A Genomics Approach to Conservation, Systematics, and Phylogeography to Understand Two Lineages of Lamiales

Research using genomic DNA data is increasingly important in understanding and conservingbiodiversity. This work considers two lineages of Lamiales of very different scales: a tribe with hundreds of species from across the tropics, and a single, rare species that is narrowly endemic and native to Southern California. Among Acanthaceae (ca. 4,000 spp.), Barlerieae (ca. 440 spp.) is a tribe that needs considerable further study. Barlerieae can be recognized by the developmental character of quincuncial corolla aestivation (i.e., the arrangement of corolla lobes, with two pairs of lobes, one enclosed inside the other, and a fifth lobe intermediate between them). The tribe contains 13 genera, the two largest and most widespread of which are Barleria (ca. 300 spp., primarily paleotropical), and the pantropical Lepidagathis (ca. 100 spp.). Many species in this group are important in tropical ecosystems and support a wide range of pollinators. Barlerieae present several taxonomic problems, and some species have intriguing biogeographic patterns. In a recent reclassification of Acanthaceae, three subtribes have been proposed based on corolla and calyx characters: (1) Barleria, (2) Crabbea and allies, and (3) Lepidagathis and allies. Using a next-generation sequencing approach (ddRADseq), this study (1) estimates a wellsampled phylogeny of the tribe, (2) tests genera and sub-generic groups for monophyly, (3) identifies morphological characters that support monophyletic groups, (4) examines patterns of biogeography and diversification, and (5) addresses conservation concerns and prospects in a phylogenetic context. Phylogenetic analyses indicate that Barlerieae is monophyletic (given our sampling) and resolve relationships among all thirteen currently recognized genera in Barlerieae. Strong support for the three proposed subtribes was observed, and formal recognition of these taxa was recommended. In addition, results suggest that a major taxonomic revision of Lepidagathis is necessary. Species of Lepidagathis are place in three clades: Lepidagathis s.s., Lophostachys s.l., and Teliostachya. These clades can be distinguished by inflorescence and stamen characters, and the phylogenetic relationships recovered here suggest each of the three clades should be classified as distinct genera. Multiple transcontinental disjunctions across the tribe have also been illuminated, and a shift in diversification rates was identified occurring in the Middle Miocene early in the history of Barleria. In addition, evolutionarily distinct and globally endangered species of Barleria were identified as high priority conservation targets. Lepechinia rossii (Ross's pitcher sage) is a highly aromatic shrub narrowly endemic to southern California chaparral. It occurs in only two known locations in the Western Transverse Ranges of Los Angeles and Ventura counties. It is listed by the California Native Plant Society with a Rare Plant Rank of 1B.2, meaning that it is rare or endangered in California and elsewhere. Lepechinia rossii is also considered "Critically Imperiled" both statewide (S1) and globally (G1) by NatureServe. It faces a range of threats from invasive species; changes in fire regimes; and human activities including off highway vehicle use, power line maintenance, and petroleum exploration. Conservation actions include resurveying known occurrences, searching for new occurrences and potential habitats, updating threat assessments, and studying genetic diversity and structure of all known populations. Field work was conducted on the Angeles National Forest and Los Padres National Forest to survey and sample Lepechinia rossii populations across its range. DNA was extracted from 132 samples of L. rossii and outgroups including L. calycina, L. cardiophylla, L. fragrans, L. ganderi, and L. hastata. Individuals of L. rossii from the two occurrences were found to form reciprocally monophyletic groups that have been isolated for an estimated 300,000 years. Population genomic analyses included samples from the entire range of L. rossii and revealed highly differentiated populations that show little sign of admixture. These findings will inform possible conservation and restoration efforts, and a report has been submitted to the ANF and LPNF for their management consideration.