A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

Olivier Maurin ,Steven Dodsworth ,I M Turner ,Vanessa Graziele Staggemeier ,Robyn S Cowan ,Renato Goldenberg ,Ed Biffin ,Catherine Mcginnie ,Thaís Vasconcelos ,Sarah K Morris ,Oscar Alejandro Pérez Escobar ,Félix Forest ,Gustavo Hiroaki Shimizu ,Yohan Pillon ,Berta Gallego ,Fabián A Michelangeli ,Andrew H Thornhill ,Sidonie Bellot ,Peter G Wilson ,Alexandre R Zuntini ,William J Baker ,Augusto Giaretta ,Grace E Brewer ,Darin S Penneys ,Tristan Charles‐Dominique ,Fiorella Fernanda Mazine ,Lisa Pokorny ,Yee Wen Low ,Peter C Hoch ,Shirley A Graham ,Niroshini Epitawalage ,Deise Josely Pereira Gonçalves ,Kyle W Tomlinson ,Artémis Anest ,Eve Lucas

doi:10.1002/ajb2.1699

Abstract

To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Highlights

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents, we tested the Angiosperms353 probe kit
High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events
V3 from exon-only gene trees, with quartet score (QS; for the main, and the first and second alternative topologies) and local posterior probabilities (LPP) values displayed. This ASTRAL tree is compared to the maximum likelihood (ML) analysis of concatenated exons, with bootstrap support (BS) values displayed at the nodes (Fig. 1)

Summary

RESULTS

Inferred in a clade sister to M. tomentosa (Aubl.) DC., of section Tomentosae E.Lucas & D.F.Lima While support for this relationship is moderate in the exon-o nly tree (LPP 0.63), it is high in the supercontig tree (LPP 0.94). The exon only analysis, instead, places Eugenia biflora sister to the clade comprising Eugenia sections Umbellateae, Jossinia, Speciosae, and Phyllocalyx with low congruence and high support (LPP 0.77). Within the Miconieae or Melastomateae the inclusion of introns does not provide a substantial increase in LPP support values, and some relationships along the internal backbone of these two clades are instead more-weakly supported

CONCLUSIONS

MATERIALS AND METHODS

DISCUSSION