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 evolution 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? What processes contribute to the formation and diversification of species? 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 topics: a) the discovery and description of biological diversity, b) the inference of evolutionary histories of genes, species, and clades, and c) the integration of these two topics 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 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, or rely on computer simulations. In the future, we look forward to incorporating experimental approaches to 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.
Projects in the lab include:
Biosystematic studies on species discovery and species delimitation integrating 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
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, 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, and P Cartwright. (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, 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 doi:10.1186/s13227-015-0018-2. Git code repository: https://bitbucket.org/caseywdunn/siebert_etal.
Weeks A, F Zapata, SK Pell, DC Daly, J Mitchell, and PVA Fine. (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, NG Wilson, M Howison, SCS Andrade, KM Jörger, M Schrödl, FE Goetz, G Giribet, and CW 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. 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. Git code repository: https://bitbucket.org/mhowison/gabi. Example analysis report: https://web3.ccv.brown.edu/mhowison/gabi-report/.
Fine PVA, F Zapata, and DC Daly (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, M Howison, and F Zapata (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).