We are a group of evolutionary biologists in the Department of Ecology and Evolutionary Biology at the University of California, Los Angeles interested in the origin, evolution and maintenance of biological diversity. We are fascinated with the diversity of life, from the sheer number of species, to the amazing diversity of phenotypic and genomic traits that organisms display. How do thousands of species come to be? What is their evolutionary history? How do species boundaries originate and are maintained (or not) in nature? What is the nature of species? What processes contribute to the diversification of species? How do genes and genomes evolve? How do phenotypic and genomic traits evolve? How is the evolution of these traits related? Why do organisms occur where they are found? To answer this kind of questions, research in the lab focuses on 3 inter-related areas: a) the discovery, analysis, and description of biological diversity, b) the inference of evolutionary histories of genes, species, and clades, and c) the integration of these two areas with other types of data (e.g., natural history, spatial, ecological or climate data) in a comparative framework to test hypotheses on what factors allow and promote biological diversity.
Most of our work is focused on flowering plants; however, research with other organisms is also welcome. Projects in the lab range from detailed evolutionary studies at the species level to broader comparative studies of large clades. To carry out our research, we use data, tools and approaches from different areas. The main motivation of our research is Natural History, so we always try to do field work to learn about the biology of the organisms we study and collect specimens for further study. We supplement our collections with Herbarium/Museum specimens to study spatial patterns of eco-phenotypic variation at different geographic scales. In the laboratory, we generate genetic and genomic data to study patterns of variation at the molecular level. Finally, we use and develop computational and statistical methods to analyze data in a comparative, quantitative framework. We aim to integrate all these approaches in our research, however some projects may emphasize one (or a few) approach more than the others. Thus, projects may involve data generation (e.g., field collections, phenotypic and ecological measurements, DNA/RNA sequencing), use publicly available data, and/or rely entirely on computer simulations. In the future, we look forward to incorporating experimental approaches in our research.
Broad research areas that we are interested include: systematic biology, plant biology, phylogenetics, quantitative taxonomy, macroevolution, bio- and phylogeography, computational biology, evolutionary comparative genomics, adaptation, speciation, and tropical biology.
Current projects in the lab deal with questions emerging from:
Biosystematic studies on species discovery and species delimitation using multiple lines of evidence
Inference of the evolutionary history of different clades using genomic-level data
Inference of the evolutionary history of genes and phenotypes
Development of statistical methods to infer species boundaries, mainly using phenotypic and spatial data
Development of computational tools for phylogenomics and evolutionary comparative genomics
See some recent publications here
Recent publications. For a full list, please visit Google scholar
Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A. (2017) Pairwise comparisons are problematic when analyzing functional genomic data across species. bioRxiv doi:10.1101/107177. Git code repository: https://github.com/caseywdunn/comparative_expression_2017.
Guang A*, Zapata F*, Howison M, Dunn CW. (2016) An integrated perspective on phylogenetic workflows. Trends in Ecology & Evolution (*equal contribution) doi: 10.1016/j.tree.2015.12.007.
Zapata F, Goetz FE, Smith SA, Howison M, Siebert S, Church SH, Sanders SM, Ames CL, McFadden CS, France SC, Daly M, Collins AG, Haddock SHD, Dunn CW, and Cartwright P. (2015) Phylogenomic analyses support traditional relationships within Cnidaria. PLOS One 10(10): e0139068. doi:10.1371/journal.pone.0139068. Git code repository: https://bitbucket.org/caseywdunn/cnidaria2014.
Siebert S, Goetz FE, Church SH, Bhattacharyya P, Zapata F, Haddock SHD , and Dunn CW. (2015) Stem Cells in a Colonial Animal with Localized Growth Zones. EvoDevo doi:10.1186/s13227-015-0018-2. Git code repository: https://bitbucket.org/caseywdunn/siebert_etal.
Weeks A, Zapata F , Pell SK , Daly DC, Mitchell J, and Fine PVA. (2014) To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in the Terebinthaceae (Anacardiaceae and Burseraceae). Frontiers in Genetics-Evolutionary and Population Genetics 5: 409. doi: 10.3389/fgene.2014.00409.
Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, and Dunn CW. (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. Git code repository: https://bitbucket.org/caseywdunn/gastropoda.
Howison M, Zapata F, Edwards EJ, and Dunn CW. (2014) Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling. PLOS One 9:e99497. doi:10.1371/journal.pone.0099497. Git code repository: https://bitbucket.org/mhowison/gabi. Example analysis report: https://web3.ccv.brown.edu/mhowison/gabi-report/.
Fine PVA, Zapata F , and Daly DC. (2014) Investigating processes of Neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae). Evolution 68: 1988-2004. doi: 10.1111/evo.12414.
Dunn CW, Howison M, and Zapata F. (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. doi:10.1186/1471-2105-14-330. Git code repository: https://bitbucket.org/caseywdunn/agalma (software), https://bitbucket.org/caseywdunn/dunnhowisonzapata2013 (analyses).
We always have an eye out for highly motivated students and postdocs with broad interests in (plant) evolutionary biology. Two main goals in the lab are to help all members to: a) become broadly trained in science, evolution, and systematics, and b) become independent, critical thinkers who develop different skills that can help them in the future. Graduate students and postdocs can either join and contribute to ongoing lab projects or pursue their own research ideas (provided there is significant overlap with those of the lab); the latter is way more rewarding. Creativity, dedication, motivation and perseverance are critical skills we value in all members of the lab. As long as everyone has a genuine interest and passion for science, things should work well and it will be a fun experience for all.
Read this excellent advice on applying to Biology PhD programs.
Prospective graduate students and postdocs: please send an email describing briefly your background, research interests and project ideas. Also include a copy of your updated CV.
Graduate students: financial support is limited in our program (more information here), so try to look for and apply for external financial aid (e.g., NSF Fellowship, Fulbright, NAS Fellowship, EPA Fellowhips, AAUW, among others).
Postdocs: there are different potential sources of funding (NSF Fellowship, LaKretz Center for Conservation, NSF Minorities Program, Life Sciences Research Foundation, Marie Curie Fellowship, Fulbright, among others)
Undergraduate students: please send an email describing briefly your background, previous research experience (if any), and motivation to join the lab.