Publications

Peer-Reviewed:

Thompson, A. W., Black, A. C., Huang, Y., Shi, Q., Furness, A. I., Braasch, I., Hoffmann. F.G., and Ortí, G. (2024). Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes. Molecular Phylogenetics and Evolution.

Domínguez-Castanedo, O., Thompson, A. W., Meredith, R. W., and Furness, A.I., (2024).

An independent origin of an annual life cycle in a North American killifish. Biological Journal of the Linnean Society.

Stareczek, S. Loureiro, M. D'Anatro, A., Thompson, A. W., and Ortí, G. (2023). River drainage rearrangements and the phylogeographic pattern of the annual fish Austrolebias arachan (Cyprinodontiformes; Rivulidae). Zoologica Scripta.

Mathavarajah, S., Thompson, A. W., Stoye, M. R., T., Quinn, T. A., Roy, S., Braasch, I., and Dellaire, G. Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates. (2024). Journal of Experimental Zoology, Part B, Molecular and Developmental Evolution.

Berbel-Filho, W. M., Pirro, S., Thompson, A. W., Lima, S. M., Consuegra, S., and Betancur, R. (2023). The Complete Genome Sequences of three species from the killifish genus Kryptolebias (Rivulidae, Cyprinodontiformes). Biodiversity Genomes.

Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Bucao, C., Floi, Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W., Zahm, M., Cabau, C., Klopp, C., Thompson, A. W., Robinson-Rechavi, M., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J. H., Berthelot, C., Crollius, H. R, and Guiguen, Y. (2023). Genome structures resolve the early diversification of teleost fishes. Genome structures resolve the early diversification of teleost fishes. Science.

Thompson, A. W., Wojtas, H., Davoll, M., and Braasch, I. (2022). Genome of the bi-annual Rio Pearlfish (Nematolebias whitei), a killifish model species for Eco-Evo-Devo. G3: Genes | Genomes | Genetics.

Thompson, A. W., Hawkins, M. B., Parey, E., Wcisel, D. J., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O. E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B. L., Childs, K. L., Fontenot, Q., Ferrara, A., David, S. R., McCune, A. R., Dornburg, A., Yoder, J. A., Guiguen, Y., Crollius, H. R., Berthelot, C., Harris, M. P., and Braasch, I. (2021). The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nature Genetics.

Mikami, M., Ineno, T., Thompson, A. W., Braasch, I., Ishiyama, M., and Kawasaki, K. (2022). Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians. Gene.

Dornburg, A., Wcisel, D. J., Zapfe, K., Ferraro, E., Roupe-Abrams, L., Thompson, A. W., Braasch, I., Ota, T., and Yoder, J. A. (2021). Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system. Immunogenetics.

Enny, A., Shanabag, A., Thompson, A. W., Racicot, B., Braasch, I., and Nakamura, T. (2021). Cellular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus).

Developmental Dynamics.

Ålund, M., Emery, N., Jarrett, B. J. M., MacLeod, K. J., McCreery, H. F., Mamoozadeh, N., Phillips, J. G., Schossau, J., Thompson, A. W., Warwick, A. R., Yule, K. M., Zylstra, E. R., and Gering, E. (2020). Academic ecosystems must evolve to support a sustainable postdoc workforce. Nature Ecology and Evolution.

Darnet, S., Dragalzew, A. C., Amaral, D. B., Sousa, J. F., Thompson, A. W., Cass, A. N., Lorena, J., Pires, E. S., Costa, C. M., Sousa, M. P., Fröbisch, N. B., Oliveira, G., Schneider, P. N., Davis, M. C., Braasch, I., and Schneider, I. (2019). Deep evolutionary origin of limb and fin regeneration. Proceedings of the National Academy of Sciences.

Hughes, L. C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C. C., Thompson, A. W., Arcila D., Betancur-R., R., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B., Zhou, Z., Huang, H., Chen, S., Venkatesh, B., and Shi, Q. (2018). Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences.

Wentworth, S. A., Thede, K., Aravindabose, V., Monroe, I., Thompson, A. W., Molyneaux, N., Owen, C. L., Burns, J. R., Vicente, A. G., Garvin, J. L., and Packer, R. K. (2018). Transcriptomic analysis of changes in gene expression of immune proteins of gill tissue in response to low environmental temperature in fathead minnows (Pimephales promelas). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics.

Thompson, A. W., Hayes, A., Podrabsky, J. E., and Ortí, G. (2017). Gene expression during delayed hatching in fish-out-of-water. Ecological Genetics and Genomics.

Thompson, A. W., Furness, A. I., Stone, C., Rade, C., and Ortí, G. (2017). Microanatomical diversification of the zona pellucida in aplochelioid killifishes. Journal of Fish Biology.

Thompson, A. W., and Ortí, G. (2016). Annual killifish transcriptomics and candidate genes for metazoan diapause. Molecular Biology and Evolution.

Thompson, A. W., Betancur-R., R., López-Fernández, H., and Ortí, G. (2014). A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods. Molecular Phylogenetics and Evolution.

Publications in Review and Revision:

Bucao, C.F., Aletti, C., Moretti, S., Thompson, A. W., Racicot, B. L., Wilson, C. A., Bobe, J., Braasch, I., Guiguen, Y., Postlethwait, J. H., Robinson-Rechavi, M. Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs.

https://www.biorxiv.org/content/10.1101/2024.11.11.623020v1.full.pdf+html

Book Chapters:

Thompson, A. W., Rohner, N. (2024) Genome Evolution’s Role in Developmental Evolution.

Theses and Dissertations:

Thompson, A. W. (2016). The evolution of chorionic ultrastructure, delayed hatching, and desiccation tolerance in annual killifishes. Doctoral Dissertation, The George Washington University, 105 pages.

Outreach and Media:

Thompson, A. W. (2022). A day in the life of a killifish lab, The Node. https://thenode.biologists.com/a-day-in-the-life-of-a-killifish-lab/lablife/

Thompson, A. W. (2016). Delayed hatching in killifish. Journal of the American Killifish Association, 49:171-185.

Photography of killifish embryo featured on the back cover of Fisheries Vol. 41 • No. 10 • October 2016.