Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores.

BACKGROUND AND AIM: Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales. METHODS: We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70% of Bocageeae species, covering its geographic range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework. KEY RESULTS: The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Its ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico, during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes. CONCLUSIONS: In Bocageeae mammals may have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal may have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity, and abundance at particular time periods and places. Hence, inter- and intracontinental dispersal may not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.

Tangled banks: A landscape genomic evaluation of Wallace's Riverine barrier hypothesis for three Amazon plant species.

Wallace's Riverine Barrier hypothesis is one of the earliest biogeographic explanations for Amazon speciation, but it has rarely been tested in plants. In this study, we used three woody Amazonian plant species to evaluate Wallace's Hypothesis using tools of landscape genomics. We generated unlinked single-nucleotide polymorphism (SNP) data from the nuclear genomes of 234 individuals (78 for each plant species) across 13 sampling sites along the Rio Branco, Brazil, for Amphirrhox longifolia (8,075 SNPs), Psychotria lupulina (9,501 SNPs) and Passiflora spinosa (14,536 SNPs). Although significantly different migration rates were estimated between species, the population structure data do not support the hypothesis that the Rio Branco-an allopatric barrier for primates and birds-is a significant genetic barrier for Amphirrhox longifolia, Passiflora spinosa or Psychotria lupulina. Overall, we demonstrated that medium-sized rivers in the Amazon Basin, such as the Rio Branco, are permeable barriers to gene flow for animal-dispersed and animal-pollinated plant species.

Contrasting patterns of diversification between Amazonian and Atlantic forest clades of Neotropical lianas (Amphilophium, Bignonieae) inferred from plastid genomic data.

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.

Phylogeny of the Neotropical tribe Jacarandeae (Bignoniaceae).

PREMISE: The tribe Jacarandeae includes Jacaranda (49 species) and Digomphia (3 species), two genera of trees and woody shrubs with Neotropical distribution. Jacarandeae is sister to the rest of the Bignoniaceae, but not much is known about interspecific and intergeneric relationships within this group. METHODS: We reconstructed the phylogeny of Jacarandeae using chloroplast (ndhF, rpl32-trnL, trnL-F) and nuclear (ETS, PPR62) markers. Evolutionary relationships within Jacarandeae were inferred using Bayesian, Maximum Likelihood, and species tree approaches. The resulting phylogenetic framework was used as the basis to interpret the evolution of key morphological character states (i.e., stamen and calyx traits) and revise the infra-generic classification of the group. RESULTS: Jacaranda and Digomphia belong to a well-supported clade, with Digomphia nested within Jacaranda. We propose the necessary taxonomic changes to recognize monophyletic taxa, including a broadly circumscribed Jacaranda divided into four sections: (1) Jacaranda sect. Nematopogon, species previously included in Digomphia and united by divided staminode apices and spathaceous calyces; (2) Jacaranda sect. Copaia, species with monothecal anthers and cupular calyces; (3) Jacaranda sect. Jacaranda, species with monothecal anthers and campanulate calyces; and (4) Jacaranda sect. Dilobos, species with dithecal anthers and cupular calyces, and including more than half of the species of the genus, all restricted to Brazil. CONCLUSIONS: As circumscribed here, Jacarandeae includes only a broadly defined Jacaranda divided into four sections. Each section is defined by a unique combination of anther and calyx morphologies.

The molecular control of tendril development in angiosperms.

The climbing habit has evolved multiple times during the evolutionary history of angiosperms. Plants evolved various strategies for climbing, such as twining stems, tendrils and hooks. Tendrils are threadlike organs with the ability to twine around other structures through helical growth; they may be derived from a variety of structures, such as branches, leaflets and inflorescences. The genetic capacity to grow as a tendrilled climber existed in some of the earliest land plants; however, the underlying molecular basis of tendril development has been studied in only a few taxa. Here, we summarize what is known about the molecular basis of tendril development in model and candidate model species from key tendrilled families, that is, Fabaceae, Vitaceae, Cucurbitaceae, Passifloraceae and Bignoniaceae. Studies on tendril molecular genetics and development show the molecular basis of tendril formation and ontogenesis is diverse, even when tendrils have the same ontogenetic origin, for example leaflet-derived tendrils in Fabaceae and Bignoniaceae. Interestingly, all tendrils perform helical growth during contact-induced coiling, indicating that such ability is not correlated with their ontogenetic origin or phylogenetic history. Whether the same genetic networks are involved during helical growth in diverse tendrils still remains to be investigated.

Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies.

Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species.

Wallace's riverine barrier hypothesis postulates that large rivers, such as the Amazon and its tributaries, reduce or prevent gene flow between populations on opposite banks, leading to allopatry and areas of species endemism occupying interfluvial regions. Several studies have shown that two major tributaries, Rio Branco and Rio Negro, are important barriers to gene flow for birds, amphibians and primates. No botanical studies have considered the potential role of the Rio Branco as a barrier, while a single botanical study has evaluated the Rio Negro as a barrier. We studied an Amazon shrub, Amphirrhox longifolia (A. St.-Hil.) Spreng (Violaceae), as a model to test the riverine barrier hypothesis. Twenty-six populations of A. longifolia were sampled on both banks of the Rio Branco and Rio Negro in the core Amazon Basin. Double-digest RADseq was used to identify 8,010 unlinked SNP markers from the nuclear genome of 156 individuals. Data relating to population structure support the hypothesis that the Rio Negro acted as a significant genetic barrier for A. longifolia. On the other hand, no genetic differentiation was detected among populations spanning the narrower Rio Branco, which is a tributary of the Rio Negro. This study shows that the strength of riverine barriers for Amazon plants is dependent on the width of the river separating populations and species-specific dispersal traits. Future studies of plants with contrasting life history traits will further improve our understanding of the landscape genetics and allopatric speciation history of Amazon plant diversity.

Complete chloroplast genome sequences contribute to plant species delimitation: A case study of the Anemopaegma species complex.

PREMISE OF THE STUDY: Bignoniaceae is an important component of neotropical forests and a model for evolutionary and biogeographical studies. A previous combination of molecular markers and morphological traits improved the phylogeny of the group. Here we demonstrate the value of next-generation sequencing (NGS) to assemble the chloroplast genome of eight Anemopaegma species and solve taxonomic problems. METHODS: Three NGS platforms were used to sequence total DNA of Anemopaegma species. After genome assembly and annotation, we compared chloroplast genomes within Anemopaegma, with other Lamiales species, and the evolutionary rates of protein-coding genes using Tanaecium tetragonolobum as the outgroup. Phylogenetic analyses of Anemopaegma with different data sets were performed. KEY RESULTS: Chloroplast genomes of Anemopaegma species ranged from 167,413 bp in A. foetidum to 168,987 bp in A. acutifolium ("typical" form). They exhibited a characteristic quadripartite structure with a large single-copy region (75,070-75,761 bp), a small single-copy region (12,766-12,817 bp) and a pair of inverted repeat regions (IRs) (39,480-40,481) encoding an identical set of 112 genes. An inversion of a fragment with ca. 8 kb, located in the IRs and containing the genes trnI-AAU, ycf2, and trnL-CAA, was observed in these chloroplast genomes when compared with those of other Lamiales. CONCLUSIONS: Anemopaegma species have the largest genomes within the Lamiales possibly due to the large amount of repetitive sequences and IR expansion. Variation was higher in coding regions than in noncoding regions, and some genes were identified as markers for differentiation between species. The use of the entire chloroplast genome gave better phylogenetic resolution of the taxonomic groups. We found that two forms of A. acutifolium result from different maternal lineages.

Phylogeny and biogeography of Tynanthus Miers (Bignonieae, Bignoniaceae).

The origin of Neotropical biodiversity represents a key question in evolutionary biology. Despite the attempts to decipher the role of ecological and historical factors to present-day distribution patterns, robust phylogenetic studies of Neotropical clades are still needed before a comprehensive picture of the origin of Neotropical biodiversity can be achieved. Tynanthus Miers (Bignonieae, Bignoniaceae) is a well-circumscribed genus of Neotropical lianas with species that are narrowly distributed, except from a few taxa. The genus is characterized by a clove odor, small bilabiate flowers with the two upper lobes almost fused, and fruits with raised margins, all of which represent morphological synapomorphies for this clade. Other distinctive characters are the thecae reflexed forward, the densely pubescent ovaries and the poorly-developed nectariferous disk. The circumscription of the genus has remained constant over the years, despite the problematic limits of most genera of tribe Bignonieae. In this study, we reconstruct the phylogeny of Tynanthus based on two plastid (ndhF and rpl32-trnL) and one nuclear (pepC) markers and use this phylogenetic framework to investigate the biogeographical history of the genus. Our phylogenetic hypothesis provides further support for the monophyly of Tynanthus, and strongly supports a series of infra-generic clades. Most species are reconstructed as monophyletic, while T. cognatus and T. polyanthus are paraphyletic. Biogeographic reconstructions suggest that Tynanthus originated between 9.4 and 21.5Mya, most likely at approximately 15.3Mya. The MRCA of the genus was likely broadly distributed through lowland Amazonia, Western South America and Central America and diversified in the Neotropics during the Miocene. Closely related species are generally distributed within the same biogeographic area, suggesting that niche conservatism has played an important role in the diversification history of the group.

Secondary phloem diversity and evolution in Bignonieae (Bignoniaceae).

BACKGROUND AND AIMS: Phloem evolution has been explored in the literature across very broad scales, either for vascular plants as a whole or for major plant groups, such as the monocotyledons or the former dicotyledons. However, it has never been examined in a way that would elucidate evolutionary shifts leading to the diversification of phloem in single lineages. Therefore, the present study explores in detail the patterns of phloem evolution in the tribe Bignonieae (Bignoniaceae). This group represents a particularly good model for phloem studies since it is known to have a very conspicuous and diverse phloem. METHODS: A total of 19 phloem characters were coded in 56 species from all 21 genera currently recognized in the tribe Bignonieae, accounting for phloem wedge growth and for all the anatomical cell diversity encountered in the phloem. Phloem evolution was explored by reconstructing ancestral character states using maximum-likelihood assumptions with a time-calibrated molecular phylogeny for the group. Directionality and the effect of phylogenetic transformations in the current variation of quantitative traits and evolutionary correlations of selected discrete phloem traits were also tested under a maximum-likelihood approach. KEY RESULTS: Individual phloem features are quite diverse in the tribe, but generally conserved within smaller clades. Contrasting phloem patterns were found when comparing major groups, with certain lineages having the phloem marked by a background of phloem fibres where all other cells are embedded, tangentially arranged sieve tubes and sieve-tubecentric parenchyma. In contrast, other lineages exhibited a scarcely fibrous phloem, regularly stratified phloem, sieve tube elements in radial or diffuse arrangement, and diffuse parenchyma. We found signals of directional evolution in fibre abundance and number of sieve areas, which increased in the 'Fridericia and allies extended clade' and decreased in the 'Multiples of four extended clade', resulting in no signal of directionality when the whole Bignonieae was considered. In contrast, no indication of directional evolution was found for the axial parenchyma, either in single clades within Bignonieae or in the entire tribe. Positive correlation was found between sieve element length and both sieve plate type and the presence of a storied structure. Correlated evolution was also found between fibre abundance and several traits, such as sieve tube arrangement, sieve plate type, parenchyma arrangement, ray lignification and number of companion cells. CONCLUSIONS: The secondary phloem of Bignonieae is extremely diverse, with sister lineages exhibiting distinct phloem anatomies derived from contrasting patterns of evolution in fibre abundance. Fibre abundance in the tribe has diversified in correlation with sieve tube arrangement, sieve tube morphology, number of companion cells and parenchyma type. The results challenge long-standing hypotheses regarding general trends in cell abundance and morphological cell evolution within the phloem, and demonstrate the need to expand studies in phloem anatomy both at a narrow taxonomic scale and at a broad one, such as to families and orders.

Acquisition and diversification of tendrilled leaves in Bignonieae (Bignoniaceae) involved changes in expression patterns of SHOOTMERISTEMLESS (STM), LEAFY/FLORICAULA (LFY/FLO), and PHANTASTICA (PHAN).

Leaves have undergone structural modifications over evolutionary time, and presently exist in many forms. For instance, in Fabaceae and Bignoniaceae, leaf parts can be modified into tendrils. Currently, no data are available on genic control of tendrilled leaf development outside Fabaceae. Here, we conducted a detailed study of three representatives of Bignonieae: Amphilophium buccinatorium, Dolichandra unguis-cati, and Bignonia callistegioides, bearing multifid, trifid, and simple-tendrilled leaves, respectively. We investigated the structure of their petioles, petiolules, leaflets, and tendrils through histological analyses. Additionally, the expression of SHOOTMERISTEMLESS (STM), PHANTASTICA (PHAN), and LEAFY/FLORICAULA (LFY/FLO) during leaf development was analyzed by in situ hybridizations. Tendrils share some anatomical similarities with leaflets, but not with other leaf parts. Transcripts of both STM and LFY/FLO were detected in leaf primordia, associated with regions from which leaflets and tendril branches originate. PHAN expression was found to be polarized in branched tendrils, but not in simple tendrils. In Bignonieae, tendrils are modified leaflets that, as a result of premature completion of development, become bladeless organs. Bignonieae leaves develop differently from those of peas, as both LFY/FLO and STM are expressed in developing leaves of Bignonieae. Moreover, PHAN is probably involved in tendril diversification in Bignonieae, as it has distinct expression patterns in different leaf types.

Macroevolution of the plant-hummingbird pollination system.

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.

Trichome structure and evolution in Neotropical lianas.

BACKGROUND AND AIMS: Trichomes are epidermal outgrowths generally associated with protection against herbivores and/or desiccation that are widely distributed from ferns to angiosperms. Patterns of topological variation and morphological evolution of trichomes are still scarce in the literature, preventing valid comparisons across taxa. This study integrates detailed morphoanatomical data and the evolutionary history of the tribe Bignonieae (Bignoniaceae) in order to gain a better understanding of current diversity and evolution of trichome types. METHODS: Two sampling schemes were used to characterize trichome types: (1) macromorphological characterization of all 105 species currently included in Bignonieae; and (2) micromorphological characterization of 16 selected species. Individual trichome morphotypes were coded as binary in each vegetative plant part, and trichome density and size were coded as multistate. Ancestral character state reconstructions were conducted using maximum likelihood (ML) assumptions. KEY RESULTS: Two main functional trichome categories were found: non-glandular and glandular. In glandular trichomes, three morphotypes were recognized: peltate (Pg), stipitate (Sg) and patelliform/cupular (P/Cg) trichomes. Non-glandular trichomes were uniseriate, uni- or multicellular and simple or branched. Pg and P/Cg trichomes were multicellular and non-vascularized with three clearly distinct cell layers. Sg trichomes were multicellular, uniseriate and long-stalked. ML ancestral character state reconstructions suggested that the most recent common ancestor (MRCA) of Bignonieae probably had non-glandular, Pg and P/Cg trichomes, with each trichome type presenting alternative histories of appearance on the different plant parts. For example, the MRCA of Bignonieae probably had non-glandular trichomes on the stems, prophylls, petiole, petiolule and leaflet veins while P/Cg trichomes were restricted to leaflet blades. Sg trichomes were not present in the MRCA of Bignonieae independently of the position of these trichomes. These trichomes had at least eight independent origins in tribe. CONCLUSIONS: The patterns of trichome evolution indicate that most morphotypes are probably homologous in Bignonieae and could be treated under the same name based on its morphological similarity and common evolutionary history, in spite of the plethora of names that have been previously designated in the literature. The trichome descriptions presented here will facilitate comparisons across taxa, allowing inferences on the relationsthips between trichome variants and future studies about their functional properties.

Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae).

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.

Human impacts outpace natural processes in the Amazon.

Amazonian environments are being degraded by modern industrial and agricultural activities at a pace far above anything previously known, imperiling its vast biodiversity reserves and globally important ecosystem services. The most substantial threats come from regional deforestation, because of export market demands, and global climate change. The Amazon is currently perched to transition rapidly from a largely forested to a nonforested landscape. These changes are happening much too rapidly for Amazonian species, peoples, and ecosystems to respond adaptively. Policies to prevent the worst outcomes are known and must be enacted immediately. We now need political will and leadership to act on this information. To fail the Amazon is to fail the biosphere, and we fail to act at our peril.

A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae.

The plant family Bignoniaceae is a conspicuous and charismatic element of the tropical flora. The family has a complex taxonomic history, with substantial changes in the classification of the group during the past two centuries. Recent re-classifications at the tribal and generic levels have been largely possible by the availability of molecular phylogenies reconstructed using Sanger sequencing data. However, our complete understanding of the systematics, evolution, and biogeography of the family remains incomplete, especially due to the low resolution and support of different portions of the Bignoniaceae phylogeny. To overcome these limitations and increase the amount of molecular data available for phylogeny reconstruction within this plant family, we developed a bait kit targeting 762 nuclear genes, including 329 genes selected specifically for the Bignoniaceae; 348 genes obtained from the Angiosperms353 with baits designed specifically for the family; and, 85 low-copy genes of known function. On average, 77.4% of the reads mapped to the targets, and 755 genes were obtained per species. After removing genes with putative paralogs, 677 loci were used for phylogenetic analyses. On-target genes were compared and combined in the Exon-Only dataset, and on-target + off-target regions were combined in the Supercontig dataset. We tested the performance of the bait kit at different taxonomic levels, from family to species-level, using 38 specimens of 36 different species of Bignoniaceae, representing: 1) six (out of eight) tribal level-clades (e.g., Bignonieae, Oroxyleae, Tabebuia Alliance, Paleotropical Clade, Tecomeae, and Jacarandeae), only Tourrettieae and Catalpeae were not sampled; 2) all 20 genera of Bignonieae; 3) seven (out of nine) species of Dolichandra (e.g., D. chodatii, D. cynanchoides, D. dentata, D. hispida, D. quadrivalvis, D. uncata, and D. uniguis-cati), only D. steyermarkii and D. unguiculata were not sampled; and 4) three individuals of Dolichandra unguis-cati. Our data reconstructed a well-supported phylogeny of the Bignoniaceae at different taxonomic scales, opening new perspectives for a comprehensive phylogenetic framework for the family as a whole.

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine.

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.

Diameters of phloem sieve elements can predict stem growth rates of woody plants.

Understanding forest dynamics is crucial to addressing climate change and reforestation challenges. Plant anatomy can help predict growth rates of woody plants, contributing key information on forest dynamics. Although features of the water-transport system (xylem) have long been used to predict plant growth, the potential contribution of carbon-transporting tissue (phloem) remains virtually unexplored. Here, we use data from 347 woody plant species to investigate whether species-specific stem diameter growth rates can be predicted by the diameter of both the xylem and phloem conducting cells when corrected for phylogenetic relatedness. We found positive correlations between growth rate, phloem sieve element diameter and xylem vessel diameter in liana species sampled in the field. Moreover, we obtained similar results for data extracted from the Xylem Database, an online repository of functional, anatomical and image data for woody plant species. Information from this database confirmed the correlation of sieve element diameter and growth rate across woody plants of various growth forms. Furthermore, we used data subsets to explore potential influences of biomes, growth forms and botanical family association. Subsequently, we combined anatomical and geoclimatic data to train an artificial neural network to predict growth rates. Our results demonstrate that sugar transport architecture is associated with growth rate to a similar degree as water-transport architecture. Furthermore, our results illustrate the potential value of artificial neural networks for modeling plant growth under future climatic scenarios.