Fabien Burki

Fabien Burki
Uppsala University

Research interests

biodiversity informatics
We aim to integrate the poorly studied protists (i.e. microbial eukaryotes) in global evolutionary models. Protists have dominated eukaryotic life since the origin of complex cellular structures, but very few species are in culture and so they have mostly remained enigmatic. As a result, we only have a very partial view of the broad eukaryotic diversity, which prevents us to derive an accurate picture of the origin and evolution of the cells that ultimately resulted in the diversity we can observe today. In my group, we explore the microbial dark matter to bridge gaps in our understanding of the deep eukaryote evolution. Our main questions relate to some of the most transformative lifestyle transitions in the evolution of complex life, such as the origin and spread of plastids or transition to parasitism. All of these lifestyle transitions have occurred repeatedly across the tree, but because we are missing key evolutionary lineages our understanding is patchy.

We use a combination of novel culture-independent genomics, transcriptomics, environmental DNA (eDNA) approaches but also more traditional protistology to identify unknown or orphan groups that represent missing evolutionary links. We attack the problem of partial sampling from two highly complementary angles: 1) phylogenomics, a gene-rich but taxon-limited method that allows to reconstruct the deep nodes in the tree of eukaryotes; 2) long-amplicon metabarcoding, a gene-poor but taxon-rich new method we are developing to phylogenetically and taxonomically resolve eDNA samples. Together, we hope that these approaches will produce a much more accurate representation of eukaryote evolution so that we can better reconstruct the history of life and the ancestral characteristics of the major eukaryotic groups.

More info on my group’s website.

Group members

Fabien Burki (PI)
Mahwash Jamy (PhD student)
Anders Alfjorden (PhD student)
Vasily Zlatogursky (postdoc)
Ioana Brännström (postdoc)

Key publications

Bass D, Ward GM, Burki F. 2019. Ascetosporea. Curr. Biol. In press

Whelan S, Irisarri I, Burki F. 2018. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics. 34(22):3929-3930.

Strassert JFH, Jamy M, Mylnikov AP, Tikhonenkov DV, Burki F. 2018. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life. bioRxiv.

Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Rohwer FL, Mylnikov AP, Keeling PJ. 2017. A new Lineage of Eukaryotes Illuminates Eraly Mitochondrial Genome Reduction. Curr. Biol. 27(23):3717-3724​.

Burki F. 2017. The Convoluted Evolution of Eukaryotes With Complex Plastids. Advances in Botanical Research. 84:1-30.

Burki F. 2016. Mitochondrial Evolution: Going, Going, Gone. Curr. Biol. 26(10):R410-412.

Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ. 2016. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc. R. Soc. B. 283:20152802.