The genus Micromonospora, a globally distributed actinomycete inhabiting diverse ecosystems, is widely recognized for its remarkable biosynthetic capacity and role as a prolific source of bioactive natural products. However, the members of the genus Micromonospora from extreme environments remain largely unstudied. In this study, we isolated 15 Micromonospora spp. strains from samples collected in desert and marine habitats. Based on polyphasic taxonomy approaches eight strains were identified and represent four novel species. Genome mining of the newly isolated strains revealed substantial biosynthetic potential for terpenes (n = 70, 22.9% of total biosynthetic gene clusters [BGCs]) and polyketides (n = 60, 19.6% of total BGCs). Subsequent pan-genomic analysis identified substantial numbers of terpene-related (n = 745, 33.8% of total biosynthetic genes [BGs]) and polyketide-related (n = 728, 33.0%) BGs in the core genome, highlighting their core biosynthetic potential. To further investigate their metabolic capacity, fermentation and metabolomic profiling were conducted to assess the secondary metabolite production capacity of all 15 strains. The results revealed a diverse array of alkaloids (averaging 75.3, 33.4% of total annotated secondary metabolites) and amino acid-derived peptides (averaging 56.3, 25.0% of total). These findings also highlight significant metabolic variations among strains and underscore the pivotal role of fermentation conditions in shaping their metabolic profiles. This study advances the taxonomic and functional understanding of Micromonospora spp. and presents a multi-omics framework combining genome mining and metabolomics to explore the biosynthetic potential of wild-type strains from extreme habitats.

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order, Lepidoptera (butterflies and moths) are central to terrestrial ecosystems and serve as important models for biologists studying ecology and evolutionary biology. However, for such an insect group, the higher-level phylogenetic relationships among its superfamilies remain poorly resolved. Here, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa), obtaining a series of amino-acid data sets from 69 680 to 400 330 aa in length for phylogenomic reconstructions. Using these data sets, we explored the effect of different taxon sampling with significant increases in gene loci on tree topology using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness of topology robustness among the three ML-based models. The results demonstrated that taxon sampling is an important determinant in tree robustness of accurate phylogenetic estimation for species-rich groups. Site-wise heterogeneity was identified as a significant source of bias, causing inconsistent phylogenetic positions among ditrysian lineages. The application of the posterior mean site frequency (PMSF) model provided reliable estimates for higher-level phylogenetic relationships of Lepidoptera. Phylogenetic inference presented a comprehensive framework among lepidopteran superfamilies, and revealed some new sister relationships with strong supports (Papilionoidea is sister to Gelechioidea, Immoidea is sister to Galacticoidea, and Pyraloidea is sister to Hyblaeoidea, respectively). The current study provides essential insights for future phylogenomic investigations in species-rich lineages of Lepidoptera and enhances our understanding on phylogenomics of highly diversified groups.

Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus′ distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro–Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro–Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro–Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro–Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.

Floral color and odor serve as attractants for pollinators. It remains unclear how changes in these traits in color-change species interact with pollinators and impact a plant's reproductive success. Lonicera calcarata flowers change from white (Night 1 [N1] and Day 1 [D1]) through yellow (Night 2 [N2]) and orange (Day 2 [D2]) to orange-red (Night 3 [N3] and Day 3 [D3]). Our research showed that floral characters, stigma activity, nectar production and floral spectral reflectance decreased through the flowering phases. Floral odor mainly comprised fatty acids, aldehydes, monoterpenes and alcohols, especially n-hexadecanoic acid, hexadecanal and 3-carene. Floral odor peaked on N1 and N3, largely due to the presence of fatty acids. The emission of n-hexadecanoic acid was higher on N1 and N3 compared with other phases, while hexadecanal emission remained constant throughout the flowering stages. The emission of 3-carene was highest on N1. Lonicera calcarata was mainly pollinated by the moth Chorodna strixaria, the butterfly Acosmeryx naga and three bumblebees (Bombus melanurus, B. eximius, B. sonani) and they all preferred to visit white (younger) flowers. Moths had a preference for 3-carene and no significant preference for n-hexadecanoic acid and hexadecanal. Seed sets of nocturnal pollination and control treatments were not significantly different. Lonicera calcarata could produce seeds by self-pollination; cross-pollination significantly increased the seed set. Floral color guides pollinators to visit younger flowers with more floral rewards and higher stigma activity. Different chemical compounds in floral odor may not only attract pollinators but also avoid herbivore damage.

In the Mountains of Southwest China (MSC), accelerated diversification triggered by mountain uplift and monsoon intensification in the Miocene is widely revealed, but less is known about the stage after the Pliocene. Thus, the tempo‐spatial evolution of the endemism of Gaoligong Shan (GLGS), a young and isolated mountain with the highest biodiversity in the MSC, was determined. Temporal patterns were inferred by the stem ages of the endemic species and spatial patterns were inferred through ancestral area reconstructions and the distributions of the sister taxa. Temporally, the calibrated origin times of 114 phylogenetically well resolved endemic species (75 plants, 33 animals and six fungi) ranged from the early Miocene to the Holecene. Spatially, 82 centric origin species (mean = 3.08 Ma) were significantly younger than 32 eccentric origin species (6.84 Ma). Eccentric origins accumulated smoothly while centric origins burst after the late Pliocene, especially after the Pleistocene (n = 52). In centric origins, most of the sister taxa showed sympatric (n = 47) or allopatric (n = 23) distributions in the GLGS. The eccentric origins were mainly dispersed from the southern lower latitude region (n = 20). Principle component analysis indicated that niche conservatism exerted greater contribution to the speciation of the endemic species. Uplift of the GLGS and monsoon intensification during the late Pliocene accelerated the formation of its endemism. The “Species pump” effect of the Pleistocene climatic fluctuations is further revealed. Speciation triggered by geological isolation by mountain and river barriers through niche conservatism exceeds adaptive evolution.

Due to the high cost of whole-genome sequencing and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum, in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The EA lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

The maintenance of species boundaries between widespread and narrow endemic congeneric species in sympatric sites remains a fundamental question in ecology and evolutionary biology. For plants with specialized pollination mechanisms, pre- and postpollination isolation mechanisms likely play distinct roles in reproductive isolation and species integrity. Parnassia (Celastraceae) is characterized by one-by-one stamen movement and has its distribution center in southwest China, where many widespread and local endemic species coexist. To quantify pre- and postpollination barriers and their relative roles in maintaining species boundaries, we conducted field experiments with the widespread Parnassia wightiana Wall. ex Wight & Arn. and the local endemic Parnassia amoena Diels over two separate years at Jinfo Mountain, southwest China. We examined four prepollination barriers (ecogeography, blooming phenology, stamen movement, and pollinator type) and three postpollination barriers (fruit set, seed production, and seed viability). Our findings indicate that prepollination barriers played a more significant role in reproductive isolation than postpollination barriers. For the widely distributed P. wightiana, ecogeographical isolation was the primary barrier, followed by phenology and pollinator type isolation. In the narrow endemic P. amoena, which exhibits slower stamen movement, this feature contributed significantly to isolation, with phenological isolation being the second most important factor. Among postpollination barriers, seed viability was the most significant for both species. Our results indicate that prepollination barriers are the predominant isolation mechanism for these two sympatric Parnassia species, and stamen movement may serve as a novel type of prepollination barrier, particularly for the narrow endemic species.

An underlying assumption for the size-dependent sex allocation (SDS) hypothesis is that the plasticity of bisexual investments in hermaphrodites would be larger in female than in male allocation, but it has rarely been critically evaluated. Among five sexual morphs in a sexually polymorphic desert herb Geranium transversale, gynomonoecious individuals were the largest, and males were the smallest, while hermaphroditic and andromonoecious plants and females did not differ significantly in plant size. The total number of flowers increased with plant size in all five sexual morphs; in gynomonoecious and andromonoecious plants this was due to an increase in the number of perfect flowers rather than pistillate or staminate flowers. Flower size increased with plant size in hermaphroditic and gynomonoecious plants (due to an increase in the size of perfect but not of unisexual flowers). The sizes of staminate flowers in andromonoecious and male plants, and pistillate flowers in gynomonoecious plants did not increase with plant size, and pistil mass increased but stamen mass decreased with plant size. The coefficient of variation (CV) in pistil and stamen mass among 210 plants in four of the sexual morphs (excluding female plants) indicated that variation in resource allocation among individuals was higher in female than male functions. Both flower number and flower size generally increased with plant size in G. transversale, supporting the SDS hypothesis. The relatively higher plasticity (CV) in female than male allocation has not been reported before, providing a cue for understanding why the female-biased allocation associated with plant size is popular in flowering plants.

This study conducted phylogenomic analyses of the higher-level phylogeny and evolution of mitogenomes and characteristics of Lycosidae Sundevall, 1833 (wolf spiders) utilizing 56 complete mitogenomes. In comparison to analyses based on target-genes, the mitogenomic phylogenies revealed Tricassinae as sister to Hippasinae and positioned Tricassinae + Hippasinae as sister to Lycosinae + Pardosinae. The findings did not support Evippinae as sister to Sosippinae and indicated uncertain phylogenetic relationships among genera (Lycosa, Trochosa, Ovia, and Alopecosa) within Lycosinae. The study proposes the validation of Wadicosinae, revisions of three species, Pardosa multivaga Simon, 1880, Arctosa ningboensis Yin, Bao & Zhang, 1996, and Alopecosa cinnameopilosa (Schenkel, 1963), and recommends placing Halocosa hatanensis (Urita, Tang, & Song, 1993) into Evippinae. Contrary to previous findings, the initial diversification of wolf spiders occurred during the Earliest Oligocene Glacial Maximum, with rapid diversification during the Miocene, both interpreted as responses to significant climate changes and grassland expansion during these periods. Within Lycosidae, mitochondrial gene rearrangements (seven patterns) were observed only in Piratula of Zoicinae and P. multivaga, primarily resulting from transfer RNA transportation and loss. Ancestral state reconstruction analyses did not support web building as the ancestral trait of lycosid prey-capture strategies, instead suggesting an evolutionary progression from vagrant hunting to web building and burrowing, with shifts to web building or burrowing occurring independently multiple times.

Members of the genus Juglans (walnuts, family Juglandaceae) are typical Tertiary relict tree species. They are widely distributed in China and are well known for their edible nuts and high‐quality wood. The genetic structure and historical gene flow patterns of Chinese Juglans still need to be resolved. Here, we collected samples from a total of 2242 trees from 142 populations of three walnut species (Juglans regia L., Juglans sigillata Dode, and Juglans mandshurica Maxim.) and a hybrid taxon Juglans × hopeiensis. These samples were distributed throughout China. We analyzed population genetic structure, interspecific relationships, lineage differentiation, and speciation using 21 EST‐SSR genetic markers. All populations of J. regia and J. sigillata clustered into one lineage, corresponding to the Juglans sect. Dioscaryon, and all J. mandshurica and Juglans × hopeiensis populations (section Cardiocaryon) clustered into a second lineage. For J. mandshurica, there was an obvious north-south genetic cline. Interestingly, except for seven populations of the hybrid Juglans × hopeiensis, there was almost no gene flow between the populations of section Juglans/Dioscaryon and section Cardiocaryon. A DIYABC analysis showed that J. regia and J. mandshurica differentiated during the Oligocene. Juglans sigillata originated during the Pliocene to the Pleistocene. Subsequently, during the Middle Pleistocene, J. regia and J. mandshurica hybridized within a narrow zone to produce Juglans × hopeiensis. These results demonstrate the impact of repeated turbulent climate changes in the Quaternary on the evolutionary history of Tertiary relict plants.

Cicadomorpha, the most diverse infraorder of hemipteran insects, is a group of plant sap-sucking insects consisting of three monophyletic superfamilies: Cercopoidea, Cicadoidea, and Membracoidea. This study aims to resolve the controversy surrounding the phylogenetic relationships between these superfamilies, specifically whether Cercopoidea is more closely related to Cicadoidea (topology H1) or Membracoidea (topology H2). To tackle this issue, we assembled four matrices, including three amino acid datasets and one nucleotide dataset, and performed comprehensive phylogenomic analyses using both coalescent and concatenation methods. Our results showed that the amino acid matrix with low ratio of missing data-based analyses strongly supported topology H2, indicating that Cercopoidea is sister to Membracoidea. However, the other three matrices yielded conflicting results. Interestingly, when site-heterogeneous models were used, the results flipped, and the datasets that previously supported topology H1 supported topology H2. Further analyses, including model comparisons, tree topology tests, and phylogenetic analyses without an outgroup, also supported the conclusion that Cercopoidea is more closely related to Membracoidea. The study highlights the importance of modeling among site compositional heterogeneity in phylogenomic analyses to mitigate systematic errors. Additionally, we noted that datasets with high missing data ratios may lead to conflicting phylogenetic relationships. Our study provides strong evidence that Cercopoidea is sister to Membracoidea and highlights the importance of careful methodological considerations in phylogenetic analyses.

Gene loss is a widespread phenomenon in species evolution, yet the evolutionary significance of large-scale gene loss—whether arising through neutral processes or adaptive evolution—remains a subject of ongoing debate. Agaricus bisporus, a globally distributed macrofungus, serves as an ideal model to investigate this phenomenon. Utilizing the “map-to-pan” method, we constructed a high-resolution pangenome comprising 30 793 genes and 143 Mb of additional sequences, including 21 370 genes absent in the reference genome. Phylogenetic and admixture analyses identified four genetic lineages: the globally distributed MIX and region-specific European, America, and Highland lineages. Core gene analyses revealed a substantially lower genetic load in MIX lineage, accompanied by a marked reduction in the frequency of deleterious mutations compared with other lineages. Presence–absence variation (PAV) analyses further demonstrated extensive gene loss in MIX lineage, with functional enrichment analyses associating these PAVs with DNA damage repair pathways. This finding suggests that gene loss could enhance tolerance to DNA damage, thereby mitigating mutation accumulation. A significantly higher proportion of lost PAVs in MIX lineage was under selective pressure, supporting gene loss as an adaptive strategy. Our findings highlight two key mechanisms facilitating the MIX lineage's broad distribution: (1) the reduction of deleterious mutations, thereby lowering genetic load, and (2) the selective loss of redundant, non-essential genes, enhancing adaptability across diverse environments. This study not only underscores the adaptive significance of large-scale gene loss in the evolution of A. bisporus but also offers a broader framework for understanding how gene loss events shape the evolutionary trajectories of other fungal species.

Allopolyploidy, involving whole genome duplication (WGD) of interspecific hybrids, is a driving force in the evolution of angiosperms, and has provided favored substrates for the domestication of major agricultural crops. This suggests allopolyploidy is a rich source of genetic variation amenable to natural and artificial selection. While allopolyploidy-induced chromosomal variation is common, its immediate phenotypic effects are challenging to delineate due to the confounding influence of postpolyploidy evolution. Newly constructed allopolyploids, having not yet undergone evolution, present suitable systems to address this issue. In this study, we synthesized five sets of allotetraploids, each with a unique genome constitution of S*S*DD, comprising a common paternal (DD) but distinct maternal (S*S*) parental diploid species of Aegilops. We observed that, except for one sterile synthetic allotetraploid, the remaining four allotetraploids exhibited high fertility, enabling the establishment of sexual lineages through selfing. Chromosomal variation in both number and structure occurred extensively, demonstrating moderate (though variable) effects on key morphological traits related to growth, development, and reproductive fitness of the nascent allotetraploids. All four sets of fertile allotetraploids can be crossed with bread wheat to generate pentaploid F1 hybrids, which as maternal parents can be further backcrossed to bread wheat. This approach promises a feasible strategy for the concomitant introgression of the vast repertoire of genetic variation from the D- and each of the four S* genome-containing species to bread wheat.

When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species in East Asia and three in the Mediterranean region. Here we used target-capture sequencing and obtained 1991 single-copy nuclear genes, plus complete plastomes, to infer the evolutionary history of Cupressus. Our phylogenomic reconstruction resolved four well supported clades in Cupressus, but revealed significant phylogenetic conflicts, with inter-lineage gene flow, incomplete lineage sorting and gene tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between the ancestors of the Himalayan–Hengduan Mountains and subtropical Asia clades, whereas orogenic and climatic changes may have facilitated gene flow within the Himalayan–Hengduan Mountains clade. Molecular dating suggested that the most recent common ancestor of Cupressus appeared in East Asia around the middle Eocene period and then became continuously distributed across Eurasia. The East Asian–Tethyan disjunction arose when the Mediterranean and Himalayan–Hengduan Mountains clades diverged, likely to have been driven by Eocene/Oligocene declines in global temperature, then reinforced by the ecogeographic barrier created by the uplift of the Qinghai–Tibet Plateau. Niche shifts in the common ancestor of the Mediterranean clade, and signatures of selection in genes for drought and salt tolerance, probably indicate adaptation of this clade to local conditions. Overall, our study suggested that in-depth phylogenomic analyses are powerful tools in deciphering the complex evolutionary history of the origin of East Asian–Tethyan disjunction of organisms, especially gymnosperms.

The genus Didymocarpus Wall. is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high-density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (external transcribed spacer [ETS], internal transcribed spacer [ITS], 18S, 26S) and five chloroplast DNAs (atpB-rbcL, rpl16, rps16, trnH-psbA, and trnL-F). The results indicated that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitated the range of the Didymocarpus sensu stricto (s. str.) with two-section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, in that it is found only in Southeast China. In addition, we proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera.

Burmoniscus Collinge, 1916, the most species-rich genus within the family Philosciidae, presents significant taxonomic challenges due to interspecific morphological convergences and intraspecific variations. This study employs an integrative taxonomic framework combining morphological examination with molecular phylogenetic analyses and species delimitations based on the sequence data of a mitochondrial COI gene and three nuclear genes (18S rRNA, 28S rRNA, and NaK) to classify Burmoniscus species. Our results reveal 21 species Burmoniscus from China, including 12 new species (Burmoniscus acutatus Li & Jiang, sp. nov., B. obscurus Li & Jiang, sp. nov., B. cuneatus Li & Jiang, sp. nov., B. rectangulatus Li & Jiang, sp. nov., B. solus Li & Jiang, sp. nov., B. spinellosus Li & Jiang, sp. nov., B. cordatus Li & Jiang, sp. nov., B. trispinatus Li & Jiang, sp. nov., B. rotundus Li & Jiang, sp. nov., B. simplicissimus Li & Jiang, sp. nov., B. rubustus Li & Jiang, sp. nov., and B. variatus Li & Jiang, sp. nov.) and firstly report two species, B. schultzi Taiti, Ferrara & Kwon, 1992 and B. comtus (Budde-Lund, 1894) from China. This work highlights the critical role of integrative taxonomy in clarifying species boundaries and uncovering hidden diversity in terrestrial isopods.

The family Primulaceae s.l. is estimated to comprise approximately 60 genera and 2600 species worldwide. Although extensive research has been conducted on the family Primulaceae and its subfamily boundaries, there is a lack of systematic studies utilizing complete plastid genome data, leading to uncertainties in the phylogenetic positions of certain key taxa, such as Stimpsonia. In this study, plastid genomic data were collected from 67 accessions representing four subfamilies and 28 genera within the Primulaceae family. Phylogenetic trees were constructed using coalescent and concatenated approaches to elucidate the evolutionary history of the family. By employing a comprehensive dataset of 67 plastid genomes from all four subfamilies, a robust phylogenetic framework for the family was established. Contentious relationships were identified at the early stages of divergence in Primula and among Cyclamen and its relatives, probably due to rapid diversification. Our plastid genomic data support the idea that Stimpsonia is sister to the remainder of the subfamily Primuloideae, in contrast with its placement in Myrsinoideae based on nuclear data. A cytonuclear discordance in the phylogenetic position was also detected in Aegiceras corniculatum. The divergence time estimates from this study align with previous findings, indicating significant diversification events during the Eocene and Oligocene epochs. These timeframes coincide with major geological and climatic changes, which were likely to have influenced the distribution and diversification of Primulaceae. These results underscore the complex evolutionary history of the Primulaceae family and lay the groundwork for future research aimed at unraveling the intricate evolutionary dynamics within this family.

Evanioidea, as a poorly known group of Hymenoptera, exhibited remarkable species diversity during the Cretaceous, especially within the basal fossil family † Praeaulacidae. Here, we describe a new genus and species, † Coronaulacus cancan gen. et sp. nov., from Cretaceous Kachin amber. Based on its unique morphological characteristics and phylogenetic analysis, we place the new genus into † Praeaulacidae. This new genus is significantly distinct from other genera of the family: it is characterized by a ring of tubercles around the median ocellus, forewing vein 3r-m absent, an unusually enlarged terminal tarsomere of the midleg, and extremely elongated hindlegs. The ring of tubercles indicate that the new taxon was a parasitoid on wood-living insects. We discuss the morphology and function of the midlegs and hindlegs. We suggest that the males of this genus might have exhibited behavior similar to dance flies (Diptera: Empididae) or hangingflies (Mecoptera: Bittacidae). During mating, the males possibly used their mid legs with the expanded distal tarsus to effectively grasp and restrain the females and their elongate hindlegs to suspend themselves and their mate from the vegetation, providing support and stability during copulation.

Pan-Himalaya, including Himalaya and its neighboring areas, hosts a rich and unique flora that is crucial for understanding the evolutionary history of mountainous biodiversity. Phylogenetic regionalization can provide novel insights into biodiversity distribution patterns and their formation mechanisms. In this study, based on comprehensive species distribution data and a species-level phylogenetic tree, we propose a phylogenetic regionalization scheme of the Pan-Himalayan vascular flora comprising 15 zones, which can be grouped into five floristic subregions and three floristic regions (i.e., the West Himalayan [WH], the Southeast Himalayan [SEH], and the Northeast Himalayan [NEH] regions). Our results reveal that the SEH and NEH regions are closely clustered, which are then grouped with the WH region. The floras of these three regions exhibit distinct evolutionary histories and phylogenetic structures. The WH region presents a phylogenetically clustered flora with Euro-Mediterranean affinities and the highest evolutionary uniqueness. The NEH region has the highest species richness and phylogenetic diversity, with most of its areas, especially at higher elevations, displaying phylogenetic clustering. In contrast, the SEH region exhibits a phylogenetically overdispersed flora, characterized by harboring species-rich families with tropical, temperate, and alpine distributions, as well as relict plant lineages. This study provides valuable insights into the evolutionary history of the Pan-Himalayan flora and informs the development of effective conservation strategies.

Five new spider fossils of the family Macrothelidae (Araneae: Mygalomorphae) are described from mid‐ Cretaceous Kachin amber, Myanmar. A new genus Acanthomacrothele gen. nov. is established for three new species: Acanthomacrothele pauciverrucae sp. nov., Acanthomacrothele geminata sp. nov., and Acanthomacrothele longicaudata sp. nov. Both male and female specimens of A. pauciverrucae sp. nov. are described, representing a rare case of a fossil spider with both sexes known. We also describe an unidentified juvenile of Macrothelidae to document different developmental stages of Cretaceous species. To test the phylogenetic position of the new fossils, we undertook phylogenetic analyses using both topology‐unconstrained and topology‐constrained methods. Our analyses supported the placement of Acanthomacrothele gen. nov. in Macrothelidae, although its phylogenetic relationship to other genera of Macrothelidae differed among different analytical methods. The fossils documented here have elongated, widely spaced posterior lateral spinnerets, compact rectangular group of eyes on a tubercle, and more spines on male tibia of anterior legs than female, similar to extant macrothelids, suggesting that they probably have similar retreat construction behavior, habitat preference, and mating position to their living relatives.

Coccoidea (Hemiptera, Sternorrhyncha) are widely distributed and agriculturally significant insects known for their distinctive morphology and biological traits. The Coccoidea are often called scales or mealybugs because many species have a shell‐like covering resembling a scale or are covered with mealy wax. Knowledge of scale insects beyond the female adult stage is limited, partly because other life stages are less conspicuous, shorter‐lived, and less impactful on host plants. This complicates accurate classification, further compounded by limited molecular phylogenetic studies. This study presents the first phylogenetic analyses combining genome and transcriptome sequence data. We sequenced five whole genomes and one transcriptome from Pseudococcidae and integrated these new genome‐scale data with existing genome and transcriptome sequences to perform phylogenomic analysis of scale insects. The analysis yielded robustly supported relationships within Coccoidea, resolving several high‐level relationships. The current genome‐scale data support the monophyly of Monophlebidae, Pseudococcidae, Kerriidae, and Diaspididae, while not supporting the monophyly of Coccidae and Eriococcidae. Bayesian inferences using site‐heterogeneous models corroborated Pseudococcidae as the sister group of all other neococcoid families. Within Pseudococcidae, two subfamilies, Phenacoccinae and Pseudococcinae, were supported. At the tribe level, Phenacoccini was found to be monophyletic, whereas Planococcini, Trabutinini, and Pseudococcini were not.

Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well-resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC, ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high-resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long-obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitatadapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section‐based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

The uplift of the Qinghai-Tibet Plateau shaped the landforms and influenced Asia's climate system and ecosystem. Vegetations on the Plateau are the first to be affected by the uplift history of the Qinghai-Tibet Plateau and related ecological impacts. However, original research on vegetation in the central Qinghai-Tibet Plateau remains limited. Here, we reconstructed the vegetation in the Lunpola Basin, central Qinghai-Tibet Plateau from 24.3 to 16 Ma based on pollen data from the Dingqinghu Formation. Pollen assemblages reveal a temperate mixed deciduous broad-leaved and coniferous forest around the Lunpola paleolake during the latest Oligocene to the Early Miocene. An obvious vegetation vertical zone existed near the Lunpola Basin. Dark coniferous forests grew in the highlands, thermophilous shrubs stayed in the lowlands. This work provides new and original data on plant composition and vegetation in the central Qinghai-Tibet Plateau and enhances our understanding of the ecological impacts of the Qinghai-Tibet Plateau uplift.

Among the lineages of the tree of life, land plants exhibit a remarkably high genomic disparity because of their distinct evolutionary trajectories in the phylogenetic history of their major lineages. The macroevolutionary pattern of genomic evolution has been mainly investigated to obtain insights into well-studied lineages such as angiosperms, but little attention has been given to many important lineages such as bryophytes. This study was designed to resolve this gap by comparing the genomic evolution trajectories of mosses and liverworts. Thus, a data set comprising chromosome number and genome size was compiled, including previously published and newly generated data that were used to trace the phylogenetic history of these two parameters among mosses and liverworts via ancestral state reconstruction and phylogenetic comparative analyses. Contrasting patterns of chromosome number and genome size evolutions were detected between the two sister lineages. Mosses accumulated high chromosome number disparity via repeated whole-genome duplications and descending dysploidy but maintained a small genome size. By contrast, the chromosome number of liverworts was highly conserved, and heterogeneous trends in genome size evolution were identified among major lineages. These contrasting patterns may be partly explained by the difference in genomic dynamics: Active dynamics enables genome downsizing and reorganization in mosses, whereas genome stability leads to the accumulation of large genomes in liverworts. The results of this study confirmed the distinct trends of genomic evolution in bryophytes.

Multimedia representations of phylogenies can only broaden the audience experiencing results of the field. I developed a bioinformatics pipeline for representation of phylogenies as audio and video, optimized to enable conversion of an extremely wide range of phylogeny structures (from tens to tens of thousands of terminals). I also compiled and standardized a set of contemporary phylogenetics results comprising only ones that were provisioned in analyzable form supplementary to a publication and that had been assigned a Creative Commons license by the authors. Fifty-six such phylogenies were audified and the resultant media files were made easily accessible. This work provisionally addresses a problematic gap in public information on phylogenetics for nonvisual modalities, and exemplifies how evolutionary biologists might better respond to obligations in widening participation.

Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of Rhododendron germplasms and showcases strong environmental adaptability. However, there remains a lack of understanding regarding Rhododendron's evolution and environmental adaptations. Rhododendron bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb., an exceedingly rare species, thrives in the alkaline karst landforms of Guizhou, southwest China, different from the typical growing environment of other Rhododendron species. In this study, we present a chromosome-level genome assembly of R. bailiense, revealing a genome size of 923.3 Mb, a contig N50 of 24.5 Mb, and a total of 47 567 predicted genes. An evolutionary analysis indicated that R. bailiense diverged from its ancestors prior to the other subgenus Hymenanthes rhododendrons, with the expanded and contracted genes being notably enriched in “stress response” and “growth,” respectively. Rhododendron bailiense is predominantly found on limestone soil in the mountains of Guizhou, with only two wild populations known. The genome of R. bailiense contained a high copy number of ankyrin repeat (ANK) and Ca²⁺-ATPase (CAP) genes, primarily involved in Ca²⁺ transport, shedding light on how R. bailiense copes with karst high-calcium stress. In contrast, the structures of the ANKs displayed unique characteristics, while the CAPs showed conservatism. The R. bailiense genome provides new insights into the adaptation and evolutionary history of Rhododendron plants in karst environments, potentially offering valuable information for adaptive breeding and ecological enhancement in such challenging settings.

Carex sect. Paniceae sensu lato (s.l.) exhibits two major disjunct centers of diversity: eastern North America and East Asia. This pattern, commonly observed in other plant groups, has been associated with trans-Pacific dispersal from Asia to America and subsequent local extinctions in western North America. This study reconstructed a phylogenetic tree using two nuclear (external transcribed spacer and internal transcribed spacer) and three plastid (matK, trnL-F, and rpl32-trnL^UAG) regions, along with 474 nuclear loci from high-throughput sequencing (Hyb-Seq). Dating analysis and ancestral area reconstruction were used to investigate the evolutionary and biogeographic history of sect. Paniceae s.l. A broader circumscription of sect. Paniceae s.l., incorporating sects. Bicolores and Laxiflorae, is established. Two primary clades were identified: one clade predominantly diversified in North America and the other in East Asia. Biogeographic analyses suggested a likely origin of sect. Paniceae s.l. in the Palearctic during the Late Miocene. The most probable scenario involved dispersal to eastern North America via the Western Palearctic, followed by subsequent dispersal into western North America, other parts of the continent, and back to the Old World. Within East Asia, the group was inferred to have diversified during the Pliocene and Pleistocene, with the basalmost nodes inferred in mainland China. Multiple dispersal events from this region to the Russian Far East, Korea, and Japan were inferred. This study highlights the underexplored role of East Asia in the biogeography of grass-like plants and the existence of alternative migration routes in explaining the East Asia–eastern North America pattern of disjunction.

To investigate the evolutionary relationships and biogeographical history among the species of Agrostis and allied genera within the subtribe Agrostidinae, we generated a phylogeny based on sequences from nuclear ribosomal DNA (ITS) and three plastid regions (rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron). We also aimed to assess the generic limits of Agrostis, characterize possible subgeneric relationships among species in the genus, identify hypothesized reticulation events, and present our biogeographical theory. Based on our phylogeny of 198 samples, representing 138 species (82 from Agrostisas currently recognized, 10 from Polypogon, and 10 from Lachnagrostis), we identify two strongly supported clades within Agrostis: clade Longipaleata (Agrostis subg. Vilfa) and clade Brevipaleata (A. subg. Agrostis). The species of Agrostis in clade Longipaleata usually have florets with paleas 2/5 to as long as the lemma, whereas species in clade Brevipaleata have florets with paleas less than 2/5 as long as the lemma, minute, orabsent. Core (species with congruent alignment using ITS and plastid data) phylogenetic analysis of Agrostis reveals three strongly supported clades within Longipaleata (European‐Northwest African, Asian,and African), three strongly supported clades within Brevipaleata (Asian, North American, and South American), and a European grade leading to the latter two. Of the six genera commonly associated with Agrostis, that is, Bromidium, Polypogon, Lachnagrostis, Linkagrostis, Chaetopogon, and Chaetotropis, only Polypogon maintained its status as a separate genus, while the remaining genera are subsumed within Agrostis or Polypogon. Polypogon is identified as an intergeneric hybrid originating via ancient hybridization between unknown representatives of Agrostis clade Longipaleata (plastid DNA) and Calamagrostis clade Americana (nrDNA). We include several species of Lachnagrostis, including the type (L. filiformis), that follow the same pattern in Polypogon, while the remaining species of Lachnagrostis in our study are identified as ancient intersubgeneric hybrids within Agrostis. We propose nine new combinations in Polypogon: P. adamsonii (Vickery) P.M. Peterson, Soreng & Romasch.; P. aemulus (R. Br.) P.M. Peterson, Soreng & Romasch.; P. billardierei (R. Br.) P.M. Peterson, Soreng & Romasch.; P. bourgaei (E. Fourn.) P.M.Peterson, Soreng & Romasch.; P. filiformis (G. Forst.) P.M. Peterson, Soreng & Romasch.; P. littoralis P.M.Peterson, Soreng & Romasch.; P. exaratus (Trin.) P.M. Peterson, Soreng & Romasch.; P. polypogonoides (Stapf) P.M. Peterson, Soreng & Romasch.; and P. reuteri (Boiss.) P.M. Peterson, Soreng & Romasch. We designate lectotypes for the names Agrostis sect. Aristatae Willd., Agrostis barbuligera Stapf, A. bourgaei E. Fourn., A. eriantha Hack., A. exarata Trin., A. lachnantha Nees, A. polypogonoides Stapf, Chaetotropis chilensis Kunth, Polypogon elongatus Kunth, P. inaequalis Trin., P. suspicatus Willd., and Vilfa muricata J. Presl.

Speciation events often occur with adaptive radiation. The factors that promote these adaptive radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used the adaptive radiated genus Ligustrum to evaluate the relative contributions of the environment, species interactions, phylogenetic diversity, and diversification rates in generating extant species diversity patterns. Using complete chloroplast genome data, we reconstructed the highly supported and dated backbone phylogenetic relationships of Ligustrum. Biogeographic results indicated that Ligustrum originated in Southwest China during the Oligocene and spread to suitable areas that were warm and humid via 18 dispersal events. For the overlapping ranges of species pairs, a smaller phylogenetic distance was detected in high species overlap than in low species overlap, which is consistent with no significant difference in niche among the different species. We found that the phylogenetic diversity and interspecies competition induced by insignificant niche divergence shaped the global pattern of Ligustrum diversity.

Taihangia rupestris Yu & Li, an early spring flowering plant of the Rosaceae family, is classified as a second-level protected species in China. Endemic to the cliff faces of the Taihang Mountains in central China, this rare species requires a comprehensive understanding and conservation approach. In this study, we analyzed population-level genetic variations in both chloroplast and nuclear genomes. Taihangia rupestris var. ciliata exhibited higher genetic diversity than T. rupestris var. rupestris in both genome types. All individuals of T. rupestris var. rupestris formed a single cluster, while individuals of T. rupestris var. ciliata were grouped into three distinct clusters. Approximately 29.82 Ma, T. rupestris diverged from its closely related species. Taihangia rupestris var. ciliata appeared first, followed by the differentiation of T. rupestris var. rupestris, which adapted to the climate of the southern Taihang Mountains, around 3.55 Ma. Additionally, our study identified several chloroplast genes potentially involved in variety adaptive differentiation. These findings enhance our understanding of environmental adaptation and differentiation in the two T. rupestris varieties, providing valuable genetic insights for the conservation and utilization of this species.

Rich materials can provide more opportunities for exploring the mechanisms of speciation driven by sexual selection. Being the fastest‐evolving arthropods to date, the sword‐tailed crickets of Nudilla Gorochov, 1988 (= Laupala Otte, 1994) have rapidly diverged primarily due to the variability of their calling songs (sexual signals). In addition, they also exhibit morphological conservatism, with little variation between species. Similar circumstances can be seen in tree crickets (Oecanthinae), which have conservative morphology and a diverse range of song variations. Thus, we believe that tree crickets could serve as a model for research on sexual selection since they share a similar evolutionary history and mode of differentiation with Nudilla. However, due to the improper methods in analyzing the calling songs and nearly identical morphological features between taxa, there are many problems with the taxonomy of Oecanthinae in China. To solve these problems, we conducted an integrative taxonomic study of Chinese Oecanthinae based on comparative morphology, species delimitation, acoustical analysis, and phylogenetic analysis. This study recognized 12 Oecanthinae species in China, including four new species, and confirmed one new synonym and two misidentifications. Meanwhile, we confirmed the morphological stability of Oecanthinae, and revealed that variation in color, size, and morphology may be intraspecific polymorphism, which sometimes does not reflect the species relationships. The result indicates that the acoustic parameter freq.median can be used for efficient and accurate species delimitation in Oecanthinae. We speculate that incomplete species divergence leads to complexity in species relationships at the genetic level of Oecanthinae. The conservation of morphological characters, the interspecificity of songs and the complexity of species relationships suggest that sexual selection have played a role in the evolution of Oecanthinae. Our study resolves some systematic and taxonomic problems of Oecanthinae, clarifies the species relationships of Oecanthinae in China, and provides clues for expanding the cricket groups to be used in speciation studies.

Toona fargesii A. Chev., a versatile tree in the Toona genus of the Meliaceae family, is renowned for its exquisite timber and medicinal properties, offering promising benefits. Due to natural regeneration obstacles and long‐term excessive exploitation, it has been threatened in China. Intriguingly, root sprouting, which may diminish the genetic diversity and hinder population development, dominates the reproductive pattern of T. fargesii in the wild. However, the lack of complete genome information has hampered basic studies on the regeneration, classification, evolution and conservation of this species. Here, we report the genome of T. fargesii, which was sequenced using the PacBio platform and assembled into a high‐quality genome with a total size of 535.24 Mb. Of this, 97.93% of the assembled contigs were anchored onto 28 pseudochromosomes, achieving a chromosomelevel genome. The long terminal repeat assembly index score was 21.34, and the consensus quality value was 39.90%, indicating the accuracy and completeness of the genome. Comparative genome analysis suggested that a recent whole genome duplication event occurred between 22.1 and 50.1 Mya in the Toona genus, with the divergence time between T. fargesii and its relative T. sinensis estimated at approximately ~16.7 Mya. Additionally, 13 TfARR genes, which play integral roles in root sprouting by mediating cytokinin signaling, underwent rapid gene expansion and showed significant enrichment in the plant hormone signal transduction pathway. Furthermore, transcriptomic analysis demonstrated that differentially expressed genes between root sprouts and nonroot sprouts were significantly enriched in the zeatin biosynthesis pathway, indicating that cytokinin regulation is involved in root sprouting development. Collectively, the findings provide valuable genomic resources for the Toona genus and genetic insights into the mechanisms of root sprouting in T. fargesii.