Molecular and Cellular Evolution of Microbial Eukaryotes

Dr. Simon R. Harris

Contact information

  • Phone number:
  • e-mail adress: sh16 (at)

Work description


The general morphology of turtles, showing the high level of similarity between Triassic and modern forms. (A) The oldest known turtle, Proganochelys quenstedti, from the Upper Triassic of Germany. (B) The extant turtle, Emys orbicularis (the European pond turtle). Figure modified from Gaffney (1990).
I completed my joint honours undergraduate degree in Biology and Geology at the University of Bristol in 2001. After graduation I began work on a NERC funded PhD, entitled "Character construction in morphological phylogenetics and the affinities of turtles" [PDF] (9.5MB), again at the University of Bristol, under the supervision of Professor Michael Benton. I was co-supervised by Dr Mark Wilkinson and Dr David Gower at the Natural History Museum, London, where I spent one year of my PhD. My research centered around issues involved in the production of characters for use in phylogenetic analysis of morpohological data, especially in relation to fossil taxa where no molecular evidence is available. I also looked into the use of alternatives to the generally used phylogenetics methods in attempting to resolve debates which appear to have reached a stalemate due to differing interpretations of morphology. As a case study I worked on the well-known debate over the phylogenetic position of turtles within Amniota.The controversy appears to stem from the highly divergent morphology of the group, and the lack of intermediate forms. The earliest known turtle, Proganochelys quenstedti Baur, 1887, possesses a derived turtle morphology, extremely similar to extant forms. This makes assessments of homology with potentially close relatives in the fossil record difficult and, to judge from the abundance of alternative interpretations in the literature, open to subjectivity and disagreement. My research showed that resolving the disagreement between authors is not the key to identification of the true position of turtles, and that the 98% of characters over whose scoring opposing authors agree contain multiple, incompatible phylogenetic signals. Resolution of the debate is likely to require new fossil discoveries or more comprehensive molecular-based phylogenetic studies. I wrote COMPASS (Compatibility Analysis Site Stripping), a compatibility boildown program for identifying fast evolving sites in an alignment during my PhD. It is available along with some supplementary information from our downloads page. I graduated in October of 2004 and moved to Newcastle in 2005.

Current Work

The origin of Eukaryotes is one of the most fundamental questions in biology. Depending on this origin, the mitochondrial endosymbiont was either one of the founding partners of the first eukaryote or was acquired subsequently by a cell with a nucleus. Whichever is true, the eukaryotic proteome should be a chimera, comprising genes from both contributing prokaryotes, but the alternative theories differ in the identities of these founding partners.

It is widely accepted that the mitochondrion is derived from an alpha-proteobacterium, based on the fact that phylogenetic analyses of genes of the mitochondrial genome usually branch with this group of prokaryotes. However, the genome of the organelle has become highly reduced, with many genes being lost to the host nucleus. How many, and what types of genes in eukaryotic genomes arise from the mitochondrial endosymbiont is currently unknown, with estimates ranging from 391 to 630 depending on selection criteria.

My research includes application of semi-automated, genome-wide analyses to construct phylogenetic trees for all of the proteins on contemporary alpha-proteobacterial genomes in an attempt to identify genes in eukaryotic genomes that are derived from the mitochondrial endosymbiont. An important part of the research is to establish the limits of what we can infer from the available genomes using the best phylogenetic methods at our disposal.

The research will also concentrate on recently identified mitochondrial homologues in anaerobic and parasitic protists that lack oxidative phosphorylation. Such evidence shows that the mitochondrial homologue is not simply retained for the purpose of oxidative phosphorylation, and along with Cedric Simillion, I will be attempting to identify what, if any, functions are fundamental to the mitochondrial homologues and hope to produce a core mitochondrial homologue proteome.

Simon has now moved to the Wellcome Trust Sanger Institute to work on the evolution of pathogens, his new contact details are:

Dr. Simon R Harris

Pathogen Sequencing Unit

Wellcome Trust Sanger Institute

Genome Campus

Hinxton CB10 1SA

Simon's publications

  • Heinz E, Williams TA, Nakjang S, Noel CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Bernhardt J, Dagan T, Hacker C, Lucocq JM, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM. The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution. PLoS Pathog. vol 8 p. e1002979 (2012). pubmed
  • Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci USA. vol 105 p. 20356-61 (2008). pubmed
  • Smid O, Matuskova A, Harris SR, Kucera T, Novotny M, Horvathova L, Hrdy I, Kutejova E, Hirt RP, Embley TM, Janata J, Tacheyy J. Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis.. PLoS Pathog.. vol 4 p. e1000243 (2008). pubmed
  • Harris SR, Pisani D, Gower DG and Wilkinson M. Investigating stagnation in morphological phylogenetics using consensus data. Systematic Biology. vol 56 p. 125-9 (2007). pubmed
  • Pisani D, Mohun SM, Harris SR, McInerney JO and Wilkinson M. Molecular evidence for dim-light vision in the last common ancestor of the vertebrates. Current Biology. vol 16 p. R318-9 (2006). pubmed
  • Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D and Thorley JL. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol. vol 54 p. 419-31 (2005). pubmed
  • Harris SR, Gower DJ and Wilkinson M. Phylogenetic methods and aetosaur interrelationships: a rejoinder. Syst Biol. vol 52 p. 851-2 (2003). pubmed
  • Harris SR, Gower DJ and Wilkinson M. Intraorganismal homology, character construction, and the phylogeny of aetosaurian archosaurs (reptilia, diapsida). Syst Biol. vol 52 p. 239-52 (2003). pubmed
  • Harris SR, Wilkinson M and Gower DJ. Countering concerted homoplasy. Cladistics. vol 19 p. 128-30 (2003).