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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.

— Monardella (Lamiaceae) is a taxonomically complex western North American genus ranging from the Pacific coast to the western slopes of the Rocky Mountains and from southern British Columbia in Canada to the Cape region of Baja California Sur in Mexico. We applied a combination of gross vegetative morphology, trichome morphology and abundance/distribution, and molecular data to clarify taxonomic discontinuities, specifically regarding the monophyly of plants formerly treated within Monardella odoratissima. The data suggest a clear distinction between the non-monophyletic M. odoratissima species complex and the M. ovata species complex, thus resolving taxonomic ambiguities within and between them. We formally recognize plants from southern Oregon, northern California, and western Nevada previously misapplied to M. odoratissima as belonging to the M. ovata species complex. We introduce the following taxonomic and nomenclatural revisions: describe M. ovata Greene subsp. lenmaniae as a novel subspecies; present M. ovata subsp. pallida at a new position and rank; recognize M. modocensis, M. ovata, and M. rubella as accepted taxa; designate lectotypes for M. modocensis and M. rubella; and designate M. californica and M. tortifolia as new synonyms under M. ovata.

The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.

Winter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal.

Lamiaceae are one of the largest and most economically important families of flowering plants. Despite focused study on relationships within subclades, higher-level relationships have been under-studied. Moreover, the herbaceous habit of much of the family has resulted in a poor fossil record and has hampered estimates of divergence times. Using a new dataset of five plastid loci from 178 members of Lamiaceae representing all subfamilies and nearly all tribes, we clarify major infrafamilial relationships and present a robust set of divergence times. We use this phylogenetic hypothesis as a platform to test previous hypotheses regarding the historical biogeography and evolution of major traits in the family. We confirm the placement of subfamily Nepetoideae, show continued uncertainty in the placement of subfamilies Ajugoideae and Premnoideae and highlight extreme discordance with recent results from nuclear data. Lamiaceae originated during the Late Cretaceous as woody plants with nutlet fruits and four stamens, probably in South-East Asia. Most subfamilies diverged during the Eocene, perhaps facilitated by climatic cooling. Our results provide a valuable set of secondary dates for Lamiaceae and highlight the need for focused study of subfamilies Callicarpoideae and Viticoideae. Our results also provide several hypotheses regarding trait or range-dependent diversification.

To investigate the value of atypical foraging behavior of honey bees (Apis mellifera) during dearth, we compared the number of days survived in vitro among young adult honey bees kept in hoarding c...

The genus Salvia is comprised of about 1000 species and has diversity hotspots in the Americas, East Asia, southwest Asia and the Mediterranean region. Central Asia also possesses considerable Salvia species diversity but is understudied relative to the aforementioned diversity hotspots. To help remedy this deficiency, we present a synopsis of Central Asian Salvia species based on extensive fieldwork, herbarium consultation, and literature surveys focusing on Uzbekistan, Kyrgyzstan, Tajikistan, Kazakhstan, and Turkmenistan (i.e., Central Asia). According to our final taxonomic revision, there are 41 species of native Salvia in the flora of Central Asia, 24 of which are endemic. Salvia ariana from Tajikistan and S. spinosa from Kazakhstan are documented from the respective countries for the first time, and the presence of S. tianschanica from Tajikistan and S. verticillata from Kazakhstan has been confirmed. In addition, the neotypification of S. deserta and three lectotypifications (Perovskia abrotanoides, S. bucharica and S. trautvetterii) are provided. Furthermore, we synonymized six species of Salvia that were previously reported from Central Asia, including S. intercedens, S. kopetdaghensis, S. linczevskii, S. lipskyi, S. semilanata and S. stepposa. Finally, a new species identification key for Central Asian Salvia is presented based on the new nomenclature changes and our taxonomic revision.

Premise of research. Previous studies based on plastid fragments and/or nuclear ribosomal DNA have had limited success resolving relationships within the genus Salvia. This study evaluates the effi...

Premise of research. Salvia grandifolia is a narrowly endemic species known only from the Hengduan Mountains of southwestern China. Previous studies have shown that East Asian Salvia species form a...

Salvia rupestris (Lamiaceae), from the Caatinga region of Pernambuco State, Brazil, is described and illustrated. Photos of the specimen dissected in stereo microscope and a distribution map are provided. The new species is compared to S. fruticetorum, a morphologically allied species.

A fundamental question in evolutionary biology is how clades of organisms exert influence on one another. The evolution of the flower and subsequent plant/pollinator coevolution are major innovations that have operated in flowering plants to promote species radiations at a variety of taxonomic levels in the Neotropics. Here we test the hypothesis that pollination by Neotropical endemic hummingbirds drove the evolution of two unique stigma traits in correlation with other floral traits in New World Salvia (Lamiaceae). We examined morphometric shapes of stigma lobing across 400 Salvia spp., scored presence and absence of a stigma brush across Salvia, and used a suite of phylogenetic comparative methods to detect shape regime shifts, correlation of trait shifts with BayesTraits and phylogenetic generalized least square regressions, and the influence of scored pollinators on trait evolution using OUwie. We found that a major Neotropical clade of Salvia evolved a correlated set of stigma features, with a longer upper stigma lobe and stigmatic brush, following an early shift to hummingbird pollination. Evolutionary constraint is evident as subsequent shifts to bee pollination largely retained these two features. Our results support the hypothesis that hummingbirds guided the correlative shifts in corolla, anther connective, style and stigma shape in Neotropical Salvia, despite repeated shifts back to bee pollination.

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 ∼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.

Paralamium(Lamiaceae) is a monotypic genus within the subfamily Lamioideae and has a sporadic distribution in subtropical mountains of southeast Asia. Although recent studies have greatly improved our understanding of generic relationships within Lamioideae, the second most species-rich subfamily of Lamiaceae, the systematic position ofParalamiumwithin the subfamily remains unclear. In this study, we investigate the phylogenetic placement of the genus using three datasets: (1) a 69,276 bp plastome alignment of Lamiaceae; (2) a five chloroplast DNA region dataset of tribe Pogostemoneae, and (3) a nuclear ribosomal internal transcribed spacer region dataset of Pogostemoneae. These analyses demonstrate thatParalamiumis a member of Pogostemoneae and sister to the monotypic genusCraniotome. In addition, generic-level phylogenetic relationships within Pogostemoneae are also discussed, and a dichotomous key for genera within Pogostemoneae is provided.

Background: A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results: We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions: Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract: [Figure not available: see fulltext.]. © 2021, The Author(s). Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province: YNWR-QNBJ-2018-279National Science Foundation, NSF: TUBITAK-BIDEB 2219, DEB-1655611RG19-172019FI009 This study was in part supported by Yunnan Fundamental Research Projects (Grant No. 2019FI009) and “Ten Thousand Talents Program of Yunnan” (Grant No. YNWR-QNBJ-2018-279) awarded to CLX, the CAS “Light of West China” program to CLX and YPC, the Australian Biological Resources Study National Taxonomy Research Grant Program (Grant No. RG19-17) awarded to TCW, CLX, and BL, NSF DEB-1655611 awarded to BTD, and the Postdoctoral Research Program (TUBITAK-BIDEB 2219) awarded to FC.

Kriebel, Ricardo/0000-0002-1138-7533; Drew, Bryan T./0000-0001-7248-2799; mahdjoub, mohamed malik/0000-0001-5584-6642; Celep, Ferhat/0000-0003-3280-8373 WOS:000540384100001 PubMed: 32484910 Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1000 species ofSalvia(Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW)Salviais largely distinct from that of Old World (OW)Salviaand that these differences are pollinator driven; shifts in floral morphology sometimes mirror shifts in pollinators; anther connectives (key constituents of theSalviastaminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever inSalviais a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion. University of Wisconsin Graduate School grant; University of Wisconsin Botany Department Hofmeister Endowment; National Science Foundation-DOB grant [DOB-1046355]; National Science Foundation-DEB grant [DEB-1655606]; CONACYTConsejo Nacional de Ciencia y Tecnologia (CONACyT) [255165]; TUBITAK-BIDEB 2219 Postdoctoral Research ProgramTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) The authors would like to thank the editors and reviewers for their time and constructive comments that improved this article. We also thank I. Cacho, E. Dariotis, and C.-L. Xiang for help obtaining floral scans in Mexico, Greece, and China, respectively, as well as the UC-Berkeley and Denver Botanical Gardens. We also thank the Phylogenetics and Evolution group in the Botany Department, University of Wisconsin, and C. Ane for statistical advice. The work was funded in part by a University of Wisconsin Graduate School grant, the University of Wisconsin Botany Department Hofmeister Endowment, a National Science Foundation-DOB grant to Sytsma (DOB-1046355), and a National Science Foundation-DEB grant to Sytsma and Drew (DEB-1655606). GG thanks financial support provided by CONACYT (project 255165). FC thanks the TUBITAK-BIDEB 2219 Postdoctoral Research Program for financial support.

Celep, Ferhat/0000-0003-3280-8373 WOS:000596023100005 Salvia L. is an ideal exemplar to demonstrate prezygotic isolation mechanisms in sympatric populations due to their well-known staminal lever mechanism. Mechanical, phenological, and ethological isolation mechanisms have been reported among sympatric species of Salvia. However, it has been shown that if closely related species are sympatric and flower at the same time, they can potentially hybridize. In this study, we describe two new hybrid species of Salvia (S. x karamanensis Celep & B.T.Drew, and S. x doganii Celep & B.T.Drew) from Turkey based on morphological and molecular evidence. Salvia x karamanensis (S. aucheri Benth. subsp. canescens (Boiss. & Heldr.) Celep, Kahraman & Dogan x S. heldreichiana Boiss. ex Benth.) is known from near Karaman city in the central Mediterranean region of Turkey, and S. x doganii (S. cyanescens Boiss. & Bal. x S. vermifolia Hedge & Hub.-Mor.) occurs near Sivas in central Anatolia, Turkey. Morphological comparisons between the hybrid species and their putative parents are given with notes on the International Union for Conservation of Nature (IUCN) red list categories, biogeography and ecology of the two hybrid species. TUBITAKBIDEB 2219 Postdoctoral Research ProgramTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK); NSF-DEB grant [DEB-1655611] We thank Dr. Ricardo Kriebel (University of WisconsinMadison) for assistance with flower scans, Prof.Dr. Esra Martin (Necmettin Erbakan University) for information about chromosome numbers of S. vermifolia, and the curators of herbaria ADO, ANK, BM, E, G, GAZI, HUB, ISTE, ISTF, K, KNYA, and LE for permitting examination of their Salvia collections. Ferhat Celep thanks the TUBITAKBIDEB 2219 Postdoctoral Research Program for financial support in the University of Wisconsin-Madison. Drew also acknowledges support from NSF-DEB grant DEB-1655611. We thank handling editor of Turkish Journal Botany and two anonymous reviewers for their constructive criticisms.

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.

International audience; Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here, we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot. Specifically, we investigated various biological, ecological, and geographical drivers of species diversification within the genus Oxera. We found that Oxera underwent an initial process of rapid cladogenesis likely triggered by a dramatic period of aridity during the early Pliocene. This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms. Finally, recent diversification of Oxera appears to have been further driven by the interplay of allopatry and habitat shifts likely related to climatic oscillations. This suggests that Oxera could be regarded as an adaptive radiation at an early evolutionary stage that has been obscured by more recent joint habitat diversification and neutral geographical processes. Diversification within Oxera has perhaps been triggered by varied ecological and biological drivers acting in a leapfrog pattern, but geographic processes may have been an equally important driver. We suspect that strictly adaptive radiations may be rare in plants and that most events of rapid clade diversification may have involved a mixture of geographical and ecological divergence.

Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.

Aim Across angiosperm families, the area occupied by a family is strongly correlated with its richness. We explore the causes of this area-richness correlation using the cosmopolitan family, Cyperaceae Juss., as a model. We test the hypothesis that, despite a proposed tropical origin, temperate lineages in the family diversified at elevated rates. We test the hypothesis that the area-richness correlation is maintained within intrafamilial clades, and that this relationship could be described as a function of niche space. We also test the hypothesis that the partitioning of geographical and ecological space, not the extent of this space, is the factor most closely associated with clade richness. Location Cosmopolitan. Methods We use molecular data from four genes sequenced in 384 taxa to develop a chronogram of Cyperaceae. We then develop a model of ancestral ranges and measure rates of diversification throughout the history of the family. Integrating data from over 4,800,000 digitized herbarium records, we characterize the range and niche of more than 4500 species and test for correlations of the species richness maintained within clades with range size, range partitioning, range overlap, niche, clade age and rate of diversification. Results Cyperaceae originated in South America in the late Cretaceous and subsequently dispersed throughout the globe. Of three increases in diversification rate, two occurred in the temperate Northern Hemisphere. The variable most closely associated with clade richness is the partitioning of geographical space by species within each clade. Main conclusions We show that species-rich clades in Cyperaceae are not only more widespread, occupy more niche space, and diversify more quickly, but also exhibit patterns that are consistent with the partitioning of geographical and ecological space as a major correlate to diversification.

Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai-Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.

Ombrocharis is the only incertae sedis genus within Lamiaceae that has not been included in a published molecular phylogenetic study. Here, we adopt a two-step approach to resolve the phylogenetic placement of the genus. Initially, the subfamilial affiliation of Ombrocharis was determined based on a combined ndhF and rbcL dataset covering all seven subfamilies of Lamiaceae. Results show that Ombrocharis is a member of Nepetoideae, a placement that is also supported by its hexacolpate pollen grains. In the second set of analyses, two nrDNA (ITS, ETS) and four cpDNA (ycf1, rps15-ycf1, trnL-F, rpl32-trnL) markers were used to explore the position of Ombrocharis within Nepetoideae. Our results demonstrate that Ombrocharis and another monotypic genus, Perillula, form a clade that is sister to the remaining genera of tribe Elsholtzieae. Ombrocharis and other taxa within Elsholtzieae share divergent stamens, a weakly 2-lipped corolla, and an asymmetric disc with an elongate anterior lobe, but it is unclear whether these features are apomorphic. This study represents both the most comprehensive phylogenetic analysis of Elsholtzieae to date and the only study to include all genera of Elsholtzieae. The monophyly of Elsholtzieae (including Ombrocharis) is well supported, and there is weak support for Elsholtzieae as sister to the rest of Nepetoideae. Additionally, our results do not support the merging of Keiskea with Collinsonia, and Elsholtzia may be polyphyletic.

The role of geography and ecology in speciation are often discussed in the context of phylogenetic niche conservatism (PNC), the propensity of lineages to retain ancestral niche related traits. However, a recent paradigm shift focuses instead on measuring divergence of these traits in conjunction with patterns of speciation. Under this framework, we analyzed the diversification of North America's third most diverse family, Cyperaceae ("sedges"), using a modified Parsimony Analysis of Endemicity approach to identify floristic regions and ordination statistics to quantify species distribution in a continuous manner. Utilizing over 200,000 georeferenced specimens, we characterized the geographical distribution and climatic and edaphic niche space occupied by each species. We constructed a supermatrix phylogeny of the North American sedge flora, aided in part by the sequencing of all sedges of Wisconsin, and employed a multifaceted approach to assess the role of geographical and ecological divergence on lineage diversification. In addition to measuring phylogenetic signal for these traits, we also measured pairwise phylogenetic distance of species within floristic regions, calculated rates of speciation, and tested for correlations of speciation rate to tempo of geographical and ecological evolution. Our analyses consistently show that evolutionarily related species tend to be geographically unrelated. Rates of geographical and ecological diversification are closely linked to tempo of speciation, and exploration of geographical place coincides with divergence in ecological niche space. We highlight the benefits of treating geography in a continuous manner, and stress the importance of employing a diverse suite of analytical approaches in testing hypotheses regarding the evolution of range and niche.

Premise of the study A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. Methods A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. Key results A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. Conclusions Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Background and aims Salvia is the largest genus within Lamiaceae, with about 980 species currently recognized. East Asia, with approx. 100 species, is one of the three major biodiversity centres of Salvia. However, relationships within this lineage remain unclear, and the staminal lever mechanism, which may represent a key innovation within the genus, has been understudied. By using six genetic markers and nearly comprehensive taxon sampling, this study attempts to elucidate relationships and examine evolutionary trends of staminal development within the East Asia (EA) Salvia clade. Methods Ninety-one taxa of EA Salvia were sampled and 34 taxa representing all other major lineages of Salvia were included for analysis. Two nuclear [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and four chloroplast (psbA-trnH, ycf1-rps15, trnL-trnF and rbcL) DNA markers were used for phylogenetic analysis employing maximum parsimony (MP), maximum likelihood (ML) and BEAST, with the latter also used to estimate divergence times. Key results All Salvia species native to East Asia form a clade, and eight major subclades (A-G) were recognized. Subclade A, comprising two limestone endemics (S. sonchifolia and S. petrophila), is sister to the remainder of EA Salvia. Six distinct stamen types were observed within the EA clade. Stamen type A, with two fully fertile posterior thecae, only occurs in S. sonchifolia and may represent the ancestral stamen type within EA Salvia. Divergence time estimates showed that the crown of EA Salvia began to diversify approx. 17.4 million years ago. Conclusions This study supports the adoption of a broadly defined Salvia and treats EA Salvia as a subgenus, Glutinaria, recognizing eight sections within this subgenus. Stamen type A is ostensibly plesiomorphic within EA Salvia, and the other five types may have been derived from it. Staminal morphology has evolved in parallel within the EA Salvia, and staminal structure alone is inadequate to delimit infrageneric categories.

In the California Floristic Province (CA-FP) and nearby deserts, 19 species of Salvia (Lamiaceae, Mentheae) form a small radiation but an important component of the chaparral and desert communities. Traditionally, two groups within these Californian Salvia have been recognized (usually treated as sections), but relationships within each, to each other, and to other Salvia are unclear. Phylogenetic relationships of all species, with multiple accessions for most, were obtained using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) markers. Ancestral character state reconstruction of both vegetative and floral features was done on the resulting nrDNA tree. Biogeographical analysis of the groups within the CA-FP and adjacent floristic provinces was done in BioGeoBEARS and species diversification assessed with BAMM. Significant conclusions drawn from the study include: 1) California Salvia should be classified into two monophyletic sections, Audibertia (15 species) and Echinosphace, (four spe...

The recently described Lepechinia flammea was originally known only from the Sierra Madre del Sur in Guerrero, Mexico. However, a new population of this species was uncovered in Jalisco during recent botanical explorations. Additionally, it was more recently described in Oaxaca as L. oaxacana , a name that in this work is synonymized with L. flammea . Meanwhile, L. glomerata , the most morphologically similar species to L. flammea , was rediscovered in Jalisco. Morphological notes on L. flammea , an extended description of L. glomerata , and photographs and distribution maps for the two species are provided. We also explore the relationships of these two species within Lepechinia , and show they are closely related to the more broadly distributed L. nelsonii .

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

Premise of the study The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. Methods Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. Key results A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. Conclusions Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.

Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.

Since the advent of molecular phylogenetics more than 25 years ago, a major goal of plant systematists has been to discern the root of the angiosperms. Although most studies indicate that Amborella trichopoda is sister to all remaining extant flowering plants, support for this position has varied with respect to both the sequence data sets and analyses employed. Recently, Goremykin et al. (2013) questioned the "Amborella-sister hypothesis" using a "noise-reduction" approach and reported a topology with Amborella + Nymphaeales (water lilies) sister to all remaining angiosperms. Through a series of analyses of both plastid genomes and mitochondrial genes, we continue to find mostly strong support for the Amborella-sister hypothesis and offer a rebuttal of Goremykin et al. (2013). The major tenet of Goremykin et al. is that the Amborella-sister position is determined by noisy data—that is, characters with high rates of change and lacking true phylogenetic signal. To investigate the signal in these noisy data further, we analyzed the discarded characters from their noise-reduced alignments. We recovered a tree identical to that of the currently accepted angiosperm framework, including the position of Amborella as sister to all other angiosperms, as well as all other major clades. Thus, the signal in the "noisy" data is consistent with that of our complete data sets—arguing against the use of their noise-reduction approach. We also determined that one of the alignments presented by Goremykin et al. yields results at odds with their central claim—their data set actually supports Amborella as sister to all other angiosperms, as do larger plastid data sets we present here that possess more complete taxon sampling both within the monocots and for angiosperms in general. Previous unpartitioned, multilocus analyses of mitochondrial DNA (mtDNA) data have provided the strongest support for Amborella + Nymphaeales as sister to other angiosperms. However, our analysis of third codon positions from mtDNA sequence data also supports the Amborella- sister hypothesis. Finally, we challenge the conclusion of Goremykin et al. that the first flowering plants were aquatic and herbaceous, reasserting that even if Amborella + water lilies, or water lilies alone, are sister to the rest of the angiosperms, the earliest angiosperms were not necessarily aquatic and/or herbaceous. (Angiosperms; Amborella; Nymphaeales; plastid genome; water lilies.)

Monardella is a western North America genus ranging from the Rocky Mountains to the Pacific Ocean and from southern Canada to the southern tip of Baja California Sur. The levels of unrecognized and cryptic taxa within Monardella are similar to other taxonomically complicated western North American genera, such as Eriogonum (Polygonaceae), Penstemon (Plantaginaceae), and Oreocarya (Boraginaceae). We present variation in trichome morphology as a taxonomic tool within Monardella, being comparable in importance to trichome variation in other plant families and genera (e.g., Brassicaceae, Draba; Loasaceae, Mentzelia; Solanaceae, Solanum). Trichome morphology within Monardella is a useful character to differentiate taxa and resolve taxonomic ambiguities. We present nomenclatural novelties and revisions for Monardella occurring in the Hells Canyon region along the lower Snake River of west-central Idaho and northeastern Oregon. We introduce the following taxonomic and nomenclatural changes. Monardella odoratissima Benth. var. neglecta Cronquist is recognized as a later homonym; a new name and rank are presented for it: M. perplexans Elvin, R. B. Kelley, & B. T. Drew. Two new species are described: M. kruckebergii Elvin, R. B. Kelley, & B. T. Drew and M. walwaamaxsia Elvin, R. B. Kelley, & B. T. Drew.

Lepechinia (Lamiaceae) is a diverse and widespread genus that is important in indigenous New World culture. We present a phylogenetic analysis of 72 accessions representing 31 species of Lepechinia using data from three plastid (trnL-F, ycf1, ycf1-rps15 spacer) and four nuclear [internal transcribed spacer (ITS), external transcribed spacer (ETS), granule-bound starch synthase I (GBSS)I, pentatricopeptide repeat region (PPR)-AT3G09060] DNA regions. Data were analysed using parsimony, maximum likelihood and Bayesian approaches. Divergence time estimation using BEAST shows Lepechinia had a mid/late Miocene origin, perhaps as a response to global cooling patterns. Cladogenesis in most South American Lepechinia is shown to have occurred within the past 5 Myr, presumably as a response to climatic and orogenic events. Dioecy has arisen multiple times in Lepechinia, once in North America and at least twice in South America, and not necessarily involving gynodioecy as an intermediary step. Dioecy and gynodioecy are demonstrated to be associated with several floral characters, including flower size, number and colour. © 2012 The Linnean Society of London

 Premise of the study: The mint family (Lamiaceae) is the sixth largest family of fl plants, with the tribe Mentheae containing about a third of the species. We present a detailed perspective on the evolution of the tribe Mentheae based on a phylogenetic analysis of cpDNA and nrDNA that is the most comprehensive to date, a biogeographic set of analyses using a fossil-calibrated chronogram, and an examination of staminal evolution.  Methods: Data from four cpDNA and two nrDNA markers representing all extant genera within the tribe Mentheae were analyzed using the programs BEAST, Lagrange, S-DIVA, and BayesTraits. BEAST was used to simultaneously estimate phylogeny and divergence times, Lagrange and S-DIVA were used for biogeographical reconstruction, and BayesTraits was used to infer staminal evolution within the tribe.  Key results: Currently accepted subtribal delimitations are shown to be invalid and are updated. The Mentheae and all fi ve of its subtribes have a Mediterranean origin and have dispersed to the New World multiple times. The vast majority of New World species of subtribe Menthinae are the product of a single dispersal event in the mid-late Miocene. At least four transitions from four stamens to two stamens have occurred within Mentheae, once in the subtribe Salviinae, once in the subtribe Lycopinae, and at least twice in the subtribe Menthinae.  Conclusions: Worldwide cooling trends probably played a large role in the diversifi cation and present day distribution of the tribe Mentheae. Additional work is needed to ascertain relationships within some Mentheae genera, especially in the subtribe Menthinae.

The evolution of the inflorescence head in Asteraceae is important in the diversification of this largest angiosperm family. The aggregation of heads into higher-order capitulescences (secondary heads or syncephalia) is considered evolutionarily advanced. The genera Moscharia, Nassauvia, Polyachyrus, and Triptilion of the subtribe Nassauviinae (Mutisieae) have syncephalia with differing degrees of capitula condensation. ITS and plastid trnL-trnF regions were analyzed separately and together using maximum parsimony and maximum likelihood to examine the evolution of syncephalia in the Nassauviinae. The four genera displaying syncephalia do not form a clade minus taxa without syncephalia, indicating that secondary heads in Nassauviinae have either convergently evolved twice in the subtribe (or, very unlikely) once with multiple reversions. Strong support was obtained for a sister relationship between Leucheria (without syncephalium) and Polyachyrus, and both sister to Moscharia. Nassauvia and Triptilion form a distinct clade but are sister to other genera, Perezia and Panphalea, without syncephalium. Previous hypotheses postulated the evolution from simple to more complex secondary heads. We show that the ancestor of Moscharia, Polyachyrus, and Leucheria, in a more arid habitat, had a complex type of secondary head, and loss of complexity occurred in response to a shift from arid to mesic conditions.

Reconstructing the phylogenetic relationships that unite all biological lineages (the tree of life) is a grand challenge of biology. However, the paucity of readily available homologous character data across disparately related lineages renders direct phylogenetic inference currently untenable. Our best recourse towards realizing the tree of life is therefore the synthesis of existing collective phylogenetic knowledge available from the wealth of published primary phylogenetic hypotheses, together with taxonomic hierarchy information for unsampled taxa. We combined phylogenetic and taxonomic data to produce a draft tree of life?the Open Tree of Life?containing 2.3 million tips. Realization of this draft tree required the assembly of two resources that should prove valuable to the community: 1) a novel comprehensive global reference taxonomy, and 2) a database of published phylogenetic trees mapped to this common taxonomy. Our open source framework facilitates community comment and contribution, enabling a continuously updatable tree when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminates significant gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point from which we can continue to improve through community contributions. Having a comprehensive tree of life will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change studies, agriculture, and genomics.