An updated and extended version of the Melastomataceae probe set for target capture.

Premise: A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae. Methods: In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version. Results: The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery. Discussion: This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.

Out of chaos: Phylogenomics of Asian Sonerileae.

Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.

Beneath a hairy problem: Phylogeny, morphology, and biogeography circumscribe the new Miconia supersection Discolores (Melastomataceae: Miconieae).

Miconia is among the largest plant genera in the Neotropics and a taxonomically complex lineage. Indeed, molecular phylogenetic data shows that none of its traditionally accepted sections are monophyletic, preventing taxonomic advances within the genus. Miconia is the largest plant genus in the Brazilian Atlantic Forest, including three main lineages, the Leandra s.s. clade (ca. 215 spp.), the Miconia sect. Chaenanthera (24 spp.), and the Miconia discolor clade (estimated 77 spp.). Out of these lineages, the Miconia discolor clade is the only currently lacking phylogenetic data, complicating its taxonomy. In this study, we reconstruct the phylogeny of the Miconia discolor clade, using three plastid (atpF-H, psbK-I, and psaI-accD) and two nuclear (ETS and ITS) markers. We sampled 60 out of the 77 species of the group, representing 78% of its diversity. Taxa were selected considering their distribution, morphology, and previous phylogenetic knowledge. We used the newly reconstructed phylogeny to better understand phylogenetic relationships among Atlantic Forest species and morphologically similar taxa, and to propose a new infrageneric classification for the Miconia discolor clade: the Miconia supersection Discolores. We further studied the evolution of seven morphological characters using a Maximum Likelihood approach, and estimated the ancestral range distribution of various lineages in order to understand the biogeographic history of this clade. We found that dichasial inflorescences represent the ancestral condition within Miconia, subsequently giving rise to scorpioid and glomerulate inflorescences in the studied group. We describe Miconia supersect. Discolores, originated in the Amazon region, which is recognized by a dense layer of branched tricomes covering young branches and non-dichasial inflorescences, including three main lineages: (i) Miconia sect. Albicantes, characterized by persistent bracts and arachnoid indument on the abaxial surface of leaves, mainly distributed in the Amazon basin; (ii) Miconia sect. Discolores, characterized by caducous calyx lobes and glomerulate inflorescences, centered in the Atlantic Forest; and (iii) Miconia sect. Multispicatae, characterized by leaves not completely covered with indument, and capitate stigma, mainly distributed in the Atlantic Forest. All three sections and the supersection originated in the Neogene, between the Late Miocene and the Early Pliocene.

A multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic Forest hotspot / Integrando disciplinas para a predição da biodiversidade da Floresta Atlântica no Brasil

Abstract: We briefly describe selected results from our thematic project focused on the biodiversity of the Atlantic Forest ("AF BIOTA"), which was jointly funded by FAPESP's BIOTA Program, the U.S. National Science Foundation Dimensions of Biodiversity Program, and the National Aeronautics and Space Administration (NASA). As one of the five most important hotspots of biodiversity in the world, the Atlantic Forest (AF) holds less than 16% of its vegetation cover, yet, amongst the hotspots, it still harbors one of the highest numbers of species, including endemics. By gathering specialists across multiple disciplines (biology, geology, engineering), we aimed to understand how this megabiodiversity was built through time, informing biodiversity science and conservation. Among the results, we trained 18 Master's and 26 Ph.D. students, published more than 400 peer-reviewed papers that improved our knowledge about the forest's biologic and climatic diversity and dynamics through time, developed new analytical methods, produced outreach videos and articles, and provided data to help define biodiversity conservation policies.

Resumo: Descrevemos de forma resumida resultados selecionados do nosso projeto temático com foco na biodiversidade da Floresta Atlântica ("AF BIOTA"), que foi financiado pelo BIOTA FAPESP e pelo programa "Dimensions of Biodiversity" da "U.S. National Science Foundation" e "National Aeronautics and Space Administration" (NASA). Devido à sua megabiodiversidade (que inclui várias espécies endêmicas), e por restar menos de 16% da vegetação original, a Floresta Atlântica (FA) é uma das cinco áreas mais importantes para a biodiversidade do planeta ("biodiversity hotspot"). Reunimos especialistas de diversas disciplinas (biologia, geologia, engenharia) visando compreender como essa megabiodiversidade evoluiu ao longo do tempo e fornecer informações científicas para a sua conservação. Dentre os resultados obtidos, nós formamos 18 mestres e 26 doutores, publicamos mais de 400 artigos científicos que aumentaram o conhecimento sobre a diversidade biológica e climática da FA e sua dinâmica ao longo do tempo, desenvolvemos novos métodos analíticos, produzimos material de divulgação científica e fornecemos dados para desenvolver políticas públicas de conservação da biodiversidade.

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Low bee visitation rates explain pollinator shifts to vertebrates in tropical mountains.

Evolutionary shifts from bee to vertebrate pollination are common in tropical mountains. Reduction in bee pollination efficiency under adverse montane weather conditions was proposed to drive these shifts. Although pollinator shifts are central to the evolution and diversification of angiosperms, we lack experimental evidence of the ecological processes underlying such shifts. Here, we combine phylogenetic and distributional data for 138 species of the Neotropical plant tribe Merianieae (Melastomataceae) with pollinator observations of 11 and field pollination experiments of six species to test whether the mountain environment may indeed drive such shifts. We demonstrate that shifts from bee to vertebrate pollination coincided with occurrence at high elevations. We show that vertebrates were highly efficient pollinators even under the harsh environmental conditions of tropical mountains, whereas bee pollination efficiency was lowered significantly through reductions in flower visitation rates. Furthermore, we show that pollinator shifts in Merianieae coincided with the final phases of the Andean uplift and were contingent on adaptive floral trait changes to alternative rewards and mechanisms facilitating pollen dispersal. Our results provide evidence that abiotic environmental conditions (i.e. mountain climate) may indeed reduce the efficiency of a plant clade's ancestral pollinator group and correlate with shifts to more efficient new pollinators.

The Herbarium 2021 Half-Earth Challenge Dataset and Machine Learning Competition.

Herbarium sheets present a unique view of the world's botanical history, evolution, and biodiversity. This makes them an all-important data source for botanical research. With the increased digitization of herbaria worldwide and advances in the domain of fine-grained visual classification which can facilitate automatic identification of herbarium specimen images, there are many opportunities for supporting and expanding research in this field. However, existing datasets are either too small, or not diverse enough, in terms of represented taxa, geographic distribution, and imaging protocols. Furthermore, aggregating datasets is difficult as taxa are recognized under a multitude of names and must be aligned to a common reference. We introduce the Herbarium 2021 Half-Earth dataset: the largest and most diverse dataset of herbarium specimen images, to date, for automatic taxon recognition. We also present the results of the Herbarium 2021 Half-Earth challenge, a competition that was part of the Eighth Workshop on Fine-Grained Visual Categorization (FGVC8) and hosted by Kaggle to encourage the development of models to automatically identify taxa from herbarium sheet images.

An algorithm competition for automatic species identification from herbarium specimens.

PREMISE: Plant biodiversity is threatened, yet many species remain undescribed. It is estimated that >50% of undescribed species have already been collected and are awaiting discovery in herbaria. Robust automatic species identification algorithms using machine learning could accelerate species discovery. METHODS: To encourage the development of an automatic species identification algorithm, we submitted our Herbarium 2019 data set to the Fine-Grained Visual Categorization sub-competition (FGVC6) hosted on the Kaggle platform. We chose to focus on the flowering plant family Melastomataceae because we have a large collection of imaged herbarium specimens (46,469 specimens representing 683 species) and taxonomic expertise in the family. As is common for herbarium collections, some species in this data set are represented by few specimens and others by many. RESULTS: In less than three months, the FGVC6 Herbarium 2019 Challenge drew 22 teams who entered 254 models for Melastomataceae species identification. The four best algorithms identified species with >88% accuracy. DISCUSSION: The FGVC competitions provide a unique opportunity for computer vision and machine learning experts to address difficult species-recognition problems. The Herbarium 2019 Challenge brought together a novel combination of collections resources, taxonomic expertise, and collaboration between botanists and computer scientists.

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae.

PREMISE: Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae). METHODS: We present a two-tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome-skimming data from within the focal clades. RESULTS: We sequenced 193 loci common to Memecylon and Tibouchina. Probes designed from 56 template sequences successfully targeted sequences in both clades. Probes designed from genome-skimming data within a focal clade were more successful than probes designed from other sources. DISCUSSION: Our pipeline successfully identified and targeted SCN loci in Memecylon and Tibouchina, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources.

Flower morphology is correlated with distribution and phylogeny in Bertolonia (Melastomataceae), an herbaceous genus endemic to the Atlantic Forest.

Several centers of endemism have been proposed for Melastomataceae, particularly in Amazonia and Atlantic Forest. Despite the high degree of human-caused degradation in the last 500 years, the Atlantic Forest still presents some of the largest levels of diversity and endemism across all angiosperms. With several recently described species in the last decade, the knowledge on Bertolonia's distribution and morphological characterization has changed, with most new species found in northern Atlantic Forest and with different flower color patterns than the species from southern Atlantic Forest. We first tested the monophyly of the genus sampling over 85% of its species to generate a reliable phylogenetic hypothesis. Afterwards, we used Bertolonia as a model group to study distribution patterns and morphological evolution of lineages in the Atlantic Forest. Bertolonia is particularly interesting to address such questions because it is endemic to this domain, with species distributed either in the southern, central or northern portions of the Atlantic Forest. The second step of our work aimed to respond (1) Do closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological traits? and (2) Are floral traits more conserved within clades than vegetative characters? We hypothesize that both (1) and (2) are true due to the low dispersal ability and consequent microendemic distribution of most species in the genus. Our results confirm the veracity of the proposed hypotheses. Three major groups were recovered in our analysis: marmorata, formosa and nymphaeifolia clades. Most species that occur in northern Atlantic Forest were recovered in the marmorata clade. Most species distributed in central Atlantic Forest were recovered in the formosa clade, and the ones from the southern Atlantic Forest in the nymphaeifolia clade. A similar pattern was recovered with reproductive characters reconstructed across the phylogeny. Generally, species with pink petals and cream-colored anthers with an extrorse pore occur in northern Atlantic Forest, and species with white petals and yellow anthers with an introrse or apical pore tend to occur in southern Atlantic Forest. Some vegetative characters also have evolutionary congruence and are restricted to one or few lineages, while other characters, such as the texture of the leaf blade surface, have a strong taxonomic value and are useful to identify species, but are not homologous. Our analysis also indicates that the division between southern and northern Atlantic Forest could also be related to ancient events, not only linked with recent phylogeographic patterns. Moreover, we suggest that the orientation of the anther pore in Bertolonia could be related with diversity of species and stability of its populations. In summary, we corroborate, based on the evolutionary history of Bertolonia, that closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological floral traits.

Miconia lucenae (Melastomataceae), a new species from montane Atlantic Forest in Espírito Santo, Brazil.

We describe Miconia lucenae R.Goldenb. & Michelang., a new species from the montane Atlantic Forest in Santa Teresa in the state of Espírito Santo. Our analysis, based on three plastid spacers (atpF-atpH, psbK-psbl and trnS-trnG), one plastid gene (ndhF, not available for M. lucenae), and two nuclear ribosomal loci (nrITS and nrETS), showed that it belongs to a small clade with Miconia paradoxa (Mart. ex DC.) Triana (Minas Gerais) and M. michelangeliana R.Goldenb. & L.Kollmann (Espírito Santo). The three species in the "Paradoxa clade" can be recognized by the plants with glabrous or glabrescent branches and leaves, white petals and yellow stamens, these with the connectives not prolonged below the thecae, ventrally unappendaged, dorsally unappendaged or with a minute tooth, the latter bilobed or not, glabrous ovary, and the fruits with a persistent calyx. Miconia lucenae can be recognized, among the species in this clade, by the shrubby plants with terete young branches, short inflorescences, usually with red axes, and the 2-bracteolate, sessile, 4-merous flowers, with a ciliolate inner portion of the sepals, lanceolate petals, and 4-celled ovaries. This species can be considered as endangered according to IUCN criteria.

Erratum: Author Correction: Modularity increases rate of floral evolution and adaptive success for functionally specialized pollination systems.

[This corrects the article DOI: 10.1038/s42003-019-0697-7.].

Modularity increases rate of floral evolution and adaptive success for functionally specialized pollination systems.

Angiosperm flowers have diversified in adaptation to pollinators, but are also shaped by developmental and genetic histories. The relative importance of these factors in structuring floral diversity remains unknown. We assess the effects of development, function and evolutionary history by testing competing hypotheses on floral modularity and shape evolution in Merianieae (Melastomataceae). Merianieae are characterized by different pollinator selection regimes and a developmental constraint: tubular anthers adapted to specialized buzz-pollination. Our analyses of tomography-based 3-dimensional flower models show that pollinators selected for functional modules across developmental units and that patterns of floral modularity changed during pollinator shifts. Further, we show that modularity was crucial for Merianieae to overcome the constraint of their tubular anthers through increased rates of evolution in other flower parts. We conclude that modularity may be key to the adaptive success of functionally specialized pollination systems by making flowers flexible (evolvable) for adaptation to changing selection regimes.

Systematics and relationships of Tryssophyton (Melastomataceae), with a second species from the Pakaraima Mountains of Guyana.

The systematics of Tryssophyton, herbs endemic to the Pakaraima Mountains of western Guyana, is reviewed and Tryssophyton quadrifolius K.Wurdack & Michelang., sp. nov. from the summit of Kamakusa Mountain is described as the second species in the genus. The new species is distinguished from its closest relative, Tryssophyton merumense, by striking vegetative differences, including number of leaves per stem and leaf architecture. A phylogenetic analysis of sequence data from three plastid loci and Melastomataceae-wide taxon sampling is presented. The two species of Tryssophyton are recovered as monophyletic and associated with mostly Old World tribe Sonerileae. Fruit, seed and leaf morphology are described for the first time, biogeography is discussed and both species are illustrated.

Beyond buzz-pollination - departures from an adaptive plateau lead to new pollination syndromes.

Pollination syndromes describe recurring adaptation to selection imposed by distinct pollinators. We tested for pollination syndromes in Merianieae (Melastomataceae), which contain bee- (buzz-), hummingbird-, flowerpiercer-, passerine-, bat- and rodent-pollinated species. Further, we explored trait changes correlated with the repeated shifts away from buzz-pollination, which represents an 'adaptive plateau' in Melastomataceae. We used random forest analyses to identify key traits associated with the different pollinators of 19 Merianieae species and estimated the pollination syndromes of 42 more species. We employed morphospace analyses to compare the morphological diversity (disparity) among syndromes. We identified three pollination syndromes ('buzz-bee', 'mixed-vertebrate' and 'passerine'), characterized by different pollen expulsion mechanisms and reward types, but not by traditional syndrome characters. Further, we found that 'efficiency' rather than 'attraction' traits were important for syndrome circumscription. Contrary to syndrome theory, our study supports the pooling of different pollinators (hummingbirds, bats, rodents and flowerpiercers) into the 'mixed-vertebrate' syndrome, and we found that disparity was highest in the 'buzz-bee' syndrome. We conclude that the highly adaptive buzz-pollination system may have prevented shifts towards classical pollination syndromes, but provided the starting point for the evolution of a novel set of distinct syndromes, all having retained multifunctional stamens that provide pollen expulsion, reward and attraction.

Amazon plant diversity revealed by a taxonomically verified species list.

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

The first complete plastid genomes of Melastomataceae are highly structurally conserved.

BACKGROUND: In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. METHODS: Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. RESULTS: The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. DISCUSSION: Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.

Miconia papillosperma (Melastomataceae, Miconieae): a new species from Amazonas, Brazil.

Miconia papillosperma, a new species of Melastomataceae shrubs from Northern Brazil is described and illustrated. This new species is characterized by elliptic lanceolate leaves with the only pair of secondary veins running close to the margin. It is also unique in having seeds with a papillose testa, a character until now unknown in the Miconieae. The description of this new species from a relatively well collected area near a major road north of Manaus, Amazonas, Brazil, is further evidence of our lack of knowledge on plants in many Neotropical areas.

Diversity and constraints in the floral morphological evolution of Leandra s.str. (Melastomataceae).

BACKGROUND AND AIMS: Putative processes related to floral diversification and its relation to speciation are still largely unaccounted for in the Melastomataceae. Leandra s.str. is one of the most diverse lineages of the Neotropical Miconieae and ranks among the ten most diverse groups in the Atlantic Forest. Here, we describe the floral diversity of this lineage in a continuous framework and address several questions related to floral evolution and putative developmental and environmental constraints in its morphology. METHODS: The morphological data set includes individual size measurements and shape scores (from elliptical Fourier analysis) for hypanthia, petals, stamens and styles. We evaluate whether there is evidence of correlation among these floral structures, shifts and convergent patterns, and association of these traits with elevation. KEY RESULTS: Leandra s.str. flower structures present a strong phylogenetic signal and tend to be conserved among close relatives. The extremes in flower regimes seem to be quite distinct, but non-overlapping discrete flower types are not observed. Overall, the morphology of Leandra s.str. floral structures is correlated, and anther colour and inflorescence architecture correlate with flower structures. Additionally, the rates of species diversification and morphological evolution are correlated in most clades. CONCLUSIONS: Although some flower regimes tend to occur in different elevational ranges, no significant association is observed. The general idea that hypanthium-ovary fusion is associated with fruit types in the Melastomataceae does not hold for Leandra s.str., where, instead, hypanthium-ovary fusion seems to be associated with anther shape. The lowest rate of flower morphological change, when compared with species diversification rates, is observed in the clade that possesses the most specialized flowers in the group. While stuck on a single general pollination system, Leandra s.str. seems to be greatly wandering around it, given the flower diversity and convergent patterns observed in this group.

Molecular phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights into their morphological evolution.

The tank-epiphytic clade of berry-fruited bromeliads, also known as the Core Bromelioideae, represents a remarkable event of adaptive radiation within the Bromeliaceae; however, the details of this radiation have been difficult to study because this lineage is plagued with generic delimitation problems. In this study, we used a phylogenetic approach to investigate a well supported, albeit poorly understood, lineage nested within the Core Bromelioideae, here called the "Ronnbergia Alliance". In order to assess the monophyly and phylogenetic relationships of this group, we used three plastid and three nuclear DNA sequence markers combined with a broad sampling across three taxonomic groups and allied species of Aechmea expected to comprise the Ronnbergia Alliance. We combined the datasets to produce a well-supported and resolved phylogenetic hypothesis. Our main results indicated that the Ronnbergia Alliance was a well-supported monophyletic group, sister to the remaining Core Bromelioideae, and it was composed by species of the polyphyletic genera Aechmea, Hohenbergia and Ronnbergia. We identified two major internal lineages with high geographic structure within the Ronnbergia Alliance. The first of these lineages, called the Pacific Clade, contained species of Aechmea and Ronnbergia that occur exclusively from southern Central America to northwestern South America. The second clade, called the Atlantic Clade, contained species of Aechmea, Hohenbergia and Ronnbergia mostly limited to the Atlantic Forest and the Caribbean. We also explored the diagnostic and evolutionary importance of 13 selected characters using ancestral character reconstructions on the phylogenetic hypothesis. We found that the combination of tubular corollas apically spreading and unappendaged ovules had diagnostic value for the Ronnbergia Alliance, whereas flower size, length of the corolla tube, and petal pigmentation and apex were important characters to differentiate the Pacific and Atlantic clades. This study opens new perspectives for future taxonomic reorganizations and provides a framework for evolutionary and biogeographic studies.