Shimeld Lab Research

Animals come in a huge diversity of body forms. We seek to understand the evolutionary origins of this diversity, using tools drawn from ecology, developmental biology, evolutionary biology, molecular biology, genomics and bioinformatics. For an introduction to some of the species we work with, see my Favourite Animals section. Below describes some of the core research questions, with links to the relevant publications detailing our findings. Scroll down or link via the list below:

 

Vertebrate origins: genes, organs, tissues and cell types

At both the genetic and morphological level vertebrates seem to be a lot more complicated than their invertebrate relatives. Vertebrates appear to have invented a number of new tissues, such as the neural crest and placodes, and to have massively elaborated others, such as the brain and spinal cord. They also have more regulatory genes than their invertebrate relatives, with most families of transcription factor and signalling molecule genes having expanded by gene duplication during early vertebrate evolution. We are investigating how both molecular and morphological complexity has evolved. Using molecular and embryological methods we are characterising the development of animals such as ascidians, amphioxus and lampreys, lineages of living creatures which span the origin of vertebrates. A special emphasis is placed on unravelling the changing roles of regulatory gene networks involved in the development of vertebrate specific morphology. Within this broad area several specific research projects are underway, including:

  • The evolution of the vertebrate lens and crystallin genes
  • The evolutionary origin of placodes
  • Transcriptomic profiling of sensory cells and the evolution of new cell types
  • The origins of complex neural patterning

Publications in this area

Chen, W.-C., Pauls, S., Elgar, G. Bacha, J., Loose, M. and Shimeld, S.M. (2014) Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Dev. Biol. 390: 261-272.
Patthey, C., Schlosser, G. and Shimeld, S,M. (2014). The evolutionary history of vertebrate cranial placodes-I: Cell type evolution. Dev. Biol. 389: 82-97
Doglio, L,. Goode, D.K., Pelleri, M.C., Pauls, S., Frabetti, F., Shimeld, S.M., Vavouri, T., Elgar, G. (2013). Parallel Evolution of Chordate Cis-Regulatory Code for Development. PLOS Genetics DOI: 10.1371/journal.pgen.1003904.
Graham, A. and Shimeld, S.M. (2013). The origin and evolution of the ectodermal placodes. J. Anat. 222: 32-40.
Shimeld, S.M. and Donoghue, P.J. (2012) Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish). Development 139: 2091-2099.
Thompson, H., Shaw, M.K., Dawe, H. and Shimeld, S.M. (2012). The formation and positioning of cilia in Ciona intestinalis embryos in relation to the generation and evolution of chordate left-right asymmetry. Dev. Biol. 364: 214-223.
Wotton, K, Mazet, F. and Shimeld, S.M. (2008). Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for Fox genes in vertebrate development. Dev Dynamics 237:1590-1603.
Shimeld, S.M., van den Heuvel, M., Dawber, R. and Briscoe, J. (2007) An Amphioxus Gli Gene Reveals Conservation of Midline Patterning and the Evolution of Hedgehog Signalling Diversity in Chordates. PLoS One 9: e864.
Riyahi, K. and Shimeld, S.M. (2007). Chordate beta-gamma crystallins and the evolutionary developmental biology of the vertebrate lens. Comp Biochem Physiol B 147: 347-357.
Shimeld, S.M., Purkiss, A.G., Dirks, R.P.H., Bateman, O.A, Slingsby, C. and Lubsen, N.H. Urochordate βγ-crystallin and the evolutionary origin of the vertebrate eye lens. Current Biology, 15: 1684-1689.
Mazet, F., Hutt, J.A., Milloz, J., Millard, J., Graham, A. and Shimeld, S.M. (2005). Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev Biol  282: 494-508.
Mazet, F. and Shimeld, S.M. (2005) Evolutionary origin of vertebrate cranial sensory placodes. J Exp Zool B Mol Dev Evol 304B: 340-346.
Shimeld, S.M. and Holland, N.D. (2005) Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms. Can J Zool 83: 90-100.
Mazet, F. Masood, S., Luke, G.N., Holland, N.D. and Shimeld, S.M. (2004) Expression of AmphiCoe, an amphioxus COE/EBF gene, in the developing central nervous system and epidermal sensory neurons. Genesis 38: 58-65.
Mazet, F. and Shimeld, S.M. (2003) Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock. Dev Genes Evol.213: 505-509.
Gostling, N.J. and Shimeld, S.M. Protochordate Zic genes define primitive somite compartments and highlight molecular changes underlying neural crest evolution. Evol Dev5: 136-144.
Mazet, F. and Shimeld, S.M. (2002) The evolution of chordate neural segmentation Dev Biol 251: 258-270.
Boorman, C.J.  and Shimeld, S.M. (2002) Cloning and expression of a Pitx homeobox gene from the lamprey, a jawless vertebrate. Dev Genes Evol 212: 349-353.
Knight, R.D., Panopoulou, G.D., Holland, P.W.H. and Shimeld, S.M. (2000). An amphioxus Krox gene: Insights into vertebrate hindbrain evolution. Dev Genes Evol 210: 518-521.

 

Axes, symmetry and asymmetry

Most living animals are members of the Bilateria and are, as the name suggests, at least superficially bilaterally symmetrical. Establishing bilateral symmetry follows from establishing definitive AP and DV axes, with midline cells often taking on an organising role. However the embryos of many species also deliberately break bilateral symmetry, forming asymmetric bodies with definitive if subtle left and right sides: the asymmetric placement of our own internal organs, and the spiral coiling of snail shells are examples of this.

We are using a variety of species (mollusc, annelid, amphioxus, lamprey) to dissect the evolution of the mechanisms that generate distinct left and right sides. We use confocal, EM and timelapse imaging to follow the initial breaking of symmetry during early cleavage, gene and signalling pathway manipulation to understand how this is transferred to asymmetric gene expression, and the tools of developmental biology to establish how such molecular asymmetry is then propagated.

 

Publications in this area

Namigai, E.O., Kenny, N.J. and Shimeld, S.M. (2014). Right across the tree of life: the evolution of left right asymmetry in the Bilateria. Genesis .
Thompson, H., Shaw, M.K., Dawe, H. and Shimeld, S.M. (2012). The formation and positioning of cilia in Ciona intestinalis embryos in relation to the generation and evolution of chordate left-right asymmetry. Dev. Biol. 364: 214-223.
Shimeld, S. M. and Levin, M. (2006). Evidence for the regulation of left-right asymmetry in Ciona by ion flux. Dev Dynamics 235: 1543-1553.
Shimeld, S.M. (2004). Calcium turns sinister in left-right asymmetry. Trends Genet 20: 277-280.
Boorman, C.J.  and Shimeld, S.M. (2002) Cloning and expression of a Pitx homeobox gene from the lamprey, a jawless vertebrate. Dev Genes Evol 212: 349-353.
Boorman, C.J.  and Shimeld, S.M. (2002) Pitx homeobox genes in Ciona and amphioxus show left-right asymmetry is a conserved chordate character and define the ascidian adenohypophysis. Evol Dev 4: 354-365.
Boorman, C.J. and Shimeld, S.M. (2002) The evolution of chordate left right asymmetry. Bioessays 24: 1004-1011.

 

Gene diversification in animal evolution

The duplication of genes is of common occurrence in evolution. For example early vertebrate evolution is marked by widespread gene duplication resulting from duplication of the entire genome. We are using molecular phylogenetic approaches, coupled with genome sequencing of key taxa, to reconstruct the evolution of complex gene families. Such approaches allow us to ask when gene duplications have occurred, and just as importantly when genes have been lost and how orthologous genes have diverged in different lineages. We focus on ‘developmental’ genes, that is those involved in transcriptional control, intercellular signalling and tissue integrity, mapping changes onto phylogeny and allowing the construction of testable hypotheses of the underlying genetic basis for macroevolutionary change.

 

Publications in this area

Paps, J., Holland, P.W.H., Shimeld, S.M. (2012). A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus? Briefings in Functional Genomics 11: 177-186.
Kenny, N. and Shimeld, S.M. (2012). Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette. Dev. Genes. Evol. DOI 10.1007/s00427-012-0416-6.
Wotton, K. and Shimeld, S.M. (2011).  Analysis of lamprey clustered Fox genes: Insight into Fox gene evolution and expression in vertebrates. Gene 489: 30-40.
Shimeld, S.M.,  Boyle, M.J., Brunet, T., Luke, G.N. and Seaver, E.C. (2010). Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster. Dev. Biol. 240: 234-248.
Shimeld, S.M., Degnan, B. and Luke, G.N. (2010). Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters. Genomics. 95: 256-260.
Yu, J.-K., Mazet, F., Chen, Y.-T., Huang, S.-W., Jung, K.-C. and Shimeld, S.M. (2008) The Fox genes of Branchiostoma floridae. Dev Genes Evol 218: 629-638.
Larroux, C., Luke, G.N.,  Koopman, P.,  Rokhsar, D.S.,  Shimeld, S.M.  and Degnan, B.M. (2008). Genesis and expansion of metazoan transcription factor gene classes Mol Biol Evol 25:980-96.
Wotton, K, Mazet, F. and Shimeld, S.M. (2008). Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for Fox genes in vertebrate development. Dev Dynamics 237:1590-1603.
Wotton, K. and Shimeld, S.M. (2006). Comparative genomics of vertebrate Fox cluster loci. BMC Genomics doi:10.1186/1471-2164-7-271.
Mazet, F., Amemiya, C. and Shimeld, S. M. (2006). An ancient Fox gene cluster in the Bilateria. Current Biology 16: R314-R316.
Mazet, F., Luke, G.N. and Shimeld, S.M. (2005) An amphioxus FoxQ1 gene is expressed in  the developing endostyle. Gene Expression Patterns 5: 313-315.
Mazet, F., Yu, J.-K.,  Liberles, D., Holland, L.Z. and Shimeld, S.M. (2003). Phylogenetic relationships of the Fox (forkhead) gene family in the Bilateria. Gene. 316: 79-89.
Yagi, K., Satou, Y, Mazet, F., Shimeld, S.M., Degnan, B., Rokhsar, D, Levine, M., Kohara, Y. and Satoh, N. (2003). A genomewide survey of developmentally relevant genes in Ciona intestinalis III.  Genes for Fox, ETS, nuclear receptors and NFκB. Dev. Genes Evol. 213: 235-244.

 

Other projects: thermotolerance in marine larvae; the evolution of shells; microRNAs in animal evolution; developmental biology of colonial ascidians

Through a combination of collaboration and exploitation of the biological, genomic and transcriptomic resources we have developed we are also investigating a number of other aspects of invertebrate evolution and development. Please see the publications below or contact me if you want to know more about any of these areas.

 

Publications in these areas

Sato, A., Bishop, J.D.D., Shimeld, S.M. (2014). Symmetrical reproductive compatibility of two species in the Ciona intestinalis (Ascidiacea) species complex, a model for marine genomics and developmental biology. Zool. Sci. 39: 369-374.
Kenny, N.J., Sin, Y.W., Shen, X., Zhe, Q., Chan, T.F., Tobe, S.S., Shimeld, S.M., Chu, K.H. and Hui, J. (2014). Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Marine Drugs. 12, 1419-1437.
Werner, G.A., Gemmell, P., Grosser, S., Hamer, R. and Shimeld, S.M. (2012). Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Mar. Biotechnol. DOI 10.1007/s10126-012-9481-0.
Kenny, N. and Shimeld, S.M. (2012). Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette. Dev. Genes. Evol. DOI 10.1007/s00427-012-0416-6.
 Gasparini, F., Shimeld, S.M., Ruffoni, E., Burighel, P. and Manni, L. (2011). Expression of a Musashi-like gene in sexual and asexual development of the colonial chordate Botryllus schlosseri and phylogenetic analysis of the protein group. J. Exp. Zool. B. 316B: 562-573.
Gasparini, F. and Shimeld, S.M. (2011) Analysis of a botryllid enriched-full-lenght cDNA library: insight into the evolution of splice leader trans-splicing in tunicates. Dev. Genes Evol. 220: 329-336.
Degasperi V, Gasparini F, Shimeld S.M., Sinigaglia, C., Burighel, P. and Manni, L. (2009) Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations. BMC Dev. Biol. 9: 48.
Takahashi, T., McDougall, C., Troscianko, J., Chen, W.C., Jayaraman-Nagarajan, A., Shimeld, S.M. and Ferrier, D.E.K. (2009) An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals. BMC Evol. Biol. 9: 240.