Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae)

The tribe Lasiopetaleae (Malvaceae subfamily Byttnerioideae) consists of nine genera largely distributed in Australia. Boundaries between genera have historically been contentious, with many species being described in one genus and variously transferred to others. Previous phylogenetic studies using morphology and plastid DNA have mostly resolved relationships within the tribe except for a group of genera allied to Lasiopetalum. To clarify generic boundaries and the phylogeny of this group, we generated and analyzed target sequence capture data for 144 samples across 8 genera, focusing on denser sampling within Guichenotia, Lasiopetalum, Lysiosepalum and Thomasia, using two bait sets: Angiosperms353 and OzBaits. Sequences for 388 nuclear loci were assembled using two approaches: HybPiper and SECAPR (with some modifications), and results were compared. We used concatenation and coalescent analyses, with and without putative hybrids, to generate new phylogenetic hypotheses for the group. Potential hybrids were investigated using HybPhaser and by assembling phased high-copy portions of the genome, as well as by quantifying potential parentage from heterozygous sites in alignments. Our results indicate that current genera in the group are paraphyletic, and there are examples of hybridization within and between them. Gene concordance for backbone relationships in the group was low, likely caused by gene tree estimation error and taxon instability among closely-related species as well as incomplete lineage sorting during rapid diversification. Despite discordance and hybridization, morphologically diagnosable genomic clades could be recognized. Paraphyly might be resolved by expanding one or two existing genera substantially (subsuming c. 108 taxa) or, for less taxonomic disruption, reinstating two former genera and recognizing two new genera.