Members of the genus Heliconia L. (Heliconiaceae) have evolved complex interactions with both insect herbivores and hummingbird pollinators in tropical forests and secondary growth where they are abundant and diverse. Many of these same species have also been cultivated as ornamentals around the world for hundreds of years because of their extraordinary colors and forms. Because of the large size, fleshy nature, and tropical distribution, and despite a long taxonomic history, the classification and phylogenetic relationships of species of Heliconia have not received sufficient attention to date. No complete classification has been published for the entire genus, although some preliminary attempts have been offered. In this paper we used tissue sampled from field and herbarium collections of 136 species for genomic sequencing to determine the phylogenetic patterns within Heliconia, which then served as the basis for a new evolutionary classification of the genus. This new classification, which is based on extensive field work and the phylogenomic insights provided here, includes 187 currently recognized species. The new classification of Heliconia is composed of 17 sections in five subgenera with all groups well-supported in the phylogenomic analysis. Four subgenera are each composed of two sections and one subgenus includes nine sections. One subgenus and 10 sections are described as new.

Total genomic DNA was extracted from either silica dried leaves or herbarium specimens using a modified CTAB protocol. Libraries were constructed using the NEBNext Ultra™ II DNA Library Prep kit with Sample Purification Beads and Multiplex oligos for Illumina (96 Index Primes). Libraries were combined in hybridization pool reactions consisting of 10–12 Heliconia species per reaction. In solution hybridization of the library pools to the target loci was performed by Arbor Biosciences LLC (Ann Arbor, Michigan) using the myBaits Custom 1-20K kit designed for Zingiberales (Carlsen et al. 2018). Sequencing was performed either in an Illumina MiSeq with v.3 chemistry kits (250 bp paired-end) or in an Illumina NovaSeq S4 system (150 bp paired-end).

Illumina raw paired-end reads were quality trimmed and adapters were removed using a combination of Trimmomatic v. 0.39 (Bolger et al. 2014) and Trim Galore v. 0.6.4 (https://github.com/FelixKrueger/TrimGalore). Cleaned reads were assembled using HybPiper v. 1.3.1 (Johnson et al. 2016). Coding sequences were extracted using Exonerate (Slater and Birney 2005) with the HybPiper retrieve_sequences.py script. Each loci recovered were separately aligned with MAFFT v. 7.407 (Katoh and Standley 2013) with “-- auto” parameter. Single locus tree reconstruction was performed using RAxML v. 8.2.12 (Stamatakis 2014), with no partition scheme, GTRCAT model of evolution, and 500 bootstrap replicates. Coalescence based species tree reconstruction was performed with ASTRAL III v. 5.7.1 (Zhang et al. 2018) using the individual trees generated with RAxML.