We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of the APG classification were largely based on uniparentally inherited markers (plastid DNA, typically maternally inherited), there has emerged since APG IV extensive evidence of widespread hybridization and inheritance of ancestral polymorphisms. Despite this evidence of gene-tree discordance, most of the APG IV classification is supported by both plastid and nuclear analyses, and only a few revisions are required in this update to make the classification parallel phylogenetic results in the literature. At the ordinal level, few changes in circumscription are required relative to the last APG version, although the fabids now comprise only the four nitrogen-fixing orders (Cucurbitales, Fabales, Fagales, and Rosales) and the malvids now include the former COM clade (Celastrales, Malpighiales, and Oxalidales), which, in nuclear DNA analyses, is no longer monophyletic. Oncothecales (with only Oncothecaceae) and Cardiopteridales (with Cardiopteridaceae and Stemonuraceae) are newly recognized, and Icacinales are restricted to Icacinaceae. Restriction of Aquifoliales and Bruniales to just Aquifoliaceae/Helwingiaceae and Bruniaceae, respectively, is also proposed. Huaceae and Columelliaceae are unplaced to order among the malvids and campanulids, respectively. At the family level, expanded circumscriptions include Tecophilaeaceae (including Ixioliriaceae, Asparagales), Frankeniaceae (including Tamaricaceae, Caryophyllales), Phytolaccaceae (including Agdestidaceae and Sarcobataceae, Caryophyllales), Helwingiaceae (including Phyllonomaceae, Aquifoliales), Gesneriaceae (including Calceolariaceae and Peltantheraceae, Lamiales), Pentaphylacaceae (including Sladeniaceae, Ericales), and Orobanchaceae (including Mazaceae, Paulowniaceae, Phrymaceae, and Wightiaceae, Lamiales). In Santalales, the limits of Santalaceae and Olacaceae are revised, and Erythropalaceae and Strombosiaceae are recognized as distinct from Olacaceae; Balanophoraceae are maintained as distinct from Santalaceae, but this is a tentative placement. Generic relationships in Dioscoreales require more analyses before a revised family classification can be proposed, so we maintain the APG IV families of this order.

We present a phylogenetic analysis of benthic ctenophores of the order Platyctenida, sampling all but one genus. Using complete mitochondrial genomes and nuclear ribosomal data and a reassessment of anatomy, our integrated analysis uncovers an unexpectedly close relationship between two unusual members of the Coeloplanidae: Coeloplana (Benthoplana) meteoris and Vallicula multiformis. These two species form a well-supported clade, deriving at or near the base of the tree of Platyctenida, distantly related to other Coeloplana, rendering Coeloplana and Coeloplanidae non-monophyletic. A unique mitochondrial gene order and a tentacle bulb with four extensions are newly identified synapomorphies of this lineage. We elevate the subgenus Benthoplana to the generic level, erect the new family Benthoplanidae for Benthoplana and Vallicula, and provide diagnoses for these taxa and their accepted species. We also show that planktonic Ctenoplana (Diploctena) neritica is the early life stage of Benthoplana meteoris, and suggest that the remaining Ctenoplanidae likely represent early life history stages of Coeloplanidae and perhaps other platyctenes. While both the nuclear ribosomal (18S and 28S) and mitochondrial protein-coding genes suggest a deep phylogenetic divergence between Benthoplanidae and Coeloplanidae, we detect conflicting phylogenetic signal between these markers, suggesting nuclear-mitochondrial discordance, leaving the placement of Tjalfiellidae and Lyroctenidae uncertain.

Neotropical catfishes of the genus Rhamdia are divided into cis- and trans-Andean/Middle American reciprocally monophyletic components, the latter notable for its considerable cave-dwelling diversity. Despite previous research, uncertainties regarding the systematics and historical biogeography of the Middle American clade remain. To test previous phylogenetic hypotheses and improve our understanding of the evolutionary history of this group of Middle American freshwater fishes, we generated and analyzed comparative mitogenome-wide data from most valid species and known cave-dwelling forms. Our results corroborate this clade as divided into two reciprocally monophyletic groups (split dated at ~9 Ma): a clade representing the species Rhamdia guatemalensis (crown group dated at ~2.8 Ma) and a clade consisting of the remaining Middle American species (i.e., the Rhamdia laticauda species group; crown group dated at ~4 Ma). Our results also confirm the notion that R. laticauda is deeply paraphyletic and that phylogenetically scattered geographic lineages of this taxon could represent different species. Our divergence time estimates, coupled with present-day distribution patterns, support the biogeographic scenario in which northward dispersal and colonization of Central America and southern North America by Rhamdia was catalyzed by the emergence of the Panamanian Isthmus land bridge and stream captures across Lower Central America. Cave colonization in Middle American Rhamdia is widespread, convergent, relatively recent (dating from the Pleistocene), and most likely opportunistic, with established cave-dwelling populations possibly representing “evolutionary dead ends.”

Accurate species delimitation is crucial for biodiversity research, as it significantly impacts taxonomy, ecology, and conservation. Recent advances in molecular phylogenetics and integrative taxonomy have improved classifications and resolved long-standing taxonomic uncertainties. Here, we use Hyb-Seq (489 nuclear loci) and phylogenomic approaches to investigate Afrocarduus, a genus endemic to tropical Afromontane and Afroalpine regions. Our analyses reveal 16 evolutionary lineages within this relatively young genus (crown age 2.3 Mya), with new morphological data strongly supporting the recognition of each lineage as a distinct species. We demonstrate that the stemless habit evolved independently in species from the Ethiopian Highlands and the East African Rift System (EARS). Notably, we show that the concept of the stemless Afrocarduus schimperi adopted by the Flora of Tropical East Africa, in fact, comprises seven clearly recognizable species, which we formally reinstate. Unexpectedly, the stemmed Afrocarduus nyassanus was recovered as paraphyletic with Afrocarduus ruwenzoriensis nested within it, probably due to incomplete lineage sorting or hybridization. Additionally, the stemmed Afrocarduus keniensis may represent a complex of cryptic species, and we describe a new stemmed species from southern Ethiopia, Afrocarduus kazmi sp. nov. We expand the number of accepted species in Afrocarduus from eight, as recognized in the Flora of Tropical East Africa, to 18 (including two species for which we were not able to obtain molecular data). Our study thus highlights a substantial prior underestimation of the diversity of Afrocarduus in Afromontane and Afroalpine habitats.

Fossil Ericales pollen from late Oligocene to Early Miocene sediments of the Ban Pa Kha Subbasin, Li Basin, northern Thailand, were examined using the single-grain method. A total of 24 different ericalean pollen types belonging to Ebenaceae (Diospyros), Ericaceae (Cassiope, Vaccinium, and Rhododendron), Pentaphylacaceae (Adinandra), Sapotaceae, Styracaceae (Rehderodendron and Styrax), and Symplocaceae (Symplocos) were identified. All the fossil pollen, except that of Sapotaceae, represent families/genera that are described for the first time from the Cenozoic of Thailand. By considering present terrestrial biome occupancy, Köppen–Geiger climate profiles, and vertical distributions of potential modern analogs of the parent plants producing the fossil pollen, the phytosociological and paleoecological preferences of the fossil taxa were assessed. Our results demonstrate that modern analogs of most of the ericalean taxa have wide ecological and climatic amplitudes with a broad zone of convergence in warm and cold temperate humid or seasonally dry climates. Exceptions are Sapotaceae, which rarely occur outside lowland tropical forests, and Cassiope, which at present occurs at high elevations and, besides Rehderodendron, is one of two modern analogs absent from the modern flora of Thailand. Along with a review of phytosociological studies in montane forests of northern Thailand and neighboring regions, this suggests that the assemblage of dispersed ericalean pollen of the Ban Pa Kha Subbasin likely derives from more than one vegetation type and possibly from different vertical zones.

While conducting a population genetic study aiming at refining previous conclusions about cladogenesis in the Oxera genus (Lamiaceae) in New Caledonia, we uncovered an unexpected result for the well-known Oxera palmatinervia Dubard species. To better understand the preliminary molecular results that revealed two distinct sister species, we performed extensive field studies in order to sample, measure, hand-pollinate, and observe the flower and fruit visitors on different populations of O. palmatinervia and other species of the “robusta” clade. We found flower morphology differences to be congruent with the molecular results, so that we propose to describe a new species as O. sympatrica Gâteblé & Karnadi sp. nov. The differences in flower morphology between the two species, which can grow in true sympatry and flower at the same time of the year, are striking so that flower visitors and pollination syndromes were investigated as far as possible. We find that two species of honeyeaters Glycifohia undulata and Philemon diemenensis are likely the preferred pollinators, respectively, of O. palmatinervia and O. sympatrica sp. nov. because of their respective sizes, bill and tongue lengths, and behavior. Even though, to date, it cannot be proven that initial speciation of both Oxera occurred in sympatry, today's sympatry is observed along with a remarkable supposed coevolution pollination syndrome. The new species is fully described, mapped, evaluated against Red List criteria, and illustrated. Pollination syndromes are discussed and illustrated.

A major obstacle to biodiversity conservation is that thousands, if not millions, of plant and animal species have yet to be discovered and described, even in historically well-explored regions. Carex sect. Lupulinae (Cyperaceae; “sedges”) is a small group of six showy Eastern North American species that, until recently, was thought to be well understood. However, a DNA barcoding study of North American Carex undertaken over a decade ago serendipitously revealed unsuspected molecular diversity, including one potentially undescribed cryptic species. Here, we test the hypothesis that this entity is a species on a separate evolutionary trajectory by expanding barcoding results with an integrative approach that combines a densely-sampled molecular phylogeny (five plastid and two nuclear markers, 112 sequenced specimens), morphometric analyses (93 characters, > 300 measured specimens), ecological field surveys, and common greenhouse observations. Results all support the recognition of a new, abundant species common in the southeastern United States' Coastal Plain that we name Carex gator. This study highlights how integrative taxonomy can help to describe cryptic plant species revealed by DNA barcoding. We provide illustrations, a distribution map, and an identification key, and discuss how C. gator may be a rare example of homoploid sympatric speciation in plants.

Maize is amongst the most agriculturally and economically important crops to human beings. It was domesticated from a wild relative called teosinte. During domestication, maize has experienced drastic morphological transformations, such that it produces fewer ears, each of which bears many more kernels covered by soft and reduced glumes. The striking differences between maize and teosinte make the origin of maize ear a fascinating question, which has been fiercely and actively debated for more than a century. Over the past few decades, the discovery of numerous key genes and genetic pathways has greatly deepened our understanding of the mechanisms underlying maize ear development and domestication. In this review, by providing an overview of the morphogenetic processes of maize and teosinte ears, and the molecular mechanisms of maize ear development, we highlight key morphodynamical distinctions between maize and teosinte ears. By recapitulating historical accounts and summarizing recent advances regarding maize domestication, we present the current understanding and propose a model for the origin of maize ear.

Encephalartos, an African endemic genus within the Zamiaceae, comprises 65 extant species whose phylogenetic relationships have remained unresolved due to limited genetic differentiation observed in previous studies. This research reconstructs the evolutionary history of Encephalartos utilizing 3545 single-copy nuclear genes derived from transcriptomes of 64 species. The study estimates divergence times and reconstructs ancestral states for 12 key morphological traits. Phylogenetic analyses definitively resolve eight major clades, supported by both molecular and morphological evidence. Although these clades partially align with previous morphology and geography based classifications, the genomic data provide novel insights, necessitating a revised infrageneric system. Biogeographic reconstructions indicate that Encephalartos originated in southern Africa during the Oligocene (~26.3 Ma), subsequently dispersing into eastern and northern Africa through the Zimbabwe–Mozambique corridor during the Miocene, followed by expansion into Central Africa. Speciation rates decreased markedly during the Pliocene and Pleistocene, potentially due to intensified climatic drying and cooling. Morphological character mapping identified ancestral traits, including aerial stems, green leaves, and red sarcotesta. Specific transitions such as subterranean stems in clade IV and bluish-green leaves in clades II and V, further substantiate clade differentiation. These findings resolve long-standing taxonomic uncertainties and emphasize the Oligocene-Miocene as a crucial period for Encephalartos diversification, influenced by Cenozoic climate change. This research establishes a robust framework for future systematic and conservation studies while demonstrating the effectiveness of transcriptome data in resolving phylogenies of slowly evolving lineages.