Plant Diversity and Evolution

Rapid floral syndrome convergence in Penstemon through independent genetic variation

This study identifies four independent origins of hummingbird syndrome in Penstemon and finds rapid floral trait convergence without stepwise modification or adaptive introgression.

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

The paper uses dual-hybridisation probes to reconstruct phylogenetic relationships in Sauvagesieae, finding evidence of polyploidisation and hybridisation affecting tree resolution.

Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera

This study presents the first plastome-scale phylogenomic analysis of the tribe Spermacoceae, clarifying generic boundaries and supporting taxonomic revisions.

Making the most out of it: shallow genome-skimming possibilities for the systematics of prickly lineages of Solanum (Solanaceae)

This study evaluates shallow genome-skimming for phylogenetic inference in Solanum, finding it effective for SNP datasets but limited in recovering complete mitochondrial genomes and low-copy nuclear genes.

A novel phylogenomics pipeline reveals extensive topological conflict in the evolution of the angiosperm order Cucurbitales

The paper introduces CAPTUS, a phylogenomics pipeline that efficiently handles mixed sequencing data, revealing topological conflicts in the evolution of Cucurbitales.

Nuclear phylogenomics clarifies the family-level backbone and gene-tree conflict in Zingiberales

This study uses nuclear phylogenomics to resolve the family-level backbone of Zingiberales, finding that deep node instability is due to rapid divergence and incomplete lineage sorting, not hybridization.

Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages

The paper designs a custom probe set to improve phylogenetic resolution in the challenging Clusioid clade, showing better performance than a universal probe set.

Puzzling parasitic plants: phylogenetics and classification of Santalales revisited

The paper revisits the phylogenetics and classification of Santalales, finding better-supported relationships and proposing a new taxonomic framework.

CHLOROPLAST GENOME AND PHYLOGENETIC ANALYSIS OF KATMON (Dillenia philippinensis Rolfe), A PHILIPPINE ENDEMIC FRUIT

This study sequences and analyzes the chloroplast genome of Dillenia philippinensis, revealing its structure, gene content, and phylogenetic relationships with related species.

Phloem evolved gradually and asynchronously to xylem in early vascular plants

This study re-examines phloem-like tissues in 407-million-year-old Rhynie chert fossils, identifying them as food-conducting cells lacking true phloem features and suggesting phloem evolved gradually after xylem.

Multiple evidence supporting a novel species amid complex phylogenomic discordance: a case of Indian Ledebouria based on Angiosperms353 target capture sequencing

The paper uses Angiosperms353 target capture sequencing to clarify phylogenetic relationships among Indian Ledebouria species, identifying L. hyderabadensis as a distinct species and other accessions as incipient species.

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne

This study investigates how hybridization, incomplete lineage sorting, and climate change shaped the evolutionary history and geographic structure of Linum bienne.

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)

This study evaluates paralog processing methods in polyploid-rich Packera genus to improve phylogenomic accuracy and understanding of evolutionary history.

Tracing Sticky Trails: The Historical Biogeography of Australia's Glandular Goose-foots (Dysphania, Chenopodioideae, Amaranthaceae)

This study reconstructs the evolutionary history of Australian Dysphania, finding that diversification was driven by ecological factors rather than polyploidy or geographic isolation.

When morphology stands still: constrained floral evolution in a mega diverse legume genus

This study investigates whether floral morphology in the legume genus Mimosa is constrained, finding that morphological uniformity is shaped by developmental and functional constraints rather than pollinator selection.

Phylogenomics and Systematics of African Sesuvium (Aizoaceae)

The paper uses genome skimming to resolve the phylogeny of African Sesuvium species, finding a C3 species sister to a C4 clade with discordant gene trees.

Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics

The paper compares RADseq and whole genome resequencing methods to resolve oak phylogeny and address uncertainties in divergence times and gene tree discordance.

Evolutionary origin of prolonged delayed fertilization in the Fagaceae

This study investigates the evolutionary origins of 2-year fruiting in Fagaceae by analyzing phylogenetic data and ancestral state reconstructions across 88 species.

The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae

This study investigates phylogenetic challenges in Rafflesiaceae and Apodanthaceae, identifying a 'danger zone' caused by incomplete lineage sorting and long-branch attraction, leading to unstable placements despite divergence time estimates suggesting a mid-Cretaceous origin.

The conquest and diversification of leafy spurges across the Holarctic and beyond: biogeography and evolution of life-history of Euphorbia subgenus Esula

This study investigates the biogeography and evolution of life-history traits in Euphorbia subgenus Esula, showing that perenniality and range expansion are linked to diversification.

Dissetangling the Vine: Phylogenomics and Historical Biogeography of Vanilla (Orchidaceae)

This study constructs a comprehensive phylogenomic framework for Vanilla, revealing evolutionary relationships, historical biogeography, and hybridization patterns.

The Speciation Continuum in Bloom: Incomplete Lineage Sorting, Gene Flow, and Reticulate Evolution in Rapidly Diverging Plant Lineages

This study examines the evolutionary history of recently diverged Petunia lineages, revealing that most are intermediate stages along a speciation continuum rather than distinct species.

A new phylogeny and phylogenetic classification for Solanaceae

A 1,474-species 10-marker phylogeny and a 110-taxon Angiosperms353 phylogenomic dataset support a rank-free PhyloCode classification defining 38 clades across Solanaceae, including 16 infrageneric clades in Solanum.

Vascular diversity in Fabaceae: evolutionary and ecological insights from a globally distributed lineage

This study examines vascular diversity in Fabaceae, revealing that over 100 species across four subfamilies have evolved atypical vascular architectures found globally.

SPECIES DELIMITATION IN AN INTRACTABLE SYNGAMEON: BRINGING ORDER TO THE POLYPHYLETIC HEUCHERA AMERICANA GROUP

The paper reassesses species limits in a syngameon of Heuchera, identifying five species and three varieties using genetic and phenotypic data.

A Phylogenetic Model of Established and Enabled Biome Shifts

The paper introduces a phylogenetic model, RFBS, to distinguish between established and enabled biome affinities in species evolution and applies it to flowering plants.

The complete chloroplast genome of Garcinia binucao (Blanco) Choisy, an indigenous fruit from the Philippines

This study reports the first complete chloroplast genome of Garcinia binucao, providing genomic resources for conservation and genetic research.

CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family

CactEcoDB provides integrated ecological, trait, and phylogenetic data for over 1,000 cactus species to support comparative research on trait evolution and macroevolutionary dynamics.

Complete chloroplast genome of African Baobab (Adansonia digitata L.): structural characterization, comparative genomics, and phylogenetic placement within Malvaceae

This paper characterizes the complete chloroplast genome of Adansonia digitata, compares it with other Adansonia species, and places it phylogenetically within Malvaceae.

Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) reveals unlikely hybrid ancestry of a New Zealand species

The paper identifies a hybrid lineage in the Austral podocarps using phylogenomic analyses, revealing that Podocarpus nivalis is a hybrid between P. laetus and P. lawrencei.