Evolution of Biological Diversity
@ UCLA


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 phenotypes, genes, and genomes 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 study evolutionary processes and test hypotheses on what factors allow and promote biological diversity.

Research


Field

Laboratory

Herbarium/Museum

Computation

Most of our work is focused on flowering plants from the Neotropics and the California Florisitic Province; however, we have worked and continue working with other groups of organisms. Thus, research projects with other taxa are certainly possible in the lab.

Projects in the lab can 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, computational biology, phylogenetic comparative functional genomics, adaptation, speciation, bio- and phylogeography, and tropical biology.

Current projects in the lab deal with questions emerging from:

  • Biosystematic studies on species discovery, species delimitation, and the speciation continuum analyzing multiple lines of evidence to better understand the nature of species, including the development and use of quantitative approaches to infer and evaluate species boundaries

  • Reconstruction of the evolutionary history of clades to study speciation, adaptation, and diversification, including the development of computational tools for phylogenomics

  • Inference of evolutionary processes in the history of genes and phenotypes across species to better understand the bases of biological diversity, including the development of computational approaches for phylogenetic comparative functional genomics

See some recent publications here

Publications


For a full list of publications, please visit Google scholar

Cadena CD, Jiménez I, Zapata F. (2017) Atlantean Evolution in Darwin's Finches - Issues and Perspectives in Species Delimitation using Phenotypic Data. bioRxiv [doi] [repo].

Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A. (2017) Pairwise comparisons are problematic when analyzing functional genomic data across species. bioRxiv [doi] [repo].

Guang A*, Zapata F*, Howison M, Dunn CW. (2016) An integrated perspective on phylogenetic workflows. Trends in Ecology & Evolution (*equal contribution) [doi].

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] [repo].

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] [repo].

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].

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] [repo].

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] [repo] [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] [repo].

Dunn CW, Howison M, and Zapata F. (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. [doi] [repo] [analysis].

People



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.

Teaching


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