Phylogenetic discordance poses significant challenges for reconstructing evolutionary relationships, particularly in recently diversified lineages where incomplete lineage sorting, hybridization, and gene flow may obscure evolutionary history. We employed a Hyb-Seq approach to generate complete plastomes and nuclear data from 295 loci to investigate phylogenetic relationships and discordance in the Tillandsia erubescens species group, a recently radiated lineage endemic to Mexico. Phylogenetic analyses confirmed the monophyly of the T. erubescens species group in both plastid and nuclear datasets. No strongly supported discordance was detected between plastome and coalescence-based nuclear trees within the group, indicating broad agreement between genomic compartments at the species level. In contrast, PhyParts analyses revealed extensive discordance among individual nuclear gene trees, with most loci supporting alternative topologies relative to both the plastome tree and nuclear species tree. Discordance was most pronounced at deeper nodes, whereas shallower relationships showed greater concordance. Low gene concordance and site concordance factor values indicate heterogeneous phylogenetic signal across loci, consistent with rapid diversification. These findings demonstrate the utility of phylogenomic approaches that integrate multiple genomic compartments and accommodate gene-tree heterogeneity when investigating recent evolutionary radiations.
Vanilla is a pantropical genus of 130 vine species, most of which are nomadic. It is most diverse in Brazil, which hosts thirteen endemic species, including two in the Amazon, its second-richest domain. Vanilla exhibits high morphological diversity, although identifying species requires flowers. Since the vegetative anatomy of Vanilla is still poorly understood, our objective was to conduct a comparative study of the leaves of eight species occurring in the Amazon, belonging to two subgenera: Vanilla subgen. Membranacea (V. acuta and V. mexicana) and Vanilla subgen. Vanilla (V. appendiculata, V. lindmaniana, V. odorata, V. phaeantha, V. planifolia and V. pompona), using standard protocols for light and scanning electron microscopy. We identified anatomical characters for Vanilla species, noting that the presence and type of crystalliferous idioblasts and crystal types proved most significant in distinguishing between them. For example, V. appendiculata lacks crystals, V. odorata has prismatic crystals, and V. phaeantha has prismatic crystals and raphides in the leaf blade. Other characters can be used to separate groups of taxa within the sample, such as the following: absence/presence of a hypodermis; and absence/presence, type, and location of crystals. The findings provide new diagnostic information for vegetative Vanilla, which is crucial for conservation efforts in Brazil’s Amazon, and offers a year-round tool for researchers studying this commercially important plant. This updated structural data is expected to guide future, larger systematic studies of the genus.
Hydnora is a highly unusual genus of holoparasitic plants in the family Hydnoraceae comprising 10 species across Africa and the Middle East. Species concepts and relationships within the genus have historically been poorly defined, in part due to a paucity of morphological characters available for species delimitation. Here, we present the most comprehensively sampled nuclear phylogenomic study of Hydnora to date. We employ the Angiosperms353 target capture approach, using 34 nuclear loci to generate the species tree. Our results provide strong molecular support for all four recently proposed subgenera of Hydnora, demonstrating that even a limited set of morphological traits can be used to delimit lineages within the genus. We estimate ancestral states for these taxonomically informative characters within the Hydnoraceae and provide molecular evidence to clarify some of the long-standing taxonomic uncertainty within the widespread Hydnora abyssinica complex. We analyse gene tree discordance in the results and discuss our results in the context of these conflicting studies. The phylogenetic hypotheses presented here are the most widely sampled to date, and provide a framework for future ecological and evolutionary research into this enigmatic family of parasitic plants.
The tribe Sorbarieae (Rosaceae) exhibits a disjunct distribution between Eastern Asia and North America, yet its infrageneric relationships and the evolutionary history of its morphological traits remain poorly understood. To address these questions, we conducted an integrative study combining molecular phylogenetics with quantitative analyses of morphological character evolution. We reconstructed the phylogeny of Sorbarieae using nuclear ribosomal ITS (nrITS) sequences and estimated divergence times under a Bayesian relaxed-clock model. Ancestral character states were reconstructed using Bayesian Binary MCMC (BBM), and phylogenetic signal was assessed using Fritz’s D statistic. Our results support the monophyly of the genus Sorbaria, which diverged from its sister genus Spiraeanthus approximately 31.57 Mya (Oligocene). Diversification within Sorbaria into two sections—sect. Sorbaria and sect. Kirilowiana—occurred around 20.75 Mya (Early Miocene). Phylogenetic signal analyses across traits revealed a mosaic pattern of evolution: Vegetative traits, including leaf retention and stomatal characteristics, exhibit strong phylogenetic conservatism (D < 0) and serve as stable diagnostic features of the genus, whereas several reproductive traits, particularly sexine ornamentation, stamen length, and fruit epicuticular wax, are associated with infrageneric divergence. Despite phylogenetic incongruence in the placement of S. grandiflora between ML and BI analyses, morphological evidence supports its affinity with sect. Sorbaria. This study provides a quantitative evolutionary framework for Sorbarieae, demonstrating the diagnostic utility of pollen micromorphology—particularly sexine ornamentation—as a reliable marker for infrageneric delimitation within the tribe.
Integrative analyses combining nrITS and trnK/matK phylogenetic analyses, palynology, ecological niche modelling, and morphology were conducted to reassess species limits within the Neotropical genus Sigmoidotropis (Leguminosae). Our phylogenetic framework recovered well-supported clades that clarify previously ambiguous relationships and revealed a distinctive lineage endemic to humid forest enclaves in northeastern Brazil. Palynological traits, together with diagnostic morphological features, provide additional evidence for its separation from closely related taxa. Ecological niche modelling further supports the ecological isolation of this lineage, indicating distribution restricted to cooler and moister upland refugia embedded within the seasonal Caatinga domain. The integration of multiple data sources consistently confirms the uniqueness of this taxon, here described as a new species, S. carolinae. Our results highlight the underestimated diversity within Sigmoidotropis and underscore the evolutionary and biogeographical significance of humid forest refugia in shaping species diversification across northeastern Brazil.
