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.

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.

Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well as between deeply diverged lineages across phylogenetic time-scales. Their strengths and limitations in the latter cases, however, remain poorly explored. This study presents a systematic evaluation of the performance of the most popular population clustering method, STRUCTURE, under a variety of cross-species hybridization scenarios, including hybrid speciation, as well as introgression involving ghost (i.e., extinct or unsampled) lineages or otherwise. Our simulations demonstrate that STRUCTURE performs well in identifying hybrids and their parental donors when admixture happens very recently between sampled extant lineages, but generally fails to detect signals of admixture when hybridization occurs in deep time or when gene flow stems from ghost lineages. We find that symmetrical parental contribution in cases of hybrid speciation will often be revealed as extremely asymmetrical in STRUCTURE, especially when the admixture event occurred a long time ago. Our results suggest that population-genetic clustering methods may be inefficient for detecting ancient or ghost admixtures, which may partly explain why ghost introgression has escaped the attention of evolutionary biologists until recently.

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.

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, that 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.

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 analogues of the parent plants producing the fossil pollen, the phytosociological and paleoecological preferences of the fossil taxa were assessed. Our results demonstrate that modern analogues 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 analogues 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.

The genetic structure and population history of ethno-linguistically diverse populations from the Yunnan-Guizhou Plateau remain underrepresented in human genomic research. We analyzed genome-wide data from 239 individuals in Guizhou, combined with modern and ancient datasets, to investigate their fine-scale genetic structure, demographic events, and functional consequences of adaptive genomic signatures. Our findings revealed three genetically distinct groups corresponding to linguistic categories, shaped by differential gene flow from ancient millet farmers and southern Chinese populations. We identified population-specific adaptive candidate genomic regions associated with immune, metabolic, and hematological functions. Additionally, we detected clinically relevant variants with implications for disease risk prediction and precision medicine. These findings underscore the importance of genetic diversity in understanding human adaptation and health disparities, offering a framework for equitable genomic research in underrepresented populations.

Karst area are well known as their extremely biodiversity and the investigation of plants adaptation in these unique environments is one of research hotspots. Previous studies primarily focused on the genomic adaptation of karst endemic species, but the special adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas, serves as a valuable model for understanding the genomic mechanisms of this issue. Here, the genome of H. subcapitata was sequenced using the PacBio and Illumina platforms and de novo assembled with contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events likely facilitated the expansion of stress-responsive gene families, which in turn influenced functional pathway regulation. Especially, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared to the karst-endemic Primulina tabacum, H. subcapitata showed upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation was the unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.