Dr Peter Foster

Dr Peter Foster

Researcher, Molecular Biology Computing Officer

Department: Life Sciences
Division: LS Diversity and Informatics Division
Phone: 020 7942 5438

Summary

I am interested in model-based methods of phylogenetic analysis --- statistical approaches to making the family tree of life --- using DNA and protein sequences. I have developed models of evolution that can accommodate changes in the process of evolution over time. Together with my colleagues Martin Embley, Cymon Cox, Tom Williams, and others, we have tested the iconic Woese three-domains tree of life using these models, which showed the surprising result that if these better models of evolution are used on the same data more support is given to the eocyte hypothesis with an origin of the eukaryotes from within the Archaea. This change in the overall shape of the tree of life has become accepted over the last decade. I have written about these methods and the Tree of Life work mentioned above, some phylogenetic commentary, on eukaryotic microbial genomics and horizontal gene transfer, several genomics projects, and Anopheles systematics in collaboration with Anice Sallum. I continue to develop a phylogenetics toolkit that implements these models, but also can be used for tree interrogation, and is a general phylogenomics toolkit that has been used in genomics pipelines to show the extent of horizontal gene transfer in eukaryotic microbes. My work on supertrees with Mark Wilkinson at the NHM has led to a maximum likelihood implementation and to my knowledge the first Bayesian implementation of supertree construction. My more recent projects have dealt with mitochondrial genome assembly and analysis, and on competition between prokaryotic and eukaryotic carbon-fixers in mid-oceanic gyres.

Qualifications

Degrees

PhD Biology, University of Ottawa, Canada, 1995 - 1997

Grants

How do eukaryotic CO2 fixers co-exist with faster growing prokaryotic CO2 fixers in the oligotrophic ocean covering 40% of Earth?
Role: Principal investigatorFoster P
Funding: NERC
Total value £135,142 (to Museum £135,142)
Dates: 2015 - 2018

Fast Supertree Construction Using Quartet Joining
Role: Principal investigatorFoster P
Co-investigator: Wilkinson M
Funding: BBSRC
Total value £121,618 (to Museum £121,618)
Dates: 2009 - 2010

Other projects

Molluscan deep-sea diversity
Role: Member
Funding: Museum development

Publications

Williams ST, Foster PG, Hughes C, Harper EM, Taylor JD, Littlewood DTJ, Dyal P, Hopkins KP, Briscoe AG (2017) Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes. Molecular Phylogenetics and Evolution, 110 : 60 - 72. doi: 10.1016/j.ympev.2017.03.004

Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, San MauroD, Day JJ, Littlewood DTJ, Foster PG, Nussbaum RA, Gower DJ (2016) Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. PLOS ONE, 11 (6) : e0156757 - e0156757. doi: 10.1371/journal.pone.0156757

Timmermans MJTN, Barton C, Haran J, Ahrens D, Culverwell CL, Ollikainen A, Dodsworth S, Foster PG, Bocak L, Vogler AP (2016) Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics. Genome Biology and Evolution, 8 (1) : 161 - 175. doi: 10.1093/gbe/evv241

Demari-silva B, Foster PG, De OliveiraTMP, Bergo ES, Sanabani SS, Pessôa R, Sallum MAM (2015) Mitochondrial genomes and comparative analyses of Culex camposi, Culex coronator, Culex usquatus and Culex usquatissimus (Diptera:Culicidae), members of the coronator group. BMC Genomics, 16 (1) : doi: 10.1186/s12864-015-1951-0

Akanni WA, Siu-ting K, Creevey CJ, Mcinerney JO, Wilkinson M, Foster PG, Pisani D (2015) Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis. Philosophical Transactions of the Royal Society B: Biological Sciences, 370 (1678) : 20140337 - 20140337. doi: 10.1098/rstb.2014.0337

Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D (2015) Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. Royal Society Open Science, 2 (8) : 140436 - 140436. doi: 10.1098/rsos.140436

Jabbar A, Littlewood DTJ, Mohandas N, Briscoe AG, Foster PG, Müller F, Von Samson-HimmelstjernaG, Jex AR, Gasser RB (2014) The mitochondrial genome of Parascaris univalens - implications for a “forgotten” parasite. Parasites & Vectors, 7 (1) : 428 - 428. doi: 10.1186/1756-3305-7-428

Li B, Lopes JS, Foster PG, Embley TM, Cox CJ (2014) Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins. Molecular Biology and Evolution, 31 (7) : 1697 - 1709. doi: 10.1093/molbev/msu105

Lewis CJ, Maddock ST, Day JJ, Nussbaum RA, Morel C, Wilkinson M, Foster PG, Gower DJ (2014) Development of anonymous nuclear markers from Illumina paired-end data for Seychelles caecilian amphibians (Gymnophiona: Indotyphlidae). Conservation Genetics Resources, 6 (2) : 289 - 291. doi: 10.1007/s12686-013-0127-y

Lloyd RE, Streeter SD, Foster PG, Littlewood DTJ, Huntley J, Beckham GT, Himmel ME, Cragg SM (2015) The complete mitochondrial genome of Limnoria quadripunctata Holthuis (Isopoda: Limnoriidae). Mitochondrial DNA, 26 (6) : 825 - 826. doi: 10.3109/19401736.2013.855912

Cox CJ, Li B, Foster PG, Embley TM, Civan P (2014) Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions. Systematic Biology, 63 (2) : 272 - 279. doi: 10.1093/sysbio/syt109

Williams ST, Foster PG, Littlewood DTJ (2014) The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene, 533 (1) : 38 - 47. doi: 10.1016/j.gene.2013.10.005

Civáň P, Foster PG, Embley MT, Séneca A, Cox CJ (2014) Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants. Genome Biology and Evolution, 6 (4) : 897 - 911. doi: 10.1093/gbe/evu061

Baselga A, Fujisawa T, Crampton-platt A, Bergsten J, Foster PG, Monaghan MT, Vogler AP (2013) Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels. Nature Communications, 4 : doi: 10.1038/ncomms2881

Alsmark C, Foster PG, Sicheritz-ponten T, Nakjang S, Martin EmbleyT, Hirt RP (2013) Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology, 14 (2) : R19 - R19. doi: 10.1186/gb-2013-14-2-r19

Cox CJ, Foster PG (2013) A 20-state empirical amino-acid substitution model for green plant chloroplasts. Molecular Phylogenetics and Evolution, 68 (2) : 218 - 220. doi: 10.1016/j.ympev.2013.03.030

Foster PG, Bergo ES, Bourke BP, Oliveira TMP, Nagaki SS, Sant’ana DC, Sallum MAM (2013) Phylogenetic Analysis and DNA-based Species Confirmation in Anopheles (Nyssorhynchus). PLoS ONE, 8 (2) : e54063 - e54063. doi: 10.1371/journal.pone.0054063

Morgan CC, Foster PG, Webb AE, Pisani D, Mcinerney JO, O’connell MJ (2013) Heterogeneous Models Place the Root of the Placental Mammal Phylogeny. Molecular Biology and Evolution, 30 (9) : 2145 - 2156. doi: 10.1093/molbev/mst117

Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin EmbleyT (2013) Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics. Genome Biology and Evolution, 5 (12) : 2285 - 2303. doi: 10.1093/gbe/evt184

Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504 (7479) : 231 - 236. doi: 10.1038/nature12779

Lloyd RE, Foster PG, Guille M, Littlewood DTJ (2012) Next generation sequencing and comparative analyses of Xenopus mitogenomes. BMC Genomics, 13 (1) : 496 - 496. doi: 10.1186/1471-2164-13-496

Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM (2012) A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences, 279 (1749) : 4870 - 4879. doi: 10.1098/rspb.2012.1795

Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences, 108 (37) : 15258 - 15263. doi: 10.1073/pnas.1105100108

Bourke BP, Foster PG, Bergo ES, Calado DC, Sallum MAM (2010) Phylogenetic relationships among species of Anopheles (Nyssorhynchus) (Diptera, Culicidae) based on nuclear and mitochondrial gene sequences. Acta Tropica, 114 (2) : 88 - 96. doi: 10.1016/j.actatropica.2010.01.009

Mureb SallumMA, Foster PG, Dos SantosCLS, Flores DC, Motoki MT, Bergo ES (2010) Resurrection of Two Species From Synonymy of Anopheles (Nyssorhynchus) strodei Root, and Characterization of a Distinct Morphological Form From the Strodei Complex (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY, 47 (4) : 504 - 526.

Alsmark UCM, Sicheritz-ponten T, Foster PG, Hirt RP, Embley TM (2009) Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis, In: Horizontal gene transfer: Genomes in flux, Gogarten P, Gogarten M (Eds). Springer Inc. : New York. 500 pp..

De SouzaRP, Foster PG, Sallum MAM, Coimbra TLM, Maeda AY, Silveira VR, Moreno ES, Da SilvaFG, Rocco IM, Ferreira IB, Suzuki A, Oshiro FOM, Petrella SMCN, Pereira LE, Katz G, Tengan CH, Siciliano MM, Dos SantosCLLS (2010) Detection of a new yellow fever virus lineage within the South American genotype I in Brazil. Journal of Medical Virology, 82 (1) : 175 - 185. doi: 10.1002/jmv.21606

Foster PG, Cox CJ, Embley TM (2009) The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philosophical Transactions of the Royal Society B: Biological Sciences, 364 (1527) : 2197 - 2207. doi: 10.1098/rstb.2009.0034

Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ (2009) Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. THE PLANT CELL ONLINE, 21 (7) : 1897 - 1911. doi: 10.1105/tpc.109.065805

Santos CLS, Ishida MA, Foster PG, Sallum MAM, Benega MA, Borges DB, Corrêa KO, Constantino CRO, Afzal MA, Paiva TM (2008) Detection of a new mumps virus genotype during parotitis epidemic of 2006–2007 in the State of São Paulo, Brazil. Journal of Medical Virology, 80 (2) : 323 - 329. doi: 10.1002/jmv.21068

Calado DC, Foster PG, Bergo ES, Santos CLSD, Galardo AKR, Sallum MAM (2008) Resurrection of Anopheles goeldii from synonymy with Anopheles nuneztovari (Diptera, Culicidae) and a new record for Anopheles dunhami in the Brazilian Amazon. Memórias do Instituto Oswaldo Cruz, 103 (8) : 791 - 799. doi: 10.1590/S0074-02762008000800009

Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM (2008) The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences, 105 (51) : 20356 - 20361. doi: 10.1073/pnas.0810647105

Longhorn SJ, Foster PG, Vogler AP (2007) The nematode?arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases. Cladistics, 23 (2) : 130 - 144. doi: 10.1111/j.1096-0031.2006.00132.x

Wilkinson M, Mcinerney JO, Hirt RP, Foster PG, Embley TM (2007) Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends in Ecology & Evolution, 22 (3) : 114 - 115. doi: 10.1016/j.tree.2007.01.002

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UCM, Besteiro S, Sicheritz-ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van dePeerY, Miranda-saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-corcuera FD, Simoes-barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu C-L, Osoegawa K, De JongPJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik S-B, Logsdon JM, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu C-H, Lee Y-S, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-liggett CM, Johnson PJ (2007) Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. Science, 315 (5809) : 207 - 212. doi: 10.1126/science.1132894

Clark CG, Alsmark UCM, Tazreiter M, Saito-nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-ponten T, Foster PG, Samuelson J, Noel CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillen N, Duchene M, Nozaki T, Hall N (2007) Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY, VOL 65, 65 : 51 - 190. doi: 10.1016/S0065-308X(07)65002-7

Foster PG (2007) Inferring phylogenetic relationships from sequence data.

Pearson T, U’ren JM, Schupp JM, Allan GJ, Foster PG, Mayo MJ, Gal D, Choy JL, Daugherty RL, Kachur S, Friedman CLC, Leadem B, Georgia S, Hornstra H, Vogler AJ, Wagner DM, Keim P, Currie BJ (2007) VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution, 7 (4) : 416 - 423. doi: 10.1016/j.meegid.2006.12.002

Sallum MAM, Foster PG, Li C, Sithiprasasna R, Wilkerson RC (2007) Phylogeny of the Leucosphyrus Group of Anopheles (Cellia) (Diptera: Culicidae) Based on Mitochondrial Gene Sequences. Annals of the Entomological Society of America, 100 (1) : 27 - 35. doi: 10.1603/0013-8746(2007)100[27:POTLGO]2.0.CO;2

Wilkinson M, Mcinerney JO, Hirt RP, Foster P, Embley TM (2007) Of clades and clans: terms for relationships in unrooted trees. Trends in Ecology and Evolution, 22 : 114 - 115.

Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, De RivaA, Mejia-chang M, Foster PG, Vogler AP (2006) Dense Taxonomic EST Sampling and Its Applications for Molecular Systematics of the Coleoptera (Beetles). Molecular Biology and Evolution, 23 (2) : 268 - 278. doi: 10.1093/molbev/msj041

Andersson JO, Hirt RP, Foster PG, Roger AJ (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC EVOLUTIONARY BIOLOGY, 6 : doi: 10.1186/1471-2148/6/27

Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, Mcleod R, Roberts CW (2006) Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements. Eukaryotic Cell, 5 (9) : 1517 - 1531. doi: 10.1128/EC.00106-06

Hampl V, Horner DS, Dyal P, Kulda J, Flegr J, Foster PG, Embley TM (2005) Inference of the Phylogenetic Position of Oxymonads Based on Nine Genes: Support for Metamonada and Excavata. Molecular Biology and Evolution, 22 (12) : 2508 - 2518. doi: 10.1093/molbev/msi245

Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, 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 MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillén N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-ponten T, Weber C, Singh U, Mukherjee C, El-sayed NM, Petri WA, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N (2005) The genome of the protist parasite Entamoeba histolytica. Nature, 433 (7028) : 865 - 868. doi: 10.1038/nature03291

Wilkerson RC, Foster PG, Li C, Sallum MAM (2005) Molecular Phylogeny of Neotropical Anopheles (Nyssorhynchus) albitarsis Species Complex (Diptera: Culicidae). Annals of the Entomological Society of America., 98 : 918 - 925.

Foster PG, Schultz T (2004) Modeling Compositional Heterogeneity. Systematic Biology, 53 (3) : 485 - 495. doi: 10.1080/10635150490445779

Hrdy I, Hirt RP, Dolezal P, Bardonová L, Foster PG, Tachezy J, Martin EmbleyT (2004) Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature, 432 (7017) : 618 - 622. doi: 10.1038/nature03149

Santos CLS, Sallum MAM, Foster PG, Rocco IM (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. Revista do Instituto de Medicina Tropical de Sao Paulo, 46 : 145 - 152.

Embley TM, Van derGiezenM, Horner D, Dyal P, Bell S, Foster P (2003) Hydrogenosomes, Mitochondria and Early Eukaryotic Evolution. IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), 55 (7) : 387 - 395. doi: 10.1080/15216540310001592834

Theodorides K, De RivaA, Gomez-zurita J, Foster PG, Vogler AP (2002) Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Molecular Biology, 11 (5) : 467 - 475. doi: 10.1046/j.1365-2583.2002.00355.x

Wilkinson M, Peres-neto PR, Foster PG, Moncrieff CB, Sanderson M (2002) Type 1 Error Rates of the Parsimony Permutation Tail Probability Test. Systematic Biology, 51 (3) : 524 - 527. doi: 10.1080/10635150290069931

Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. SYSTEMATIC BIOLOGY, 50 (4) : 525 - 539. doi: 10.1080/106351501750435086

Anderson FE, Foster PG (2000) Tests of ecdysozoan monophyly using molecular sequence data. AMERICAN ZOOLOGIST 40 (6) : 929 - 930.

Horner DS, Foster PG, Embley TM (2000) Iron Hydrogenases and the Evolution of Anaerobic Eukaryotes. Molecular Biology and Evolution, 17 (11) : 1695 - 1709. doi: 10.1093/oxfordjournals.molbev.a026268

Introduction

Summary

I am interested in model-based methods of phylogenetic analysis --- statistical approaches to making the family tree of life --- using DNA and protein sequences. I have developed models of evolution that can accommodate changes in the process of evolution over time. Together with my colleagues Martin Embley, Cymon Cox, Tom Williams, and others, we have tested the iconic Woese three-domains tree of life using these models, which showed the surprising result that if these better models of evolution are used on the same data more support is given to the eocyte hypothesis with an origin of the eukaryotes from within the Archaea. This change in the overall shape of the tree of life has become accepted over the last decade. I have written about these methods and the Tree of Life work mentioned above, some phylogenetic commentary, on eukaryotic microbial genomics and horizontal gene transfer, several genomics projects, and Anopheles systematics in collaboration with Anice Sallum. I continue to develop a phylogenetics toolkit that implements these models, but also can be used for tree interrogation, and is a general phylogenomics toolkit that has been used in genomics pipelines to show the extent of horizontal gene transfer in eukaryotic microbes. My work on supertrees with Mark Wilkinson at the NHM has led to a maximum likelihood implementation and to my knowledge the first Bayesian implementation of supertree construction. My more recent projects have dealt with mitochondrial genome assembly and analysis, and on competition between prokaryotic and eukaryotic carbon-fixers in mid-oceanic gyres.

Qualifications

Degrees

PhD Biology, University of Ottawa, Canada, 1995 - 1997

Projects

Grants

How do eukaryotic CO2 fixers co-exist with faster growing prokaryotic CO2 fixers in the oligotrophic ocean covering 40% of Earth?
Role: Principal investigatorFoster P
Funding: NERC
Total value £135,142 (to Museum £135,142)
Dates: 2015 - 2018

Fast Supertree Construction Using Quartet Joining
Role: Principal investigatorFoster P
Co-investigator: Wilkinson M
Funding: BBSRC
Total value £121,618 (to Museum £121,618)
Dates: 2009 - 2010

Other projects

Molluscan deep-sea diversity
Role: Member
Funding: Museum development

Publications

Publications

Williams ST, Foster PG, Hughes C, Harper EM, Taylor JD, Littlewood DTJ, Dyal P, Hopkins KP, Briscoe AG (2017) Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes. Molecular Phylogenetics and Evolution, 110 : 60 - 72. doi: 10.1016/j.ympev.2017.03.004

Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, San MauroD, Day JJ, Littlewood DTJ, Foster PG, Nussbaum RA, Gower DJ (2016) Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. PLOS ONE, 11 (6) : e0156757 - e0156757. doi: 10.1371/journal.pone.0156757

Timmermans MJTN, Barton C, Haran J, Ahrens D, Culverwell CL, Ollikainen A, Dodsworth S, Foster PG, Bocak L, Vogler AP (2016) Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics. Genome Biology and Evolution, 8 (1) : 161 - 175. doi: 10.1093/gbe/evv241

Demari-silva B, Foster PG, De OliveiraTMP, Bergo ES, Sanabani SS, Pessôa R, Sallum MAM (2015) Mitochondrial genomes and comparative analyses of Culex camposi, Culex coronator, Culex usquatus and Culex usquatissimus (Diptera:Culicidae), members of the coronator group. BMC Genomics, 16 (1) : doi: 10.1186/s12864-015-1951-0

Akanni WA, Siu-ting K, Creevey CJ, Mcinerney JO, Wilkinson M, Foster PG, Pisani D (2015) Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis. Philosophical Transactions of the Royal Society B: Biological Sciences, 370 (1678) : 20140337 - 20140337. doi: 10.1098/rstb.2014.0337

Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D (2015) Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. Royal Society Open Science, 2 (8) : 140436 - 140436. doi: 10.1098/rsos.140436

Jabbar A, Littlewood DTJ, Mohandas N, Briscoe AG, Foster PG, Müller F, Von Samson-HimmelstjernaG, Jex AR, Gasser RB (2014) The mitochondrial genome of Parascaris univalens - implications for a “forgotten” parasite. Parasites & Vectors, 7 (1) : 428 - 428. doi: 10.1186/1756-3305-7-428

Li B, Lopes JS, Foster PG, Embley TM, Cox CJ (2014) Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins. Molecular Biology and Evolution, 31 (7) : 1697 - 1709. doi: 10.1093/molbev/msu105

Lewis CJ, Maddock ST, Day JJ, Nussbaum RA, Morel C, Wilkinson M, Foster PG, Gower DJ (2014) Development of anonymous nuclear markers from Illumina paired-end data for Seychelles caecilian amphibians (Gymnophiona: Indotyphlidae). Conservation Genetics Resources, 6 (2) : 289 - 291. doi: 10.1007/s12686-013-0127-y

Lloyd RE, Streeter SD, Foster PG, Littlewood DTJ, Huntley J, Beckham GT, Himmel ME, Cragg SM (2015) The complete mitochondrial genome of Limnoria quadripunctata Holthuis (Isopoda: Limnoriidae). Mitochondrial DNA, 26 (6) : 825 - 826. doi: 10.3109/19401736.2013.855912

Cox CJ, Li B, Foster PG, Embley TM, Civan P (2014) Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions. Systematic Biology, 63 (2) : 272 - 279. doi: 10.1093/sysbio/syt109

Williams ST, Foster PG, Littlewood DTJ (2014) The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene, 533 (1) : 38 - 47. doi: 10.1016/j.gene.2013.10.005

Civáň P, Foster PG, Embley MT, Séneca A, Cox CJ (2014) Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants. Genome Biology and Evolution, 6 (4) : 897 - 911. doi: 10.1093/gbe/evu061

Baselga A, Fujisawa T, Crampton-platt A, Bergsten J, Foster PG, Monaghan MT, Vogler AP (2013) Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels. Nature Communications, 4 : doi: 10.1038/ncomms2881

Alsmark C, Foster PG, Sicheritz-ponten T, Nakjang S, Martin EmbleyT, Hirt RP (2013) Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology, 14 (2) : R19 - R19. doi: 10.1186/gb-2013-14-2-r19

Cox CJ, Foster PG (2013) A 20-state empirical amino-acid substitution model for green plant chloroplasts. Molecular Phylogenetics and Evolution, 68 (2) : 218 - 220. doi: 10.1016/j.ympev.2013.03.030

Foster PG, Bergo ES, Bourke BP, Oliveira TMP, Nagaki SS, Sant’ana DC, Sallum MAM (2013) Phylogenetic Analysis and DNA-based Species Confirmation in Anopheles (Nyssorhynchus). PLoS ONE, 8 (2) : e54063 - e54063. doi: 10.1371/journal.pone.0054063

Morgan CC, Foster PG, Webb AE, Pisani D, Mcinerney JO, O’connell MJ (2013) Heterogeneous Models Place the Root of the Placental Mammal Phylogeny. Molecular Biology and Evolution, 30 (9) : 2145 - 2156. doi: 10.1093/molbev/mst117

Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin EmbleyT (2013) Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics. Genome Biology and Evolution, 5 (12) : 2285 - 2303. doi: 10.1093/gbe/evt184

Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504 (7479) : 231 - 236. doi: 10.1038/nature12779

Lloyd RE, Foster PG, Guille M, Littlewood DTJ (2012) Next generation sequencing and comparative analyses of Xenopus mitogenomes. BMC Genomics, 13 (1) : 496 - 496. doi: 10.1186/1471-2164-13-496

Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM (2012) A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences, 279 (1749) : 4870 - 4879. doi: 10.1098/rspb.2012.1795

Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences, 108 (37) : 15258 - 15263. doi: 10.1073/pnas.1105100108

Bourke BP, Foster PG, Bergo ES, Calado DC, Sallum MAM (2010) Phylogenetic relationships among species of Anopheles (Nyssorhynchus) (Diptera, Culicidae) based on nuclear and mitochondrial gene sequences. Acta Tropica, 114 (2) : 88 - 96. doi: 10.1016/j.actatropica.2010.01.009

Mureb SallumMA, Foster PG, Dos SantosCLS, Flores DC, Motoki MT, Bergo ES (2010) Resurrection of Two Species From Synonymy of Anopheles (Nyssorhynchus) strodei Root, and Characterization of a Distinct Morphological Form From the Strodei Complex (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY, 47 (4) : 504 - 526.

Alsmark UCM, Sicheritz-ponten T, Foster PG, Hirt RP, Embley TM (2009) Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis, In: Horizontal gene transfer: Genomes in flux, Gogarten P, Gogarten M (Eds). Springer Inc. : New York. 500 pp..

De SouzaRP, Foster PG, Sallum MAM, Coimbra TLM, Maeda AY, Silveira VR, Moreno ES, Da SilvaFG, Rocco IM, Ferreira IB, Suzuki A, Oshiro FOM, Petrella SMCN, Pereira LE, Katz G, Tengan CH, Siciliano MM, Dos SantosCLLS (2010) Detection of a new yellow fever virus lineage within the South American genotype I in Brazil. Journal of Medical Virology, 82 (1) : 175 - 185. doi: 10.1002/jmv.21606

Foster PG, Cox CJ, Embley TM (2009) The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philosophical Transactions of the Royal Society B: Biological Sciences, 364 (1527) : 2197 - 2207. doi: 10.1098/rstb.2009.0034

Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ (2009) Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. THE PLANT CELL ONLINE, 21 (7) : 1897 - 1911. doi: 10.1105/tpc.109.065805

Santos CLS, Ishida MA, Foster PG, Sallum MAM, Benega MA, Borges DB, Corrêa KO, Constantino CRO, Afzal MA, Paiva TM (2008) Detection of a new mumps virus genotype during parotitis epidemic of 2006–2007 in the State of São Paulo, Brazil. Journal of Medical Virology, 80 (2) : 323 - 329. doi: 10.1002/jmv.21068

Calado DC, Foster PG, Bergo ES, Santos CLSD, Galardo AKR, Sallum MAM (2008) Resurrection of Anopheles goeldii from synonymy with Anopheles nuneztovari (Diptera, Culicidae) and a new record for Anopheles dunhami in the Brazilian Amazon. Memórias do Instituto Oswaldo Cruz, 103 (8) : 791 - 799. doi: 10.1590/S0074-02762008000800009

Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM (2008) The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences, 105 (51) : 20356 - 20361. doi: 10.1073/pnas.0810647105

Longhorn SJ, Foster PG, Vogler AP (2007) The nematode?arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases. Cladistics, 23 (2) : 130 - 144. doi: 10.1111/j.1096-0031.2006.00132.x

Wilkinson M, Mcinerney JO, Hirt RP, Foster PG, Embley TM (2007) Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends in Ecology & Evolution, 22 (3) : 114 - 115. doi: 10.1016/j.tree.2007.01.002

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UCM, Besteiro S, Sicheritz-ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van dePeerY, Miranda-saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-corcuera FD, Simoes-barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu C-L, Osoegawa K, De JongPJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik S-B, Logsdon JM, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu C-H, Lee Y-S, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-liggett CM, Johnson PJ (2007) Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. Science, 315 (5809) : 207 - 212. doi: 10.1126/science.1132894

Clark CG, Alsmark UCM, Tazreiter M, Saito-nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-ponten T, Foster PG, Samuelson J, Noel CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillen N, Duchene M, Nozaki T, Hall N (2007) Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY, VOL 65, 65 : 51 - 190. doi: 10.1016/S0065-308X(07)65002-7

Foster PG (2007) Inferring phylogenetic relationships from sequence data.

Pearson T, U’ren JM, Schupp JM, Allan GJ, Foster PG, Mayo MJ, Gal D, Choy JL, Daugherty RL, Kachur S, Friedman CLC, Leadem B, Georgia S, Hornstra H, Vogler AJ, Wagner DM, Keim P, Currie BJ (2007) VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution, 7 (4) : 416 - 423. doi: 10.1016/j.meegid.2006.12.002

Sallum MAM, Foster PG, Li C, Sithiprasasna R, Wilkerson RC (2007) Phylogeny of the Leucosphyrus Group of Anopheles (Cellia) (Diptera: Culicidae) Based on Mitochondrial Gene Sequences. Annals of the Entomological Society of America, 100 (1) : 27 - 35. doi: 10.1603/0013-8746(2007)100[27:POTLGO]2.0.CO;2

Wilkinson M, Mcinerney JO, Hirt RP, Foster P, Embley TM (2007) Of clades and clans: terms for relationships in unrooted trees. Trends in Ecology and Evolution, 22 : 114 - 115.

Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, De RivaA, Mejia-chang M, Foster PG, Vogler AP (2006) Dense Taxonomic EST Sampling and Its Applications for Molecular Systematics of the Coleoptera (Beetles). Molecular Biology and Evolution, 23 (2) : 268 - 278. doi: 10.1093/molbev/msj041

Andersson JO, Hirt RP, Foster PG, Roger AJ (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC EVOLUTIONARY BIOLOGY, 6 : doi: 10.1186/1471-2148/6/27

Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, Mcleod R, Roberts CW (2006) Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements. Eukaryotic Cell, 5 (9) : 1517 - 1531. doi: 10.1128/EC.00106-06

Hampl V, Horner DS, Dyal P, Kulda J, Flegr J, Foster PG, Embley TM (2005) Inference of the Phylogenetic Position of Oxymonads Based on Nine Genes: Support for Metamonada and Excavata. Molecular Biology and Evolution, 22 (12) : 2508 - 2518. doi: 10.1093/molbev/msi245

Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, 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 MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillén N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-ponten T, Weber C, Singh U, Mukherjee C, El-sayed NM, Petri WA, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N (2005) The genome of the protist parasite Entamoeba histolytica. Nature, 433 (7028) : 865 - 868. doi: 10.1038/nature03291

Wilkerson RC, Foster PG, Li C, Sallum MAM (2005) Molecular Phylogeny of Neotropical Anopheles (Nyssorhynchus) albitarsis Species Complex (Diptera: Culicidae). Annals of the Entomological Society of America., 98 : 918 - 925.

Foster PG, Schultz T (2004) Modeling Compositional Heterogeneity. Systematic Biology, 53 (3) : 485 - 495. doi: 10.1080/10635150490445779

Hrdy I, Hirt RP, Dolezal P, Bardonová L, Foster PG, Tachezy J, Martin EmbleyT (2004) Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature, 432 (7017) : 618 - 622. doi: 10.1038/nature03149

Santos CLS, Sallum MAM, Foster PG, Rocco IM (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. Revista do Instituto de Medicina Tropical de Sao Paulo, 46 : 145 - 152.

Embley TM, Van derGiezenM, Horner D, Dyal P, Bell S, Foster P (2003) Hydrogenosomes, Mitochondria and Early Eukaryotic Evolution. IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), 55 (7) : 387 - 395. doi: 10.1080/15216540310001592834

Theodorides K, De RivaA, Gomez-zurita J, Foster PG, Vogler AP (2002) Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Molecular Biology, 11 (5) : 467 - 475. doi: 10.1046/j.1365-2583.2002.00355.x

Wilkinson M, Peres-neto PR, Foster PG, Moncrieff CB, Sanderson M (2002) Type 1 Error Rates of the Parsimony Permutation Tail Probability Test. Systematic Biology, 51 (3) : 524 - 527. doi: 10.1080/10635150290069931

Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. SYSTEMATIC BIOLOGY, 50 (4) : 525 - 539. doi: 10.1080/106351501750435086

Anderson FE, Foster PG (2000) Tests of ecdysozoan monophyly using molecular sequence data. AMERICAN ZOOLOGIST 40 (6) : 929 - 930.

Horner DS, Foster PG, Embley TM (2000) Iron Hydrogenases and the Evolution of Anaerobic Eukaryotes. Molecular Biology and Evolution, 17 (11) : 1695 - 1709. doi: 10.1093/oxfordjournals.molbev.a026268