Abstract Detail

Phylogenomics

Carlsen, Monica [1], Fer, Tomas [2], Kress, John [3].

A fully resolved phylogeny of the tropical Zingiberales using targeted gene enrichment.

The primarily tropical order Zingiberales, which includes eight families, approx. 100 genera and 2,000 species, has traditionally been a group where phylogenetic relationships among the advanced taxa have been generally accepted, but reconstructions have been difficult to establish among the basal branches of the clade due to rapid lineage radiation. Previous attempts to recover a fully resolved phylogeny for the order have suffered in part from the lack of comprehensive generic sampling within families. In this study, hybridization-based target enrichment was used to obtain sequences from 4,618 exons (longer than 120 bp) from 1,180 orthologous nuclear loci (longer than 960 bp), and plastome DNA (86 coding regions). Putative orthologous loci were selected based on comparison of genome skimming data of Curcuma ecomata and transcriptome of C. longa. Processing of 150 bp paired-end MiSeq reads and phylogenomic analysis followed a combination of established pipelines and custom scripts. Concatenated data matrices were analyzed using RAxML and supported individual gene trees were merged using a coalescent framework in ASTRAL. All analyses accounted for differences in gene evolutionary rates and minimized the amount of missing data per species and per locus. Only one fully supported topology was recovered in all analyses, with no significant conflicts found among data type and/or analysis type. This topology recognizes two clades, sister to each other, splitting at the base of the order. One clade contains the families Musaceae (Heliconiaceae (Lowiaceae + Strelitziaceae)), whereas the second clade includes (Costaceae + Zingiberaceae) (Marantaceae + Cannaceae). This second clade has been traditionally well-resolved in all previous studies. However, the placement of Musaceae, and in some cases Heliconiaceae, has until now been contested, even in studies using other genomic scale datasets, where these families were previously placed as the basal lineages to all other families in the order. Among individual gene trees, the previous basal placement of Musaceae was only seen in 7% of the genes included in our study, and not well supported in any analysis. Consequently, concatenated and coalescent analyses performed here did not support that relationship, but instead placed Musaceae as a member of the clade containing Heliconiaceae, Lowiaceae and Strelitziaceae, finally resolving one of the most elusive relationships in the order Zingiberales.

1 - Smithsonian Institution, Botany Department, National Museum of Natural History, Washington, DC, 20560, USA
2 - Charles University, Department of Botany, Faculty of Science, Prague, Czech Republic
3 - Smithsonian Institution, Botany, MRC-166 National Museum Of Natural History, PO Box 37012, WASHINGTON, DC, 20013-7012, USA

Keywords:
target enrichment
Zingiberales
rapid diversification
Musaceae
phylogenomics
Heliconiaceae
Next generation sequencing.

Presentation Type: Oral Paper
Session: 16, Phylogenomics II
Location: 202/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 10:45 AM
Number: 16011
Abstract ID:631
Candidate for Awards:None