Staff Profile

Areas of expertise

• The investigation of early eukaryotic evolution using genomics, cell and molecular biology
• Computational evolution, particularly the use of phylogenetics to explore gene and genomic origins
• Parasites and their minimal mitochondria (mitosomes and hydrogenosomes) as models for understanding the essential functions of mitochondria for all eukaryotes
  

Awards and roles

• Awarded Darwin Medal of the Royal Society (2022)
  
• Elected Fellow of the Royal Society (FRS 2019)
• Vice Chair, Marie Sklodowska-Curie International Training Networks, Environment Panel (2018 - to date)
  
• Elected to the European Academy for Microbiology (2016)
• Vice Chancellor’s Award for Academic Distinction (2016)
• Member of Editorial Board, Genome Biology and Evolution (2011 - to date)
• Vice Chair, Marie Sklodowska-Curie Individual Fellowships, Environment Panel (2011 - 2018)
• Elected Fellow of the UK Academy of Medical Sciences (FMedSci 2011)
• ERC Advanced Investigator Award (2011-2017)
• Wellcome Trust Programme Grant (2010-2016)
  
• Elected Member of the European Molecular Biology Organization (2009)
• Elected Fellow of the American Academy for Microbiology (2008)
• Royal Society Wolfson Research Merit Award (2006-2011)
• Scientific Associate, Department of Life Sciences, The Natural History Museum (2004 to date)
• Associate Editor, Molecular Biology and Evolution (2002-2011)
• Member of Editorial Board, Environmental Microbiology (2000-2006)
• Member of the Canadian Institute of Advanced Research (1996-2007)
• Visiting Professor to the Universities of Aberdeen, Essex, Kings College, Liverpool and Newcastle (1996-2004)
• Senior Principal Scientific Officer IMP (Individual Merit Promotion), the Natural History Museum (2001-2004)
• Principal Scientific Officer, Dept. Zoology, the Natural History Museum (1992-2001)
• Senior Scientific Officer, Dept. Zoology, the Natural History Museum, London (1991-1992)
• Principal Lecturer in Microbiology, University of East London (1988-1991)
• Lecturer in Microbiology, University of East London (1983-1988)
• PhD in Microbiology, Newcastle University (1979-1983)
  

Google scholar: Click here.

Research Interests

We are interested in the early evolution of eukaryotic cells, their genomes and their organelles related to mitochondria (hydrogenosomes and mitosomes).  We use anaerobic and parasitic eukaryotes including Giardia, Trichomonas and particularly Microsporidia as our models.  We also investigate how reductive evolution has affected the biology of obligate intracellular Microsporidia parasites that infect most animal groups including humans.  Our work has the following broad themes:

Genomics

We use whole genome data to investigate the contrasting roles of vertical and horizontal inheritance, including genes of endosymbiotic origins, in shaping eukaryotic genomes. We also study the effects of reductive evolution on parasite genomes.

Phylogenetics

We are developing better methods, based upon likelihood and Bayesian approaches, for phylogenetic analysis of molecular data. Our aim is to improve the reconstruction of phylogenetic trees relevant to understanding the early evolution of eukaryotes.

Cell Biology

We have a long term interest in the discovery and characterisation of reduced organelles (hydrogenosomes, mitosomes) related to mitochondria.  Our investigations are aimed at identifying the essential functions of mitochondria for eukaryotes.  In these studies we have often used the tiny minimal mitochondria (mitosome) of Microsporidia - which we discovered - as a model system.  More recently we have become interested in how Microsporidia use transport proteins to steal resources from infected host cells.

Two reviews that give an overview of our interests in eukaryotic evolution:

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

Embley, TM and Martin W. (2006). Eukaryotic evolution, changes and challenges.  Nature 440: 623-630.

Two recent papers that give an insight into our work on Microsporidia molecular cell biology:

Dean, P, Sendra, KM, Williams, TA, Watson , AK,  Major, P, Nakjang, S, Kozhevnikova, E, Goldberg, AV, Kunji, ERS, Hirt, RP and Embley, TM. (2018).  Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites. Nature Communications 9: 1709.  (there is also a commentary on this paper by Lukes and Husnik in Current Biology: Microsporidia: A single horizontal gene transfer drives a great leap forwards.  doi.org/10.1016/j.cub.2018.05.031).

Freibert, SA, Goldberg, AV, Hacker, C, Molik, S, Dean, P, Williams, TA, Nakjang, S, Long, S, Sendra, K, Heinz, E, Hirt, RP, Lucocq, JM, Embley, TM and Lill R. (2017).  Evolutionary conservation and in vitro reconstitution of microsporidian iron-sulphur cluster biosynthesis.  Nature comunications 8: 13932.

Undergraduate Teaching

I no longer lead undergraduate modules as I retired in October 2022.  I still give occasional lectures on evolution on the modules of other colleagues.

International workshops

We have run an EMBO-funded workshop on Computational Molecular Evolution since 1998. The teaching material including all of the slides and practicals for the 2018 EMBO course (in Faro, Portugal) can be downloaded using the link below (copy it into your browser it will not work from here).

EMBO 2017 Workshop on Computational Molecular Evolution, Teaching Materials:

http://att.ccmar.ualg.pt/embo2018/.

• Articles

  • Williams TA, Cox CJ, Foster PG, Szollosi GJ, Embley TM. Phylogenomics provides robust support for a two-domains tree of life. Nature Ecology & Evolution 2020, 4, 138-147.
  • Lewis WH, Lind AE, Sendra KM, Onsbring H, Williams TA, Esteban GF, Hirt RP, Ettema TJG, Embley TM. Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss. Molecular Biology and Evolution 2020, 37(2), 524-539.
  • Major P, Sendra K, Dean P, Williams TA, Watson AK, Thwaites DT, Embley TM, Hirt RP. A new family of cell surface located purine transporters in Microsporidia and related fungal endoparasites. eLife 2019, 8, e47037.
  • Dean P, Sendra KM, Williams TA, Watson AK, Major P, Nakjang S, Kozhevnikova E, Goldberg AV, Kunji ERS, Hirt RP, Embley TM. Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites. Nature Communications 2018, 9, 1709.
  • Lind AE, Lewis WH, Spang A, Guy L, Embley TM, Ettema TJG. Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle. ISME Journal 2018, 12(11), 2655-2667.
  • Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM. Integrative modelling of gene and genome evolution roots the archaeal tree of life. Proceedings of the National Academy of Sciences of the United States of America 2017, 114(23), E4602-E4611.
  • Freibert SA, Goldberg AV, Hacker C, Molik S, Dean P, Williams TA, Nakjang S, Long SJ, Sendra K, Bill E, Heinz E, Hirt RP, Lucocq JM, Embley TM, Lill R. Evolutionary conservation and in vitro reconstitution of microsporidian iron–sulfur cluster biosynthesis. Nature Communcations 2017, 8, 13932.
  • Embley TM, Williams TA. Only two domains, not three: Changing views on the tree of life. Microbiology Today 2016, 43(2), 70-73.
  • Domman D, Horn M, Embley TM, Williams TA. Plastid establishment did not require a chlamydial partner. Nature Communications 2015, 6, 6421.
  • Williams TA, Heaps SE, Cherlin S, Nye TMW, Boys RJ, Embley TM. New substitution models for rooting phylogenetic trees. Philosophical Transactions of the Royal Society B: Biological Sciences 2015, 370(1678), 20140336.
  • Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proceedings of the National Academy of Sciences of the United States of America 2015, 112(30), 9370-9375.
  • Heinz E, Hacker C, Dean P, Mifsud J, Goldberg AV, Williams TA, Nakjang S, Gregory A, Hirt RP, Lucocq JM, Kunji ER, Embley TM. Plasma Membrane-Located Purine Nucleotide Transport Proteins are Key Components for Host Exploitation by Microsporidian Intracellular Parasites. PLoS Pathogens 2014, 10(12), e1004547.
  • Williams TA, Embley TM. Archaeal "Dark Matter" and the Origin of Eukaryotes. Genome Biology and Evolution 2014, 6(3), 474-481.
  • Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Embley T. Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics. Genome Biology and Evolution 2013, 5(12), 2285-2303.
  • Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology 2013, 14(2), R19.
  • Heinz E, Williams TA, Nakjnag S, Noël 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 ParasiteTrachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution. PLoS Pathogens 2012, 8(10), e1002979.
  • Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences 2012, 279(1749), 4870-4879.
  • Williams TA, Embley TM, Heinz E. Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses. PLoS One 2011, 6(6), e21080.
  • Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philosophical Transactions of The Royal Society B: Biological Sciences 2009, 364(1527), 2197-2207.
  • Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences 2008, 105(51), 20356-20361.
  • Smid O, Matuskova A, Harris SR, Kucera T, Novotny M, Horvathova L, Hrdy I, Kutejova E, Hirt RP, Embley TM, Janata J, Tachezy J. Reductive Evolution of the Mitochondrial Processing Peptidases of the Unicellular Parasites Trichomonas vaginalis and Giardia intestinalis. PLoS Pathogens 2008, 4(12), e1000243.
  • Goldberg AV, Molik S, Tsaousis AD, Neumann K, Kuhnke G, Delbac F, Vivares CP, Hirt RP, Lill R, Embley TM. Localization and functionality of microsporidian iron-sulphur cluster assembly proteins. Nature 2008, 452(7187), 624-628.
  • Tsaousis AD, Kunji ERS, Goldberg AV, Lucocq JM, Hirt RP, Embley TM. A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi. Nature 2008, 453(7194), 553-556.
  • 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 De Peer Y, 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 Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik S-B, Logsdon Jr 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. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 2007, 315(5809), 207-212.
  • Embley TM. Multiple secondary origins of the anaerobic lifestyle in eukaryotes. Philosophical Transactions of the Royal Society of London B: Biological Sciences 2006, 361(1470), 1055-1067.
  • 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, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri Jr WA, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N. The genome of the protist parasite Entamoeba histolytica. Nature 2005, 433(7028), 865-868.
  • Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UCM, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth T-J, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, MacLeod A, Mooney PJ, Moule S, Martin DMA, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream M-A, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CMR, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM. The genome of the African trypanosome Trypanosoma brucei. Science 2005, 309(5733), 416-422.
  • El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran A-N, Wortman JR, Alsmark UCM, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N. Comparative genomics of trypanosomatid parasitic protozoa. Science 2005, 309(5733), 404-435.
  • Chan KW, Slotboom D-J, Cox S, Embley TM, Fabre O, Van Der Giezen M, Harding M, Horner DS, Kunji ERS, Leon-Avila G, Tovar J. A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica. Current Biology 2005, 15(8), 737-742.
  • Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J, Embley TM. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 2004, 432(7017), 618-622.
  • van der Giezen M, Slotboom DJ, Horner DS, Dyal PL, Harding M, Xue GP, Embley TM, Kunji ER. Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. The EMBO Journal 2002, 21(4), 572-579.
  • Williams BA, Hirt RP, Lucocq JM, Embley TM. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 2002, 418(6900), 865-869.
  • Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF, Embley TM. Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings Of the National Academy Of Sciences Of the United States Of America 1999, 96(2), 580-585.

• Editorials

  • Embley TM, Williams TA. Steps on the road to eukaryotes. Nature 2015, 521(7551), 169-170.
  • Williams TA, Embley TM. Changing ideas about eukaryotic origins. Philosophical Transactions of the Royal Society B. Biological Sciences 2015, 370(1678).

• Note

  • Martin W, Embley TM. Early evolution comes full circle. Nature 2004, 431(7005), 134-137.

• Reviews

  • Dean P, Hirt RP, Embley TM. Microsporidia: why make nucleotides if you can steal them?. PLoS Pathogens 2016, 12(11), e1005870.
  • Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 2013, 504, 231-236.
  • Embley TM, Martin W. Eukaryotic evolution, changes and challenges. Nature 2006, 440(7084), 623-630.