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    East Asian-North American disjunctions and phylogenetic relationships within subtribe Nepetinae (Lamiaceae)
    (Academic Press Inc Elsevier Science, 2023) Rose, Jeffrey P.; Wiese, Joshua; Pauley, Nicole; Dirmenci, Tuncay; Celep, Ferhat; Xiang, Chun-Lei; Drew, Bryan T.
    Biogeographic disjunctions, including intercontinental disjunctions, are frequent across plant lineages and have been of considerable interest to biologists for centuries. Their study has been reinvigorated by molecular dating and associated comparative methods. One of the classic disjunction patterns is that between Eastern Asia and North America. It has been speculated that this pattern is the result of vicariance following the sundering of a widespread Acrto-Teritary flora. Subtribe Nepetinae in the mint family (Lamiaceae) is noteworthy because it contains three genera with this disjunction pattern: Agastache, Dracocephalum, and Meehania. These disjunctions are ostensibly the result of three separate events, allowing for concurrent testing of the tempo, origin, and type of each biogeographic event. Using four plastid and four nuclear markers, we estimated divergence times and analyzed the historical biogeography of Nepetinae, including comprehensive sampling of all major clades for the first time. We recover a well-supported and largely congruent phylogeny of Nepetinae between genomic compartments, although several cases of cyto-nuclear discordance are evident. We demonstrate that the three disjunctions are pseudo-congruent, with unidirectional movement from East Asia at slightly staggered times during the late Miocene and early Pliocene. With the possible exception of Meehania, we find that vicariance is likely the underlying driver of these disjunctions. The biogeographic history of Meehania in North America may be best explained by long-distance dispersal, but a more complete picture awaits deeper sampling of the nuclear genome and more advanced biogeographical models.
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    Model selection, hummingbird natural history, and biological hypotheses: a response to Sazatornil et al.
    (Oxford Univ Press, 2023) Kriebel, Ricardo; Rose, Jeffrey P.; Drew, Bryan T.; Gonzalez-Gallegos, Jesus G.; Celep, Ferhat; Heeg, Luciann; Mahdjoub, Mohamed M.
    We have previously suggested that a shift from bee to hummingbird pollination, in concert with floral architecture modifications, occurred at the crown of Salvia subgenus Calosphace in North America ca. 20 mya (Kriebel et al. 2020 and references therein). Sazatornil et al. (2022), using a hidden states model, challenged these assertions, arguing that bees were the ancestral pollinator of subg. Calosphace and claiming that hummingbirds could not have been the ancestral pollinator of subg. Calosphace because hummingbirds were not contemporaneous with crown subg. Calosphace in North America. Here, using a variety of models, we demonstrate that most analyses support hummingbirds as ancestral pollinators of subg. Calosphace and show that Sazatornil et al. (2022) erroneously concluded that hummingbirds were absent from North America ca. 20 mya. We contend that biological realism - based on timing and placement of hummingbirds in Mexico ca. 20 mya and the correlative evolution of hummingbird associated floral traits - must be considered when comparing models based on fit and complexity, including hidden states models.
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    Phylogeny, biogeography and character evolution of origanum L. (Lamiaceae)
    (Nova Science Publishers, Inc., 2021) Celep, Ferhat; Özcan, Taner; Rose, Jeffrey P.; Yazici, Türker; Dirmenci, Tuncay
    Origanum L. (Lamiaceae) comprises perennial herbs with medicinal and culinary uses and is largely confined to the Mediterranean Basin. Despite the economic importance of this genus, phylogenetic relationships and species boundaries are unclear and insufficiently studied. We sequenced the nuclear internal transcribed spacer (ITS) DNA region from 40 Origanum taxa and 32 outgroup specimens. Using this data, we tested sectional and species relationships in Origanum together with molecular dating, biogeographical and character evolution analysis. Molecular results shown that Origanum is a monophyletic genus, however sections of the genus proposed by morphological data are not monophyletic. Thymus L. is sister to Origanum (PP = 1), and the two genera diverged 5.14-6.5 mya. Origanum diversified during the Pliocene, 3.05-5.33 mya. Biogeographic analysis shows and Eastern Mediterranean region is the center of diversity and origin of the genus. In addition, we reconstructed the evolution of four morphological characters which have been used as diagnostic characters in previous infrageneric classifications of Origanum. © 2022 Nova Science Publishers, Inc.
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    Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
    (Frontiers Media Sa, 2021) Rose, Jeffrey P.; Kriebel, Ricardo; Kahan, Larissa; DiNicola, Alexa; Gonzalez-Gallegos, Jesus G.; Celep, Ferhat; Lemmon, Emily M.
    Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with similar to 1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.