Dr Dave Ferrier


tel: 01334 463480
email: dekf@st-andrews.ac.uk
room: 1.10  (SOI)
Scottish Oceans Institute
East Sands
University of St Andrews
St Andrews
KY16 8LB

General Information


Research Overview. We aim to understand how the diversity of form in the animal kingdom evolved. The focus of our research is the connection between the evolution of animal genome organisation and development, with a particular concentration on the homeobox-containing genes. The Hox gene cluster is established as a corner-stone of Evolutionary Developmental Biology, but much about the evolution of its organisation and mode of operation remains unknown. Also the Hox cluster is not unique as a homeobox gene cluster controlling animal development, further clusters being the ParaHox and NK clusters, all of which evolved within larger arrays of homeobox genes (the Mega-cluster and Super-Hox cluster). We utilize a variety of organisms in our research (including amphioxus, sea squirts, polychaetes and priapulids), chosen from key points in the phylogeny of the animals to enable reconstruction of the ancestral conditions at major nodes in the animal kingdom; the origin of bilaterians, protostomes, deuterostomes, chordates and vertebrates.


Recent Publications

MacKintosh, C & Ferrier, DEK 2017, 'Recent advances in understanding the roles of whole genome duplications in evolution' F1000Research, vol 2017, no. 6, 1623. DOI: 10.12688/f1000research.11792.1
Ferrier, DEK 2016, 'The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal' Briefings in Functional Genomics, vol 15, no. 5, pp. 333-341. DOI: 10.1093/bfgp/elv056
Ferrier, DEK 2016, 'Evolution of homeobox gene clusters in animals: the Giga-cluster and primary versus secondary clustering' Frontiers in Ecology and Evolution, vol 4, 36. DOI: 10.3389/fevo.2016.00036
Garstang, MG, Osborne, P & Ferrier, DEK 2016, 'TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates' BMC Evolutionary Biology, vol 16, 57. DOI: 10.1186/s12862-016-0614-3
Plöschner, M, Kollárová, V, Dostál, Z, Nylk, J, Barton-Owen, T, Ferrier, DEK, Chmelík, R, Dholakia, K & Čižmár, T 2015, 'Multimode fibre: light-sheet microscopy at the tip of a needle' Scientific Reports, vol 5, 18050. DOI: 10.1038/srep18050
Yang, Z, Piksarv, P, Ferrier, DEK, Gunn-Moore, FJ & Dholakia, K 2015, 'Macro-optical trapping for sample confinement in light sheet microscopy' Biomedical Optics Express, vol 6, no. 8, pp. 2778-2785. DOI: 10.1364/BOE.6.002778
Szabo, R & Ferrier, DEK 2015, 'Another biomineralising protostome with an msp130 gene and conservation of msp130 gene structure across Bilateria' Evolution and Development, vol 17, no. 3, pp. 195-197. DOI: 10.1111/ede.12122
Chipman, AD, Ferrier, DEK, Brena, C, Qu, J, Hughes, DST, Schröder, R, Torres-Oliva, M, Znassi, N, Jiang, H, Almeida, FC, Alonso, CR, Apostolou, Z, Aqrawi, P, Arthur, W, Barna, JCJ, Blankenburg, KP, Brites, D, Capella-Gutiérrez, S, Coyle, M, Dearden, PK, Du Pasquier, L, Duncan, EJ, Ebert, D, Eibner, C, Erikson, G, Evans, PD, Extavour, CG, Francisco, L, Gabaldón, T, Gillis, WJ, Goodwin-Horn, EA, Green, JE, Griffiths-Jones, S, Grimmelikhuijzen, CJP, Gubbala, S, Guigó, R, Han, Y, Hauser, F, Havlak, P, Hayden, L, Helbing, S, Holder, M, Hui, JHL, Hunn, JP, Hunnekuhl, VS, Jackson, L, Javaid, M, Jhangiani, SN, Jiggins, FM, Jones, TE, Kaiser, TS, Kalra, D, Kenny, NJ, Korchina, V, Kovar, CL, Kraus, FB, Lapraz, F, Lee, SL, Lv, J, Mandapat, C, Manning, G, Mariotti, M, Mata, R, Mathew, T, Neumann, T, Newsham, I, Ngo, DN, Ninova, M, Okwuonu, G, Ongeri, F, Palmer, WJ, Patil, S, Patraquim, P, Pham, C, Pu, L-L, Putman, NH, Rabouille, C, Ramos, OM, Rhodes, AC, Robertson, HE, Robertson, HM, Ronshaugen, M, Rozas, J, Saada, N, Sánchez-Gracia, A, Scherer, SE, Schurko, AM, Siggens, KW, Simmons, D, Stief, A, Stolle, E, Telford, MJ, Tessmar-Raible, K, Thornton, R, van der Zee, M, von Haeseler, A, Williams, JM, Willis, JH, Wu, Y, Zou, X, Lawson, D, Muzny, DM, Worley, KC, Gibbs, RA, Akam, M & Richards, S 2014, 'The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima' PLoS Biology, vol 12, no. 11, e1002005. DOI: 10.1371/journal.pbio.1002005
Szabo, R, Calder, A & Ferrier, DEK 2014, 'Biomineralisation during operculum regeneration in the polychaete Spirobranchus lamarcki' Marine Biology, vol 161, no. 11, pp. 2621-2629. DOI: 10.1007/s00227-014-2534-3
Fortunato, S, Adamski, M, Mendivil Ramos, O, Leininger, S, Liu, J, Ferrier, DEK & Adamska, M 2014, 'Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes' Nature, vol 514, pp. 620-623. DOI: 10.1038/nature13881
Yang, Z, Prokopas, M, Nylk, J, Coll Llado, C, Gunn-Moore, FJ, Ferrier, DEK, Vettenburg, T & Dholakia, K 2014, 'A compact Airy beam light sheet microscope with a tilted cylindrical lens' Biomedical Optics Express, vol 5, no. 10, pp. 3434-3442. DOI: 10.1364/BOE.5.003434
Szabo, R & Ferrier, DEK 2014, 'Cell proliferation dynamics in regeneration of the operculum head appendage in the annelid Pomatoceros lamarckii' Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol 322B, no. 5, pp. 257-268. DOI: 10.1002/jez.b.22572
Vettenburg, T, Dalgarno, HIC, Nylk, J, Coll-Lladó, C, Ferrier, DEK, Cizmar, T, Gunn-Moore, FJ & Dholakia, K 2014, 'Light-sheet microscopy using an Airy beam' Nature Methods, vol 11, no. 5, pp. 541-544. DOI: 10.1038/nmeth.2922
Ferrier, DEK 2014, 'The Hox-TALE has been wagging for a long time' eLife, vol 3, e02515. DOI: 10.7554/eLife.02515
Szabo, R & Ferrier, DEK 2014, 'The dynamics of alkaline phosphatase activity during operculum regeneration in the polychaete Pomatoceros lamarckii' International Journal of Developmental Biology, vol 58, no. 6/7/8, pp. 635-642. DOI: 10.1387/ijdb.140116df
Barker, D, Ferrier, DEK, Holland, PWH, Mitchell, JBO, Plaisier, H, Ritchie, MG & Smart, SD 2013, '4273π: bioinformatics education on low cost ARM hardware' BMC Bioinformatics, vol 14, 243. DOI: 10.1186/1471-2105-14-243
Garstang, MG & Ferrier, DEK 2013, 'Time is of the essence for ParaHox homeobox gene clustering.' BMC Biology, vol 11, no. 72, 72. DOI: 10.1186/1741-7007-11-72
Mendivil Ramos, O, Barker, D & Ferrier, DEK 2012, 'Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals' Current Biology, vol 22, no. 20, pp. 1951-1956. DOI: 10.1016/j.cub.2012.08.023
Ferrier, DEK 2012, Evolution of the Hox gene cluster. in eLS. John Wiley and Sons, Chichester. DOI: 10.1002/9780470015902.a0023989
Tinti, M, Johnson, C, Toth, R, Ferrier, DEK & MacKintosh, C 2012, 'Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates' Open Biology, vol 2, 120103. DOI: 10.1098/rsob.120103
Hui, JHL, McDougall, C, Monteiro, AS, Holland, PWH, Arendt, D, Balavoine, G & Ferrier, DEK 2012, 'Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization' Molecular Biology and Evolution, vol 29, no. 1, pp. 157-165. DOI: 10.1093/molbev/msr175
Mendivil Ramos, O & Ferrier, DEK 2012, 'Mechanisms of gene duplication and translocation and progress towards understanding their relative contributions to animal genome evolution' International Journal of Evolutionary Biology, vol 2012, 846421. DOI: 10.1155/2012/846421
Ferrier, DEK 2012, 'Evolutionary crossroads in developmental biology: annelids.' Development, vol 139, pp. 2643-2653. DOI: 10.1242/dev.074724
McDougall, C, Korchagina, N, Tobin, J & Ferrier, DEK 2011, 'Annelid Distal-less/Dlx duplications reveal varied post-duplication fates' BMC Evolutionary Biology, vol 11, pp. 241. DOI: 10.1186/1471-2148-11-241
Torres, ML, Antkowiak, M, Cizmarova, H, Ferrier, DEK, Dholakia, K & Gunn-Moore, FJ 2011, 'Integrated holographic system for all-optical manipulation of developing embryos' Biomedical Optics Express, vol 2, no. 6, pp. 1564-1575 . DOI: 10.1364/BOE.2.001564
Ferrier, DEK 2011, 'Tunicates push the limits of animal evo-devo' BMC Biology, vol 9, 3. DOI: 10.1186/1741-7007-9-3
Ferrier, DEK 2011, 'Hox and ParaHox genes in evolution, development and genomics.' Genomics Proteomics & Bioinformatics, vol 9, no. 3, pp. 63-64. DOI: 10.1016/S1672-0229(11)60009-0
Butts, T, Holland, PWH & Ferrier, DEK 2010, 'Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression' Proceedings of the Royal Society B: Biological Sciences, vol 277, no. 1699, pp. 3381-3389. DOI: 10.1098/rspb.2010.0647
Ferrier, DEK & Martinez, P 2010, 'Evolutionary Developmental Genomics: At the 2008 meeting of the European Society for Evolutionary Developmental Biology' Genomics, vol 95, no. 5, pp. 247-249. DOI: 10.1016/j.ygeno.2009.07.001
Shigenobu, S, Bickel, RD, Brisson, JA, Butts, T, Chang, C-C, Christiaens, O, Davis, GK, Duncan, EJ, Ferrier, DEK, Iga, M, Janssen, R, Lin, G-W, Lu, H-L, McGregor, AP, Miura, T, Smagghe, G, Smith, JM, van der Zee, M, Velarde, RA, Wilson, MJ, Dearden, PK & Stern, DL 2010, 'Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes' Insect Molecular Biology, vol 19, pp. 47-62. DOI: 10.1111/j.1365-2583.2009.00944.x
Ferrier, DEK & The International Aphid Genomics Consortium 2010, 'Genome sequence of the pea aphid Acyrthosiphon pisum' PLoS Biology, vol 8, no. 2, e1000313. DOI: doi:10.1371/journal.pbio.1000313
Osborne, PW & Ferrier, DEK 2010, 'Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content' Molecular Biology and Evolution, vol 27, no. 2, pp. 217-220. DOI: 10.1093/molbev/msp235
Ferrier, DEK 2010, Evolution of Hox complexes. in J Deutsch (ed.), Hox Genes: studies from the 20th to the 21st century.: Advances in experimental medicine and biology. vol. 689, Landes Bioscience, pp. 91-100.
Takahashi, T, McDougall, C, Troschianko, J, Chen, W-C, Nagarajan, AJ, Shimeld, SM & Ferrier, DEK 2009, 'An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals.' BMC Evolutionary Biology, vol 9, 240. DOI: 10.1186/1471-2148-9-240
Hui, JHL, Raible, F, Korchagina, N, Dray, N, Samain, S, Magdelenat, G, Jubin, C, Segurens, B, Balavoine, G, Arendt, D & Ferrier, DEK 2009, 'Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes' BMC Biology, vol 7, 43. DOI: 10.1186/1741-7007-7-43
Osborne, PW, Benoit, G, Laudet, V, Schubert, M & Ferrier, DEK 2009, 'Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae).' Developmental Biology, vol 327, pp. 252-262. DOI: doi:10.1016/j.ydbio.2008.11.027
Takatori, N, Butts, T, Candiani, S, Pestariono, M, Ferrier, DEK, Saiga, H & Holland, PWH 2008, 'Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.' Development Genes and Evolution, vol 218, pp. 579-590. DOI: 10.1007/s00427-008-0245-9
Hui, JHL, Holland, PWH & Ferrier, DEK 2008, 'Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster.' Evolution and Development, vol 10, pp. 725-730. DOI: 10.1111/j.1525-142X.2008.00286.x
McDougall, C, Hui, JHL, Monteiro, A, Takahashi, T & Ferrier, DEK 2008, 'Annelids in evolutionary developmental biology and comparative genomics.' Parasite, vol 15, no. 3, pp. 321-328. DOI: 10.1051/parasite/2008153321
Amemiya, CT, Prohaska, SJ, Hill-Force, A, Cook, A, Wasserscheid, J, Ferrier, DEK, Pascual-Anaya, J, Garcia-Fernandez, J, Dewar, K & Stadler, PF 2008, 'The amphioxus Hox cluster: characterization, comparative genomics, and evolution' Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol 310B, no. 5, pp. 465 - 477. DOI: 10.1002/jez.b.21213
Holland, LZ, Albalat, R, Azumi, K, Benito-Gutierrez, E, Blow, MJ, Bronner-Fraser, M, Brunet, F, Butts, T, Candiani, S, Dishaw, LJ, Ferrier, DEK, Garcia-Fernandez, J, Gibson-Brown, JJ, Gissi, C, Godzik, A, Hallbook, F, Hirose, D, Hosomichi, K, Ikuta, T, Inoko, H, Kasahara, M, Kasamatsu, J, Kawashima, T, Kimura, A, Kobayashi, M, Kozmik, Z, Kubokawa, K, Laudet, V, Litman, GW, McHardy, AC, Meulemans, D, Nonaka, M, Olinski, RP, Pancer, Z, Pennacchio, LA, Pestarino, M, Rast, JP, Rigoutsos, I, Robinson-Rechavi, M, Roch, G, Saiga, H, Sasakura, Y, Satake, M, Satou, Y, Schubert, M, Sherwood, N, Shiina, T, Takatori, N, Tello, J, Vopalensky, P, Wada, S, Xu, A, Ye, Y, Yoshida, K, Yoshizaki, F, Yu, J-K, Zhang, Q, Zmasek, CM, de Jong, PJ, Osoegawa, K, Putnam, NH, Rokhsar, DS, Satoh, N & Holland, PWH 2008, 'The amphioxus genome illuminates vertebrate origins and cephalochordate biology' Genome Research, vol 18, pp. 1100-1111. DOI: 10.1101/gr.073676.107
Putnam, NH, Butts, T, Ferrier, DEK, Furlong, RF, Hellsten, U, Kawashima, T, Robinson-Rechavi, M, Shoguchi, E, Terry, A, Yu, J-K, Benito-Gutierrez, E, Dubchak, I, Garcia-Fernandez, J, Gibson-Brown, JJ, Grigoriev, IV, Horton, AC, de Jong, PJ, Jurka, J, Kapitonov, VV, Kohara, Y, Kuroki, Y, Lindquist, E, Lucas, S, Osoegawa, K, Pennacchio, LA, Salamov, AA, Satou, Y, Sauka-Spengler, T, Schmutz, J, Shin-I, T, Toyoda, A, Bronner-Fraser, M, Fujiyama, A, Holland, LZ, Holland, PWH, Satoh, N & Rokhsar, DS 2008, 'The amphioxus genome and the evolution of the chordate karyotype.' Nature, vol 453, pp. 1064 - 1071. DOI: 10.1038/nature06967
Butts, T, Holland, PWH & Ferrier, DEK 2008, 'The Urbilaterian Super-Hox cluster.' Trends in Genetics, vol 24, no. 6, pp. 259 - 262. DOI: 10.1016/j.tig.2007.09.006
Tribolium Sequencing Consortium, Richards et al., S & Ferrier, DEK 2008, 'The genome of the developmental model beetle and pest Tribolium castaneum' Nature, vol 452, pp. 949 - 955. DOI: 10.1038/nature06784
Ferrier, DEK 2008, When is a Hox gene not a Hox gene? The importance of gene nomenclature. in A Minelli & G Fusco (eds), Evolving Pathways: key themes in Evolutionary Developmental Biology.. Cambridge University Press, pp. 175-193.
Denes, AS, Jekely, G, Steinmetz, PRH, Raible, F, Snyman, H, Prud'homme, B, Ferrier, DEK, Balavoine, G & Arendt, D 2007, 'Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria.' Cell, vol 129, no. 2, pp. 277-288. DOI: 10.1016/j.cell.2007.02.040
Hui, J, Kortchagina, N, Arendt, D, Balavoine, G & Ferrier, DEK 2007, 'Duplication of the ribosomal gene cluster in the marine polychaete Platynereis dumerilii correlates with ITS polymorphism.' Journal of the Marine Biological Association of the United Kingdom, vol 87, pp. 443-449. DOI: 10.1017/S002531540705566X
Ferrier, DEK 2007, Evolution of Hox gene clusters. in S Papageorgiou (ed.), HOX gene expression. Landes Bioscience, pp. 53-67.
Osborne, PW, Luke, GN, Holland, PWH & Ferrier, DEK 2006, 'Identification and Characterisation of five novel Miniature Inverted-repeat Transposable Elements (MITEs) in amphioxus (Branchiostoma floridae).' International Journal of Biological Sciences, vol 2, pp. 54-60.
Monteiro, A & Ferrier, DEK 2006, 'Hox genes are not always Colinear.' International Journal of Biological Sciences, vol 2, pp. 95-103.
McDougall, C, Chen, W-C, Shimeld, SM & Ferrier, DEK 2006, 'The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes.' Frontiers of Zoology, vol 3, pp. 16. DOI: 10.1186/1742-9994-3-16
Raible, F, Tessmar-Raible, K, Osoegawa, K, Wincker, P, Jubin, C, Balavoine, G, Ferrier, DEK, Benes, V, de Jong, P, Weissenbach, J, Bork, P & Arendt, D 2005, 'Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.' Science, vol 310, no. 5752, pp. 1325-1326. DOI: 10.1126/science.1119089
Ferrier, DEK, Dewar, K, Cook, A, Chang, JL, Hill-Force, A & Amemiya, C 2005, 'The chordate ParaHox cluster' Current Biology, vol 15, no. 20, pp. R820-R822. DOI: doi:10.1016/j.cub.2005.10.014
Ferrier, DEK 2004, 'Hox genes: did the vertebrate ancestor have a Hox14?' Current Biology, vol 14, pp. R210-R211. DOI: doi:10.1016/j.cub.2004.02.025
Ferrier, DEK 2004, 'Review of the 4th UK Evolutionary Developmental Biology meeting.' Evolution and Development, vol 6, pp. 65-66. DOI: 10.1111/j.1525-142X.2004.04010.x
Ferrier, DEK & Minguillón, C 2003, 'Evolution of the Hox/ParaHox gene clusters.' International Journal of Developmental Biology, vol 47, pp. 605-611.
Ferrier, DEK & Holland, PWH 2002, 'Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity' Molecular Phylogenetics and Evolution, vol 24, no. 3, pp. 412-417. DOI: 10.1016/S1055-7903(02)00204-X
Minguillón, C, Ferrier, DEK, Cebrián, C & Garcia-Fernàndez, J 2002, 'Gene duplications in the prototypical cephalochordate amphioxus.' Gene, vol 287, pp. 121-128. DOI: doi:10.1016/S0378-1119(01)00828-9
Ferrier, DEK & Shimeld, SM 2002, 'Evolution of developmental mechanisms.' Genome Biology, vol 3, pp. reports4020.1-4020.3. DOI: 10.1186/gb-2002-3-7-reports4020
Ferrier, DEK 2002, Homeobox. in M Pagel (ed.), The Encyclopedia of Evolution.. Oxford University Press.
Ferrier, DEK, Minguillon, C, Cebrian, C & Garcia-Fernandez, J 2001, 'Amphioxus Evx genes: implications for the evolution of the Midbrain-Hindbrain Boundary and the chordate tailbud' Developmental Biology, vol 237, no. 2, pp. 270-281. DOI: 10.1006/dbio.2001.0375
Ferrier, DEK & Holland, PWH 2001, 'Sipunculan ParaHox genes' Evolution and Development, vol 3, no. 4, pp. 263-270. DOI: 10.1046/j.1525-142x.2001.003004263.x
Ferrier, DEK, Brooke, NM, Panopoulou, G & Holland, PWH 2001, 'The Mnx homeobox class defined by HB9, MNR2 and amphioxus AmphiMnx.' Development Genes and Evolution, vol 211, pp. 103-107. DOI: 10.1007/s004270000124
Ferrier, DEK & Holland, PWH 2001, 'Ancient origin of the Hox gene cluster.' Nature Reviews Genetics, vol 2, no. 1, pp. 33-38. DOI: 10.1038/35047605
Garcia-Fernàndez, J, Ferrier, DEK, Minguillón, C & Cebrián, C 2001, 'The amphioxus genome in Evo-Devo: archetype or “cul de sac”?' International Journal of Developmental Biology, vol 45, no. S1, pp. S137-S138.
Ferrier, DEK, Minguillón, C, Holland, PWH & Garcia-Fernàndez, J 2000, 'The amphioxus Hox cluster : deuterostome posterior flexibility and Hox14.' Evolution and Development, vol 2, pp. 284-293. DOI: 10.1046/j.1525-142x.2000.00070.x
Ferrier, DEK & Akam, MEA 1996, 'Organization of the Hox gene cluster in the grasshopper, Schistocerca gregaria.' Proceedings of the National Academy of Sciences of the United States of America, vol 93, pp. 13024-13029.
Averof, M, Dawes, R & Ferrier, DEK 1996, 'Diversification of arthropod Hox genes as a paradigm for the evolution of gene functions' Seminars in Cell and Developmental Biology, vol 7, no. 4, pp. 539-551. DOI: 10.1006/scdb.1996.0068
Akam, ME, Averof, M, Castelli-Gair, J, Dawes, RE, Falciani, F & Ferrier, DEK 1994, 'The evolving roles of the Hox genes in arthropods.' Development, vol Supplement, pp. 209-215.

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