Billie Swalla

Billie Swalla

Research areas

Research years

Marine Genomics allows insights into the mechanisms by which evolutionary novelty evolves in animal body plans. My lab is interested in the evolution of animal body plans and uses comparative genomic approaches to understand the evolution of specific cell types and structures. We study the evolution and development of the chordates, a unique group of animals that includes vertebrates. We are studying how chordates evolved from marine invertebrates using tunicates and hemichordates. We use phylogenies and the expression of developmental genes to infer ancestral traits. We are also studying the development and evolution of ctenophores, a group of very basal metazoans. in collaboration with Professor Leonid Moroz and Dr. Andrea Kohn at the University of Florida‚ Whitney Marine Labs.

Selected publications

2017

Makabe, K. W., Hsu, J., Swalla, B. J., Satoh N., Jeffery, W. R. (2017) Cymric, a new member of the shark family of non-receptor tyrosine kinases, is expressed differentially in ascidians with different larval phenotypes. (in preparation)

2017

Wu, P.X., Seufert, D.W. and Swalla B. J. (2017) Molgulid ascidians share a unique gene complex. J. Exp. Zoolog. B Mol. Dev. Evol. (in revision)

2017

Maliska, M. E., Lowe, E., Pavangadkar, K., Weber, C., Serra, N., Brown, C. T. and Swalla B. J. (2017) Molgulid ascidians have a radical heterochronic shift in the metamorphic gene network. Mol. Biol. Evol. (in revision)

2017

Lowe, E.K., Swalla, B.J. and Brown, C.T. (2017) Assembly on Cloud 9: Transcriptome assembly of closely related Ascidian species. Genome Research (to be submitted soon)

2017

Racioppi, C. Valoroso M. C., Coppola, U., Lowe, E.K., Brown, C.T., Swalla, B.J., Christiaen, L., Stolfi, A. and Ristoratore, F. (2017) Evolutionary loss of  melanogenesis in the tunicate Molgula occulta. EvoDevo 8:11

2016

Luttrell, S., Gotting, K., Ross, E., Sánchez Alvarado, A., Swalla, B.J. (2016) Head    regeneration in hemichordates Is not a strict recapitulation of head development.  Develop. Dynamics 245:1159–1175.

2016

Presnell, J.S., Vandepas, L.E., Warren, K.J., Swalla, B.J., Amemiya, C.T. and Browne,        W.E. (2016) The presence of a functionally tripartite through-gut in Ctenophora has implications for metazoan character trait evolution. Current Biology 26:1-7        http://dx.doi.org/10.1016/j.cub.2016.08.01

2016

Tassia M.G., Cannon J.T., Konikoff C.E., Shenkar N., Halanych K.M., Swalla B.J.  (2016) The Global Diversity of Hemichordata. PLoS ONE 11(10): e0162564. doi:10.1371/journal.pone.0162564

2016

Davies, N., Field, D., Gavaghan, D., Holbrook, S. J., Planes, S., Troyer, M., Bonsall, M., Claudet, J., Roderick, G., Schmitt, R. J., Zettler, L. A., Berteaux, V., Bossin, H. C.,   Cabass, C., Collin, A., Deck, J., Dell, T., Dunne, J., Gates, R., Harfoot, M., Hench,           J.L., Hopuare, M., Kirch, P., Kotoulas, G., Kosenkov, A., Kusenko, A., Leichter, J.J., Lenihan, H., Magoulas, A., Martinez, N., Meyer, C., Stoll, B., Swalla, B.,     Tartakovsky, D.M., Murphy, H.T., Turyshev, S., Valdvinos, F., Williams, R., Wood,   S. and IDEA Consortium (2016) Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium. GigaScience 5:14 DOI 10.1186/s13742-016-0118-5

2015

Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B,     Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi    C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C,   McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P. (2015)  ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res. doi: 10.1093/nar/gkv966

2015

Stolfi, A., Sasakura, Y., Chalopin, D., Satou, Y., Christiaen, L., Dantec, C., Endo T., Naville, M., Nishida, H., Swalla, B. J., Volff,J.-N., Voskoboynik, A., Dauga, D. and Lemaire, P. (2015) Guidelines for the nomenclature of genetic elements in tunicate genomes. Genesis 53: 1-14. doi:10.1002/dvg.22822.

2015

Vandepas, L.E., Serina Lee, S.C., Oliveira, L.M., Hirose, E., Rocha, R.M. and Swalla, B.J. (2015) The native range of Phallusia nigra: Is it really black and white? Biol. Bull. (in press)

2015

Karaiskou, A. Swalla, B. J, Sasakura, Y. and Chambon J.-P. (2015) Metamorphosis in solitary ascidians. Genesis. 53: 34-47.

2014

Padilla, D.K., Daniel, T.L., Dickinson, P.S., Grünbaum, D., Hayashi, C., Manahan, D.T., Marden, J.H., Swalla, B.J. and Tsukimura, B. (2014) Addressing Grand Challenges In Organismal Biology – The Need For Synthesis. BioScience 64: 1178-1187. doi:10.1093/biosci/biu164

2014

Lowe, E. K., Swalla, B. J., and Brown, C. T. (2014) Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species. Peer J preprint.

2014

Stolfi, A., Sasakura, Y., Chalopin, D., Satou, Y., Christiaen, L., Dantec, C., Endo T., Naville, M., Nishida, H., Swalla, B. J., Volff,J.-N., Voskoboynik, A., Dauga, D. and Lemaire, P. (2014) Guidelines for the nomenclature of genetic elements in tunicate genomes. Genesis. 53: 1-14. doi:10.1002/dvg.22822.

2014

Cannon, J.T. Kocot, K. M., Waits, D. S., Weese, D. A., Swalla, B. J., Santos, S. R., and Halanych, K. M. (2014) Phylogenomic resolution of the hemichordate and echinoderm Clade. Current Biology. 24: 1-6.

2014

Stolfi, A., Lowe, E., Racioppi, C., Ristoratore, F., Swalla, B.J., Brown, C.T. and Christiaen, L. (2014) Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. eLife 2014:3:e03728

2014

Moroz, L.L., K.M. Kocot, M.R. Citarella, S. Dosung, T.P. Norekian, I.S. Povolotskaya, A.P. Grigorenko, C. Dailey, E. Berezikov, K. M. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T.P. Moroz, Y. Bobkova, F. Yu, V.V. Kapitonov, J. Jurka, Y.V. Bobkov, J.J. Swore, D.O. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.E. Mills, J.P. Rast, R. Derelle, V.V. Solovyev, F.A. Kondrashov, B.J. Swalla, J.V. Sweedler, E.I. Rogaev, K.M. Halanych, and A.B. Kohn, 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature (June 5, 2014): 109-114. Published online May 21, 2014; corrected online June 4, 2014.

2013

Cannon J. T., Swalla, B.J., and Halanych, K. M. (2013) Hemichordate molecular phylogeny reveals a novel cold-Water clade of Harrimaniid acorn worms. Biol. Bull. 225: 194–204.

2013

Halanych, K. M., Cannon J. T., Mahon A. R., Swalla, B. J., and Smith, C. R. (2013) Modern Antarctic acorn worms form tubes. Nature Comm. 3738: 1-4.

2013

Peterson, K. J., Su Yi-H., Arnone M. I., Swalla B. J., and King B. (2013) microRNAs support the monophyly of enteropneust hemichordates. J. Exp. Zoolog. B Mol. Dev. Evol. 9999B: 1–7.

2013

Maliska, M. E., Pennell, M. W. and Swalla B.J. (2013) Developmental mode influences diversification in ascidians. Biology Letters 9: 20130068.

2012

Appeltans, W., S.T. Ahyong, G. Anderson, M.V. Angel, T. Artois, N. Bailly, R. Bamber, A. Barber, I. Bartsch, A. Berta, M. B_azewicz-Paszkowycz, P. Bock, G. Boxshall, C.B. Boyko, S. Nunes Brandão, R.A. Bray, N.L. Bruce, S.D. Cairns, T-Y. Chan, L. Cheng, A.G. Collins, T. Cribb, M. Curini-Galletti, F. Dahdouh-Guebas, P.J.F. Davie, M.N. Dawson, O. De Clerck, W. Decock, S. De Grave, N.J. de Voogd, D.P. Domning, C.C. Emig, C. Erséus, W. Eschmeyer, K. Fauchald, D.G. Fautin, S.W. Feist, C.H.J.M. Fransen, H. Furuya, O. Garcia-Alvarez, S. Gerken, D. Gibson, A. Gittenberger, S. Gofas, L. Gómez-Daglio, D.P. Gordon, M.D. Guiry, F. Hernandez, B.W. Hoeksema, R.R. Hopcroft, D. Jaume, P. Kirk, N. Koedam, S. Koenemann, J.B. Kolb, R.M. Kristensen, A. Kroh, G. Lambert, D.B. Lazarus, R. Lemaitre, M. Longshaw, J. Lowry, E. Macpherson, L.P. Madin, C. Mah, G. Mapstone, P.A. McLaughlin, J. Mees, K. Meland, C.G. Messing, C.E. Mills, T.N. Molodtsova, R. Mooi, B. Neuhaus, P.K.L. Ng, C. Nielsen, J. Norenburg, D.M. Opresko, M. Osawa, G. Paulay, W. Perrin, J.F. Pilger, G.C.B. Poore, P. Pugh, G.B. Read, J.D. Reimer, M. Rius, R.M. Rocha, J.I. Saiz-Salinas, V. Scarabino, B. Schierwater, A. Schmidt-Rhaesa, K.E. Schnabel, M. Schotte, P. Schuchert, E. Schwabe, H. Segers, C. Self-Sullivan, N. Shenkar, V. Siegel, W. Sterrer, S. Stöhr, B.J. Swalla, M.L. Tasker, E.V. Thuesen, T. Timm, M.A. Todaro, X. Turon, S. Tyler, P. Uetz, J. van der Land, B. Vanhoorne, L.P. van Ofwegen, R.W.M. van Soest, J. Vanaverbeke, G. Walker-Smith, T.C. Walter, A. Warren, G.C. Williams, S.P. Wilson, and M.J. Costello, 2012. The magnitude of global marine species diversity. Current Biology, 22: 1-14.

2012

Luttrell, S., Konikoff, C., Byrne, A., Bengtsson, B., and Swalla B.J. (2012) Ptychoderid hemichordate neurulation without a notochord. Integrative Comparative Biology 52 (6): 829-834.

2012

Brown, F.D. and Swalla, B.J. (2012) Evolution and development of budding by stem cells: Ascidian coloniality as a case study. Develop. Biology 369(2):151- 162.

2012

Fedonkin M.A., Vickers-Rich P., Swalla, B.J., Trusler P. and Hall M. (2012) A new metazoan from the Vendian of the White Sea, Russia, with possible affinities to the ascidians. Paleontological Journal 46:1-11.

2011

Oyarzun, F.X., Mahon A.R., Swalla, B.J. and Halanych, K.M. (2011) Phylogeography and reproductive variation of the poecilogonous polychaete Boccardia proboscidea (Annelida: Spionidae) along the West Coast of North America. Evolution & Development 13:6 489-503.

2011

Shenkar, N. and Swalla, B.J. (2011) Global Diversity of Ascidiaea. PLoS 1. 6:6 e20657

2010

Maliska, M. E. and Swalla, B. J. (2010) Molgula pugetiensis is a Pacific tailless ascidian within the Roscovita clade of molgulids. Biological Bulletin 219: 277-282.

2010

Lambert G., Shenkar, N. and Swalla B.J. (2010) First Pacific record of the north Atlantic ascidian Molgula citrina—bioinvasion or circumpolar distribution? Aquatic Invasions 5(4): 369-378.

2010

Shenkar, N. and Swalla, B.J. (2010) Molecular data confirm synonomy of Roscovite molgulid ascidians. Cahiers de Biologie Marine 51: 85-87.