Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

• Published in: American journal of botany 2020-12, Vol.107 (12), p.1710-1735
• Main Authors: Koenen, Erik J. M., Kidner, Catherine, Souza, Élvia R., Simon, Marcelo F., Iganci, João R., Nicholls, James A., Brown, Gillian K., Queiroz, Luciano P., Luckow, Melissa, Lewis, Gwilym P., Pennington, R. Toby, Hughes, Colin E.
• Format: Article
• Language: English
• Subjects: Angiosperms; Biological Evolution; Caesalpinioideae; Cell Nucleus - genetics; Fabaceae; Fabaceae - genetics; Genera; Genes; hard polytomy; hybrid capture; incomplete lineage sorting; ingoid clade; lack of phylogenetic signal; Legumes; Leguminosae; Loci; mimosoid clade; Network analysis; Nuclear capture; Phylogenetics; phylogenomics; Phylogeny; Radiation; Reclassification; Species
• ISSN: 0002-9122; 1537-2197
• DOI: 10.1002/ajb2.1568

PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species‐rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low‐copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well‐supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.