Evolution of resinous dots in the fern genus Elaphoglossum (Dryopteridaceae) and the systematics of the Elaphoglossum petiolatum complex
Data files
May 25, 2026 version files 407.67 KB
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Martinez-Becerril_May_26.csv
8.62 KB
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Martinez-Becerril_May_26.nex
395.92 KB
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README.md
3.13 KB
Abstract
Elaphoglossum is one of the most species-rich fern genera, yet species delimitation is challenging because diagnostic characters are few and often require microscopy. Morphological study has nonetheless been central for distinguishing closely related taxa and informing phylogenetic hypotheses. The Elaphoglossum petiolatum complex was informally defined within E. sect. Lepidoglossa subsect. Pilosa by the presence of resinous dots on leaves and/or petioles, black rhizome scales with entire margins, and scales on the proximal portion of the petiole with dark-apices. Earlier molecular phylogenetic analyses suggested that the complex is not monophyletic and that all Mexican representatives form a clade (the Mexican-petiolatum clade), challenging both the definition of the complex and the homology of its diagnostic characters. To clarify the evolutionary history of resinous dots, evaluate relationships among species of the E. petiolatumcomplex, and test the monophyly of the Mexican-petiolatum clade, we conducted maximum likelihood analyses using three non-coding chloroplast spacers (atpβ–rbcL, rps4–trnS, trnL–trnF). Our sampling included nine of the 11 species of the complex, 43 Mexican species, 37 taxa with resinous dots, and totaled 176 Elaphoglossum taxa. Our analyses show that resinous dots evolved independently at least six times within sect. Lepidoglossa, and that the E. petiolatum complex is not monophyletic. Its species fall into three non-sister clades, here termed the Ciliatum (11 spp.), Lancifolium (20 spp.), and Petiolatum (7 spp.) clades. Although species with resinous dots are consistently present within these three clades, no single morphological character uniquely diagnoses any of them. Relationships within each clade remain poorly resolved, likely reflecting low plastid divergence and/or recent rapid diversification. Despite their repeated evolution, resinous dots remain informative for circumscribing the Ciliatum, Lancifolium, and Petiolatum clades, with implications for the circumscription of subsect. Pilosa and the E. petiolatum complex.
Dataset DOI: 10.5061/dryad.tb2rbp0hr
Description of the data and file structure
This dataset contains the molecular and morphological data necessary to replicate the phylogenetic analyses and ancestral state reconstructions presented in Martínez-Becerril and Vasco (2026). The study investigates the evolutionary history of resinous dots in the fern genus Elaphoglossum (Dryopteridaceae), tests the monophyly of the E. petiolatum complex, and clarifies relationships within the Petiolatum Clade of Elaphoglossum sect. Lepidoglossa.
The dataset includes: (1) a combined molecular matrix comprising three non-coding chloroplast regions (atpB-rbcL, rps4-trnS, and trnL-F) for 234 individuals representing 176 Elaphoglossum taxa, including newly generated and previously published GenBank sequences; and (2) a morphological matrix coding the presence/absence of resinous dots. Outgroups used for phylogenetic analyses were Mickelia nicotianifolia and Bolbitis serratifolia.
Phylogenetic analyses indicate that resinous dots evolved independently multiple times within E. sect. Lepidoglossa and that the E. petiolatum complex is not monophyletic.
Files and variables
File: Martinez-Becerril_May_26.csv
Description: Resinous dots presence/absence matrix
Variables
- Species name ("E_"): Elaphoglossum
- Caracter1: Resinous dots
File: Martinez-Becerril_May_26.nex
Description: Combined molecular matrix
Code/software
The Maximum Likelihood analyses were conducted using the IQ-Tree web server (iqtree.cibiv.univie.ac.at). Dataset was divided into four partitions previously estimated by the ModelFinder option implemented in the same web server. To assess branch support, a fast bootstrap analysis (ultrafast bootstrap) with 1000 replicates was applied.
The evolutionary history of resinous was reconstructed on the tree obtained from the ML analyses, by using the R package phytools v. 2.4-4 (Revell 2024). The original tree was pruned to retain a single representative per species in section Lepidoglossa. The functions drop.tip and ladderize, were implemented to prune and sort the original ML tree, respectively. A stochastic mapping approach was used to infer ancestral states, by applying the function make.simmap, running 100 iterations and summarizing the results with countSimmap. The posterior probabilities at the nodes were plotted using plotSimmap.
Access information
Other publicly accessible locations of the data:
Data was derived from the following sources:
- 230 sequences are new and were generated for this study: 63 of atpβ-rbcL, 85 of rps4-trnS, and 82 of trnL-F.
- 374 additional sequences were downloaded from GenBank: 90 of atpβ-rbcL, 141 of rps4-trnS, and 143 of trnL-F.
