The Research Department hosts a seminar series that feature speakers on a wide range of topics in evolutionary biology and ecology.
Seminars are open to all and held on select Fridays at 4:00 pm during the academic year.
Please check in at the Kiosk and tell Admissions staff that you are here for the seminar. You will be admitted at no charge and directed to the venue. Out of respect for seminar speakers and to limit disruptions, guests of the Botany Seminar Series will not be admitted to the Garden after 4:10 pm.
Amanda Fisher, Ph.D.
California State University - Long Beach
Combining genome skims and transcriptomes for a phylogenomic framework of Acanthaceae
Acanthaceae is a family of tropical flowering plants with over 4000 species, including Barleria (ca.300 spp.), Justicia (ca.400 spp.), and Ruellia (ca. 300 spp.). A 2008 estimate of phylogeny across the family by McDade et al. used four chloroplast loci (trnL-Fregion, rps16 intron, trnT-LandtrnS-Gintergenic spacers) and the nuclear ribosomal internal transcribed spacer.Several branches in the resulting tree had low support, particularly relationships between Barlerieae, Andrographideae, Neuracanthus, and Whitfieldieae. Totest these relationships we used genome-scale sequence data from 16 species:four publicly available transcriptomes, seven newly sequenced leaf and flower transcriptomes, and five newly sequenced genome skims, to estimate a primaril ynuclear phylogeny of the family. We de novo assembled transcriptomes using Trinity and identified coding regions using TransDecoder. Genome skims were de novo assembled using SPAdes and coding regions were predicted in Augustus. Amino acid sequences were used in OrthoFinder2 to identify 1,257,148 orthologous loci. Using several combinationsof the data (6,136 orthogroups with all 16 species present, allowing for multiple copies; 587 single-copy loci forat least 9 out of 16 species; 10 single-copy loci with all species present) andestimation methods (STAG, RAxML, neighbor-net networks, PCAs) we explored phylogenetic signal in the data. A single topology was consistently recovered with high ML bootstrap support. The genome + transcriptome phylogeny corroborates the chloroplast + nrITS estimate, with the exception of the placement of Crabbea. The increased resolution and support for evolutionary relationships in the family will now allow us to infer patterns of character evolution, especially trends in flower color, anther, and pollen morphology.
Lynn C. Sweet, Ph.D.
University of California, Riverside
Monitoring the impact of climate change on desert species in the Joshua Tree National Park region
In the region surrounding Joshua Tree National Park (JTNP), which straddles the Colorado and Mojave Deserts in southern California, previous research has predicted the widespread demise of its namesake iconic species, the Joshua tree (Yucca brevifolia). These climate change predictions point to hotter, drier deserts, which may be a challenge for even drought-adapted species. We have gathered field measurements, with community scientists, from across the Park’s broad elevation gradient for Joshua trees as well as other flora and fauna as part of a research partnership between UC Riverside, JTNP and Earthwatch Institute. We used historic gridded datasets representing the conditions where this species has occurred to predict the distribution of still-suitable conditions (refugia) at the end-of-century under a several future climate change model scenarios. We then used statistical models to identify climate refugia for Joshua trees as well as other mid elevation Mojave Desert species. In order to validate model predictions, using the community science data, we analyzed the demographic patterns of Joshua tree stands from low elevations to upper elevations within JTNP. Recruitment within stands show a strong concurrence with modeled mitigated climate refugia. Mapped refugia provide land stewards with targets for focusing protective management, giving native species a space to persist into the future. As well, collaboration with citizen science NGO’s provides a powerful tool for boosting data-gathering capacity for anticipating and responding to management challenges.