ground floor)

Teachers: Chris Barratt & Laura Mendez Cuellar, sDiv and Evolution and Adaptation (iDiv)

Course summary | Course website

All powerpoint slides available here


Day 1 (20th June): 09:00 - 15:00

Day 2 (21st June): 09:00 - 15:00

Hands on sessions to analyse population structure, phylogeny and genetic diversity - using Leptopelis flavomaculatus data (an African treefrog):


Before the course, please:

Please contact us if you have any questions!


  1. Understand best practices on planning and executing a population genomics project based on ddRAD-seq (short read) type data

  2. Learn how to download genomic sequence data from the European Nucleotide Archive

  3. Familiarise yourself with the Stacks 2 bioinformatic pipeline to process raw reads

  4. Be able to generate your own output files after Stacks processing for downstream analyses of population structure, phylogeny and genetic diversity

  5. Run analyses to perform (Admixture, sNMF, DAPC, RAxML, F-statistics), understand what you’ve done and how to interpret the outputs


The reduction in costs for genomic data generation has reduced drastically in recent years. This cost reduction has led to the large-scale adoption of ddRAD-seq as a method for denovo Single Nucleotide Polymorphism (SNP) discovery in non-model organisms, where thousands of molecular markers can be used to answer ecological, evolutionary and conservation questions that were previously not possible to answer.

In this course you’ll learn how to plan a ddRAD-seq style project effectively, learn the data types, how to analyse them and what the outputs mean. There’s also the chance to analyse your own data (if you already have it) and earn an extra 0.5 ECTS.


Andrews et al 2016. Harnessing the power of RADseq for ecological and evolutionary genomics

Rochette et al. 2019. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics

Paris et al. 2017. Lost in parameter space: a road map for stacks

Rochette and Catchen 2017. Deriving genotypes from RAD-seq short-read data using Stacks

Cerca et al. 2021. Removing the bad apples: A simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms


Barratt et al. 2018. Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians

Razgour et al. 2019. Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

Mendez et al. (in prep)