We study how evolution has produced a diversity of life. We are interested in learning about the actual history of life on Earth as well as the general properties of evolution that have contributed to these historical patterns. The type of questions we ask require field (marine), laboratory, and computational work. Our research falls into several domains.
Siphonophores are unique marine animals found throughout the oceans of the world. They are colonial - each siphonophore starts as a single embryo that asexually produces many genetically identical, physiologically integrated bodies. The many bodies in a siphonophore are each specialized for particular functions, such as feeding or swimming. We study the morphology, evolution, and development of siphonophores to understand this unique functional specialization.
Phylogenetics is the study of evolutionary relationships. We develop new methods and tools for understanding phylogenetic relationships, and apply these tools to animals to understand the evolution of complex traits. We are particularly interested in deep animal phylogeny, but also work on subgroups of animals including cnidarians and molluscs.
Many of the questions we are work on require new computational methods and tools. We develop and implement new methods, connect existing analysis tools in new ways, and are particularly interested in engineering analyses so that they are open, transparent, reproducible, and easy to extend. Our data analysis tools are available at bitbucket.
We sequence transcriptomes to build phylogenies and to identify genes that are differentially expressed between tissues and developmental stages. We have integrated these two approaches to now study the evolution of differential gene expression. This work provides new ways to understand the relationships between genome and phenotype evolution.
In addition to the specific domains highlighted above, we are very interested in the basic biology of animals. Since many of the animals we work on are so poorly known, these studies include descriptions of lifecycles, natural history, development, alpha taxonomy, functional biology, and morphology.
Osborn Memorial Labs, Yale, September 2017.
My CV is available here.
The evolution of development, organogenesis, and gene-phenotype relationships. My site.
Evolution and diversification of trophic niches and predatory strategies in siphonophores.
Cell type evolution, origin and evolution of complex characters, broad patterns of gene-phenotype relationships.
Evolutionary origins of mesoglea and functional morphology of siphonophore nectophores.
Body plan development and axial patterning in Hydractinia
Robotics for marine natural history observations
Origin and evolution of new levels of biological organization. Evolution and development of functional specialization in siphonophores.
Evolutionary processes, applied math. Phylogenetic algorithms and the reproducibility and accuracy of their results.
As an application scientist, I help researchers better utilize high performance computing resources.
Impacts of organic matter inputs and sea ice retreat on marine bacterial community structure in Antarctica.
Using HIV phylogenetics to better understand transmission networks.
Phylogenetics, diversity, and computational biology. I am a botanist, but enjoy animals too. My site.
The developmental biology and diversity of hydrozoans (Cnidaria).
Comparative biology and phylogenetics, as well as developmental biology. Histology and development of siphonophores.
Comparative biology with additional interests in conservation. Inspired by the diversity of life.
Smith, SD, MW Pennell, CW Dunn, SV Edwards (2020) Phylogenetics is the New Genetics (for Most of Biodiversity). Trends in Ecology and Evolution. doi:10.1016/j.tree.2020.01.005.
Li-Gen Wang, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, Casey W Dunn, Bradley R Jones, Tyler Bradley, Huachen Zhu, Yi Guan, Yong Jiang, Guangchuang Yu. (2019) treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. doi:10.1093/molbev/msz240. Git code repository: https://guangchuangyu.github.io/software/treeio/.
Pugh, PR, CW Dunn, SHD Haddock (2018) Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals. Zootaxa 4415(3):452–472. doi:10.11646/zootaxa.4415.3.3.
Haddock, SHD, Christianson LM, Francis WR, Martini S, Dunn CW, Pugh PR, Mills CE, Osborn KJ, Seibel BA, Choy CA, Schnitzler CE, Matsumoto GI, Messié M, Schultz DT, Winnikoff JR, Powers ML, Gasca R, Browne WE, Johnsen S, Schlining KL, von Thun S, Erwin BE, Ryan JF, Thuesen EV (2018) Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology. Oceanography 30:38-47. doi:10.5670/oceanog.2017.422.
Munro, C, S Siebert, F Zapata, M Howison, A Damian-Serrano, SH Church, FE Goetz, PR Pugh, SHD Haddock, CW Dunn (2018) Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2018.06.030. bioRxiv preprint: doi:10.1101/251116. Git code repository: https://github.com/caseywdunn/siphonophore_phylogeny_2017.
Dunn, CW, F Zapata, C Munro, S Siebert, A Hejnol (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. PNAS. doi:10.1073/pnas.1707515115. bioRxiv preprint: doi:10.1101/107177. Git code repository: https://github.com/caseywdunn/comparative_expression_2017. (pdf)
Dunn, CW (2017) Ctenophore trees. Nature Ecology and Evolution. doi:10.1038/s41559-017-0359-4.
Zapata, F, FE Goetz, SA Smith, M Howison, S Siebert, S Church, SM Sanders, CL Ames, CS McFadden, SC France, M Daly, AG Collins, SHD Haddock, CW Dunn, P Cartwright (2015) Phylogenomic analyses support traditional relationships within Cnidaria. PLoS One 10(10): e0139068. doi:10.1371/journal.pone.0139068. bioRxiv preprint: doi:10.1101/017632. Git code repository: https://bitbucket.org/caseywdunn/cnidaria2014. (pdf)
Siebert, S, FE Goetz, SH Church, P Bhattacharyya, F Zapata, SHD Haddock, and CW Dunn. (2015) Stem Cells in a Colonial Animal with Localized Growth Zones. EvoDevo 6:22. doi:10.1186/s13227-015-0018-2. bioRxiv preprint: doi:10.1101/001685. Git code repository: https://bitbucket.org/caseywdunn/siebert_etal. (pdf)
Zapata, F, NG Wilson, M Howison, SCS Andrade, KM Jörger, Michael Schrödl, Freya E Goetz, Gonzalo Giribet, Casey W Dunn (2014) Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proceedings of the Royal Society B: Biological Sciences 281:1471-2954. doi:10.1098/rspb.2014.1739 (pdf). bioRxiv preprint: doi:10.1101/007039. Git code repository: https://bitbucket.org/caseywdunn/gastropoda.
Howison, M, F Zapata, EJ Edwards, and CW Dunn (2014) Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling. PLoS One 9:e99497. doi:10.1371/journal.pone.0099497. arXiv preprint: 1308.1388. Git code repository: https://bitbucket.org/mhowison/gabi. Example analysis report: https://web3.ccv.brown.edu/mhowison/gabi-report/ (pdf)
Ryan, JF, K Pang, CE Schnitzler, A Nguyen, RT Moreland, DK Simmons, BJ Koch, WR Francis, P Havlak, NISC Comparative Sequencing Program, SA Smith, NH Putnam, SHD Haddock, CW Dunn, TG Wolfsberg, JC Mullikin, MQ Martindale, AD Baxevanis (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 432:1242592. doi:10.1126/science.1242592, PMC3920664 (pdf)
CW Dunn, M Howison, and F Zapata (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. doi:10.1186/1471-2105-14-330. arXiv preprint: 1307.6432. Git code repository: https://bitbucket.org/caseywdunn/agalma (software), https://bitbucket.org/caseywdunn/dunnhowisonzapata2013 (analyses). (pdf)
Siebert, S, MD Robinson, SC Tintori, F Goetz, RR Helm, SA Smith, N Shaner, SHD Haddock, CW Dunn (2011) Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows. PLoS One 6(7): e22953. doi:10.1371/journal.pone.0022953 (pdf)
Hejnol, A, M Obst, A Stamatakis, M Ott, G Rouse, G Edgecombe, P Martinez, J Baguñà, X Bailly, U Jondelius, M Wiens, WEG Müller, Elaine Seaver, WC Wheeler, MQ Martindale, G Giribet, and CW Dunn (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B. 276:4261-4270 doi:10.1098/rspb.2009.0896 (pdf). Git repository: https://bitbucket.org/caseywdunn/hejnol_etal_2009.
Giribet, G, CW Dunn, GD Edgecombe, A Hejnol, MQ Martindale, and GW Rouse (2009) Assembling the spiralian tree of life (p 52-64) In: Animal Evolution. MJ Telford and DTJ Littlewood (eds). Oxford University Press.
Dunn, CW, A Hejnol, DQ Matus, K Pang, WE Browne, SA Smith, E Seaver, GW Rouse, M Obst, GD Edgecombe, MV Sorensen, SHD Haddock, A Schmidt-Rhaesa, A Okusu, RM Kristensen, WC Wheeler, MQ Martindale, and G Giribet (2008) Broad phylogenomic sampling improves resolution of the Animal Tree of Life. Nature. 452:745-749. doi:10.1038/nature06614 (pdf)
Giribet, G, CW Dunn, GD Edgecombe, and GW Rouse (2007) A modern look at the Animal Tree of Life. Zootaxa 1668:61-79. (pdf)
Mills, CE, AC Marques, AE Migotto, DR Calder, C Hand, JT Rees, SHD Haddock, CW Dunn, and PR Pugh. (2007) Hydrozoa: Polyps, Hydromedusae, and Siphonophora. In: The Light & Smith manual: intertidal invertebrates from central California to Oregon, 4th edition. JT Carlton (ed). University of California Press.
Dunn, CW, PR Pugh, and SHD Haddock (2005) Molecular phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization. Systematic Biology 54:916-935. doi:10.1080/10635150500354837 (pdf). Git repository: https://bitbucket.org/caseywdunn/siphonophores_2005.
Dunn, CW, PR Pugh, and SHD Haddock (2005) Marrus claudanielis, a new species of deep-sea physonect siphonophore (Siphonophora, Physonectae). Bull. Mar. Sci. 76:699-714. (pdf)
Haddock, SHD and CW Dunn (2005) The complex world of siphonophores. JMBA Global Marine Environment 2005(2):24-25. (pdf)