The study reconstructs the molecular phylogeny and biogeographical history of Stizophyllum (Bignonieae, Bignoniaceae), a small genus of Neotropical lianas, distributed from southern Brazil to Central America. We sampled 33 individuals representing the breadth of morphological variation and geographical distribution of the three species recognized to date, i.e., Stizophyllum inaequilaterum, Stizophyllum perforatum, and Stizophyllum riparium. Bayesian and maximum likelihood approaches led to congruent topologies. A putative new species from Amazonia collected in the Brazilian state of Para, Stizophyllum coriaceum, sp. nov., was recovered as sister to the remaining species of the genus, confirming that it represents a distinct taxon. Furthermore, all Stizophyllum riparium from Central America emerged as a separate clade, leading to the reestablishment of Stizophyllum punctifolium. These findings corroborate a broader circumscription of Stizophyllum perforatum (including all Stizophyllum from the Brazilian Atlantic Forest and Dry Diagonal) and a narrower circumscription of Stizophyllum inaequilaterum (restricted to Western Amazonia and Central America), while indicating that Stizophyllum riparium is not monophyletic and best divided into two taxa: Stizophyllum riparium and Stizophyllum punctifolium. The molecular phylogenetic findings are corroborated by morphological data, and the appropriate taxonomic changes are proposed. In sum, a broader Stizophyllum, with five species is recognized, and an updated synopsis of the genus is presented. Divergence time estimates indicate that the stem node of Stizophyllum originated during the late Eocene, while most of the diversification within the genus occurred much later during the Miocene and Pliocene, periods of intense geological activity in South America. Ancestral area reconstructions inferred Lowland Amazonia as the most likely distribution of the MRCA of Stizophyllum. Five dispersal events and three local extinction events led to the current distribution of the genus.

This study describes two new species of Glechon from the state of Rio Grande do Sul, Brazil: G. rupestris and G. villosissima. Comprehensive morphological descriptions, geographical distribution data, and a preliminary assessment of their conservation status are provided. Additionally, photographic documentation of each species is included. A comparative analysis is presented in tables, highlighting and distinguishing morphologically similar species in the region.

We use a hybrid approach that combines high-throughput sequencing (HTS) data with traditional targeted loci data to infer the phylogeny of Martinella Baill. (Bignonieae, Bignoniaceae), a group of Neotropical lianas. The genus traditionally included three species, but two new species were described recently. We sequenced, assembled, and annotated six complete or nearly complete plastomes representing four of the five known species. In addition, we obtained sequences of the plastid ndhF and rpl32-trnL and the nuclear pepC markers via Sanger sequencing for 15 additional individuals of Martinella, representing all known species and covering their range of geographic distribution. Two outgroups were sampled, leading to a final dataset with 23 individuals. We used these data to assemble five different dataset combinations to evaluate tree topology and support values. Targeted loci data alone led to a poorly resolved topology, while HTS data recovered a fully resolved tree with maximum support in most branches. Combining HTS and Sanger sequencing data maximized taxon and character sampling, leading to a fully resolved tree with moderate support. This tree is considered the most robust and reliable estimate of the phylogeny of Martinella to date and is used as a basis to evaluate the taxonomy of the group. This phylogeny supports the recognition of five taxa, including the previously recognized M. obovata, M. insculpta, and M. insignis, plus the two newly described Amazonian species, M. lanuginosa and M. tomentosa. Our study highlights the importance of in-depth studies of individual lineages, especially in Amazonia, where important sampling lacunae remain.

While studying Vellozo’s Verbenaceae names in Floræ Fluminensis, the name Verbena cunha Vell. was suspected to be the oldest name for a species usually identified as Verbena phlogiflora Cham./Glandularia phlogiflora (Cham.) Schnack Covas. An expedition was made to observe and collect specimens in the most likely type locality, given the interpretation of the original locality in São Paulo. As a result, a new combination, Glandularia cunha, is provided. This taxonomic novelty is presented along with typification, nomenclatural and taxonomic notes, photographs and a distribution map.

Species of Tanaecium (Bignonieae, Bignoniaceae) are lianas distributed in the Neotropics and centered in the Amazon. Members of the genus exhibit exceptionally diverse flower morphology and pollination systems. Here, we sequenced, assembled, and annotated 12 complete and four partial chloroplast genomes representing 15 Tanaecium species and more than 70% of the known diversity in the genus. Gene content and order were similar in all species of Tanaecium studied, with genome sizes ranging between 158,470 and 160,935 bp. Tanaecium chloroplast genomes have 137 genes, including 80–81 protein-coding genes, 37 tRNA genes, and four rRNA genes. No rearrangements were found in Tanaecium plastomes, but two different patterns of boundaries between regions were recovered. Tanaecium plastomes show nucleotide variability, although only rpoA was hypervariable. Multiple SSRs and repeat regions were detected, and eight genes were found to have signatures of positive selection. Phylogeny reconstruction using 15 Tanaecium plastomes resulted in a strongly supported topology, elucidating several relationships not recovered previously and bringing new insights into the evolution of the genus.

Recent phylogenetic results strongly suggest that neither Lantana nor Lippia are monophyletic. This has a direct impact on taxonomy and nomenclature in the tribe Lantaneae and it underscores the need to revise its classification. However, any generic recircumscription following the International Code of Nomenclature for algae, fungi, and plants will require substantial nomenclatural changes. As a solution, a phylogenetic classification following the PhyloCode is applied to the whole Lantaneae, and 28 rank-free names are proposed and defined for clades. Clade /Lantaneae is defined to exclude Coelocarpum. Traditional taxon names previously recognized at the ranks of tribe, genus, and section are maintained when associated with clades. Discussion about fruit and corolla morphology, the basis of most previous classifications, within the group is presented along with a key to the clades of /Lantaneae. A useful classification of the plant diversity in tribe Lantaneae consistent with the phylogenetic relationships within the group is provided. This rank-free system promotes name stability as new data become available and avoids name changes to well-known species.

Aim The biotic assembly of one of the most species-rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity. We investigated the timing and routes of species movements between wet or seasonally dry habitats across Neotropical regions and assessed the potential for ecological adaptation by evaluating the habitat transitions correlated with morphological shifts. Location Neotropics. Taxon The plant genus Anemopaegma (Bignonieae, Bignoniaceae). Methods We inferred a Bayesian molecular phylogeny of Anemopaegma using one nuclear and two chloroplast markers. We sampled more than 90% of the known species diversity of Anemopaegma, covering its full geographical range. We estimated divergence times using a Bayesian relaxed-clock approach and inferred ancestral ranges as well as shifts in habitat and morphological characters. Results Phylogenetic analyses recovered seven main clades within Anemopaegma. The genus likely originated in Amazonia in the late Oligocene. Early-diverging lineages diversified in situ in Amazonia, particularly during the Miocene, with independent dispersal events to the Andes, Atlantic Forest and Cerrado. Shifts from seasonally dry forest to savanna habitats were correlated with shifts from liana to shrub and the loss of tendrils. Main Conclusions The timing of diversification of major lineages within Anemopaegma is consistent with major geological and climatic events that occurred during the late Palaeogene and Neogene, such as the Andean uplift and the Middle Miocene Climatic Optimum. Movements across different regions within the Neotropics were relatively common but shifts between habitats were not. The correlation in the evolution of the shrubby habit, the loss of tendrils and the shifts from forest to savanna are consistent with a scenario of ecological adaptation.

The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.

We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole.

Evolutionary and ecological processes that influenced the assembly of the New World flora are best understood through investigation of spatio-temporal processes of specific lineages, but some groups still lack a historical overview. Here, we produced a well-sampled dated tree, reconstructed ancestral ranges and performed diversification analyses for Sisyrinchium (Iridaceae) to elucidate its evolution in the Americas. Eight molecular markers and samples representing its full geographical range and morphological diversity were used to estimate divergence times with a Bayesian relaxed clock with secondary calibrations. Ancestral range reconstruction under likelihood methods and diversification analyses were performed. Sisyrinchium originated in a broad range including the Andes and Mesoamerica in the Mid-Miocene. Diversification at high elevations occurred in the early diverging lineages, which feature the highest extinction rates. Increase in diversification rate was detected during the Pliocene/Pleistocene after the colonization of lower elevations. Later sympatric speciation in south-eastern Brazil was followed by movements to other regions, including a long-dispersal event to North America. Higher extinction rates were followed by movements to lower elevations, with periods of accelerated Andean orogeny and global temperature decrease. Our results indicate that palaeoclimate and changes in elevational range influenced diversification in Sisyrinchium.

Background and aims – The last comprehensive study that estimated the number of Verbenaceae genera and species was published in 2004, and included 34 genera and around 1200 species. Since then, several publications based on morphology and/or molecular data have proposed important changes within the family. Due to the lack of updated literature to cite when referring to the number of Verbenaceae taxa, a review of these estimates is necessary.Key results and conclusion – We present a detailed list of genera currently accepted in Verbenaceae with the number of species contained in each and compare our numbers with the previous estimate. In addition, we indicate the geographic distribution and the most recent important taxonomic or phylogenetic works for each genus. Our compilation shows that Verbenaceae have 32 genera and 800 species currently accepted.This work provides up-to-date numbers and brings a holistic view of the family.

PREMISE Lantana and Lippia (Verbenaceae) are two large Linnean genera whose classification has been based on associated fruit traits: fleshy vs. dry fruits and one vs. two seed-bearing units. We reconstruct evolutionary relationships and the evolution of the two fruit traits to test the validity of these traits for classification. METHODS Previous studies of plastid DNA sequences provided limited resolution for this group. Consequently, seven nuclear loci, including ITS, ETS, and five PPR loci, were sequenced for 88 accessions of the Lantana/Lippia clade and three outgroups. RESULTS Neither Lantana nor Lippia is monophyletic. Burroughsia, Nashia, Phyla, and several Aloysia species are included within the clade comprising Lantana and Lippia. We provide a hypothesis for fruit evolution and biogeographic history in the group and their relevance for classification. CONCLUSIONS Fleshy fruits evolved multiple times in the Lantana/Lippia clade and thus are not suitable taxonomic characters. Several sections of Lantana and Lippia and the small genera are monophyletic, but Lippia section Zappania is broadly paraphyletic, making circumscription of genera difficult. Lippia sect. Rhodolippia is a polyphyletic group characterized by convergence in showy bracts. Species of Lantana sect. Sarcolippia, previously transferred to Lippia, are not monophyletic. The clade originated and diversified in South America, with at least four expansions into both Central America and the Caribbean and two to Africa. The types species of Lantana and Lippia occur in small sister clades, rendering any taxonomy that retains either genus similar to its current circumscription impossible.

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.

The accurate analyses of massive amounts of data obtained through next-generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate "supergene" approach. The effects of molecular evolutionary models and character partition strategies on plastome-based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well-supported conflicting topologies). We compared different datasets (e.g., non-coding regions, exons, and codon-aligned and translated amino acids) using concatenated approaches under site-heterogeneous and site-homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

Lippia subracemosa var. harleyi Moldenke and Verbena subpetiolata N.O’Leary, previously considered synonyms of Lippia lasiocalycina Chamisso and Glandularia jordanensis (Moldenke) N.O’Leary & P.Peralta, respectively, are being here recognized as distinct species in the genera Lippia and Glandularia. The nomenclatural changes needed are herein proposed: Lippia deltata I.N.Santana & T.R.S.Silva stat. & nom. nov. and Glandularia subpetiolata (N.O’Leary) P.H.Cardoso & V.Thode comb. nov. Comments on the distribution and morphological characters to differentiate these species from their most similar congeneric taxa are provided.

Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.

Two species of Glandularia from Rio Grande do Sul Brazilian state are described, G. rupestris V. Thode & Bordignon and G. sessilifolia V. Thode & Bordignon. Detailed morphological descriptions, geographical distribution, evaluation of their IUCN conservation status and photographs are presented. Comparison tables with morphologically similar species occurring in Rio Grande do Sul and an identification key to the species occurring in Brazil are also provided.

The mechanisms and processes underlying patterns of species distributions have intrigued ecologists and biogeographers for a long time. The Neotropics is the most species-rich region in the World, representing an excellent model for studying the drivers of diversification. In this study, we used a phylogenomic approach to infer relationships and examine the role of major geological and climatic events in shaping biogeographic patterns within Amphilophium (Bignonieae, Bignoniaceae), a genus of Neotropical lianas. Even though Amphilophium is broadly distributed across the Neotropics, it is centered in Amazonia and the Atlantic rainforest. We generated nearly-complete plastome sequences for 32 species of Amphilophium, representing 70% of the species diversity in the genus. The final dataset included 78 plastid-coding regions and was analyzed under Maximum Likelihood and Bayesian approaches to reconstruct the phylogeny of Amphilophium. We also used this dataset to estimate divergence times using a Bayesian relaxed-clock approach. We further inferred ancestral ranges, migration events, and shifts in diversification rates using a branch-specific diversification model and the Dispersal-Extinction-Cladogenesis (DEC) model implemented in a Bayesian phylogenetic framework. Overall, we obtained a well-resolved and strongly supported phylogeny for Amphilophium, with five main clades that are well characterized by morphological features. Amphilophium originated in the Early Oligocene, and started to diversify in the Late Oligocene. The first diversification event involved a split between Amazonian and Atlantic forest clades. These two clades showed very different diversification scenarios. Divergence within the Atlantic forest clade began in the Mid-Oligocene, while the Amazonian clade underwent rapid diversification starting in the Late Miocene. In-situ speciation characterized the Amazonian clade, whereas allopatric speciation driven by migration events into other Neotropical biomes were mostly inferred within the Atlantic forest clade. The diversification of Amphilophium in the Neotropics was triggered by major geological events and changes in landscape that occurred during the Late Paleogene and Neogene, with little influence of the climatic changes of the Pleistocene ice ages. The divergence times and range inferences support the role of the Western Amazonian "megawetlands" and the formation of the South American "dry diagonal" as key climatic and geological barriers that separated the Atlantic forest from the Amazonian lowlands. Timing of migration events agrees with a Mid-Miocene closure of the Central American Seaway.

Abstract Glandularia J. F. Gmel. (Verbenaceae) is the largest genus in the tribe Verbeneae, with ca. 84 species distributed mainly in temperate North and South America. A complete taxonomic revision of Glandularia in Brazil is provided. Thirty-one species and one variety are present in Brazil, 11 of these being endemic, principally in the southern area of the country. A detailed morphological description is given for each taxon as well as a key for their identification, illustrations, synonymy, distribution, lists of selected specimens, and discussions about the relationships among closely related taxa. A new combination, G. tomophylla (Briq.) N. O'Leary & V. Thode, is here proposed, six new synonyms are suggested, and two lectotypes are designated for Verbena chamaedryfolia Juss. f. strigosa Chodat and V. humifusa Cham.

Glandularia J. F. Gmel. (Verbenaceae) is the largest genus in the tribe Verbeneae, with ca. 84 species distributed mainly in temperate North and South America. A complete taxonomic revision of Glandularia in Brazil is provided. Thirty-one species and one variety are present in Brazil, II of these being endemic, principally in the southern area of the country. A detailed morphological description is given for each taxon as well as a key for their identification, illustrations, synonymy, distribution, lists of selected specimens, and discussions about the relationships among closely related taxa. A new combination, G. tomophylla (Brig.) N. O'Leary & V. Thode, is here proposed, six new synonyms are suggested, and two lectotvpes are designated for Verbena ehamaedryfolia Juss. f. strigosa Chodat and V humifitsa Cham.