Dr Peter Foster

Biography

Employment history

• 1999-present   Molecular Biology Computing Officer, NHM
• 1997-1999 Molecular Systematics Fellow, Laboratory of Molecular Systematics, National Museum of Natural History, Smithsonian Institution

Qualifications 

• 1997  PhD,  University of Ottawa

Research

I have a long-standing interest in phylogenetic methods, especially
in the problems of data heterogeneity in phylogenetic analysis. This
includes the development of better models to accommodate heterogeneous
data, and also the development of statistical tests for model choice
and model adequacy. These new models and methods are implemented in
my p4, a freely available software toolkit. Another thread of my
research is in phylogenomics. I was co-Investigator on the BBSRC
funded project, "Expressed sequence tags for molecular systematics'',
that looked into the feasibility of using ESTs for molecular
systematics. I was part of the analysis team for the
Entamoeba histolytica and Trichomonas vaginalis genome
projects, showing the extent of horizontal gene transfer from bacteria
to these protists.

I have recently led a BBSRC-funded study, with Cymon Cox,Martin
Embley, and Robert Hirt, to use the best available phylogenetic
methods to assess the support for different hypotheses of the origin
of eukaryotes. This phylogenomic study has led to the surprising
result that when better phylogenetic methods are used, support for the
iconic 3-domain Tree of Life disappears, and strong support is given
to the eocyte hypothesis, where eukaryotes are sister taxa to the
Crenarchaeota. More recently I have been working with Mark Wilkinson
and Tobias Hill at the NHM on the implementation and testing of fast supertree
methods, and has been awarded a BBSRC grant to pursue this.

Publications

Foster, PG, Cox, CJ, and Embley, TM (2009) The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil Trans Roy Soc B. 364: 2197–2207.

Richards, T.A., Soanes, D.M., Foster, P.G., Leonard, G., Thornton, C.R., and Talbot, N.J. 2009. Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. Plant Cell 21: 1897–1911.

de Souza, R.P., Foster, P.G., Sallum, M.A.M., Coimbra, T.L.M., Maeda, A.Y., Silveira, V.R., Moreno, E.S., da Silva, F.G., Rocco, I.M., Ferreira, I.B., Suzuki, A., Oshiro, F.M., Petrella, S.M.C.N., Pereira, L.E., Katz, G., Tengan, C.H., Siciliano, M.M., and dos Santos, C.L.S. (2009) Detection of a new Yellow Fever Virus lineage within the South American genotype I in Brazil. J. Med. Virol. In press.

Alsmark, U. C. M., Sicheritz-Ponten, T., Foster, P.G., Hirt, R. P., and Embley, T. M. (2009) Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. in Horizontal gene transfer: Genomes in flux edited by P.Gogarten and M.Gogarten. Springer.

Cox, C.J., Foster, P.G., Hirt, R.P., Harris, S.R., and Embley, T.M. (2008) The archaebacterial origin of eukaryotes. Proc. Nat. Acad. Sci. USA. 105:20356–20361.

Santos, C.L.S., Ishida, M.A., Foster, P.G., Sallum, M.A.M., Benega, M.A., Borges, D.B., Correa, K.O., Constantino, C.R.O., M. A. Afzal, M.A., Paiva, T.M. (2008). Detection of a new mumps virus genotype during parotitis epidemic of 2006-2007 in the state of Sao Paulo, Brazil. J. Med. Virol. 80:323–329

Clark, C.G., Alsmark, U.C.M., Hofer, M., Saito-Nakano, Y., Ali, V., Marion, S., Weber, C., Mukherjee, C., Bruchhaus, I., Tannich, E., Leippe, M., Sicheritz-Ponten, T., Foster, P.G., Samuelson, J., Noel, C.J., Hirt, R.P., Embley, T.M., Gilchrist, C.A., Mann, B.J., Singh, U., Ackers, J.P., Bhattacharya, S., Bhattacharya, A., Lohia, A., Guillen, N., Duchene, M., Nozaki, T., and Hall, N. (2007). Structure and content of the Entamoeba histolytica genome. Advances In Parasitology 65:1–358.

Foster, P.G. (2007) Inferring phylogenetic relationships from sequence data. in Dear, P. Bioinformatics: Methods Express. Scion, Bloxham, Oxfordshire.

Pearson, T., U'Ren, J.M., Schupp, J.M., Allan, G.J., \foster, P.G., Mayo, M.J., Gal, D., Choy, J.L., Daugherty, R.L., Kachur, S., Friedman, C.L.C., Leadem, B., Georgia, S., Hornstra, H., Vogler, A.J., Wagner, D.M., Keim, P., and Currie, B.J. (2007). VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution 7:416–423.

Longhorn, S.J., Foster, P.G., and Vogler, A.P. (2007) The nematode-arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases. Cladistics 23:130-144.

Wilkinson M, McInerney J.O., Hirt R.P., Foster, P.G., Embley T.M. (2007) Of clades and clans: terms for phylo- genetic relationships in unrooted trees. Trends Ecol. Evol. 22:114-5.

Carlton, J.M., Hirt, R.P., Silva, J.C., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark. U.C.M., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van de Peer, Y., Miranda-Saavedra, D., Barton, G.J., Westrop, G.D., Muller, S., Dessi, D., Fiori, P.L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F.D., Simoes-Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, R., Smith, A.J., Vanacova, S., Villalvazo, M., Haas, B.J., Pertea, M., Feldblyum, T.V., Utterback, T.R., Shu, C.-L., Osoegawa, K., de Jong, P.J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S.-B., Logsdon, J.M., Jr., Henze, K., Gupta, A., Wang, C.C., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tang, P., Chiu, C.-H., Lee, Y.-S., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., and Johnson, P.J. (2007). Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis Science 315: 207-212.

Sallum, M.A.M., Foster, P.G., Li, C., Sithiprasasna, R., Wilkerson, R.C. (2007). Phylogeny of the Leucosphyrus Group of Anopheles (Cellia) (Diptera: Culicidae) based on Mitochondrial Gene Sequences. Ann. Entomol. Soc. Am. 100: 27–35.

Richards, T.A., Dacks, J.B., Campbell, S.A., Blanchard, J.L., Foster, P.G., McLeod, R., and Roberts, C.W. (2006). Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer and endosymboitic replacements. Eukaryotic Cell 5:1517–1531

Andersson, J.O., Hirt, R.P., Foster, P.G., and Roger, A.J. (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evolutionary Biology 2006, 6:27

Hughes, J., Longhorn, S.J., Papadopoulou, A., Theodorides, K., de Riva, A., Mejia-Chang, M., Foster, P.G., and Vogler, A.P. (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol. Biol. Evol. 23: 268–278.

Wilkerson, R.C., Foster, P.G., Li, C., and Sallum, M.A.M. (2005). Molecular Phylogeny of Neotropical Anopheles (Nyssorhynchus) albitarsis Species Complex (Diptera: Culicidae). Ann. Entomol. Soc. Am. 98(6): 918–925.

Hampl, V., Horner, D. S., Dyal, P., Kulda, J., Flegr, J., Foster, P.G., and Embley T.M. (2005) Inference of the phylogenetic position of oxymonads based on 9 genes: Support for monophyly of Metamonada and Excavata. Mol. Biol. Evol. 22: 2508 - 2518.

Loftus, B., Anderson, I., Davies, R., Alsmark, C. M., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R. P., Mann, B. J., Nozaki, T., Suh, B., Pop, M., Duchene, M., Ackers, J., Tannich, E., Leippe, M., Hofer, M., Bruchhaus, I., Willhoeft, U., Bhattacharya, A., Chillingworth, T., Churcher, C., Hance, Z., Harris, B., Harris, D., Jagels, K., Moule, S., Mungall, K., Ormond, D., Squares, R., Whitehead, S., Quail, M. A., Rabbinowitsch, E., Norbertczak, H., Price, C., Wang, Z., Guilln, N., Gilchrist, C., Stroup, S. E., Bhattacharya, S., Lohia, A., Foster, P. G., Sicheritz-Ponten, T., Weber, C., Singh, U., Mukherjee, C., El-Sayed, N. M., Petri, W. A. Jnr., Clark, C. G., Embley, T. M., Barrell, B., Fraser, C. M., Hall, N. (2005) The genome of the protist parasite Entamoeba histolyica. Nature 433: 865–868.

Hrdy, I., Hirt, R.P., Dolezal, P., Bardonov, L., Foster, P.G., Tachezy J., and Embley, T.M. (2004) Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 434: 29–31. Discussed in “News and Views” MW Gray (2005) The hydrogenosome’s murky past. Nature 434: 29-31.

Foster, P.G. (2004) Modeling compositional heterogeneity. Syst Biol 53, 485–495.

Santos, C.L., Sallum, M.A., Foster, P.G., Rocco, I.M. (2004) Molecular analysis of the dengue virus type 1 and 2 in Brazil based on sequences of the genomic envelope-nonstructural protein 1 junction region. Rev Inst Med Trop Sao Paulo 46(3):145-52.

Walker, G., Silberman, J.D., Karpov, S.A., Preisfeld, A., Foster, P., Frolov, A.O., Novozhilov, Y., and Sogin, M. (2003) An ultrastructural and molecular study of Hyperamoeba dachnaya, n. sp., and its relationship to the mycetozoan slime moulds. Eur J Protistol 39:319–336.

Embley, T.M., Van Der Giezen, M., Horner, D.S., Dyal, P.L., Bell, S., and Foster, P.G. (2003) Hydrogenosomes, mitochondria, and early eukaryotic evolution. IUBMB Life 55:387–395.

Embley, T.M., Van Der Giezen, M., Horner, D.S., Dyal, P.L., and Foster, P. (2003) Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Phil. Trans. R. Soc. Lond. B 358:191–203

Theodorides, K., De Riva, A., Gomez-Zurita, J., Foster, P.G., and Vogler, A.P. (2002) Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Mol. Biol 11(5):467–475

Wilkinson, M., Peres-Neto, P.R., Foster, P.G., Moncrieff, C.B. (2002) Type I error rates of the parsimony PTP test. Syst Biol 51(3):524–527

Sallum, M.A.M., Schultz, T.R., Foster, P.G., Aronstein, K., Wirtz, R.A., Wilkerson, R.C. (2002) Phylogeny of Anophelinae (Diptera: Culicidae) based on nuclear ribosomal and mitochondrial DNA sequences. Syst Entomol 27(3):361–382

Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., Rogers, J.S. (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 50(4): 525-539

Horner, D.S., Foster, P.G., and Embley, T.M. (2000) Iron [Fe] hydrogenases and the evolution of anaerobic eukaryotes. Mol Biol Evol 17(11): 1695-709

Foster, P.G., and Hickey, D.A. (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48: 284-290

Foster, P.G., Jermiin, L.S., and Hickey, D.A. (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44: 282-288

Jermiin, L.S., Foster, P.G., Graur, D., Lowe, R.M., and Crozier, R.H. (1996) Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA. J Mol Evol 42: 476-480