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Data from: Ancestral area analyses reveal Pleistocene-influenced evolution in a clade of Coastal Plain endemic plants

Cite this dataset

Naranjo, Andre (2024). Data from: Ancestral area analyses reveal Pleistocene-influenced evolution in a clade of Coastal Plain endemic plants [Dataset]. Dryad.


AIM: The North American Coastal Plain is currently recognized as a global biodiversity hotspot. However, the mechanisms driving high levels of species richness in a region with relatively low topographic relief and homogeneous climate are unclear. We investigated the evolutionary processes driving ancestral area evolution and diversification in a biodiversity hotspot from both a systematic and biogeographic context using a clade endemic to the hotspot.

LOCATION: North American Coastal Plain

TAXON: The Scrub Mint clade comprises Dicerandra, Conradina, Piloblephis, Stachydeoma, and four species of Clinopodium (Mentheae; Lamiaceae), almost all of which are endemic to the North American Coastal Plain. 

METHODS: We generated a dated phylogeny using a target enrichment/capture dataset and then calculated ancestral area using biogeographic models. We uncovered neo- and paleo-endemism hotspots and inferred ancestral potential ranges at each node based on ancestral niche reconstructions and paleoclimatic data to understand the geographic range evolution of subclades. 

RESULTS: Ancestral area for the SMC was inferred to be the Florida Panhandle/Apalachicola River basin. A diversification event likely happened around the mid-Pleistocene Transition. Endemism hotspots were recovered in NE Florida, the Atlantic Coastal Ridge, and along the Lake Wales Ridge. Reconstructions of potential ranges support biogeographic findings, with the ancestor of the SMC likely located in the vicinity of the northeastern Gulf Coast during interglacial and glacial periods.

MAIN CONCLUSIONS: The timing of diversification events and colonization of new areas by ancestors of the SMC is consistent with the timing of major geological events in the region. The presence of multiple types of endemism highlights the complexity of evolutionary and ecological processes that foster the large number of endemic taxa found in this region. Efforts to identify hotspots in this region will be critical to preserving the remaining pockets of biodiversity threatened by global change.

Provenance for this README

  • File name:
  • Authors: Andre A Naranjo
  • Other contributors: Ryan Folk, Matthew Gitzendanner, Douglas Soltis, Pamela Soltis
  • Date created: 2022-04-19
  • Date modified: 2023-11-28

Dataset Version and Release History

  • Current Version:
    • Number: 2.0.0
    • Date: 2023-11-28
    • Persistent identifier: DOI: 10.5061/dryad.prr4xgxp6
    • Summary of changes: n/a

README: Data and File Overview

Details for: supermatrix_species.nxs

Description: an aligned Nexus file with all genes and loci used to run phylogenetic analyses.

Size: 8.56 MB

Notes on this file:
There are 242 genes included in this matrix for 24 species (g010 failed to be sequenced entirely). Of those, 238 were used to build the gene trees for subsequent analyses. The genes that were left out are as follows:

DNA, g017.FNA = 20212-21966

DNA, g098.FNA = 130980-131237

DNA, g163.FNA = 218581-218870

DNA, g191.FNA = 265276-266230

Details for: Partitions.txt

Description: A list of the gene partitions used to build the individual gene trees used in our analyses.

Size: 7.10 KB

Notes on this file: None

Details for: all_bipart_names.tre

Description: A file containing all of the nuclear gene trees used in our analyses. Displayed in Newick format.

Size: 150 KB

Notes on this file: None



National Science Foundation

American Society of Plant Taxonomists

Botanical Society of America

Florida Native Plant Society