Forskningsområde - endast på engelska

Early evolutionary patterns identify fundamental principles in biology. One of those most fundamental of these patterns is the identity of the major groups of eukaryotes and the relationships among them, most important of which is the root of the eukaryote tree of life. Accurately recovering these relationships requires broadly sampling the diversity of living organisms. Molecular methods such as whole transcriptome sequencing (RNAseq) from orphan taxa makes it possible to begin filling in the vast unpopulated regions of the tree of tree of life. We are particularly focused on two major taxa that have been traditionally under-sampled, the Amoebozoa and Excavata. This includes genomics and transcriptomics of the only multicellular excavate, the acrasid slime molds. Below, specific aspects of our work are highlighted:

  • Deep phylogeny of eukaryotes
  • Evolutionary patterns in mitochondrial proteomes
  • Mechanisms of aggregative multicellularity in the acrasid amoebae


We have recently developed a novel set of eukaryotic proteins of recent bacterial ancestry. Our analyses of these data define a novel neozoan-excavate root for eukaryotes and show that similar data purported to test the eukaryote root are highly contaminated with horizontally transferred genes (HGT). We are now characterizing this HGT more fully and developing new data sets to further test the eukaryote root.

Deep Phylogeny of Eukaryotes

Selected publications:

  • He, D., Fiz-Palacios, O., Fu, C.-J., Fehling, J., Tsai, C.-C., & Baldauf, S. L. (2014). An Alternative Root for the Eukaryote Tree of Life. Current Biology, 24(4), 465–470.
  • Carr M, Leadbeater BSC, Hassan R, Nelson M and Baldauf SL (2008b) Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proc Natl Acad Sci USA 105: 16641-16646
  • Baldauf, S. L. (2003). The deep roots of eukaryotes. Science (New York, NY), 300(5626), 1703–1706.
  • Baldauf, S. L. (2000). A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data. Science, 290(5493), 972–977.


Aggregative multicellularity is a non-growth based developmental process whereby multi-cellular structures are built by the massive aggregation of formerly free-living cell (mostly amoebae). This process is well studied in the dictyostelids (formerly “cellular slime molds”). However, it is has evolved independently multiple times, including once in the Excavata, the least well characterized of the three major divisions of eukaryotes. We have sequenced and are now in the process of annotating the genome of one of these transiently multicellular excavates, Acrasis kona. This also represents only the second genome sequence from a free-living member of eukaryotic supra-kingdom Excavata.

Selected publications:

  • Sheikh, S., Gloeckner, G., Kuwayama, H., Schaap, P., Urushihara, H., Baldauf, S. (2015). The root of Dictyostelia based on 213 universal proteins. Molecular Phylogenetics and Evolution [in press].
  • Fu, C.-J., Sheikh, S., Miao, W., Andersson, S. G. E., & Baldauf, S. L. (2014). Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA. Genome Biology and Evolution, 6(9), 2240–57.
  • Romeralo, M., Cavender, J. C., Landolt, J. C., Stephenson, S. L., & Baldauf, S. L. (2011). An expanded phylogeny of social amoebas (Dictyostelia) shows increasing diversity and new morphological patterns. BMC Evolutionary Biology, 11(1), 84.
  • Schaap, P., Winckler, T., Nelson, M., Alvarez-Curto, E., Elgie, B., Hagiwara, H., … Baldauf, S. L. (2006). Molecular phylogeny and evolution of morphology in the social amoebas. Science (New York, N.Y.), 314(5799), 661–3.


Mitochondrial genome phylogeny gives strong evidence of an alpha- proteobacterial ancestry for mitochondria. However, nuclear-encoded mitochondrial genes show a mixed bacterial origin. This suggests that the nuclear-encoded portion of the mitochondrial proteome has a complex evolutionary history. We are trying to understand this better through characterizing the role of hortizontal gene transfer in mitochondrial proteome evolution. One group we are focusing on are the Jakobid excavates, which are unique among eukaryotes in possessing gene-rich bacterial-like mitochondrion genomes (mtDNAs). Our recent evidence suggests that these mtDNAs may not entirely reflect a primitive state.

Selected publications:

  • He et al. (MBE in review)
  • He, D., Fiz-Palacios, O., Fu, C.-J., Fehling, J., Tsai, C.-C., & Baldauf, S. L. (2014). An Alternative Root for the Eukaryote Tree of Life. Current Biology, 24(4), 465–470.