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This is the OLD website: the NEW web site is at Please go there for information about the 2020 Workshop.

Taken on Tuesday 6 Aug 2019

Above: Group Photo from 2019 (key, mouse-over to see names). Photos from previous years: 2012, 2013, 2014, 2015, 2016, 2017, 2018

Workshop Values and Ethics (please read)

MBL Course Page (to apply)

How to prepare for the Workshop on Molecular Evolution

Co-director: Paul Lewis (University of Connecticut) Co-director: Peter Beerli (Florida State University)


Please click on the link above to go to the new web site. The one you are currently looking at is obsolete and may have incorrect information.

Course Dates: THE COURSE HAS BEEN CANCELED FOR 2020 because of the Coronavirus; we anticipate to run the course in 2021.

Applications: (not open yet).

Course Facebook Page




Course Description

MBL’s Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology. The workshop also welcomes participants from federal agencies and science journalists. A priority of this workshop is to foster an environment where students can learn from each other as well from the course faculty.

Content has been carefully selected to provide participants with the background and practical skills required by modern molecular datasets. The schedule addresses the following subject areas, with each subject having one or more exercises focused on practical data analysis and interpretation skills.

  • An evolutionary perspective on molecular data: protein sequence versus protein structure; homology, orthology and parology; multiple sequence alignment; information resources
  • Foundations of phylogenetic analysis: theoretical, mathematical, and statistical principles; sampling properties of sequence data; Maximum likelihood theory and practice; Bayesian analysis; hypothesis testing
  • Species-level phylogenomics: species trees from gene trees; species delimitation; multi locus and SNP data; empirical examples
  • Deep phylogenomics: deep evolutionary relationships; lateral gene transfer; modeling approaches; topology testing; sequencing strategies
  • Foundations of population genetic analysis: neutral theory; coalescence theory; maximum likelihood and Bayesian estimation of population genetic parameters; empirical examples
  • Population genomics: phylogeography; molecular ecology; next-generation population genetics; signatures of natural selection; natural populations of non-model organisms
  • Comparative genomics: genome content; genome structure; gene and genome evolutionary dynamics; prediction of gene function
  • Molecular evolution integrated at organism and higher levels: population biology and ecology; natural selection; systematics and conservation
  • Molecular evolution integrated at lower levels: biochemistry; cell biology; physiology; natural selection; relationship of genotype to phenotype

As the course progresses, participants learn how to use the following software to address questions concerning the origins, maintenance, and function of molecular variation: PAUP*, IQTree, SVD Quartets, ASTRAL, SNaQ, RevBayes, MIGRATE, PAML, and other tools for data preparation and interpreting results. Students will work with software on their own laptops and learn how to run analyses on a high-performance computer cluster. Training in programming with specific examples in phylogenetics is provided too.

Recent changes

  • Connection to the wiki is now encrypted (https). Depending on your browser you may be asked to accept an untrusted certificate. It is OK to say yes to this. If you're reading this you've probably figured this out.
  • All students now have editing rights on the wiki! Most of the existing pages are still protected, but you can create and edit new pages, and add to some pages like Resources and Participants.
  • Navigation Menu customized to be more useful (thanks Peter)

Schedule Faculty Participants Software Resources