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 A. schimperi adopted by the Flora of Tropical East Africa, in fact, comprises seven clearly recognizable species, which we formally reinstate. Unexpectedly, the stemmed A. nyassanus was recovered as paraphyletic with A. ruwenzoriensis nested within it, probably due to incomplete lineage sorting or hybridization. Additionally, the stemmed A. keniensis may represent a complex of cryptic species, and we describe a new stemmed species from southern Ethiopia, A. 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.

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.

Identification of Fabaceae family Plants, traditionally relies on either morphological traits or DNA barcoding, each with limitations in accuracy and efficiency. Deep learning has emerged as a promising tool for integrating multiple data sources, but its full potential remains underexplored. This study aimed to utilize a deep learning model that integrates morphological and molecular data for species identification within Fabaceae family, bridging the gap between the two methods of identification. The research involved four main phases: (i) data collection, (ii) data preprocessing, (iii) training and testing the model, and (iv) results analysis. The data comprised DNA barcode sequences retrieved from the BOLD database, and images were collected from different websites. The model was trained for identification on the genera and species level, with two different barcodes, ITS2 and matK+rbcL. Only species with four available copies of ITS2, matK, and rbcL sequences were selected to ensure consistent input across samples.  The final dataset included 7 genera and 21 species. While the model achieved high accuracy during training, test accuracy remained low (14–19%), indicating overfitting, likely due to the limited dataset size. However, the model demonstrated the ability to evaluate barcode discrimination across genera. Specifically, it highlighted ITS2 and matK+rbcL as having varying levels of effectiveness depending on the genus. These findings introduce a new application for deep learning in plant systematics not only for species identification but also for evaluating barcodes. This approach could help reduce the reliance on trial-and-error in barcode selection and enhance the efficiency of molecular taxonomy. 

The tribe Trichosporeae is the most species-rich, systemically complex, and morphologically diverse tribe in the Old World Gesneriaceae. It has long been a focal point and a challenge in the phylogeny of Trichosporeae, with frequent unclear relationships and delimitations among a lot of genera. Here, we conducted a molecular phylogenetic analysis by employing nine DNA fragments with a high sampling coverage for key clades in the tribe Trichosporeae. Meanwhile, we carried out a comprehensive morphological and anatomical investigation on vegetative and floral organs in related genera and species, and tried to uncover morphological synapomorphies associated with molecular clades. Our results demonstrated a well-supported phylogeny of major clades in the tribe, strongly corroborated by morphological data. We find that some genera, such as Raphiocarpus, Briggsia and Boeica, are not monophyletic. Based on molecular phylogenetic and morphological analyses, we established five new genera and revived a genus in the tribe Trichosporeae, including Neoraphiocarpus, Anisophyllaea, Hispidopalata, Pseudobriggsia and Kaiyua with revival of Boeicopsis. We further redefined the genera Raphiocarpus and Briggsiopsis. Our results would deepen our understanding about the phylogeny of the Old World Gesneriaceae.

The genus Kineococcus is primarily found in extreme environments and plant-associated habitats, suggesting its potential for stress tolerance and plant growth promotion. However, the diversity and functional potential of this genus remain largely unexplored, mainly due to the limited availability of strains and genomic resources. In this study, 33 Kineococcus strains were isolated from the Gurbantunggut Desert and Shanshan Kumtag Desert in Xinjiang, China. Based on the overall genome relatedness indices (OGRI) and sampling origins, 12 representative Kineococcus strains were selected for polyphasic taxonomy and assessment of plant growth promoting traits. By integrating phylogenetic, morphological, physiological, chemotaxonomic, and genomic analyses, these strains were classified into nine novel species (one with two subspecies). The representative isolates exhibited various key plant growth-promoting traits, including siderophore production, cellulose degradation, organophosphate solubilization, and indole-3-acetic acid (IAA) production. This study significantly expands the strains, species, and genome resources of the genus Kineococcus, providing valuable insights into its ecological adaptation, particularly in saline-alkali tolerance, and growth-promoting potential for sustainable agriculture.

Pseudoscorpiones are a group of small to medium-sized arachnids under the species-rich Chelicerata. They are found in many terrestrial habitats, normally cryptic, including leaf litter and soil, under tree bark or rocks. The fossil record of pseudoscorpiones is mainly composed of species belonging to extinct genera in extant families, with a small number of taxa described from the famous Kachin amber, sometimes referred to as Burmese amber or Burmite (12 species in six families). Here, we describe a well-preserved male specimen of pseudoscorpion from mid-Cretaceous Kachin amber, representing the first fossil record of Cheliferidae from Burmese amber. This new taxon, Echinochelifer curvatus gen. et sp. nov., is characterized by elongate tubercle-bearing pedipalps and several trichobothrial features. Based on these, we discuss the systematic placement and palaeoecological implications of the new taxon in Burmese amber.

Many genera were erected without phylogenetic validation in Bittacidae, a cosmopolitan family in Mecoptera, leaving their generic statuses contentious. Here, we investigated the phylogenetic relationships and reconstructed the ancestral states of chromosome numbers and key morphological characters for 26 species in three genera of Bittacidae using an integrative approach combining molecular, cytogenetic, and morphological data. The phylogenetic analyses reveal that all three genera studied are paraphyletic, but cytogenetic evidence supports the generic status of Terrobittacus Tan & Hua with haploid chromosome numbers ≥ 20. In contrast, the genus Bittacus Latreille, 1805 exhibits an extensive chromosomal variation from n = 8 to n = 22. Ancestral state reconstruction suggests that the diagnostic character of Bicaubittacus Tan & Hua may represent an apomorphy restricted to a few species. The cytogenetic investigation indicates that n = 22 was the ancestral chromosome number in Bittacidae. Chromosome fusions were likely responsible for numerical reduction in chromosomes of Terrobittacus, whereas more complex structural and numerical variations accounted for the chromosome diversity of Bittacus and Bicaubittacus. To satisfactorily resolve the generic problem of Bittacidae, taxon sampling should be greatly expanded at the global scale, and more attention should be paid to the integrative taxonomy.

Meiogyne is a genus of trees and treelets occurring in India, tropical Southeast Asia and Australasia-Pacific, an unusually wide distribution across Australasia and the Western Pacific compared to other genera of Annonaceae. Previous chloroplast phylogenies of the genus offered poor resolution and support. Here, a molecular phylogeny was reconstructed based on 27 described Meiogyne species (ca. 70% sampling) using seven chloroplast and 11 nuclear markers. The combined dataset generated a well-resolved and well-supported phylogeny. Estimation of divergence time utilised two fossil calibrations and an uncorrelated lognormal relaxed clock model. Trait-dependent and trait-independent biogeographical models in BioGeoBEARS were compared using AICc weight and likelihood ratio test. The results suggest that narrow monocarp width is correlated with increased macroevolutionary dispersal. Under the best-fitting trait-dependent DEC+j+t₁₂+t₂₁+m₂ model, a single colonisation event from Sunda to Sahul during the middle Miocene and two dispersal events from New Guinea and Australia into the Pacific during the late Miocene to early Pliocene were detected. BayesTraits analysis strongly supports a correlation between narrow monocarp width and bright fruit colours. Bird dispersal and the associated traits (narrow monocarp width) may have driven macroevolutionary dispersal for Meiogyne with fleshy fruits in Australasia-Pacific.

A new species, Sinocurvicubitus haotianus Xu, Shih, Ren et Wang, sp. nov. (Curvicubitidae), is described from the Upper Permian Leping Formation in Jiangxi Province, South China. This constitutes the second definitive occurrence of Curvicubitidae in the Late Permian. Through comparative wing morphology and cladistic analyses, we resolve phylogenetic relationships within the superfamily as ((Ignotalidae + Pereboriidae^*) + Curvicubitidae) and validate the exclusion of Scytophara extensa from Pereboriidae. Additionally, we estimate divergence times across Pereborioidea lineages, reconstruct ancestral distribution ranges, and elucidate the origin centers and dispersal routes for Curvicubitidae. Wing eyespots and bands suggest predator mimicry, a novel defense strategy in Permian insects.

The generic delimitation of the Caesalpinia group continues to be under contention, similar to several other lineages of the hyper diverse legume family. Despite its ecological and economic importance and role as a model to explore correlations between ecological diversification and genomic traits, intergeneric and infrageneric relationships remain unresolved, even after recent phylogenetic analyses. While phylogenomic approaches have elucidated complex relationships within the angiosperm tree of life, the phylogenetic backbone of the Caesalpinia group remains poorly defined owing to limited genomic data. To address this gap, we combined de novo assembled plastomes from 19 samples across nine genera, along with 27 previously published plastomes, resulting in 46 plastomes from 16 of the 26 genera. The phylogenomic analysis generated a robust phylogenetic hypothesis, distinguishing two main clades, one in the Neotropics and the other Pantropical, and resolving several previously ambiguous relationships. Notable changes in plastome gene content were observed, including six gene losses (psbL, rpl22, rps2, rpl32, ycf1, ycf2) and duplications (ndhB, rpl23, rps7, rps12, ycf1, ycf2). Other changes included shifts in inverted repeat (IR) boundaries and genome rearrangements, indicating lineage-specific plastome evolution. Hypervariable regions were identified as potential mini-barcodes, with cpSSRs providing valuable resources for species delimitation and population genetics studies. Codon usage revealed a strong AT bias and relaxed purifying selection in genes like accD, clpP, and rps16. These findings offer novel insights into Caesalpinia group evolution, emphasizing plastome data’s utility for resolving complex evolutionary questions and establishing a genomic toolkit for future research on the systematics, conservation, and evolutionary biology of legumes

Investigating the evolutionary history and species diversification patterns in hyperdiverse lineages is essential for understanding how species diversity accumulates and how floras assemble historically across diverse regions. A large angiosperm family Apocynaceae exhibits remarkable diversity in functional traits including growth form, fruit types, and pollen aggregation, which may have a substantial impact on species diversification rates. However, the lack of a robust and well-dated phylogeny has hindered our understanding of Apocynaceae diversification. To address this gap, we reconstructed a robust phylogeny covering 22 of 25 tribes using plastome sequences, then employed this framework to estimate divergence times, analyze diversification patterns, and investigate associations between species diversification and functional traits. The plastome phylogenies received strong nodal support across most branches. Among higher taxonomic groupings, three clades (Asclepiadoideae, Secamonoideae, and Periplocoideae) were monophyletic. At tribal levels, 19 tribes were strongly supported as monophyletic except Melodineae, Willughbeieae, and Vinceae. Additionally, five genera (Vincetoxicum, Cynanchum, Hoya, Marsdenia, and Aganosma) were identified as non-monophyletic. Our analyses revealed that Apocynaceae originated in the paleotropics during the middle Late Cretaceous. Integrating BiSSE, HiSSE, and FiSSE analyses, we found that species with pollinia had a higher speciation rate than those without. Dry-fruited species had a higher speciation rate than those with fleshy fruits. Furthermore, BAMM analyses detected a diversification rate increase coinciding with evolution of pollinia with clip-type attachment mechanisms. Herbs had the highest speciation rate, followed by climbers and self-supporting species. Our findings contribute to understanding the historical assembly of floras in tropical and subtropical Asia.

Carpesium (Asteraceae) represents the largest Asian genus within the subtribe Inulinae of the tribe Inuleae, exhibiting maximum species diversity in China. This study presents the first comprehensive phylogenetic analysis of Carpesium, utilizing nuclear ribosomal ITS, specific chloroplast DNA sequences (rps16-trnQ, rpl32-trnL and ndhF-rpl32), whole chloroplast genomes and chloroplast coding sequence (CDS). The results demonstrate that Carpesium, excluding C. abrotanoides, constitutes a monophyletic group. The Carpesium s.str. clade contains two well-supported lineages with distinct morphological characteristics. Based on morphological analyses, molecular phylogenetic evidence, and karyotypic studies, this research establishes Cladocarpesium gen. nov. to accommodate Carpesium abrotanoides. The comprehensive sampling approach has facilitated a thorough phylogenetic reconstruction of the Inula complex, establishing a robust systematic framework that clarifies previously uncertain relationships among constituent species. This multilocus methodology provides essential insights for reassessing infrageneric classifications within this taxonomically complex group.