Methods: We generate transcriptomes to select low-copy nuclear genes, enrich the sevia hybrid capture for representative species of most mimosoid genera and analyse 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.
Key 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 hyper-fast 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 tax on sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.
- hard polytomy
- hybrid capture
- incomplete lineage sorting
- ingoid clade
- lack of phylogenetic signal
- mimosoid clade