People of Baldauf Lab


Sandra L. Baldauf

Professor and Head of Program

I have been studying molecular evolution and phylogeny since 1985, and received my PhD from the University of Michigan in 1990 (Nature 1990, PNAS 1990, PNAS 1993). I continued to study deep phylogeny of eukaryotes and molecular evolution as a postdoc in Nova Scotia (PNAS 1996, PNAS 1997, Science 2000), and later as lecturer and then professor of Bioinformatics at the University of York (UK). My research focus is a combination of molecular phylogeny, patterns of protein sequence evolution, and systematics of major understudied orphan taxa such as Dictyostelia (Science 2006, with P Schaap) and Choanoflagellata (PNAS 2008, with B Leadbeater). I moved to Uppsala University in 2007 to head the program in systematic biology.


Sanea Sheikh

My PhD project focuses on the annotation of the genome of Acrasis kona. I am interested in the identification and analyses of genes, proteins, metabolic pathways and gene expression patterns in Acrasis kona genome in order to define the nature of the last common ancestor of eukaryotes, how features unique to eukaryotes have evolved, how some proteins are different over the branches of eukaryotic tree and how cells communicate and cooperate to form multicellular structures.


Cheng-Jie Fu

Single-celled eukaryotes (protists) account for most of eukaryotic diversity, in terms of numbers of cells, numbers of major taxa and depth of evolutionary history. My major research interests are to investigate the origin of fundamental and unique eukaryotic traits using cultured and non-cultured experimental models. This includes developing culture methods for non-model organisms for DNA/RNA/protein extraction and sequencing. These data are then used to investigate evolutionary patterns using a combination of bioinformatics and laboratory experimentation.  My current research projects are: 1) genomics of Acrasis kona, in order to understand the origins of aggregative multicellularity and the extent and directionality of illegitimate genetic exchange between soil microbes. 2) the role of endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT) in shaping mitochondrial proteomes.

Former Members

Ding He 

The mitochondrion is universal among eukaryotes, yet in some ways it is also one of the most divergent cellular units. I am interested in molecular evolution of ancient eukaryotic proteins, especially those involved in mitochondrial function. I am also interested in deep eukaryote phylogeny using phylogenomic approaches with evolutionarily conserved genetic markers and to investigate possible sources of phylogenetic artifact. In the conjunction of these two interests, I have used mitochondrial proteins to test the root of the eukaryote tree, in the process identifying some unexpected patterns of molecular evolution. One of my current projects is to investigate anomalous evolutionary patterns of mitochondrial genes in jakobids, a group of protists with strikingly ancestral-like mitochondrial genomes.