The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal
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A key aim in evolutionary biology is to deduce ancestral states to better understand the evolutionary origins of clades of interest and the diversification process(es) that has/have elaborated them. These ancestral deductions can hit difficulties when undetected loss events are misinterpreted as ancestral absences. With the ever-increasing amounts of animal genomic sequence data, we are gaining a much clearer view of the preponderance of differential gene losses across animal lineages. This has become particularly clear with recent progress in our understanding of the origins of the Hox/ParaHox developmental control genes relative to the earliest branching lineages of the animal kingdom: the sponges (Porifera), comb jellies (Ctenophora) and placozoans (Placozoa). These reassessments of the diversity and complexity of developmental control genes in the earliest animal ancestors need to go hand-in-hand with complementary advances in comparative morphology, phylogenetics and palaeontology to clarify our understanding of the complexity of the last common ancestor of all animals. The field is currently undergoing a shift from the traditional consensus of a sponge-like animal ancestor from which morphological and molecular elaboration subsequently evolved, to a scenario of a more complex animal ancestor, with subsequent losses and simplifications in various lineages.
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If sponges are monophyletic, sponge-like characters might be limited to sponges and not necessarily expected in other early metazoans, which may have been morphologically more complex.
“If, on the other hand, sponges are monophyletic then such characters might be limited to the sponges and would not necessarily be expected in other early metazoans, which may have been morphologically more complex [111].”
From The origin of animals: Can molecular clocks and the fossil record be reconciled? (2017) · cites this paper as [111]
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Cites
Darwin, C. R. (1859) · J. Murray eBooks · doi:10.5962/bhl.title.68064 · Cited by 4,628 · see citing works
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · see citing works
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science · doi:10.1126/science.1139158 · Cited by 1,555 · see citing works
The origin of species, by Charles Darwin.
Darwin, C. R. (1900) · doi:10.5962/bhl.title.46292 · Cited by 1,181 · see citing works
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129 · see citing works
The Amphimedon queenslandica genome and the evolution of animal complexity
Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., Richards, G. S., Conaco, C., Dacre, M., Hellsten, U., et al. (2010) · Nature · doi:10.1038/nature09201 · Cited by 1,049 · see citing works
From DNA to diversity: molecular genetics and the evolution of animal design
Carroll, S., Grenier, J., & Weatherbee, S. D. (2002) · Choice Reviews Online · doi:10.5860/choice.39-5182 · Cited by 986 · see citing works
The Trichoplax genome and the nature of placozoans
Srivastava, M., Begovic, E., Chapman, J., Putnam, N. H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M. L., et al. (2008) · Nature · doi:10.1038/nature07191 · Cited by 889 · see citing works
The evolutionary dynamics of eukaryotic gene order
Hurst, L. D., Pál, C., & Lercher, M. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1319 · Cited by 719 · see citing works
The ctenophore genome and the evolutionary origins of neural systems
Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716 · see citing works
The Genome of the Ctenophore <i>Mnemiopsis leidyi</i> and Its Implications for Cell Type Evolution
Ryan, J. F., Pang, K., Schnitzler, C. E., Nguyen, A.-D., Moreland, R. T., Simmons, D. K., Koch, B. J., Francis, W. R., Havlak, P., Program, N. C. S., et al. (2013) · Science · doi:10.1126/science.1242592 · Cited by 702 · see citing works
The zootype and the phylotypic stage
Slack, J. M. W., Holland, P. W. H., & Graham, C. F. (1993) · Nature · doi:10.1038/361490a0 · Cited by 699 · see citing works
Phylogenomics Revives Traditional Views on Deep Animal Relationships
Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., Quéinnec, E., et al. (2009) · Current Biology · doi:10.1016/j.cub.2009.02.052 · Cited by 695 · see citing works
Duboule, D. (1994) · Development · doi:10.1242/dev.1994.supplement.135 · Cited by 634 · see citing works
Primate segmental duplications: crucibles of evolution, diversity and disease
Bailey, J. A., & Eichler, E. E. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1895 · Cited by 586 · see citing works
On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota
Xiao, S., & Laflamme, M. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.07.015 · Cited by 543 · see citing works
The rise and fall of Hox gene clusters
Duboule, D. (2007) · Development · doi:10.1242/dev.001065 · Cited by 525 · see citing works
Organizing Axes in Time and Space; 25 Years of Colinear Tinkering
Kmita, M., & Duboule, D. (2003) · Science · doi:10.1126/science.1085753 · Cited by 522 · see citing works
The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster
Brooke, N. M., Garcia-Fernàndez, J., & Holland, P. W. H. (1998) · Nature · doi:10.1038/31933 · Cited by 468 · see citing works
Classification and nomenclature of all human homeobox genes
Holland, P. W., Booth, H. A. F., & Bruford, E. A. (2007) · BMC Biology · doi:10.1186/1741-7007-5-47 · Cited by 443 · see citing works
More than just orphans: are taxonomically-restricted genes important in evolution?
Khalturin, K., Hemmrich, G., Fraune, S., Augustin, R., & Bosch, T. C. G. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.07.006 · Cited by 426 · see citing works
Genomic Evolution of Hox Gene Clusters
Lemons, D., & McGinnis, W. (2006) · Science · doi:10.1126/science.1132040 · Cited by 385 · see citing works
Evo-Devo: Variations on Ancestral Themes
Robertis, E. M. D. (2008) · Cell · doi:10.1016/j.cell.2008.01.003 · Cited by 335 · see citing works
Error, signal, and the placement of Ctenophora sister to all other animals
Whelan, N. V., Kocot, K. M., Moroz, L. L., & Halanych, K. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1503453112 · Cited by 331 · see citing works
The Capsaspora genome reveals a complex unicellular prehistory of animals
Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M. W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., et al. (2013) · Nature Communications · doi:10.1038/ncomms3325 · Cited by 317 · see citing works
Genesis and Expansion of Metazoan Transcription Factor Gene Classes
Larroux, C., Luke, G. N., Koopman, P. A., Rokhsar, D. S., Shimeld, S. M., & Degnan, B. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn047 · Cited by 275 · see citing works
Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G., & Leys, S. P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu057 · Cited by 266 · see citing works
Ancient origin of the Hox gene cluster
Ferrier, D. E. K., & Holland, P. W. H. (2001) · Nature Reviews Genetics · doi:10.1038/35047605 · Cited by 260 · see citing works
Self-citationMarlow, H. Q., Srivastava, M., Matus, D. Q., Rokhsar, D., & Martindale, M. Q. (2009) · Developmental Neurobiology · doi:10.1002/dneu.20698 · Cited by 247 · see citing works
Ryan, J. F., Mazza, M. E., Pang, K., Matus, D. Q., Baxevanis, A. D., Martindale, M. Q., & Finnerty, J. R. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000153 · Cited by 241 · see citing works
Asymmetric Sequence Divergence of Duplicate GenesPreprint
Conant, G. C., & Wagner, A. (2003) · Genome Research · doi:10.1101/gr.1252603 · Cited by 232 · see citing works
Control of Hoxd genes' collinearity during early limb development
Tarchini, B., & Duboule, D. (2006) · Developmental Cell · doi:10.1016/j.devcel.2005.11.014 · Cited by 222 · see citing works
The advent of animals: The view from the Ediacaran
Droser, M. L., & Gehlîng, J. G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1403669112 · Cited by 215 · see citing works
Phylogenomic Insights into Animal Evolution
Telford, M. J., Budd, G. E., & Philippe, H. (2015) · Current Biology · doi:10.1016/j.cub.2015.07.060 · Cited by 213 · see citing works
The hidden biology of sponges and ctenophores
Dunn, C. W., Leys, S. P., & Haddock, S. H. D. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.03.003 · Cited by 212 · see citing works
Cellular and Subcellular Structure of Neoproterozoic Animal Embryos
Hagadorn, J. W., Xiao, S., Donoghue, P. C. J., Bengtson, S., Gostling, N. J., Pawlowska, M., Raff, E. C., Raff, R. A., Turner, F. R., Chongyu, Y., et al. (2006) · Science · doi:10.1126/science.1133129 · Cited by 199 · see citing works
Sebe-Pedros, A., de Mendoza, A., Lang, B. F., Degnan, B. M., & Ruiz-Trillo, I. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq309 · Cited by 195 · see citing works
The phylogenetic position of ctenophores and the origin(s) of nervous systems
Jákely, G., Paps, J., & Nielsen, C. (2015) · EvoDevo · doi:10.1186/2041-9139-6-1 · Cited by 189 · see citing works
Serial translocation by means of circular intermediates underlies colour sidedness in cattle
Durkin, K., Coppieters, W. R., Drögemüller, C., Ahariz, N., Cambisano, N., Druet, T., Fasquelle, C., Haile, A., Hořín, P., Huang, L., et al. (2012) · Nature · doi:10.1038/nature10757 · Cited by 179 · see citing works
Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?
Nora, E. P., Dekker, J., & Heard, É. (2013) · BioEssays · doi:10.1002/bies.201300040 · Cited by 177 · see citing works
TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis
Ikmi, A., McKinney, S. A., Delventhal, K. M., & Gibson, M. C. (2014) · Nature Communications · doi:10.1038/ncomms6486 · Cited by 165 · see citing works
Ryan, J. F., Pang, K., Program, N. C. S., Mullikin, J. C., Martindale, M. Q., & Baxevanis, A. D. (2010) · EvoDevo · doi:10.1186/2041-9139-1-9 · Cited by 160 · see citing works
Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbnessPreprint
Montavon, T., Garrec, J. L., Kerszberg, M., & Duboule, D. (2008) · Genes & Development · doi:10.1101/gad.1631708 · Cited by 148 · see citing works
Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy
Pegueroles, C., Laurie, S., & Albà, M. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst083 · Cited by 125 · see citing works
Evolution of the Hox/ParaHox gene clusters
Ferrier, D. E. K., & Minguillón, C. (2003) · The International Journal of Developmental Biology · doi:10.1387/ijdb.14756336 · Cited by 118 · see citing works
Self-citationThe Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary
Jakob, W., Sagasser, S., Dellaporta, S. L., Holland, P. W. H., Kuhn, K., & Schierwater, B. (2004) · Development Genes and Evolution · doi:10.1007/s00427-004-0390-8 · Cited by 116 · see citing works
Reconstructing the reproductive mode of an Ediacaran macro-organism
Mitchell, E. G., Kenchington, C. G., Liu, A. G., Matthews, J. J., & Butterfield, N. J. (2015) · Nature · doi:10.1038/nature14646 · Cited by 109 · see citing works
Not Born Equal: Increased Rate Asymmetry in Relocated and Retrotransposed Rodent Gene Duplicates
Cusack, B. P., & Wolfe, K. H. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl199 · Cited by 107 · see citing works
Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes
Fortunato, S., Adamski, M., Ramos, O. M., Leininger, S., Liu, J. L., Ferrier, D. E. K., & Adamska, M. (2014) · Nature · doi:10.1038/nature13881 · Cited by 104 · see citing works
Self-citationFernández-Valverde, S. L., Calcino, A., & Degnan, B. M. (2015) · BMC Genomics · doi:10.1186/s12864-015-1588-z · Cited by 101 · see citing works
Ferrier, D. E. K., & Holland, P. W. H. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00204-x · Cited by 101 · see citing works
Self-citationOu, Z., Stankiewicz, P., Xia, Z., Breman, A. M., Dawson, B., Wiszniewska, J., Szafrański, P., Cooper, M. L., Rao, M., Shao, L., et al. (2011) · Genome Research · doi:10.1101/gr.111609.110 · Cited by 97 · see citing works
Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology
Mah, J. L., Christensen‐Dalsgaard, K. K., & Leys, S. P. (2014) · Evolution & Development · doi:10.1111/ede.12060 · Cited by 96 · see citing works
The evolution of the Hox cluster: insights from outgroups
Finnerty, J. R., & Martindale, M. Q. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80037-3 · Cited by 92 · see citing works
Hox genes are not always Colinear
Monteiro, A. S., & Ferrier, D. E. K. (2006) · International Journal of Biological Sciences · doi:10.7150/ijbs.2.95 · Cited by 87 · see citing works
Self-citationPrimate genome architecture influences structural variation mechanisms and functional consequences
Gökçümen, Ö., Tischler, V., Tica, J., Zhu, Q., Iskow, R. C., Lee, E., Fritz, M. H.-Y., Langdon, A. E., Stütz, A. M., Pavlidis, P., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305904110 · Cited by 81 · see citing works
<i><scp>E</scp>oandromeda</i>and the origin of<scp>C</scp>tenophora
Tang, F., Bengtson, S., Wang, Y., Wang, X., & Yin, C. (2011) · Evolution & Development · doi:10.1111/j.1525-142x.2011.00499.x · Cited by 76 · see citing works
Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan
Hoyal Cuthill, J. F., & Conway Morris, S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408542111 · Cited by 73 · see citing works
Evolution: Ctenophore Genomes and the Origin of Neurons
Marlow, H., & Arendt, D. (2014) · Current Biology · doi:10.1016/j.cub.2014.06.057 · Cited by 71 · see citing works
Novel scenarios of early animal evolution--is it time to rewrite textbooks?
Dohrmann, M., & Worheide, G. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict008 · Cited by 71 · see citing works
Ghisalberti, M., Gold, D. A., Laflamme, M., Clapham, M. E., Narbonne, G. M., Summons, R. E., Johnston, D. T., & Jacobs, D. K. (2014) · Current Biology · doi:10.1016/j.cub.2013.12.017 · Cited by 70 · see citing works
A three-dimensionally preserved fossil polychaete worm from the Silurian of Herefordshire, England
Sutton, M. D., Briggs, D. E. G., Siveter, D. J., & Siveter, D. J. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1788 · Cited by 68 · see citing works
Characterization of taxonomically restricted genes in a phylum-restricted cell type
Milde, S., Hemmrich, G., Anton‐Erxleben, F., Khalturin, K., Wittlieb, J., & Bosch, T. C. G. (2009) · Genome biology · doi:10.1186/gb-2009-10-1-r8 · Cited by 64 · see citing works
Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity
Gaiti, F., Fernández-Valverde, S. L., Nakanishi, N., Calcino, A., Yanai, I., Tanurdžić, M., & Degnan, B. M. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv117 · Cited by 62 · see citing works
A low diversity of ANTP class homeobox genes in Placozoa
Monteiro, A. S., Schierwater, B., Dellaporta, S. L., & Holland, P. W. H. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00087.x · Cited by 61 · see citing works
Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization
Hui, J. H. L., McDougall, C., Monteiro, A. S., Holland, P. W. H., Arendt, D., Balavoine, G., & Ferrier, D. E. K. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr175 · Cited by 60 · see citing works
Self-citationDid the ctenophore nervous system evolve independently?
Ryan, J. F. (2014) · Zoology · doi:10.1016/j.zool.2014.06.001 · Cited by 55 · see citing works
Genesis and evolution of the Evx and Moxgenes and the extended Hox and ParaHox gene clusters
Minguillón, C., & García‐Fernàndez, J. (2003) · Genome biology · doi:10.1186/gb-2003-4-2-r12 · Cited by 55 · see citing works
Ghost Loci Imply Hox and ParaHox Existence in the Last Common Ancestor of Animals
Ramos, O. M., Barker, D., & Ferrier, D. E. K. (2012) · Current Biology · doi:10.1016/j.cub.2012.08.023 · Cited by 53 · see citing works
Self-citationNew tricks with old genes: the genetic bases of novel cnidarian traits
Forêt, S., Knack, B., Houliston, E., Momose, T., Manuel, M., Quéinnec, É., Hayward, D. C., Ball, E. E., & Miller, D. J. (2010) · Trends in Genetics · doi:10.1016/j.tig.2010.01.003 · Cited by 51 · see citing works
A century of homeosis, a decade of homeoboxes.
McGinnis, W. J. (1994) · Genetics · doi:10.1093/genetics/137.3.607 · Cited by 51 · see citing works
The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon
Lorenzen, M. D., Gnirke, A., Margolis, J. S., Garnes, J. A., Campbell, M., Stuart, J. J., Aggarwal, R., Richards, S., Park, Y., & Beeman, R. W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800444105 · Cited by 50 · see citing works
The Early ANTP Gene Repertoire: Insights from the Placozoan Genome
Schierwater, B., Kamm, K., Srivastava, M., Rokhsar, D. S., Rosengarten, R. D., & Dellaporta, S. L. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002457 · Cited by 44 · see citing works
A vanished history of skeletonization in Cambrian comb jellies
Ou, Q., Xiao, S., Han, J., Sun, G., Zhang, F., Zhang, Z., & Shu, D. (2015) · Science Advances · doi:10.1126/sciadv.1500092 · Cited by 43 · see citing works
Takahashi, T., McDougall, C., Troscianko, J. T., Chen, W.-C., Jayaraman-Nagarajan, A., Shimeld, S. M., & Ferrier, D. E. K. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-240 · Cited by 41 · see citing works
Self-citationRamos, O. M., & Ferrier, D. E. K. (2012) · International Journal of Evolutionary Biology · doi:10.1155/2012/846421 · Cited by 40 · see citing works
Self-citationHui, J. H. L., Holland, P. W. H., & Ferrier, D. E. K. (2008) · Evolution & Development · doi:10.1111/j.1525-142x.2008.00286.x · Cited by 36 · see citing works
Self-citationCircular DNA Intermediate in the Duplication of Nile Tilapia vasa Genes
Fujimura, K., Conte, M. A., & Kocher, T. D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0029477 · Cited by 33 · see citing works
Fortunato, S. A. V., Adamski, M., & Adamska, M. (2015) · Marine Genomics · doi:10.1016/j.margen.2015.07.008 · Cited by 31 · see citing works
Ferrier, D. E. K. (2010) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-6673-5_6 · Cited by 19 · see citing works
Self-citationStatistical Tests between Competing Hypotheses of Hox Cluster Evolution
Lanfear, R., & Bromham, L. D. (2008) · Systematic Biology · doi:10.1080/10635150802430079 · Cited by 16 · see citing works
Wonderful Ediacarans, wonderful cnidarians?
Erwin, D. H. (2008) · Evolution & Development · doi:10.1111/j.1525-142x.2008.00234.x · Cited by 14 · see citing works
Remodelling of a homeobox gene cluster by multiple independent gene reunions in Drosophila
Chan, C., Jayasekera, S., Kao, B., Páramo, M., von Grotthuss, M., & Ranz, J. M. (2015) · Nature Communications · doi:10.1038/ncomms7509 · Cited by 13 · see citing works
Katju, V. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-73 · Cited by 10 · see citing works
Early evolutionary history and genomic features of gene duplicates in the human genome
Bu, L., & Katju, V. (2015) · BMC Genomics · doi:10.1186/s12864-015-1827-3 · Cited by 7 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- Ryan JF, Pang K, Schnitzler CE, et al. The genome of the cteno- hore Mnemiopsis leidyi and its implications for cell type evolu- tion. Science 2013;342:1242592.
- Valentine JW. On the Origin of Phyla. Chicago and London: University of Chicago Press, 2004, 75.
- Tang F, Bengtson S, Wang Y, et al. Eoandromeda and the origin of Ctenophora. Evol Dev 2011;13(5):408-14.
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Self-citationEvolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication
Aase-Remedios, M. E., Janßen, R., Leite, D. J., Sumner‐Rooney, L. H., & McGregor, A. P. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad239 · Cited by 35 · see citing works
Li, Y., Nong, W., Baril, T., Yip, H. Y., Swale, T., Hayward, A., Ferrier, D. E. K., & Hui, J. H. L. (2020) · BMC Genomics · doi:10.1186/s12864-020-07027-6 · Cited by 36 · see citing works
Self-citationThe enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge
Schierwater, B., Osigus, H., Bergmann, T., Blackstone, N. W., Hadrys, H., Hauslage, J., Humbert, P. O., Kamm, K., Kvansakul, M., Wysocki, K., et al. (2021) · BioEssays · doi:10.1002/bies.202100080 · Cited by 32 · see citing works
“[61,73,74] Other speculations even comprise the potential loss of a Hox gene in this context.[75] However, in the absence of any confirmed fossil records and solid phylogenetic trees for early metazoan radiation the way from such speculations to valid scientific hypotheses in sensu stricto”
BackgroundPhylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum
Tessler, M., Neumann, J. S., Kamm, K., Osigus, H., Eshel, G., Narechania, A., Burns, J. A., DeSalle, R., & Schierwater, B. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.1016357 · Cited by 28 · see citing works
“…also suggests that the bauplan of placozoans has remained the same for hundreds of millions of years, they certainly underwent genome evolution between their origin and the more recent radiation (Ax, 1996; Dohrmann and Wörheide, 2013; Ferrier, 2016; Laumer et al., 2018; Schierwater et al., 2021a).”
BackgroundCtenophores: an evolutionary-developmental perspective
Jager, M., & Manuel, M. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.05.020 · Cited by 25 · see citing works
Seeking Sense in the Hox Gene Cluster
Gaunt, S. J. (2022) · Journal of Developmental Biology · doi:10.3390/jdb10040048 · Cited by 21 · see citing works
Naked chancelloriids from the lower Cambrian of China show evidence for sponge-type growth
Cong, P., Harvey, T. H. P., Williams, M., Siveter, D. J., Siveter, D. J., Gabbott, S. E., Li, Y., Wei, F., & Hou, X. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.0296 · Cited by 20 · see citing works
Hox, homology, and parsimony: An organismal perspective
Wanninger, A. (2023) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2023.01.007 · Cited by 16 · see citing works
A Look Back Over 20 Years of Evo-Devo Studies on Sponges: A Challenged View of Urmetazoa
Schenkelaars, Q., Vernale, A., Fierro‐Constaín, L., Borchiellini, C., & Renard, E. (2019) · Springer eBooks · doi:10.1007/978-3-030-30363-1_7 · Cited by 13 · see citing works
Two more Posterior Hox genes and Hox cluster dispersal in echinoderms
Szabó, R., & Ferrier, D. E. K. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1307-x · Cited by 14 · see citing works
“Hox genes encode a family of homeodomain-containing transcription factors that are renowned for conserved roles in the patterning of the anterior-posterior axis of bilaterian animals, and they may well have more ancient roles in animal axial development [1, 2].”
BackgroundSelf-citationEvolution: Directives from Sea Anemone Hox Genes
Technau, U., & Genikhovich, G. (2018) · Current Biology · doi:10.1016/j.cub.2018.09.040 · Cited by 14 · see citing works
Symmetry Transformations in Metazoan Evolution and Development
Isaeva, V. V., & Kasyanov, N. V. (2021) · Symmetry · doi:10.3390/sym13020160 · Cited by 13 · see citing works
“The emergence and evolutionary expansion of Hox genes, and their clusters, as well as the related genes of the ParaHox and NK clusters, accompanied by the loss of some genes, provided the genetic basis for the evolutionary transformations and diversifications of body plans in Bilateria [35,36,66,72,79].”
BackgroundInfluentialKostyuchenko, R. P., & Amosov, A. V. (2023) · Genes · doi:10.3390/genes14071501 · Cited by 5 · see citing works
Marine genomics: insights and challenges
Oleksiak, M. F. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw028 · Cited by 5 · see citing works
On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model
He, C., Han, T., Liao, X., Guan, R., Chen, J.-Y., Tremblay, K. D., & Lu, Z. (2020) · Gene Expression Patterns · doi:10.1016/j.gep.2020.119125 · Cited by 3 · see citing works
Evolutionary Trends in Hox Cluster Genes Utilization: Whether Common Genes Play by General Rules?
Kulakova, M. A. (2018) · Paleontological Journal · doi:10.1134/s0031030118140101 · Cited by 4 · see citing works
“The discovery of ghost clusters in genomes of Trichoplax and sponge results in a special intrigue (Mendivil Ramos et al., 2012; Fortunato et al., 2014; Ferrier, 2016).”
BackgroundThe Homeobox Genes: Classification, Regulation, Biological Functions, and Diseases
Dadzadi, M., Ramazi, S., Darvazi, M., Yoosefi, S., Abbasi, M., & Farsad, S. (2026) · MedComm · doi:10.1002/mco2.70651 · Cited by 6 · see citing works
Glutamate and GABA Receptors of Nerveless Animals (Placozoa): Preadaptation to Neurotransmission
Nikitin, M. A., & Borman, S. I. (2024) · Biology Bulletin Reviews · doi:10.1134/s2079086424010067 · Cited by 2 · see citing works
Glutamate and GABA receptors in non-neural animals (Placozoa): Preadaptation to neural transmission
Nikitin, M. A., & Borman, S. I. (2023) · Журнал общей биологии · doi:10.31857/s0044459623030053
Li, Y., Nong, W., Baril, T., Yip, H. Y., Swale, T., Hayward, A., Ferrier, D. E. K., & Hui, J. H. L. (2020) · Figshare · doi:10.6084/m9.figshare.13100695
Self-citationLi, Y., Nong, W., Baril, T., Yip, H. Y., Swale, T., Hayward, A., Ferrier, D. E. K., & Hui, J. H. L. (2020) · Figshare · doi:10.6084/m9.figshare.13100692
Self-citationBuckenmeyer, A., Abalde, S., Ryan, J. F., & Jondelius, U. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag094
- Authors
- Ferrier, D. E. K.
- Affiliations
- University of St Andrews (GB)
- Corresponding author
- Ferrier, David E.K.
- ORCID
- Ferrier, David E.K.
- Venue
- Briefings in Functional Genomics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-12-04
- Volume
- 15
- Issue
- 5
- Pages
- 333-341
- ISSN
- 2041-2647 (ISSN-L)
- 2041-2649
- 2041-2657
- OpenAlex
- W2190160250
- Cited by
- 28
- References
- 87
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 4 · 2022: 2 · 2021: 2 · 2020: 4 · 2019: 1 · 2018: 5 · 2017: 2 · 2016: 5
- FWCI
- 0.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Briefings in Functional Genomics (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- St Andrews Research Repository (St Andrews Research Repository) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Hox genes, ParaHox genes, developmental control genes, animal origins, gene loss, comb jellies, placozoans, sponges, Ctenophora, Placozoa, ancestral state reconstruction
- MeSH terms
- Animals, Gene Expression Regulation, Genes, Homeobox, Porifera, Genome, Gene Expression Regulation, Developmental, Evolution, Molecular
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