Using herbarium data for niche modeling to study phylogenetic diversity and endemism of Florida plants

Charlotte Germain-Aubrey, Julie M. Allen, Kurt M. Neubig, Shawn Laffan, Robert Guralnick, Thomas Lamy, Lucas Majure, Brent Mishler, Douglas Soltis, Jose Miguel Ponciano, Richard Abbott, Pamela Soltis

Research output: Chapter in Book/Report/Conference proceedingConference contribution


The effort to digitize all biological collections in the USA is quickly leading to an online dataset of over one billion specimens, available for addressing questions at unprecedented scales. Florida hosts several biodiversity hotspots and is home to over 4,100 species of plants. Using herbarium collections, we took advantage of the historical data linked with the specimens and constructed a pipeline that extracts environmental variables at the time of the collection for each of over 1,500 species. Using this temporally fine-scale information, we built niche models for those species. In parallel, we sequenced two genes for those same species and constructed a dated ultrametric tree and a non-ultrametric tree. We combined the niche models with both phylogenies to examine patterns of phylogenetic diversity (PD) and endemism (PE) across Florida and applied a randomization test to find significant centers of paleo- and neo-endemism using Categorical Analysis of Neo- And Paleo-Endemism (CANAPE). We then examined the effect of phylogenetic uncertainty on these methods by randomly selecting 100 trees from the posterior distribution of both the ultrametric tree and the non-ultrametric tree and recalculating the phylogenetic diversity metrics. We visualize the spatial component of phylogenetic uncertainty and discuss how to take it into account. We also compared the results obtained using the ultrametric tree versus the non-ultrametric tree. PD measured on the dated ultrametric tree reflects the amount of evolutionary history in a location, while PD measured on the non-ultrametric tree reflects the amount of feature diversity in a location. We will discuss how each of these metrics shows a unique pattern and identifies different features of Florida’s phylogenetic landscape. Lastly, we examined phylogenetic beta diversity among identified centers of significantly high PE and show how this measure can be used for applied conservation purposes.
Original languageEnglish (US)
Title of host publicationBotany 2015, Botanical Society of America Annual Meeting; 25-29 July 2015, Edmonton, Alberta, Canada
StatePublished - 2015


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