Organellar Genomes, Resolution, and Support for Deep Relationships Among the Palms

Palms are a hallmark of the tropics, and are of significant ecological and economic importance. The order Arecales encapsulates immense morphological diversity, including variation in growth form, inflorescence structure, and leaf structure. The ecological significance and morphological diversity of palms has prompted over a century of anatomical/morphological, physiological, ecological, and systematic studies. Palm evolutionary biology has a rich history, and has experienced nearly constant advancement, especially with the publication of Genera Palmarum and, more recently, several molecular phylogenies that include all palm genera. Despite such major progress in the understanding of palm evolutionary relationships, some regions of the palm tree of life lack robust support.  Furthermore, relationships among tribes of Coryphoideae and Calamoideae are only partially resolved in the most comprehensive recent multigene analyses.  Thirty eight representative palms were sequenced using Illumina technology to generate complete plastomes, sets of mitochondrial genes, and complete ribosomal DNA operons (rDNA), with the objective of fully resolving and establishing support for relationships among subfamilies and tribes (focusing on non-Arecoid tribes).  Based on 83 protein coding genes of the plastid genome, high resolution and strong support is observed among the five palm subfamilies.  Nypa fruticans—the sole member of subfamily Nypoideae—is strongly supported as sister to (Coryphoideae, (Ceroxyloideae, Arecoideae)), and Calamoideae sister to the rest of the family.  This finding is in agreement with other recent molecular phylogenies.  Relationships among Calamoid and Coryphoid tribes are also highly resolved with strong support.  Mitochondrial genes and rDNA displayed largely congruent relationships, but with some key disagreements.  In addition, organellar genome evolutionary patterns were assessed across the order.