Welcome to the Dunn Lab
Evolution/ Zoology
About

About

-

The Dunn Lab is in the Department of Ecology and Evolutionary Biology at Brown University.

- -

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.

CreatureCast - How Siphonophores Grow. A CreatureCast animation by Riley Thompson that explains some of what we have learned about how siphonophores grow. See our medium post for more.

  • Siphonophores

    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.

  • Animal phylogenetics

    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.

  • Methods and tools

    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.

  • Evolution of gene expression

    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.

  • Zoology

    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.

People

Lab members

Brown University Green, fall of 2013.

Casey Dunn

Principal Investigator

My CV is available here.

Zack Lewis

Postdoc

The evolution of development, organogenesis, and gene-phenotype relationships. My site.

Mark Howison

Application Scientist

As an application scientist, I help researchers better utilize high performance computing resources.

Cat Munro

Graduate Student

Origin and evolution of new levels of biological organization. Evolution and development of functional specialization in siphonophores.

August Guang

Graduate Student

Evolutionary processes, applied math. Phylogenetic algorithms and the reproducibility and accuracy of their results.

Cat Luria

Graduate Student

Impacts of organic matter inputs and sea ice retreat on marine bacterial community structure in Antarctica.

Alex Damian Serrano

Graduate Student

Evolution and diversification of trophic niches and predatory strategies in siphonophores.

Felipe Zapata (alum, 2016)

Postdoc

Phylogenetics, diversity, and computational biology. I am a botanist, but enjoy animals too. My site.

Stefan Siebert (alum, 2015)

Postdoc

The developmental biology and diversity of hydrozoans (Cnidaria).

Rebecca Helm (alum, 2015)

Graduate Student

Evolution of development in cnidarians, as well as their systematics and natural history. My site, my contributions to Deep Sea News.

Sam Church (alum, 2015)

Undergrad Student

Comparative biology and phylogenetics, as well as developmental biology. Histology and development of siphonophores.

Nicola Malakooti (alum, 2016)

Undergraduate Student

Comparative biology with additional interests in conservation. Inspired by the diversity of life.

Links

Some projects and resources

Practical Computing

A book about computing skills

CreatureCast

Cartoons about science

Open Content

Images, code, teaching resources

Siphonophores.org

A site about siphonophores

Agalma

A phylogenetics tool

Brown EEB

Our home department

Publications

Dunn, CW, C Munro (2016) Comparative genomics and the diversity of life. Zoologica Scripta 45:5-13. doi:10.1111/zsc.12211.

Hejnol, A, CW Dunn (2016) Animal Evolution: Are Phyla Real? Current Biology 26:R424–R426. doi:10.1016/j.cub.2016.03.058.

Guang, A, F Zapata, M Howison, CE Lawrence, CW Dunn (2016) An Integrated Perspective on Phylogenetic Workflows. Trends in Ecology and Evolution 31:116-126. doi:10.1016/j.tree.2015.12.007.

Dunn, CW (2015) Acorn worms in a nutshell. Nature 527:448-449. doi:10.1038/nature16315.

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.

Dunn, CW, JT Ryan (2015) The evolution of animal genomes. Current Opinion in Genetics and Development 35:25-32. doi:10.1016/j.gde.2015.08.006.

Haddock, SH, CW Dunn (2015) Fluorescent proteins function as a prey attractant: experimental evidence from the hydromedusa Olindias formosus and other marine organisms. Biology Open 4:1094-1104. doi:10.1242/​bio.012138.

Church, SH, JF Ryan, CW Dunn (2015) Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT. Systematic Biology 64(6): 1048-1058. doi:10.1093/sysbio/syv055. bioRxiv preprint: doi:10.1101/005264. Git code repository: https://github.com/josephryan/sowhat.

Laumer, CE, N Bekkouche, A Kerbl, F Goetz, RC Neves, MV Sørensen, RM Kristensen, A Hejnol, CW Dunn, G Giribet, K Worsaae (2015) Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15):2000-2006. doi:10.1016/j.cub.2015.06.068.

Church, SH, S Siebert, P Bhattacharyya, CW Dunn (2015) The Histology of Nanomia bijuga (Hydrozoa: Siphonophora). J. Exp. Zool. (Mol. Dev. Evol.) 324(5):435-449. doi:10.1002/jez.b.22629. bioRxiv preprint: doi:10.1101/010868.

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.

Salinas-Saavedra, M, TQ Stephenson, CW Dunn, MQ Martindale (2015) Par system components are asymmetrically localized in ectodermal epithelia, but not during early development in the sea anemone Nematostella vectensis. EvoDevo 6:20. doi:10.1186/s13227-015-0014-6.

Helm, RR, S Tiozzo, MKS Lilley, F Lombard, CW Dunn (2015) Comparative muscle development of scyphozoan jellyfish with simple and complex life cycles. EvoDevo 6:11. doi:10.1186/s13227-015-0005-7.

Dunn, CW, SP Leys, SHD Haddock (2015) The hidden biology of sponges and ctenophores. Trends in Ecology and Evolution 30:282-291. doi:10.1016/j.tree.2015.03.003

Reich, A, CW Dunn, K Akasaka, G Wessel (2015) Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa. PLoS One 10:e0119627. doi:10.1371/journal.pone.0119627

Gonzalez, VL, SCS Andrade, R Bieler, TM Collins, CW Dunn, PM Mikkelsen, JD Taylor, G Giribet (2015) A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proceedings of the Royal Society B: Biological Sciences 282:20142332. doi:10.1098/rspb.2014.2332 (pdf).

Dunn, CW, G Giribet, GD Edgecombe, A Hejnol (2014) Animal Phylogeny and its Evolutionary Implications. Annual Review of Ecology, Evolution, and Systematics 45:371–395. doi:10.1146/annurev-ecolsys-120213-091627. Supplemental summary figure.

Dunn, CW (2014) Reconsidering the phylogenetic utility of miRNA in animals. PNAS 111:12576–12577. doi:10.1073/pnas.1413545111 (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/

Lopez, J, H Bracken-Grissom, A Collins, T Collins, K Crandall, D Distel, C Dunn, et al. (2014) Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity 105:1-18. doi:10.1093/jhered/est084 (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).

Howison, M, F Zapata, CW Dunn (2013) Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 29:2959-2963. doi:10.1093/bioinformatics/btt525 (pdf)

Siebert, S, PR Pugh, SHD Haddock, CW Dunn (2013) Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa 3702: 201–232. doi:10.11646/zootaxa.3702.3.1 (pdf)

Dunn, CW, X Luo, Z Wu (2013) Phylogenetic analysis of gene expression. Integrative and Comparative Biology 53:847-856. doi:10.1093/icb/ict068 (pdf). arXiv preprint: 1302.2978. Git code repository: https://bitbucket.org/caseywdunn/sicb2013.

Helm, RR, S Siebert, S Tulin, J Smith, CW Dunn (2013) Characterization of differential transcript abundance through time during Nematostella vectensis development. BMC Genomics 14:266. doi:10.1186/1471-2164-14-266. Git code repository: https://bitbucket.org/caseywdunn/helm_etal_2013.

Dunn, CW (2013) Evolution: Out of the Ocean. Current Biology 23:R242-R243. doi:10.1038/10.1016/j.cub.2013.01.06 (pdf)

Howison, M, N Sinnott-Armstrong, CW Dunn (2012) BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP12). video, pdf. Git code repository: https://bitbucket.org/caseywdunn/biolite.

Smith, SA, NG Wilson, F Goetz, C Feehery, SCS Andrade, GW Rouse, G Giribet, CW Dunn (2011) Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367. doi:10.1038/nature10526 (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)

Edgecombe, GD, G Giribet, CW Dunn, A Hejnol, RM Kristensen, RC Neves, GW Rouse, K Worsaae, and MV Sørensen (2011) Higher-level metazoan relationships: recent progress and remaining questions. Organisms, Diversity, and Evolution 11:151-172. doi:10.1007/s13127-011-0044-4 (pdf)

Haddock, SHD and CW Dunn (2011) Practical Computing for Biologists. Sinauer Associates (Sunderland, MA). Book Site, Read more at the publisher's site

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.

Dunn, CW (2009) Siphonophores. Current Biology 19:R233-R234. doi:10.1016/j.cub.2009.02.009 (pdf)

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.

Cartwright, P, NM Evans, CW Dunn, AC Marques, MP Miglietta, P Schuchert, and AG Collins (2008) Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria). Journal of the Marine Biological Association of the United Kingdom. 88:1663-1672. doi:10.1017/S0025315408002257 (pdf)

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)

Smith, SA and CW Dunn (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24:715-716. doi:10.1093/bioinformatics/btm619 (pdf). Code repository: https://code.google.com/p/phyutility

Giribet, G, CW Dunn, GD Edgecombe, and GW Rouse (2007) A modern look at the Animal Tree of Life. Zootaxa 1668:61-79. (pdf)

Oota, H, CW Dunn, WC Speed, AJ Pakstis, MA Palmatier, JR Kidd and KK Kidd (2007) Conservative evolution in duplicated genes of the primate Class I ADH cluster. Gene. 392:64-76. doi:10.1016/j.gene.2006.11.008 (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 and GP Wagner (2006) The evolution of colony-level development in the Siphonophora (Cnidaria:Hydrozoa). Development, Genes, and Evolution. 216:743-754. doi:10.1007/s00427-006-0101-8 (pdf)

Matus, DQ, K Pang, H Marlow, CW Dunn, GH Thomsen, and MQ Martindale (2006) Deep evolutionary roots for bilaterality in the metazoa. Proceedings of the National Academy of Sciences USA 103:11195-11200. doi:10.1073/pnas.0601257103 (pdf)

Matus, DQ, RR Copley, CW Dunn, A Hejnol, H Eccleston, KM Halanych, MQ Martindale, and MJ Telford (2006) Broad Taxon and Gene Sampling Indicate that Chaetognaths Are Protostomes. Current Biology 16:R575-R576 doi:10.1016/j.cub.2006.07.017 (pdf)

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 (2005) The complex colony-level organization of the deep-sea siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) is directionally asymmetric and arises by the subdivision of pro-buds. Developmental Dynamics. 234:835-834. doi:10.1002/dvdy.20483 (pdf)

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, CW Dunn, PR Pugh. and C.E. Schnitzler. (2005) Bioluminescent and red-fluorescent lures in a deep-sea siphonophore. Science. 309:263. doi:10.1126/science.1110441 (pdf)

Haddock, SHD, CW Dunn, and PR Pugh (2005) A reexamination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties. J. Mar. Biol. Assoc. U.K. 85:695-707. doi:10.1017/S0025315405011616 (pdf)

Haddock, SHD and CW Dunn (2005) The complex world of siphonophores. JMBA Global Marine Environment 2005(2):24-25. (pdf)

Lynch, VJ, JJ Roth, K Takahashi, CW Dunn, DF Nonaka, G Stopper and GP Wagner (2004) Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society B: Biological Sciences 271:2201-2207. doi:10.1098/rspb.2004.2848 (pdf)