Revised taxonomy for two species complexes of Western Australian Isopogon (Proteaceae) using RADseq

Abstract The Australian genus Isopogon (Proteaceae) consists of approximately 39 species, most of which occur in southwestern Australia, a region of considerable endemism and biodiversity. Unresolved taxonomic issues exist for two species complexes (nine suspected taxa) allied to I . spathulatus and I . polycephalus . There is uncertainty in how to delimit species in these two complexes due to unclear or overlapping morphological characters, although recognition of four phrase‐named taxa provide starting hypotheses for potential new taxa. We used a genomic approach (ddRAD) to generate SNPs for 146 samples from 32 populations across the two complexes to evaluate the genomic distinction of taxa and delimit species. We used an optimised ipyrad assembly of the sequenced libraries, followed by custom filtering of samples and SNPs for ordination, genetic structure, distance and concatenation and coalescent phylogenetic analyses. Population genetic and phylogenetic analyses consistently supported three geographically overlapping yet genomically distinct groups, two of which showed additional genomic divergence consistent with multiple distinct species. Existing morphological hypotheses were congruent with genomic groupings in some cases but discordant in others, where genomic admixture suggested existing taxa were conspecific. Evaluating morphological characters, geographic distribution and genomic distinction, we recognise five species and three subspecies from nine original taxa. We provide a key to species in the complexes and related taxa, updated descriptions for existing taxa, and describe two new species, I. elatus sp. nov. and I. pallidus sp. nov., and two new subspecies, I. spathulatus subsp. obovatus stat. nov. and I . spathulatus subsp. elongatus subsp. nov.