Plant Diversity and Evolution

Gene tree conflict between genomic and functional partitions impacts phylogenetic inference in Zygophylloideae

This study investigates gene tree conflicts in Zygophylloideae by analyzing chloroplast and nuclear ribosomal data to understand challenges in phylogenetic inference.

Traits and hidden states: is self-fertilization associated with rates of diversification across mating and sexual systems?

The paper examines how mating and sexual systems affect diversification rates across 18 plant families, finding that sexual systems better explain diversification than mating systems.

Solving Paleobotany's 200-year problem with fluorescence and artificial intelligence

This paper uses fluorescence and AI to solve paleobotany's 200-year problem by revealing detailed leaf venation in fossils.

Diversification and coexistence amid widespread and persistent gene flow in Andean trees

The paper investigates gene flow and species boundaries in Andean Prunus, finding extensive ancient introgression and recent admixture despite Miocene divergence.

Comprehensive Phylogenomic Inference of Eucalypts Reveals Taxonomic Limits through Gene Tree Concordance

This study evaluates the accuracy of eucalypt taxonomy by comparing gene tree topologies to a concatenated species tree, revealing inconsistencies in taxonomic groupings.

Towards an understanding of the taxonomy of the Eurasian montane riparian genus Myricaria (Tamaricaceae) through Angiosperms353 herbariomics

This study uses phylogenomic analysis to clarify the taxonomy of the genus Myricaria, identifying two infrageneric sections and synonymizing several species.

Bayesian inference of global land plant diversification dynamics across the Phanerozoic

This study uses Bayesian methods to analyze land plant diversification dynamics across the Phanerozoic, identifying key patterns and drivers of diversification and extinction.

Panic at the Discordance: the Asparagaceae Phylogenetic Backbone

This study investigates phylogenetic discordance in the Asparagaceae family using nuclear gene data, identifying sources like incomplete lineage sorting and ancient hybridization.

Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs

This study examines how very long branch taxa affect phylogenetic inference in Dioscoreales, finding that they reduce branch support and challenge current classifications.

Reticulate Evolution and Plastome Restructuring Shape Asian Passiflora Diversification

This study investigates the evolutionary relationships and plastome evolution of Asian Passiflora species, revealing reticulate evolution, incomplete lineage sorting, and population differentiation.

The diversity, evolution, and conservation of African plants

The paper evaluates diversification rates and phylogenetic diversity across African plant genera, revealing mismatches between diversification hotspots and conservation priorities.

Phylogenomics reveals distinct evolutionary lineages of Japanese Cinnamomum species in the Nansei Islands

The paper uses genomic data to identify distinct evolutionary lineages of Japanese Cinnamomum species in the Nansei Islands, revealing genomic differentiation shaped by deep-sea barriers and isolation.

Disentangling enabler and adaptive traits across habitat shifts in a large neotropical plant clade

The paper investigates how vegetative and reproductive traits contribute to habitat shifts in Neotropical Myrtaceae, finding vegetative traits act as enablers while reproductive traits show both enabler and adaptive patterns.

An explicit birth-death-reticulation model for studying the diversification of phylogenetic networks

The paper develops a birth-death-reticulation model to analyze phylogenetic networks and applies it to study diversification in ferns, finding evidence that polyploids have lower diversification rates than diploids.

Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia

This study uses molecular phylogenetics to analyze Begonia species in Peninsular Malaysia, finding that speciation into limestone habitats occurred three times and climate, not substrate, was more important for diversification.

Reticulate History of Southern South American Wild Potatoes: Recurrent Hybridization, Cytonuclear Discordance, and Phylogenetic Placement of Solanum malmeanum

This study investigates the evolutionary history of wild potatoes in the Petota clade, revealing recurrent hybridization, cytonuclear discordance, and chloroplast capture affecting species boundaries.

Painting the evolutionary history of a multicompartmentalized syngameon in North American Castilleja (Orobanchaceae)

This study uses phylogenomic data to show that Castilleja forms a multicompartmentalized syngameon with ongoing gene flow and hybridization across geographically structured compartments.

Why woodiness repeatedly evolves--and disappears

The paper investigates the evolution and reversal of woodiness in flowering plants, finding that drought supports persistence while reduced frost drives gains and increased frost leads to loss.

Madagascar as an evolutionary source for the Paleotropical flora: New insights from the biogeography of Grewia (Malvaceae)

This study reconstructs the evolutionary history of Grewia, showing a Malagasy origin and dispersal to Africa, Arabia, and Asia via fleshy fruits.

Phylogeny and Species Delimitation in Isoxylosteum, a Lonicera Clade Endemic to the Himalayan-Tibetan-Hengduan Region

This study resolves the phylogeny and species boundaries of the Isoxylosteum clade using RADseq and morphology, identifying five species and reclassifying one as sister to L. spinosa.

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys)

This study uses phylotranscriptomics to distinguish between gene flow and incomplete lineage sorting in Ophrys orchids, revealing ancient adaptive gene flow events.

Synchronizing speciation, extinction, and dispersal to island paleodynamics through Bayesian phylogenetics in a Hawaiian plant radiation

The paper introduces a Bayesian phylogenetic framework to infer divergence times, ancestral ranges, and diversification rates in Hawaiian plants without fossil calibration.

Phylogenomics supports the reinstatement of Sinia (Ochnaceae)

The paper uses phylogenomic data to reinstate Sinia as a distinct genus within Ochnaceae, resolving taxonomic uncertainty by showing its close relationship to Indosinia and distant relationship to Sauvagesia.

Environmental variation is related to morphotype differentiation in a Brunfelsia (Solanaceae) complex

This study integrates morphological and environmental data to identify ecological factors shaping morphotype boundaries in a Brunfelsia species complex, revealing two distinct morphotypes with different habitat suitability.

Cytonuclear Conflict and Reticulate Evolution in the Morelloid Clade (Solanum, Solanaceae): Insights from Genome Skimming and Network Phylogenomics

The paper investigates reticulate evolution in the Morelloid clade using genome skimming and phylogenomic methods, revealing widespread chloroplast capture events.

From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum

This study investigates the evolution of distyly and stigma-height dimorphism in Jasminum using phylogenetic analysis and morphology, finding that distyly originated in the common ancestor and SHD arose multiple times through reversion.

Hierarchical constraints and trade-offs in the evolution of reproductive traits in neotropical myrtles

The paper examines evolutionary correlations among reproductive traits in neotropical myrtles, finding hierarchical constraints and trade-offs between flowers, fruits, and seeds.

The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

The paper analyzes gene tree topology space in the plant genus Glycine, finding a flat distribution of topologies with no clear peak at the species tree, suggesting complex historical signals from introgression and polyploidy.

Phylogenomics of the mega genus Bulbophyllum (Orchidaceae) with implications for infrageneric classification in the Asian clade

This study reconstructs the phylogenetic relationships of Bulbophyllum using plastid genes, revealing five major lineages and clarifying infrageneric classification in the Asian clade.

A tribal-scale phylogenomic perspective on ancestry and major lineages of the allotetraploid Hawaiian silversword alliance (Madieae, Compositae)

The paper uses phylogenomic analysis to resolve the ancestry and subgenome origins of the allotetraploid Hawaiian silversword alliance, identifying its allopolyploid origin and relationships to diploid relatives.