Phylogenomic and morphological data reveal hidden patterns of diversity in the national tree of Brazil, Paubrasilia echinata.

PREMISE: Paubrasilia echinata (common names, pau brasil, brazilwood) is the national tree of Brazil and an endangered species endemic to the Brazilian Atlantic Forest. Over its wide distribution of 2000 km, its leaflets morphology exhibits extensive plasticity. Three morphotypes are commonly identified based on leaf size, but it is unclear if they represent distinct taxa or a single polymorphic species. This study aims to clarify the taxonomic position of the three morphotypes to inform conservation decisions. METHODS: A morphometric study of leaf characters of herbarium specimens was coupled with genetic analyses using genotype-by-sequencing data. We used maximum-likelihood and coalescent methods to evaluate the phylogenetic and population structure of the species. We compared these with a morphological dendrogram built from hierarchical clustering. RESULTS: Two of the three morphotypes formed separately evolving lineages, the third morphotype formed two geographically separate lineages, and northern trees with intermediate leaf morphology formed a separate fifth lineage. Leaflet size varied by over 35-fold, and although morphological clustering generally matched the genetic patterns, there were some overlaps, highlighting the cryptic diversity within this group. CONCLUSIONS: Our genetic and morphological results provide some evidence that cultivated trees from different states in Brazil seem to have a limited genetic origin and do not reflect the broader genetic and geographical diversity of the species. As a result, more care is likely needed to preserve the overall genomic diversity of this endangered and iconic species.

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes.

Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2 -fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical legume clade.

SNP Markers as a Successful Molecular Tool for Assessing Species Identity and Geographic Origin of Trees in the Economically Important South American Legume Genus Dipteryx.

Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy-Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber.

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages.

PREMISE OF STUDY: Phylogenetic relationships of the papilionoid legumes (Papilionoideae) reveal that the early branches are more highly diverse in floral morphology than are other clades of Papilionoideae. This study attempts for the first time to comprehensively sample the early-branching clades of this economically and ecologically important legume subfamily and thus to resolve relationships among them. • METHODS: Parsimony and Bayesian phylogenetic analyses of the plastid matK and trnL intron sequences included 29 genera not yet sampled in matK phylogenies of the Papilionoideae, 11 of which were sampled for DNA sequence data for the first time. • KEY RESULTS: The comprehensively sampled matK phylogeny better resolved the deep-branching relationships and increased support for many clades within Papilionoideae. The potentially earliest-branching papilionoid clade does not include any genus traditionally assigned to tribe Swartzieae. Dipterygeae is monophyletic with the inclusion of Monopteryx. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade within papilionoids. The quinolizidine-alkaloid-accumulating genistoid clade is expanded to include a strongly supported subclade containing Ormosia and the previously unplaced Clathrotropis s.s., Panurea, and Spirotropis. Camoensia is the first-branching genus of the core genistoids. • CONCLUSIONS: The well-resolved phylogeny of the earliest-branching papilionoids generated in this study will greatly facilitate the efforts to redefine and stabilize the classification of this legume subfamily. Many key floral traits did not often predict phylogenetic relationships, so comparative studies on floral evolution and plant-animal interactions, for example, should also benefit from this study.

Evaluating the nodulation status of leguminous species from the Amazonian forest of Brazil.

Numerous leguminous species are used or have potential uses for timber production, pharmacological products, or land reclamation. Through N(2)-fixation, many leguminous trees contribute to the N-balance of tropical wetlands and rainforests. Therefore, studies of the N(2)-fixation ability of leguminous species appear to be crucial for the better use and conservation of these resources. The global nodulation inventory in the Leguminosae family is constantly being enriched with new records, suggesting the existence of undiscovered nodulated species, especially in tropical natural ecosystems and other hot spots of biodiversity. In this respect, the nodulation of leguminous species from the Amazonian forest of Porto Trombetas (Brazil) was surveyed. Overall, 199 leguminous species from flooded and non-flooded areas, were examined for their nodulation status by combining field observations, seedling inoculations, and screening of N(2)-fixing bacterial strains from the collected nodules. The results revealed a tendency for a higher relative frequency of nodulation in the species from the flooded areas (74%) compared with those from the non-flooded areas (67%). Nodulation was observed in the Caesalpinioideae, Mimosoideae, and Papilionoideae, with 25, 88, and 84% of the examined species in each subfamily, respectively. Of the 137 nodulated leguminous species, 32 including three Caesalpinoideae, 19 Mimosoideae, and 10 Papilionoideae are new records. One new nodulated genus (Cymbosema) was found in the Papilionoideae. Twelve non-nodulating leguminous species were also observed for the first time. The results are discussed based on the systematics of the Leguminosae family and the influence of available nutrients to the legume-bacteria symbiosis.