Spatial phylogenetics of the Vernonieae (Asteraceae) in North America
Data files
Jul 15, 2025 version files 493.53 KB
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concat_Vern_EG.nex
228.24 KB
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README.md
2.38 KB
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Vernonieae_North_America.csv
260.29 KB
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Vernonieae_tree_phylogram.nex
2.62 KB
Abstract
In North America, the tribe Vernonieae (Asteraceae) comprises 92 species distributed mainly in mountain ranges. Combining molecular data for 62 species and herbarium records (N=5424), spatial phylogenetics was used to identify regions of high phylodiversity, centers of endemism, and patterns of phylogenetic turnover in North America. The study region was divided into 1° latitude and longitude grid cells; four molecular markers (ndhF, trnL, rpl32-trnL, and ITS) were used to construct a phylogram and alpha phylodiversity indices were calculated (phylogenetic diversity and relative phylogenetic diversity) along with categorical analysis of neo- and paleo-endemism (CANAPE). Beta phylodiversity was examined using the PhyloβSimpson and PhyloβRWTurnover indices to determine major phyloregions. A randomization test of phylogenetic diversity revealed phylogenetic clustering in the north and south of North America, while overdispersion was concentrated in the south. Relative phylogenetic diversity showed significant concentrations of long branches in the north and south, whereas central Mexico exhibited concentrations of short branches. The CANAPE analysis revealed centers of paleo-endemism in southeastern Mexico, with long-branching lineages in genera such as Cyrtocymura and Lepidonia. Neo-endemism centers with short-branching species, such as those in genera Eremosis and Vickianthus were also identified, as well as areas with mixed endemism in different regions of Mexico. Phylogenetic turnover patterns determined 16 phyloregions (PhyloβSimpson) and 17 phyloregions (PhyloβRWTurnover).
Dataset DOI: https://doi.org/10.5061/dryad.v9s4mw75p
Description of the data and file structure
Files and variables
File: Vernonieae_North_America.csv
Description: Treated dataset of Vernonieae of North America
Variables
- Name: Contains the names of North American species.
- Long: Contains longitude coordinates in decimal units.
- Lat: Contains latitude coordinates in decimal units.
Access information
Data was derived from the following sources:
- IBdata. 2024. Herbario Nacional de México (MEXU) IBUNAM. https://ibdata.abaco2.org/web/ (last accessed 7 November 2024).
- GBIF.org (2022) GBIF Occurrence Download https://doi.org/10.15468/dl.vt2z4q (Consulted June 2022).
- Maitner, B. S., B. Boyle, N. Casler, R. Condit, J. Donoghue, S. M. Durán, D. Guadarrama, C. E. Hinchliff, P. M. Jørgensen, N. J. B. Kraft, B. McGill, C. Merow, N. Morueta-Holme, R. K. Peet, B. Sandel, M. Schildhauer, S. A. Smith, J.-C. Svenning, B. Thiers, C. Violle, S. Wiser, and B. J. Enquist. 2018. The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods in Ecology and Evolution 9: 373-379.
File: concat_Vern_EG.nex
Description: Concatenated matrix of the four molecular markers used for the spatial phylogenetic analysis. (the ndhF chloroplast gene, the spacer trnL region, the rpl32-trnL, and the nuclear ribosomal cistron ITS 1, 5.8S, and ITS 2). Each marker was aligned using MAFFT.
Access information
Data was derived from the following sources:
- https://www.ncbi.nlm.nih.gov/
- Keeley, S. C., J. T. Cantley, J. T., and T. J. Gallaher. 2021. The “evil tribe” spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae). American Journal of Botany 108: 505-519.
File: Vernonieae_tree_phylogram.nex
Description: A nexus file containing one phylogenetic tree in Newick format of 63 taxa (62 Vernonieae and one outgroup). Branch lengths represent the amount of evolutionary change.
North America was defined following Brummitt et al. (2001); thus, the study area includes Canada, the conterminous United States of America, and Mexico. Distribution data for 92 Vernonieae species from 20 genera were analyzed. Geographic data for Canada and the United States were obtained from the online databases BIEN (Maitner et al. 2017) and GBIF (2022). For Mexico, two public databases available in electronic format were consulted. The first is the National Biodiversity Information System (SNIB-REMIB) of the National Commission for the Knowledge and Use of Biodiversity (CONABIO 2024: www.snib.mx), which includes digital information from numerous herbaria both in Mexico and abroad. The second is the National Herbarium (MEXU) digital repository at the National Autonomous University of Mexico (MEXU-IBdata 2024: https://www.ibdata.abaco3.org). Only those records based on herbarium specimens were used. They are kept in around 100 herbaria.