Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

Abstract

Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic uncertainty affect these metrics and test existing hypotheses regarding geographic biodiversity patterns across the diverse vascular plant flora of Florida, US. Ecological niche models for 1,490 Florida species were combined with a "purpose-built" phylogenetic tree (phylogram and chronogram), as well as with trees derived from community resources (Phylomatic and Open Tree of Life). There were only modest differences in phylodiversity metrics given the phylogenetic source tree and taking into account the level of phylogenetic uncertainty; we identify similar areas of conservation interest across Florida regardless of the method used.

Keywords: Biogeography; Plant Biology; Spatial Phylogenetics.

Graphical abstract

Figure 1

Phylogram, Chronogram and Species Richness of Vascular Plants in Florida (A) Phylogeny of 1,490 vascular plants in Florida, shown as both chronogram (left) and phylogram (right). The black dots on the chronogram indicate the positions of the 17 calibration points. (B) A map showing species richness, with PD from one grid cell highlighted in red on the phylogram and the chronogram.

Figure 2

Phylogenetic Diversity of Vascular Plants in Florida Observed (top panel) and significant (bottom panel) phylogenetic diversity measured from phylogram (left) and chronogram (right) for vascular plants. On the top panel, the Environmental Protection Agency Level III ecoregions are mapped with the darker lines, Level IV are mapped with the lighter lines, and areas of interest, e.g., Lake Wales Ridge and Miami Ridge, are identified.

Figure 3

Phylogenetic Diversity by Latitude The study region was binned by 0.5° into 13 latitudinal sections represented by the lines on the maps on the right. Bean plots on the left represent the phylogenetic diversity values for the pixels within each section for both the phylogram (top) and chronogram (bottom).

Figure 4

Relative Phylogenetic Diversity Observed (top panel) and significant (bottom panel) relative phylogenetic diversity measured from (A and C) phylogram and (B and D) chronogram for vascular plants.

Figure 5

Diversity Hypothesis Tests Comparing Chronograms and Phylograms for Vascular Plants Built Using Either Our Purpose-Built Tree, Phylomatic, or Open Tree In the top panel are phylograms and chronograms for the purpose-built tree pruned to the (A) Phylomatic and (B) Open Tree taxon dataset. In the middle panel are the (A) Phylomatic and (B) Open Tree trees. In the lower panel are the differences between the two maps. Gray pixels are those that changed in significance level between the Phylomatic and purpose-built tree and the Open Tree and purpose-built tree.

Figure 6

Uncertainty of Phylogenetic Diversity Top: Standard deviation of observed Phylogenetic Diversity across all (A) 100 phylograms and (B) 100 chronograms selected from the post-burn-in distribution of trees in our Bayesian analysis. (C) Difference between the two on the right in blue. Bottom: Areas in light blue are those for which 91 (of 100) or more of the trees had the same level of significance. Areas in yellow are mostly consistent, with 71–90 (of 100) of the trees finding the same level of significance. Areas in red are the relatively inconsistent pixels, with only 50–70 of the trees having the same level of significance for (D) 100 phylograms and (E) 100 chronograms.

Figure 7

Uncertainty of Phylogenetic Diversity by Latitude The study region was binned by 0.5° into 13 latitudinal sections represented by the lines on the maps on the right. Bean plots represent the phylogenetic diversity values for all 100 trees for each of the pixels within each section for both the phylogram (left) and chronogram (right).