A tribal‐scale phylogenomic perspective on ancestry and major lineages of the allotetraploid Hawaiian silversword alliance (Madieae, Compositae)

PREMISE: Disentangling the ancestry of insular plant lineages is important for resolving their evolutionary histories but often complicated by polyploidy, an overrepresented condition in remote island floras. We used a phylogenomic approach to study the origin of subgenomes of the tetraploid Hawaiian silversword alliance and advance understanding of this major example of adaptive radiation. METHODS: We phased sequences from 461 target-capture nuclear loci to subgenomes of the tetraploid silversword alliance (Compositae) using assemblies from diploid North American tarweeds as clade references. We conducted maximum-likelihood and multispecies-coalescent analyses of phased loci with and without representatives of diploid lineages throughout tribe Madieae. RESULTS: An allopolyploid origin of the silversword alliance was corroborated, with subgenome A phased consistently to Anisocarpus madioides and subgenome B phased to diploid representatives of each of three other sublineages of the "Madia" lineage. Phylogenomic analyses indicate Anisocarpus madioides is more closely related to subgenome A than to other tarweeds, including Anisocarpus scabridus. Subgenome trees for the silversword alliance are highly congruent with each other and with structural genomic differences between lineages. CONCLUSIONS: These results indicate an even closer relationship of the silversword alliance to extant California tarweeds than previously understood. Anisocarpus madioides has chromosomal and ecological traits anticipated in an ancestor of the silversword alliance, with the widest geographic range among perennial tarweeds and sticky bracts completely enveloping fruits. Within the silversword alliance, robust support for four major clades reinforces the phylogenetic value of chromosomal interchanges and taxonomic insights by Asa Gray regarding the enigmatic liana Dubautia latifolia.