Background: Balanophoraceae plastomes are known for their highly condensed and re-arranged nature alongside the most extreme nucleotide compositional bias known to date, culminating in two independent reconfigurations of their genetic code. Currently, a large portion of the Balanophoraceae diversity remains unexplored, hindering, among others, evolutionary pattern recognition. Here, we explored newly sequenced plastomes of Sarcophyte sanguinea and Thonningia sanguinea. The reconstructed plastomes were analyzed using various methods of comparative genomics based on a representative taxon sampling. Results: Sarcophyte, recovered sister to the other sampled Balanophoraceae s. str., has plastomes up to 50% larger than those currently published. Its gene set contains five genes lost in any other species, including matK. Five cis-spliced introns are maintained. In contrast, the Thonningia plastome is similarly reduced to published Balanophoraceae and retains only a single cis-spliced intron. Its protein-coding genes show a more biased codon usage compared to Sarcophyte, with an accumulation of in-frame TAG stop codons. Structural plastome comparison revealed multiple, previously unknown, structural rearrangements within Balanophoraceae. Conclusions: For the “minimal plastomes” of Thonningia, we propose a genetic code change identical to sister genus Balanophora. Sarcophyte however differs drastically from our current understanding on Balanophoraceae plastomes. With a less-extreme nucleotide composition, there is no evidence for an altered genetic code. Using comparative genomics, we identified a hotspot for plastome reconfiguration in Balanophoraceae. Based on previously published and newly identified structural reconfigurations, we propose an updated model of evolutionary plastome trajectories for Balanophoraceae, illustrating a much greater plastome diversity than previously known.

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.

Aim: Studying beta diversity, or the variation in species composition among communities, can give insights into plant community assembly over space and time. If different biomes show contrasting large‐scale beta‐diversity patterns, this can indicate divergent evolutionary histories or ecological processes that then drive species turnover among communities. Here, we examine phylogenetic beta‐diversity patterns across Africa in forest and savanna assemblages, the two most widespread tropical biomes on the continent. We hypothesise that savannas will show lower phylogenetic beta diversity due to their younger evolutionary history. Location: Tropical Africa. Taxon: Woody angiosperms. Methods: We gathered 301,159 occurrences of woody angiosperms representing 1883 forest species and 1302 savanna species. We compared levels of phylogenetic beta diversity between forest and savanna assemblages, analysed spatial patterns of phylogenetic beta diversity using 1° grid cells and modelled their relationship with climate, disturbance and geographical distance. Results: We found that savannas show greater relative regional phylogenetic beta diversity, whereas forest assemblages show greater relative local phylogenetic beta diversity. The spatial distribution of beta diversity showed strong East–West patterns for both forests and savannas, aligned with a major floristic discontinuity associated with the Albertine rift. Our results also highlighted West Africa as showing a high amount of compositional change for both biomes, arranged along an aridity gradient. Variance partitioning showed that predictors linked to precipitation were the main drivers of compositional change for both forests and savannas, but the importance of individual predictors was different in each biome. Main Conclusions: Contrary to our expectations, our results indicate that savannas may have a deeper and richer evolutionary history than suggested by previous studies and that individual regions of both forest and savanna have high conservation value. Finally, our results demonstrate that environmental filtering is the dominant force influencing the assembly of these two important biomes at a continental spatial scale.

In tropical Africa, forests and savannas are the two most widespread biomes and potentially represent alternative stable states with a divergent species composition. A classic, but untested, hypothesis posited by White (1983) suggests that the transition zones between forests and savannas contain a floristically impoverished assemblage, with few representatives from each biome. Further, the evolutionary dimension of diversity has received limited attention, despite its importance for understanding the biogeographic history of biomes. Here, we quantified species richness and several measures of evolutionary diversity in 1° grid cells, using c. 300,000 occurrence records of trees and shrubs combined with biome affiliation data for 3203 species. We found that assemblages in transition zones hold fewer woody species than assemblages in forest and savanna zones, as posited by White. However, transition zones hold more phylogenetic diversity than expected given their species richness, whether one considers forest and savanna assemblages separately or together. We also show that the Congo Basin forest has low levels of phylogenetic diversity, given the number of species, and highlight south-eastern African savannas as a centre of savanna woody species richness and phylogenetic diversity. Regions with high phylogenetic diversity, given the number of both forest and savanna species, were centred around the Dahomey Gap and Cameroon, mainly in transition zones. Overall, our study shows that even if floristically impoverished, transition zones hold unexpectedly high evolutionary diversity. This suggests that they are important centres of evolutionary innovation and diversification and/or serve as evolutionary crossroads, where lineages that diversified in contrasting environments coexist within a single area.

Identification of plants is a challenging task which aims to identify the family, genus, and species level according to morphological features. Automated deep learning-based computer vision algorithms are widely used for identifying plants and can help users to narrow down the possibilities. However, numerous morphological similarities between and within species make the classification difficult. In this paper, we tested a custom convolution neural network (CNN) and vision transformer (ViT) based models using the PyTorch framework to classify plants. We used a large dataset of 88K and 16K images for classifying plants at genus and species levels respectively. Our results show that for classifying plants at the genus level, ViT models perform better compared to CNN-based models ResNet50 and ResNet-RS-420, and other state-of-the-art CNN-based models suggested in previous studies on a similar dataset. The ViT model achieved top accuracy of 83.3% for classifying plants at the genus level. ViT models also perform better for classifying plants at the species level compared to CNN-based models ResNet50 and ResNet-RS-420, with a top accuracy of 92.5%. We show that the correct set of augmentation techniques plays an important role in classification success.

In tropical Africa, forests and savannas are the two most widespread biomes and potentially represent alternative stable states with divergent species composition. A classic, but untested, hypothesis posited by White (1983) suggests that the transition zones between forests and savannas contain a floristically impoverished assemblage with few representatives from each biome. Further, the evolutionary dimension of diversity has received limited attention, despite its importance for understanding the biogeographic history of biomes. Here, we quantify species richness and several measures of evolutionary diversity in 1° grid cells, using c. 300K occurrence records of trees and shrubs combined with biome affiliation data for 3,125 species. We find that assemblages in transition zones hold fewer woody species than assemblages in forest and savanna zones, as posited by White. However, transition zones hold more phylogenetic diversity than expected given their species richness, whether one considers forest and savanna assemblages separately or together. We also show that the Congo basin forest has low levels of phylogenetic diversity given the number of species and highlight south-eastern African savannas as a centre of savanna woody species richness and phylogenetic diversity. Regions with high phylogenetic diversity given the number of both forest and savanna species were centred around the Dahomey Gap and Cameroon, mainly in transition zones. Overall, our study shows that even if floristically impoverished, transition zones lead to unexpectedly high evolutionary diversity, suggesting they are important centres of evolutionary innovation and diversification.