The first phylogenomic study of the tribe Spermacoceae based on plastome-scale data and expanded sampling of Neotropical taxa is presented, providing the most robust phylogenetic framework yet available for the tribe and establishing a foundation for future systematic, biogeographic, and evolutionary research.
Museum collections offer valuable resources for phylogenetic research, especially in taxonomically challenging groups. Here, we present a phylogenetic study of the South American Apocynaceae subtribe Orthosiinae, based on sequencing 835 nuclear genes and chloroplast genomes from ~120 species using a family‐specific probe set and multiple herbarium samples per species. Our results confirm generic relationships within Orthosiinae with
Monsanima
(2 species) sister to
Scyphostelma
(>50 species), and
Jobinia
(25 species) +
Orthosia
(55 species). Data were processed with the HybPhyloMaker pipeline, providing a reproducible framework for phylogenetic reconstructions using concatenation and coalescent‐based methods. The final dataset comprised 204 samples, 810 nuclear genes (1.2 Mb) and complete chloroplast genomes (0.16 Mb) after excluding samples with signals of admixture. Phylogenetic analysis identified several cryptic lineages with little morphological differentiation, highlighting the need for further systematic research in the Andes. Evolutionary placement of 107 additional samples confirmed
Monsanima
as sister to the rest of Orthosiinae. Divergence‐time estimates placed the crown age of Orthosiinae at ~13 Ma. Morphological analysis revealed high variability in leaf and floral traits traditionally used for taxon delimitation but also identified floral characters that are diagnostic for generic identification. Ancestral state reconstructions show no clear directional changes in leaf morphology, whereas several floral traits tend to evolve toward smaller sizes along the youngest branches of the phylogeny. Our integrated museomic approach contributes to a better understanding of evolutionary patterns and taxonomic relationships in this still understudied lineage of South American Apocynaceae.
Yam M. Pineda, M. Kandziora, María Pinilla Vargas et al.· Taxon· 0 citations
The utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae is highlighted, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.
Sadaf Habib, Yong Shi, Jie Zhang et al.· Frontiers in Plant Science· 0 citations
A phylogenomic framework to clarify the evolutionary origin of Guzmania within the broader Tillandsioideae is presented, suggesting a possible hybrid origin for G. monostachia and a distinct evolutionary trajectory for Florida populations.
Shelby Krupar, Grant T. Godden, Andrew A. Crowl et al.· American-Eurasian journal of...· 0 citations
The evolutionary history of Amaranthaceae sensu stricto (s.s.) has been shaped by multiple whole-genome duplications and rapid radiations, producing an ecologically diverse lineage whose internal relationships have long remained unresolved. Earlier studies, constrained by limited genomic resources and sparse taxon sampling, left the relationships of higher-level classification of this economically important lineage incomplete and its reticulate evolutionary history undiscovered. Using a customized bait set targeting 1000 low-copy nuclear loci of Amaranthaceae s.s., we reconstructed a globally sampled phylogeny representing 96% of all recognized genera. This sampling includes many rare and previously inaccessible taxa obtained largely from herbarium collections. Our results reveal the sources of a strongly reticulate and highly polyploid evolutionary history, involving at least two deep hybridization events and up to six ancient whole genome duplications. These processes generated substantial gene tree discordance along the backbone of the phylogeny, clarifying the sources of previous analytical instability. However, the major clades recovered are consistently and strongly supported across phylogenetic inferences. Based on these results, we recognize 11 tribes within Amaranthaceae s.s., including the formal circumscription of the newly identified tribes Allmaniopseae and Wadithamneae. This provides a robust framework for future phylogenetically informed research within Amaranthaceae s.s.
T. Kiedaisch, A. Žerdoner Čalasan, Ross A. McCauley et al.· Cladistics· 0 citations
Speciation is often considered as a prolonged, continuous and complex process shaped by interactions among multiple evolutionary forces, including both biotic and abiotic factors. Robust species delimitation is fundamental for understanding the basic biology and ecology of organisms and of course the implementation of effective conservation policies. The red bamboo ratsnake (Oreocryptophis porphyraceus) is a polytypic species in the family Colubridae widely distributed across Asia with a subspecific taxonomy has long been complex and controversial. Here, we integrated double-digest restriction-site associated DNA sequencing (ddRAD-Seq) with mitochondrial DNA (mtDNA) data to re-evaluate the subspecific taxonomy of this species primarily using samples from China and Vietnam. Phylogenetic relationships, population structure, tests of gene flow and species delimitation analyses consistently revealed that the species comprises at least four highly divergent, geographically structured lineages (five in the mtDNA phylogeny). Notably, these distinct evolutionary lineages are inconsistent with current taxonomic classifications. We propose a revised taxonomy that integrates genomic evidence with morphological data, and we discuss the distribution boundaries for each delineated species.
The pantropical genus Diospyros L. (Ebenaceae) includes many economically valuable species prized for ebony timber and edible fruits. However, its high species diversity and morphological similarity pose significant challenges for understanding its evolutionary history. Previous phylogenetic studies have suggested a rapid adaptive radiation in Diospyros, but relationships among major lineages remain poorly resolved. Here, we reconstruct a comprehensive species-level phylogeny for Chinese Diospyros using whole genome sequencing data from 69 individuals representing 65 species. Phylogenomic analyses of a concatenated nuclear SNP matrix recovered six strongly supported major clades. Notably, we found substantial cytonuclear discordance between nuclear and plastid phylogenies. To investigate this conflict, we conducted extensive gene-tree concordance analyses (Phytop, MSCquartets) and quantified introgression and incomplete lineage sorting (ILS) using Dsuite, QuIB, and PhyloNet. These analyses revealed widespread, statistically significant gene-tree conflict, particularly at deep nodes. Our results demonstrate that the evolutionary history of Chinese Diospyros has been likely shaped by deep ILS-a probable genomic signature of rapid early radiation-alongside localized ancient hybridization, most prominently within the morphologically diverse Asian clade F. Recent gene flow appears to have played a limited role, although the relative contributions of ILS and introgression remain challenging to fully disentangle. These findings provide insights into the drivers of cytonuclear discordance and offer a robust phylogenetic framework for understanding the mechanistic role of ILS in diversification, with implications for adaptive radiation dynamics in species-rich tropical lineages.
