Incorporating paleogenomes into evolutionary genomics studies


13-16 November 2023


To foster international participation, this course will be held online



Course overview

This course is aimed at Masters or PhD students as an introduction into including ancient DNA data into their genomic analyses. The course will cover mapping, filtering and quality control checks of ancient DNA. Inference of population structure when including ancient DNA samples. Inferring demographic histories using of ancient samples. And lastly, assigning genomic regions under selection to distinct adaptive haplotypes of known association with specific habitats. The practical examples will largely be based around the analyses and data from the recent Kirch et al. study on ancient threespine sticklebacks.


Course eligibility

Course is free of charge and funded by the ADAPT ESEB special topic network. Participants must be student members of ESEB (The European Society of Evolutionary Biology). Student membership costs 30 euros and comes with a range of benefits, including reduced open access publishing and conference fees:

The maximum allowable number of students is: 18!


To enrol for this course, kindly complete this form. The deadline for registration is the 15th of September. The 18 successful students will be notified a few days after the registration deadline.




3 hours each day, starting at 1 pm  EU time.



Monday– Classes from 1-4 PM Berlin time - MAPPING

We will discuss options for mapping short-read ancient DNA data to a reference and how different parameters can affect downstream analyses. We will work through an example of mapping using BWA aln, and will follow-up with various Q.C. checks and coverage estimation of our generated bam file.

Tuesday– Classes from 1-4 PM Berlin time - POPULATION STRUCTURE

On the second day we will compare the mapped ancient DNA from day 1 to a reference panel of modern samples using common methods such as Admixture, PCA and MDS plots. We will discuss the various options and which type of data they may be best suited to. We will discuss alternative options such as Factor Analysis, which can account for biases due to sampling through time.

Wednesday– Classes from 1-4 PM Berlin time - DEMOGRAPHIC HISTORY

We will continue to explore the genetic variation in the ancient sample on Day 3, with the goal of better understanding the demographic history of the ancient sample relative to modern populations. We will estimate several summary statistics including Tajima's D, Pi, and Theta and will discuss how best to interpret these. We will also introduce admixture graphs, such as QP-graph and Treemix. For the practical sessions, we will work with the tree-based D-statistic, also known as the ABBA-BABA test.

Thursday– Classes from 1-4 PM Berlin time -SELECTION

On the final day, we will discuss how incorporating ancient samples into your study can provide new insights into the chronology and tempo of adaptation. In the practical session we estimate the PC weightings of each SNP at a known adaptive region from a PCA of modern samples. We will then use Bamscorer to screen our ancient sample and to assign it to a PC cluster, where the clusters are associated with haplotypes adapted to two different environments.

We will finish with a review of what we have covered during the week and there will be time throughout the course for Q&A.





Should you have any further questions, please send an email to

Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.