DOI: 10.5061/dryad.q2bvq83xt
title: Angiosperms353 data for the epidendroid orchid base

description: Parasites present fascinating examples of evolutionary modification that
 simultaneously pose challenges for systematics. This is exemplified by
 fully mycoheterotrophic orchids, which are completely dependent on fungi,
 constituting nearly half of all mycoheterotrophic plant species. A large
 concentration of mycoheterotrophic lineages is found among the eight
 tribes comprising the base of the megadiverse orchid subfamily
 Epidendroideae, here referred to as the early diverging Epidendroideae
 (EDE). To date, relationships among the EDE have been problematic.
 Previous analyses have suffered from sparse taxon sampling, weak support
 from limited loci, or long-branch attraction in plastid-based analyses. We
 conducted the most comprehensive nuclear phylogenomic analysis of the EDE
 to date, using Angiosperms353 loci, coalescent analyses, and deep
 exploration of support, conflict, saturation, and introgression. Our study
 is the first to include phylogenomic sampling from all eight EDE tribes,
 with 22 of 26 EDE genera represented. We took a novel approach, selecting
 best-fit mixture model configurations at the individual locus level, which
 provided significantly better fit overall and required fewer parameters
 than all other models, with implications for clades characterized by
 lineage-specific rate heterogeneity. We recovered strong support for
 monophyly of all EDE tribes except for Neottieae, which were inferred to
 be paraphyletic. Information content was generally rich for deep
 relationships among the EDE tribes, but overall support was weak. We found
 evidence of saturation and putative introgression, with two inferred
 reticulation events. We conclude that short internal branches associated
 with rapid diversification, incomplete lineage sorting, and putative
 introgression resulted in low concordant signal among EDE tribes,
 underscoring the continued difficulty in resolving their relationships.
 Nonetheless, we provide the first strongly supported phylogenetic
 hypothesis for the five genera of Gastrodieae, representing the largest
 known diversification of fully mycoheterotrophic plants. We discuss our
 findings considering recent phylogenomic studies, taxonomy, morphology,
 and biogeographic implications.
description: # Angiosperms353 data for the epidendroid orchid base Dataset DOI:
 [10.5061/dryad.q2bvq83xt](10.5061/dryad.q2bvq83xt) Supplementary data
 files for "Nuclear Phylogenomic Insights Into Relationships, Support,
 and Conflict Among the Early Diverging Lineages of the Megadiverse
 Epidendroid Orchids." Craig F. Barrett1*, John V. Freudenstein2,
 Samuel V. Skibicki1, Brandon T. Sinn3,4, Hana L. Thixton-Nolan1, William
 J. Baker5, Vincent S. F. T. Merckx6,7, Oscar Alejandro Pérez-Escobar5,
 Matthew C. Pace8, Paul M. Peterson9, Kenji Suetsugu10,11, Tomohisa
 Yukawa12 1Department of Biology, West Virginia University, 5218 Life
 Sciences Building, 53 Campus Drive, Morgantown, West Virginia, USA 26506 
 2Department of Evolution, Ecology, and Organismal Biology, Ohio State
 University, 1315 Kinnear Road, Columbus, Ohio, USA 43212. 3Department of
 Biology and Earth Science, Otterbein University, 1 South Grove Street,
 Westerville, Ohio, USA. 4Faculty of Biology, University of Latvia,
 Jelgavas iela 1, Riga, LV-1004, Latvia 5Royal Botanic Gardens, Kew TW9
 3AB, Surrey, UK 6Naturalis Biodiversity Center, Darwinweg 2, Leiden, 2333
 CR, The Netherlands 7Institute of Biology Leiden, Leiden University,
 Sylviusweg 72, Leiden, 2333 BE, The Netherlands 8New York Botanical
 Garden, 2900 Southern Boulevard, Bronx, New York, New York, USA 10458
 9Department of Botany, National Museum of Natural History, Smithsonian
 Institution, Washington, DC, 20560-0166, USA 10Department of Biology,
 Graduate School of Science, Kobe University, Kobe, 1-1 Rokkodai, Nada-ku,
 Kobe, Hyogo 657-8501, Japan. 11The Institute for Advanced Research, Kobe
 University, Kobe, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan.
 12Tsukuba Botanical Garden, National Museum of Nature and Science,
 Amakubo, Tsukuba 305-0005, Japan.  ## Description of the data and file
 structure File 1: Concatenated data (filtered_concat.fasta, filtered to
 remove sites with &gt; 50% missing data) from 318 genes generated by the
 Angiosperms353 sequence capture kit. File 2: Concatenated data
 (unfiltered_concatenated.fasta) from 318 genes generated by the
 Angiosperms353 sequence capture kit. File 3: Zip archive of all 318
 individual gene alignments generated by the Angiosperms353 sequence
 capture kit (trimal_min1004471.fna.fasta_prank.best.zip). ### Files and
 variables #### File: trimal_min1004471.fna.fasta_prank.best.zip
 **Description:** Zip archive of all 318 individual gene alignments
 generated by the Angiosperms353 sequence capture kit
 (trimal_min1004471.fna.fasta_prank.best.zip). This is a .zip archive of
 individual Angiosperm353 gene alignments. Each file has a unique name.
 Angiosperms353 loci were processed with CAPTUS v1.1.0
 ([https://edgardomortiz.github.io/captus.docs/](https://edgardomortiz.github.io/captus.docs/)), a flexible environment for handling sequence capture and genome skimming data that cleans, assembles, extracts, aligns, and filters the input data including putative paralogs (Supplementary methods S3). We further filtered the resulting alignments to remove taxa represented in fewer than 50 total alignments and filtered out loci that contained fewer than 40 taxa. We also filtered out taxa that had less than 10% sequence representation in total base pairs based on the concatenated dataset. We then realigned all loci individually with the phylogenetically aware program PRANK v170427 (Löytynoja, 2014). #### File: filtered_concat.fasta **Description:** Concatenated data (filtered_concat.fasta, filtered to remove sites with &gt; 50% missing data) from 318 genes generated by the Angiosperms353 sequence capture kit. #### File: unfiltered_concatenated.fasta **Description:** Concatenated data (unfiltered_concatenated.fasta) from 318 genes generated by the Angiosperms353 sequence capture kit. #### File: Code_Epibase_2025_Dryad.txt **Description**: All code used in the manuscript (text file format). The code processes `.fna` files to count taxon occurrences, keeps only those present in ≥50 alignments, and filters out specific unwanted taxa (listed in `taxa_to_remove`) from the output FASTA files. ## Access information Other publicly accessible locations of the data: * **Raw data were submitted to the US National Center for Biotechnology Information Sequence Read Archive under BioProject PRJNA1262965, with BioSample accessions SAMN48490488- SAMN48490521 ([https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/)).**