Stephan Schiffels

Population Genetics – Computational Methods - Human History


Many Blog posts also appear on my Medium Blog

  • newsAnnouncement: Summer school on History and Genetics
    March 20, 2024

    I am excited to announce our upcoming summer school “Bridging Archaeogenetics and Medieval Studies: Using aDNA as a source for migration, demographics, kinship and pathology” in Berlin and Leipzig in September 23-27, 2024.

    I’m co-organising the summer school with Historian Jörg Feuchter from the Berlin-Brandenburg Academy of Sciences, and several colleagues from the MPI-EVA are scheduled as speakers as well.

    We are seeking master students and senior PhD students from both science and humanities backgrounds to apply until April 30th.

    More information can be found on our website

  • blogXerxes's cutlery - enjoying your dinner?
    October 27, 2023

    This post was originally published on the Poseidon Blog

    Image credit by Unsplash

    So, you’ve ordered your food, now what?

    Often, we want to summarise the genetic data through summary statistics. Examples for such summary statistics are F-Statistics. Our tool xerxes fstats, which is part of the Poseidon ecosystem, provides a powerful and expressive tool to compute such summary statistics from genetic data described in Poseidon packages.

    ... Read more

  • blogTrident's restaurant - your order please?
    October 4, 2023

    This post was originally published on the Poseidon Blog

    Image credit by Unsplash

    Today we’re releasing a new major release for trident, our command-line tool and workhorse for working with Poseidon packages.

    If you haven’t checked it out yet, take a look at our documentation. With trident, you can download packages from our web-server, initialise new packages, perform validations, list summaries of packages, and - most importantly - forge new packages out of existing ones. This functionality, forge is more than a merge, and more than a subset tool. It is both. Perhaps a working analogy for what it does is a restaurant. At a restaurant, you order a specific meal, but you don’t care how the ingredients have been packaged, and with which other ingredients they are stored. You just want the chefs to assmble the meal, no matter whether the beans are stored together with the peas or not.

    ... Read more

  • newsTwo Podcast episodes recorded in German
    September 29, 2023

    I recorded two Podcast episodes (in German) in Luca Beutel’s fabulous Show “Inspirierend anders”.

    First Episode: Apple Podcasts, Google Podcasts and Spotify.

    Second Episode: Apple Podcasts, Google Podcasts and Spotify.

    ... Read more

  • newsArticle in "The Conversation" by Victoria Gibbon on the Sutherland project
    July 14, 2023

    Victoria Gibbon from University of Cape Town wrote a nice article piece about our project on the Sutherland Nine, which we published earlier this year.

  • newsRecording of short talk available (in German)
    April 21, 2023

    On March 16, 2023, I participated in a panel discussion about the topic of “What is saxonian” in at the Deutsche Hygiene-Museum in Dresden, Germany. There is now a short video available on Youtube.

  • newsCurrent Archaeology Project of the Year - Vote now!
    December 2, 2022

    We are honored for having been nominated as one of the projects that can be voted on as “Research Project of the Year 2023” in this year’s Current Archaology Awards”

    ... Read more

  • newsCurrent Archaeology Special Issue
    November 5, 2022

    Alongside our recent publication on early medieval ancient DNA from England, we are honored to having been invited to be featured in a Special Issue of the magazine “Current Archaeology”.

    ... Read more

  • blogDesigning Command Line Interfaces in Haskell
    March 24, 2021

    Command line tools are essential in many computational fields of science, not the least because command lines are often the only interface on a high-performance compute cluster or server. Particularly critical in command-line tools is a well-defined interface between the user and the program, the command line interface (CLI). A command line interface is like a contract. The user promises to provide input parameters in the right shape and type, and the tool promises to work with this input the way it is expected to. A breach of contract from the caller may result - at best - in a refusal of the program to run, and at worst in undefined behavior.

    ... Read more

  • newsDISQUS available on my webpage
    November 30, 2020

    I have finally gotten around to install DISQUS on my webpage’s blog posts. When you view my blog, you will now find below every post a section where you can comment and discuss with other users via DISQUS. DISQUS is an online tool that provides discussion forum-like capabilities to any webpage. It’s an awesome service that spares webpage authors the annoyance of having to provide a database and fully fledged backend usually required to provide user-management and forum-functionality.

    ... Read more

  • newsTwo talks from my group at Virtual EAA conference
    July 30, 2020

    Two PhD students from my group will present at this years 26th Annual Meeting of the European Association of Archaeologists (EAA) from August 24-30.

    ... Read more

  • newsNew Video (in german) on TEDx talk
    February 18, 2020

    I gave a talk at the TEDxTHBrandenburg, which you can now enjoy on Youtube.

  • newsAddressing injustice with the science of human history
    December 10, 2019

    We are engaged in a one-of-a-kind project on the genetic analyses of the Sutherland Nine.

    ... Read more

  • blogBye bye Wordpress
    October 16, 2019

    I recently rebuilt my website. I had previously used Wordpress, and while that was perfect to get started, I soon got annoyed by its relative inflexibility. While Wordpress has a huge community with tons of free templates for nicely designed websites, the templates themselves are often very opinionated in a sense that they encourage certain archetypes, like Blogging sites, or magazine-style sites. Customization is possible, but it comes in the form of plugins (again, thousands are available for free), and the more customization you want, the more plugins you end up using. This at some point makes the whole system a bit bloated, and still not quite right in the end.

    ... Read more

  • blogFunded ERC Grant MICROSCOPE
    September 23, 2019

    Stephan Schiffels’ project MICROSCOPE will investigate the pre-Roman European Iron Age with new genetic methods. The challenge in most periods of European prehistory since the Bronze Age is a high degree of genetic homogeneity among European populations. This is due to millennia of mixing and amalgamation of the originally diverse ancestry lines that make up Europeans today. In order to address this, a significant part of the project is devoted to the development of new statistical genomic methods, based on shared rare genetic variation, which will help investigating the subtle population dynamics needed to infer population movements in the past.

    ... Read more

  • blogTracking your time helps you stay mentally sane.
    August 29, 2019

    Working in academia comes with unique freedoms and challenges. I would argue that in no other job we have so much freedom to define our own work. At least at the Post-doctoral level and beyond, you mostly can choose what problems you want to work on, how to solve them, and in what pace. Even as a PhD student, in many cases there is a lot of freedom to choose projects and set your own goals and deadlines (this may not be the case for everybody, but it was for me).

    ... Read more

  • newsWebinar available as Youtube-Video
    June 11, 2019

    A Webinar that I gave to the Regional Student Group of Turkey is available on Youtube.

  • newsInterview on German Radio about Paleo-Eskimo paper (in German)
    June 7, 2019

    A brief interview with me on our newly published study on Paleo-Inuit genetic history of the North-Ameerican arctic appeared today on German television.

  • blogBehind the paper: Paleo-Eskimo ancestry in North America
    June 5, 2019

    This post appeared originally on the Nature Ecology & Evolution Community blog.


    In October 2015 — I had just started my new job as Group Leader at the newly founded Max Planck Institute for the Science of Human History in Jena, Germany — we were visited by a young researcher, Pavel Flegontov, from Ostrava University in Czech Republic. Pavel is a computational biologist who a few years ago got himself interested in human population genetics and prehistory. I was at the time about to publish our paper on Anglo-Saxon ancient DNA from England, for which we developed new methodology to investigate fine-scale population structure based on rare genetic variation. Pavel wanted to apply this new methodology to an open genetic question in the literature about Athabaskans, an ethnic group from North America. David Reich, a geneticist from Harvard University, had shown previously in a paper in 2012 that Athabaskans have a distinct ancestry component not shared with many other Native Americans and which could be related to Paleo-Eskimos.

    ... Read more

  • newsShort Radio appearance on ancestry testing (in German)
    April 12, 2019

    A short interview with me on genetic ancestry testing (in German) appeared on German radio today.

  • newsThree talks from my group at the upcoming EMBO/EMBL Symposium on Reconstructing the Human Past
    March 15, 2019

    I’m excited to announce that there are now three talks from my group at the upcoming EMBO | EMBL Symposium on Reconstructing the Human Past – Using Ancient and Modern Genomics. My students Ke Wang and Joscha Gretzinger both have their abstracts accepted for a talk at the symposium. Congratulations!

  • news16 open PhD positions at the MPI-SHH
    December 18, 2018

    (Cross-posting from the original ad at the MPI-SHH Webpage, offline now)

    The MPI-SHH pursues an integrative approach to the study of human history. “Hard” facts as bones, teeth, plants, stones and “soft” facts as languages, history, or religions can say a lot about human history. It is our task to understand and interpret them. The International Max Planck Research School for the Science of Human History (IMPRS-SHH) is seeking for researchers knowing well how to decode such facts and data and looking for new ways of decoding them. The IMPRS-SHH is a cooperation of the Max Planck Institute for the Science of Human History and Friedrich Schiller University, both situated in Jena, a traditional as well as a modern university town in the heart of Germany. The IMPRS-SHH is offering 16 PhD positions for 14 projects.

    ... Read more

  • blogUnd nun die Wahlvorhersage...
    August 12, 2017

    Vorhersagen von Wahlergebnissen aufgrund von Umfragen gehören zum Standardgeschäft des politischen Betriebes. Etwa wöchentlich veröffentlichen die großen Fernsehsender Umfragen, zum Beispiel zur sogenannten “Sonntagsfrage”: “Wenn am nächsten Sonntag Bundestagswahl wäre, wen würden Sie wählen?”

    ... Read more

  • blogHypothesis testing without Alternatives
    June 9, 2017

    So, I am reading this book called “Probability Theory; The logic of Science” by E.T. Jaynes. It is an excellent read, highly recommended, and quite an eye-opener to me in terms of understanding statistics and data analysis from first principles. Here I am sharing a few particularly interesting insights from chapter 9.11 (“Significance Tests”, p. 293).

    ... Read more

  • blogHow rare genetic mutations help us understand human history (Part II)
    May 24, 2017

    In my last blog post I have shown how we estimated the Anglo-Saxon genetic contribution to modern English from rare variants. Here I’ll show more generally how we can use rare genetic variants to learn more details about population history.

    ... Read more

  • blogHow rare genetic mutations help us understand human history (Part I)
    January 22, 2016

    Human history is deeply imprinted in our genomes, through patterns of common ancestry. These patterns can be studied by looking at mutations that are shared between people living in different times in different places. In this post I will summarize our recent genetic study on Anglo-Saxon immigration history in Britain, and in doing so,will describe some new methodology that we have developed for this project, which is based on rare mutations.

    ... Read more

  • blogA brief introduction to neutral theory
    January 6, 2016

    This is a response to this creationist’s post on Human evolution, in which I found so many flaws that I have to at least correct the most obvious factual errors for general readers. At the same time, this may serve as a quick primer into neutral theory.

    ... Read more