Allopolyploid origin and diversification of the Hawaiian endemic mints

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai’i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin’s thinking about the evolutionary process.

Methods
We generated a genome assembly of Stenogyne calaminthoides using Oxford Nanopore Technology long read sequencing, Hi-C scaffolding, as well as gene model predictions based on transcriptome assembly and homology-based gene predictors. Illumina resequencing was performed from 45 taxa of Hawaiian mints taxa and Stachys relatives (~30 Gb per sample), in addition to 110 samples of Stenogyne rugosa and S. microphylla and their purported hybrids (~15 Gb per sample).

The data and our analyses were sued to (i) generate a high-quality, chromosome-level genome of Stenogyne calaminthoides to investigate polyploid history of the Hawaiian mint lineage, (ii) use this reference genome and resequencing of multiple species to establish the origin and phylogeny of the Hawaiian mints and their mainland relatives, as well as potential admixture history, and (iii) investigate recent introgression among Stenogyne species that co-occur at high elevation on Mauna Kea.