DOI: 10.5061/dryad.4mw6m90k6
title: Phylogenomics and macroevolution of a florally diverse Neotropical plant clade

description: Hillieae is a group of ~30 florally diverse, Neotropical epiphyte species.
 Species richness peaks in southern Central America, and taxa display bat,
 hawkmoth, or hummingbird pollination syndromes. A phylogenetic framework
 is needed to understand floral and biogeographic evolution. We used target
 enrichment data to infer a species tree and a Bayesian time-calibrated
 tree including ~83% of the species in the group. We inferred ancestral
 biogeography and pollination syndromes, described species realized
 bioclimatic niches via a principal component analysis, and estimated
 significant niche shifts using Ornstein-Uhlenbeck models to understand how
 different abiotic and biotic variables have shaped Hillieae evolution. We
 estimated that Hillieae originated in southern Central America 19 Ma and
 that hawkmoth pollination is the ancestral character state. Multiple
 independent shifts in pollination syndrome, biogeographic distribution,
 and realized bioclimatic niche have occurred, though the bioclimatic niche
 is largely conserved. Using generalized linear models, we identify two
 interactions— between species' biogeographic ranges and pollination
 syndromes, and between phylogenetic covariance and pollination syndromes—
 that additively affect the degree of bioclimatic niche overlap between
 species. Regional variation in pollination syndrome diversity and patterns
 of species bioclimatic niche overlap indicate a link between biogeography
 and species ecology in driving Hillieae diversification and syndrome
 evolution.
description: # Phylogenomics and macroevolution of a florally diverse Neotropical plant
 clade Dataset DOI:
 [10.5061/dryad.4mw6m90k6](https://doi.org/10.5061/dryad.4mw6m90k6) ##
 Description of the data and file structure This dataset includes cleaned
 and filtered multiple sequence alignments in nexus format, gene trees and
 species trees. Sequences were aligned using the program macse (version
 2.07; Ranwez et al. 2018) under default settings, and the alignments were
 cleaned with the programs TAPER (version 1.1.1; Zhang et al. 2021), phyx
 (version 1.1; Brown et al. 2017), and trimAl (version 1.2;
 Capella-Gutiérrez et al. 2009), after being visually inspected with
 Geneious Prime (version 2021.1.1). Gene trees were inferred with
 RAxML-NG (Kozlov et al. 2019) under the GTR+G nucleotide evolution model.
 We inferred two species trees: a concatenated sequence tree using the
 program RAxML-NG, and a tree inferred under the multispecies coalescent
 model with weighted-ASTRAL (i.e., wASTRAL; Zhang and Mirarab 2022). The
 wASTRAL tree was time-calibrated with RevBayes (version 1.2.1; Höhna et
 al. 2016). ### Files and variables #### File: Hillieae_wASTRAL_rooted.tre
 **Description:** Rooted species tree inferred with weighted-ASTRAL ####
 File: Hillieae_RAxML_rooted.tre **Description:** Rooted concatenated
 sequence tree inferred with RAxML-NG #### File: gene_trees.tre
 **Description:** Unrooted gene trees inferred with RAxML-NG #### File:
 Alignments_nexus.zip **Description:** Cleaned multiple sequence alignments
 (DNA) for 1375 loci, in nexus format. Alignments include 25–42 taxa and
 are of 99–4791 bp in length. Alignment gaps are represented with dashes.
 #### File: Hillieae_time_tree.tre **Description:** Rooted and
 time-calibrated species tree ## Code/software 1. **Programs needed** *
 RAxML-NG * Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., &
 Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool
 for maximum likelihood phylogenetic inference. *Bioinformatics*, *35*(21),
 4453-4455. * Weighted-ASTRAL (wASTRAL) * Zhang, C., & Mirarab, S.
 (2022). Weighting by gene tree uncertainty improves accuracy of
 quartet-based species trees. *Molecular biology and evolution*, *39*(12),
 msac215. * RevBayes * Höhna, S., Landis, M. J., Heath, T. A., Boussau, B.,
 Lartillot, N., Moore, B. R., ... & Ronquist, F. (2016). RevBayes:
 Bayesian phylogenetic inference using graphical models and an interactive
 model-specification language. *Systematic biology*, *65*(4), 726-736. ##
 Access information Other publicly accessible locations of the data: *
 Figshare:
 [https://doi.org/10.6084/m9.figshare.26110573.v1](https://doi.org/10.6084/m9.figshare.26110573.v1) * Data and scripts are also provided via GitHub: [https://github.com/laymonb/Hillieae_macroevolution](https://github.com/laymonb/Hillieae_macroevolution)