While sex-biased gene expression and its evolutionary dynamics across taxa have been extensively investigated, systematic separate characterization of the evolutionary patterns in transcriptome divergence between male and female lineages remains underexplored. Here, we analyze a comprehensive RNA-seq data set from the house mouse complex, spanning multiple organs across subspecies and species, to delineate the evolutionary trajectories of gene expression in males and females in intra- and inter-species contrasts. For both sexes, we find specific gene expression divergence patterns across the surveyed organs, with a particularly high divergence rate at early evolutionary stages of separation. Comparative analysis between sexes demonstrates male reproductive organs, particularly the testis, displaying accelerated evolutionary rates of expression divergence. Strikingly, testicular long non-coding RNA genes show the most pronounced acceleration, with differences emerging already after a few thousand years of population separation. In contrast, somatic organs and female reproductive auxiliary tissues show no major sex-specific evolutionary dynamics. Genes with sex-biased expression substantially contribute to differentially expressed genes across evolutionary transitions, though without predominant directional bias toward either sex. Notably, these differentially expressed genes display significant over-representation on autosomes. A general functional divergence process is found between male and female transcriptomes across organs mainly driven by sex-specific differentially expressed genes. Collectively, our findings establish a new evolutionary framework for sex-specific expression divergence and provide novel insights into the role of reproductive constraints in shaping transcriptome evolution in mammals.

Body size is among the key subjects in macroecology and macroevolution with important implications for conservation. Two major rules have been proposed to explain how body size changes over evolutionary time (Cope’s rule) and across temperature gradients (Bergmann’s rule). To date, however, the applicability of both rules to global terrestrial vertebrates (tetrapod) remains elusive. Here, using the newly available data, we comparatively examined the temporal variation in species body size of the world’s extant tetrapod species (tetrapoda as a whole) and of each class, amphibians (Amphibia), reptiles (Reptilia), mammals (Mammalia), and birds (Aves), through the Cenozoic Era. When all four classes were considered together, the species’ body size had increased over time and was negatively correlated with global surface temperature. However, separate analyses on each of the four classes showed that reptiles and mammals tended to support Cope’s rule while birds and amphibians did not. Also, we found no clear difference in temporal body size variation between endothermic and ectothermic species. Overall, the support for Bergmann’s rule was much stronger than that for Cope’s rule. Future research using more complete and compatible body size data from fossils is needed to better understand how species’ body size evolves over time and across space.

Chimonocalamus is distinguished by pachymorph rhizome, lower culm nodes with a ring of root thorns, and semelauctant inflorescence. However, species identification in this genus can be confused due to similar morphological features and overlapped geographical distribution. To confirm the identities of Chimonocalamus species in China, plastome and nuclear ribosomal (nrDNA) of 49 accessions of 10 known species and three putative new species were newly retrieved by genome skimming. Distance-based and tree-based methods were conducted to analyze the species discrimination rate of six datasets. The Skmer method was also applied. The results indicated that Skmer analyses had the highest discriminatory power with nine species identified (69.23%). The plastome showed much higher discriminatory success rate than the combination of three standard plastid DNA barcodes, which performed worst among the six datasets. The three potentially new species of Chimonocalamus were confirmed by the plastome and nrDNA datasets, and Skmer analysis, together with morphological differences. Herein, we describe and illustrate the three species as new to science, that is, Chimonocalamus hekouensis Y. X. Zhang, Gui L. Zhang & D. Z. Li, Chimonocalamus hsuehiorum D. Z. Li & Y. X. Zhang, and Chimonocalamus shuangjiangensis D. Z. Li & Y. X. Zhang. Moreover, the Chimonocalamus fimbriatus complex was designated, calling for further investigation. Taken together, plastome and nrDNA could serve as effective super-barcodes for species discrimination of Chimonocalamus, playing important roles in recognition of cryptic new species, and Skmer analysis can be adopted in molecular identification. Our study provides an empirical case for molecular discrimination of bamboos and can be meaningful for other plant groups.

Oxidative stress, triggered by hypoxia during repetitive diving, represents a notable environmental adaptation of marine mammals. Glutathione (GSH) is a widely acknowledged antioxidant that protects crucial cellular elements from damage by reactive oxygen species (ROS). Nevertheless, the role of the glutathione metabolism pathway in shaping the adaptation to oxidative stress in marine mammals is not fully elucidated. In this study, we conducted evolutionary analyses on 37 genes related to the GSH metabolism pathway in marine and terrestrial mammals. We found that in comparison with their terrestrial relatives, marine mammals showed convergently accelerated evolution on the core modules of GSH metabolism. Specifically, we identified a total of 16 genes with significant evolution signals unique to marine mammals, and several genes (e.g., accelerated evolution genes: RRM1 and SMS, positively selected genes: ANPEP and GCLC) were shared in marine mammal lineages. Eight genes were discovered to possess specific amino acid modifications that are common among all marine mammals. Functional assays of marine mammal GCLC showed a downregulation of HIF-1α and enhanced GSH levels under hypoxic conditions, suggesting heightened protection of marine mammals against oxidative stress induced by hypoxia. Our study identified key genes with significant evolutionary signals in marine mammals, providing genomic and functional support for convergent hypoxia adaptation mechanisms within this taxon.

Understanding the genetic diversity and genetic load of endangered species is essential for developing effective conservation strategies, particularly in ecologically sensitive regions such as the Himalayas. Cupressus austrotibetica, a rare conifer and the tallest recorded tree in Asia, reaching up to 102.3 m, faces substantial anthropogenic and environmental threats. To evaluate its genetic status, we sequenced transcriptomes of 54 individuals sampled across its restricted range and compared them with 96 individuals of C. gigantea, a closely related endangered species with broader distribution at higher elevations. Our analysis reveals that C. austrotibetica exhibits higher genetic diversity (π = 0.0091) compared to C. gigantea (π = 0.0042). Demographic analyses identified three historical bottleneck events in C. austrotibetica and two in C. gigantea, with two of these events coinciding with Quaternary climatic oscillations. Despite its relatively high genetic diversity, C. austrotibetica has a smaller effective population size based on Stairway Plot 2 (N_e ≈ 7200) than C. gigantea (N_e ≈ 17 600). Furthermore, C. austrotibetica harbors a higher proportion of severe deleterious mutations, while C. gigantea retains more moderate deleterious variants. These findings indicate that a recent anthropogenic bottleneck event has likely driven the reduced population size and increased genetic load in C. austrotibetica, emphasizing the urgent need for conservation priorities for this imperiled species.

Weasels represent the most widely distributed and diverse lineage within the family Mustelidae. They have experienced adaptive radiation and have long been the subject of significant taxonomic debates. This study undertakes a comprehensive study of this group, employing morphological measurements, mitochondrial genomes, nuclear genes, and single copy orthologs extracted from whole genome data. Based on the outcomes of phylogenetic tree construction using orthologous genes, it is ultimately verified that the genera Mustela and Neogale are independent genera, thereby resolving the controversy regarding the species they encompass. Through molecular systematics and morphological studies, a putative Mustela species collected from Mabian Dafengding National Nature Reserve in Sichuan is confirmed as a new species, designated Mustela mopbie sp. nov. This new species exhibits molecular phylogenetic affinity with M. altaica and M. nivalis, yet shares morphological similarities with M. kathiah, M. nivalis and M. aistoodonnivalis. Notably, it is considerably smaller than these species and possesses distinctive body coloration and tail morphology. This study provides a detailed description of this new species and demonstrates that larger datasets yield more robust phylogenetic signal. Furthermore, we observed substantial incongruence between mitochondrial and nuclear gene trees, suggesting potential genomic introgression between this new species and its closely related congeners (M. altaica and M. nivalis).

Sex ratio plays a critical role in population survival. Dioecious plants may simultaneously display sexual dimorphism and deviations from the equilibrium expectation of 1:1 sex ratio in populations, that is, biased sex ratio. However, whether biased sex ratios can be attributed to sexual dimorphism has not been well investigated. Here, we conducted experiments using a three-water-depth gradient to examine sexual dimorphism performance and population sex ratios for Vallisneria natans, and investigated the variations in natural population sex ratios for it and two other congeners V. spinulosa and V. denseserrulata along water depth changes. Females of V. natans had higher reproductive investment than males, and the degree of sexual dimorphism increased with increasing water depth. At greater water depths, increased reproductive expenditure led to higher mortality in females, resulting in a male-biased sex ratio. The sex ratios of natural V. natans and V. spinulosa populations did not significantly deviate from 1:1. In contrast, populations of V. denseserrulata exhibited markedly a female-biased sex ratio, which may be attributed to female plants producing more clonal ramets. Furthermore, no evidence was found for variation in sex ratios along water depth gradients in natural populations of any of the three species. These findings highlight the plasticity both of sexual dimorphism and sex ratios in dioecious plants, indicating that sex ratios are species-specific and depend on sex-specific life-history strategy shaped by their growth environments.

The peppered moth Biston betularia L., widely distributed across the Northern Hemisphere, represents an ideal organism for exploring phylogeographic patterns and evolutionary history. In this study, we integrated molecular, morphological, and distributional data of this species to reconstruct its phylogenetic relationships, estimate divergence times, infer the geographic origin, and trace dispersal routes. Molecular analyses identified six monophyletic lineages (HM, NC, HD, E, NA I, and NA II). With the exception of the sympatric North American lineages NA I and NA II, the remaining lineages exhibit allopatric distributions across Eurasia. Ancestral area reconstruction and approximate Bayesian computation (ABC) analyses supported a southern Xizang origin within the Himalayan Mountains, consistent with the “Xizang-origin hypothesis.” The colonization of North America occurred twice via the Bering Land Bridge during the Pleistocene glaciation. Collectively, the current genetic pattern is best explained by gradual allopatric differentiation following long-distance dispersal and subsequent isolation. Furthermore, we reconstructed the global dispersal history of B. betularia. These results indicated that in situ speciation within the Himalaya may be more common than previously recognized, challenging the notion that Himalayan fauna are predominantly considered “immigrant.” This study enhances our understanding of Himalayan zoogeography and biodiversity through the resolved evolutionary history of a widely distributed species.

The genus Magnolia belongs to Magnoliaceae, an early diverging lineage of the Magnoliales, and is cultivated globally for its high ornamental and commercial values. As a large genus in the family Magnoliaceae, Magnolia species are regarded as highly valuable in phylogenetic and conservation biological studies. However, the whole genome data of Magnolia is still relatively insufficient. Here, we present a high-quality, chromosome-level genome sequence of Magnolia sinostellata (1.86 Gb) with a scaffold N50 of 85.33 Mb. The 19 M. sinostellata genome chromosomes revealed 11 main duplications representing the subgenome. Comparative genomics analysis revealed that the variance in the number of abiotic stress resistance genes among Magnoliid species are related to different environmental adaptations. Most of the genes related to MAPK signaling and stress resistance pathways in the investigated M. sinostellata species are expanded, compared to the other species. Furthermore, the comparative genomics analysis of three Magnolia assemblies, M. sinostellata, Magnolia biondii, and Magnolia sieboldii revealed that large inversions were enriched in terpenoid metabolic pathways, stress resistance and flavonoid biosynthesis, and DNA replication proteins. Using transcriptome sequencing data, we analyzed the expression levels of genes related to terpenoid biosynthesis (terpene synthase) and ICE–CBF–COR gene models related to cold tolerance in various tissues and the buds under different temperature conditions. The high-quality assembly of M. sinostellata and the ICE–CBF–COR bioinformatic analysis cascade provide valuable resources for studying the phylogeny and evolution of Magnoliaceae and angiosperms, while the candidate genes will provide foundational support for molecular breeding in Magnolia species.

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.

Pseudoscorpiones are a group of small-sized 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 pseudoscorpions 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. & 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.

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 the 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) analysis of results. 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 levels, 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 data set included seven 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 data set 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 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 insight into its ecological adaptation, particularly in saline–alkali tolerance, and growth-promoting potential for sustainable agriculture.

Meiogyne is a genus of shrubs, 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 data set generated a well-resolved and well-supported phylogeny. Estimation of divergence time utilized two fossil calibrations and an uncorrelated log-normal relaxed clock model. Trait-dependent and trait-independent biogeographical models in BioGeoBEARS were compared using corrected Akaike information criterion weight and the 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 colonization 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 colors. Bird dispersal and the associated traits (narrow monocarp width) may have driven macroevolutionary dispersal for Meiogyne in Australasia–Pacific.

A new species, Sinocurvicubitus haotianus Xu, Shih, Ren & 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 resolved phylogenetic relationships within the superfamily as ((Ignotalidae + Pereboriidae*) + Curvicubitidae) and validated the exclusion of Scytophara extensa from Pereboriidae. Additionally, we estimated divergence times across Pereborioidea lineages, reconstructed ancestral distribution ranges, and elucidated the origin centers and dispersal routes for Curvicubitidae. Wing eyespots and bands suggested predator mimicry, a novel defense strategy in Permian insects.

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 internal transcribed spacer (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 C. 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.

The unique geomorphology of rivers in the eastern Himalaya has long intrigued geologists, yet their drainage history remains debated. Drainage reorganization can have a significant impact on genetic differentiation in freshwater taxa. This study employs the cold-adapted fish genus Schizothorax as a biogeographic proxy to reconstruct the evolutionary history of the Yarlung Tsangpo–Brahmaputra River (YTB), with a focus on a prominent hanging valley tributary-trunk stream system. Phylogeographic analyses of mitochondrial cyt b gene sequences identified a monophyletic QTP–YGP clade comprising species from the Qinghai–Tibet Plateau (QTP) and the Yunnan–Guizhou Plateau (YGP). Within the QTP–YGP lineage, YTB species represent the earliest diverging clade. In contrast, species from the Indus and Ganges basins are more closely related to congeners from the southeastern QTP and YGP. The YTB assemblage is further subdivided into two distinct clades. Molecular dating suggests that the YTB lineage diverged from the broader QTP–YGP group during the early Late Miocene, with the two YTB clades separating in the Late Miocene. We propose that a paleo-Yarlung Tsangpo–Dingba (Dibang)–Brahmaputra river and a Yigong–Parlung–Zayul (Lohit) river were established prior to the Late Miocene and were subsequently captured by the lower Yarlung Tsangpo River—via the Siang and Zhaqu, respectively—during the late Miocene and Quaternary. The modern YTB drainage configuration was established by the late Early Pleistocene. This study underscores the importance of integrating genetic, fauna and geomorphological data to understand the complex evolution of drainages in the eastern Himalayas.

The Hindu Kush Himalayan (HKH) region sustains the headwaters of major Asian rivers and harbors unique alpine biodiversity, and yet, it is highly sensitive to climate change. Biodiversity organization and community assembly processes across trophic levels within its river ecosystems remain poorly understood. Here, we used multi-marker environmental DNA (eDNA) metabarcoding targeting four biological groups (cyanobacteria, diatoms, invertebrates, and vertebrates) to assess multi-trophic biodiversity patterns in two alpine rivers of the region: the Yellow River source region (YR) and the middle–upper Nujiang River (NJ). These two systems differ markedly in geography, hydroclimate, vegetation, and human disturbance intensity. We identified 1695 operational taxonomic units and revealed pronounced differences in biodiversity pattern and community composition between rivers. Phototrophs and invertebrates showed higher α diversity in NJ, whereas vertebrates were richer in YR. β diversity was mainly driven by species turnover in both rivers, with a stronger distance–decay pattern in YR. Correlations between environmental variables and α and β diversity varied across groups and rivers, with geographic and climatic factors exerting stronger effects in NJ. iCAMP and pNST analyses revealed that stochastic processes dominated community assembly in both rivers, whereas deterministic processes were relatively stronger in YR compared to NJ. Accordingly, co-occurrence networks revealed cohesive communities in YR but more modular ones in NJ, indicating contrasting ecological stability regimes. Overall, our study provides an integrated, multi-trophic perspective on how environmental gradients shape riverine biodiversity and ecological interactions, informing adaptive conservation strategies under accelerating environmental change in the HKH region.

East Asia's largest inland arid ecological region—the Tarim Basin and Hexi Corridor—serves as an independent evolutionary center for highland ichthyofauna. However, systematic studies on the evolutionary patterns of fishes in this region remain limited. In this study, we integrated mitochondrial cytochrome b (Cyt b) and nuclear SNP data to investigate the demographic structure and historical dynamics of three desert fish species: Triplophysa tenuis, Triplophysa bombifrons, and Hedinichthys yarkandensis. Our results indicate that populations in the Hexi Corridor and Tarim Basin diverged approximately 0.8 million years ago (Ma), coinciding with a period of increasing aridity, followed by alternating phases of population contraction and secondary contact. Demographic fluctuations were likely driven by westerly atmospheric circulation interacting with regional geological activity. Furthermore, this study provides evidence for the existence of an ancient South Tarim River and suggests the need for taxonomic re-evaluation of T. bombifrons. These findings offer critical insights into the evolutionary processes shaping fish diversity in arid regions of China and inform strategies for their conservation.

Aquatic angiosperms represent an important but underexplored lineage for understanding genome evolution, particularly in species with exceptionally large genomes. Here, we present a chromosome-scale genome assembly of the endangered aquatic monocot Ottelia songmingensis (~10.8 Gb), providing a valuable genomic resource for studying genome gigantism and conservation. Using ONT and Hi-C technologies, we anchored 87.7% of the assembly to 11 pseudochromosomes and predicted 35362 protein-coding genes. Comparative genomics revealed two whole-genome duplication events, including a more recent duplication and an ancestral triplication shared within Alismatidae. Repetitive elements constitute 94.3% of the genome, with long terminal repeat retrotransposons alone accounting for over 90%. A recent burst of LTR activity (~6 Mya) combined with a low solo-to-intact ratio (0.61) suggests inefficient transposon removal as a driver of genome expansion. Whole-genome bisulfite sequencing showed globally high DNA methylation levels (CG ~ 85%, CHG ~ 78%), particularly enriched in transposable element-rich regions, highlighting the role of epigenetic regulation in stabilizing large genomes. Population resequencing further indicated extremely low nucleotide diversity (π = 5.31 × 10⁻⁴) and a long-term decline in effective population size since the Middle Pleistocene. Together, these resources provide a genomic foundation for exploring the evolutionary forces underlying genome gigantism and for guiding conservation genomics in endangered aquatic plants.

Cavefishes display pronounced troglomorphic adaptations, such as visual degeneration, depigmentation, and scale reduction, as specialized responses to subterranean environments. Among these, the cave loaches (CLS) of the family Nemacheilidae represent China′s second most diverse cavefish group; however, their evolutionary history remains poorly understood. To bridge this knowledge gap, we conducted whole-genome resequencing of 62 CLS species and two closely related taxa, complementing these data with published genomic resources. The reconstructed phylogeny identified ancient introgression as the primary driving force behind phylogenetic discordance, with incomplete lineage sorting as a secondary contributor. Pleistocene climatic fluctuations, coupled with species-specific genetic architectures, generated four distinct demographic trajectories across populations. Additionally, we delineated four distinct phases of lineage diversification in CLS, shaped by tectonic–climatic interactions, with alternating periods of acceleration and decline synchronized with the Asian orogenic and monsoonal cycles. This study provides the first integrated genomic perspective on the evolution of the CLS, demonstrating how biotic and abiotic factors have collectively shaped subterranean biodiversity.

Magnoliaceae, a typical boreotropical relict lineage, shows striking species richness in tropical regions, making it an important model for testing the time-for-speciation and diversification rate hypotheses for present-day diversity patterns. Here, we reconstructed a time-calibrated phylogeny using plastomes from 123 species, representing Liriodendron and all 15 sections of Magnolia, and investigated its colonization and diversification history. Our results reveal that Magnoliaceae likely experienced peak extinction during the mid-Eocene, accompanied by a range contraction from high latitudes to the amphi-Pacific tropics, followed by the rise of tropical clades with rapid diversification. Phylogenetic generalized least squares analysis demonstrates that diversification rate explains clade-level diversity variation more strongly than time for speciation. Tropical regions, such as South America and Southeast Asia, with high Magnoliaceae diversity consistently show elevated diversification rates and shorter time for speciation. These results indicate that higher diversification rate, rather than longer time for speciation, explains the high diversity of Magnoliaceae in tropical clades and regions. Our findings not only shed light on the evolutionary history of Magnoliaceae but also provide important insights into the broader processes that shape tropical biodiversity.

Sexual dimorphism in dioecious plants is common in reproductive tissues. Genes expressed in these tissues often show sex bias and differ between sexes in their protein evolutionary rates. At the same time, sex-linked genes often balance their expression levels between sexes through dosage compensation. We compared gene expression between males and females in floral and leaf tissues of eight dioecious Salicaceae species whose sex chromosomes are young to understand the level of conservation and diversity of genes with sex-biased expression. Our results revealed that sexually dimorphic gene expression showed large numbers of differences among these species, with only 6% of the genes remaining conserved, showing a consistent sex-biased direction in at least seven species. Protein evolutionary rates depended on their degree of conservation and the direction of sex bias in expression. Non-core sex-biased genes showed elevated evolutionary rates and core male-biased genes showed higher nonsynonymous and synonymous substitutions than unbiased genes. Detailed studies in three willow species revealed that the expression dosage of most sex-linked genes was partially (0.5 < X_male/XX_female < 1) or excessively (Z_female/ZZ_male > 1) compensated through reducing gene expression in the homogametic sex. Our results provide novel insights into how sexually dimorphic gene expression evolves during repeated turnovers of sex chromosomes in plants and confirm that dosage compensation mechanisms evolve relatively early in the development of sex chromosomes.

Chenopodiaceae s.s. (Amaranthaceae s.l.) contains the largest number of C₄ species among eudicots. Despite this, plastome evolution within this family has been investigated in only a few species. Here, we analyzed 119 plastomes from 115 species, including 78 newly sequenced plastomes, representing all subfamilies and most C₄ lineages of Chenopodiaceae s.s. Plastome structural variants, rearrangements, and codon usage bias were compared across subfamilies and photosynthetic types. Multiple phylogenetic approaches were employed to reconstruct the evolutionary relationships within Chenopodiaceae s.s., and Bayesian divergence time estimation was performed. Various Mk models for discrete character evolution were tested to investigate the evolution of C₄ photosynthesis, and stochastic character mapping simulations were used to reconstruct shifts in photosynthetic pathways through time. Several plastome structural variants and rearrangements were identified, but associations with photosynthetic types were observed only in the subfamily Suaedoideae. Codon usage bias analysis revealed significant bias exclusively in C₄ species, suggesting enhanced translational efficiency and accuracy as an adaptation to environmental conditions. We inferred multiple independent origins of the C₄ pathway, with the oldest lineages—Bienertia (Suaedoideae) and Caroxyleae (Salsoloideae)—dating to approximately 34 and 32 million years ago (Ma), respectively, during the Oligocene. A marked increase in the number of C₄ lineages occurred between 20 and 15 Ma. Declining atmospheric CO₂ concentrations, combined with genetic, ecological, and environmental factors, likely promoted the expansion of C₄ photosynthesis until recently. Finally, we identified five new hypervariable regions that will be valuable for phylogenetic and DNA barcoding applications in Chenopodiaceae s.s.

Liverworts, with approximately 7300 species worldwide, exhibit remarkable morphological diversity in terms of growth form, ontogeny, and architecture. Their mitochondrial genome exhibits lower average substitution rates compared to their nuclear and plastid genomes, and shows less structural variation, suggesting its suitability for inferring relationships at higher taxonomic levels. In this study, we substantially expanded mitochondrial sampling in liverworts by adding complete mitochondrial gene sets from 97 species across 25 families, thereby increasing family-level coverage to 71%. Among these, we newly assembled 23 complete mitochondrial genomes. Although four species with structural variants were newly identified, the overall architecture of liverwort mitochondrial genomes remains highly conserved, with taxa that diverged over 470 million years ago still having collinearity. Phylogenetic inferences from mitochondrial genome sequences confirmed the monophyly of most suprafamilial taxa, with the exceptions of Porellales, Ptilidiales, and Pelliidae. Herzogianthus (Ptilidiales) was well-supported as a sister group to Jungermanniales sensu lato, rather than forming a monophyletic lineage with Ptilidium (Ptilidiales). This work provides an important resource for future genetic and phylogenetic studies of liverworts.

Conifers have about 670 species worldwide but are one of the ecologically and economically most important plant groups. Their current distributions resulted from the interplay of speciation, dispersal, and extinction, with some major clades restricted to the Northern Hemisphere, whereas others are restricted to the Southern Hemisphere. Here, we explore global geographic patterns of mean diversification rate (MDR), representing recent speciation dynamics, within genera of conifers, and relate MDR to regional species richness and climatic conditions. We find that MDR is negatively correlated with species richness and latitude at a global scale; that latitudinal patterns and relationships of MDR to climatic factors differ between the Northern and Southern Hemispheres; that MDR is correlated positively with mean annual temperature and negatively with annual precipitation; that temperature-related variables explain less variation in MDR than precipitation-related variables in the Northern Hemisphere but more variation in the Southern Hemisphere; and that climate extreme variables explain more variation in MDR than climate seasonality variables. These patterns differ in many important aspects from those seen in angiosperms. We hypothesize that small land surface area and the associated paucity of broadly fragmented habitats may limit speciation in the wind-dispersed conifers, which requires broad spatial separation between diverging populations. Furthermore, conifer diversification peaks in arid habitats, probably related to numerous anatomical, physiological, and life strategy traits. Such differences between conifers and other major groups of land plants allow us to infer generalities of how geographic and climatic drivers and life history traits interact to determine the diversification dynamics of plants.

Dalbergia (Leguminosae) is a pantropical genus that serves as an ideal system for studying pantropical biogeography and diversification. However, limited taxon sampling and molecular data have hindered the resolution of intrageneric relationships and understanding of its evolutionary history. Here, we reconstruct a densely sampled phylogeny of Dalbergia based on hybrid capture of 89 low-copy nuclear loci, including 98 species spanning all major biogeographic regions and most previously recognized taxonomic clades. Phylogenetic analyses using concatenated and coalescent approaches support the monophyly of Dalbergia and consistently identify six major clades, including a distinct and newly identified Africa-Madagascar lineage (clade E) with potential taxonomic significance. Our results propose merging two of its sections, sect. Dalbergia and sect. Selenolobium, and expanding sect. Ecastaphyllum to include some African species. Topological incongruences observed between concatenated and coalescent trees, together with the high gene tree conflict at certain nodes, are consistent with localized effects of hybridization and/or incomplete lineage sorting. Divergence dating and model-based biogeographic analyses support a Neotropical origin of Dalbergia in the middle Eocene (~39 Ma), followed by repeated long-distance dispersal events from Africa to Asia, Neotropics, and Madagascar, and back into the Neotropics. An early diversification burst in Africa during the late Oligocene–early Miocene (~27–18 Ma) preceded the genus′s intercontinental expansion. Diversification rates were high across all four regions, with Madagascar showing the highest speciation rate. These macroevolutionary dynamics coincided with Eocene–Miocene climatic changes and habit shifts. This study provides a robust phylogenetic framework for Dalbergia, refines its temporal and biogeographic history, and illustrates how dispersal, climatic change, and lineage-specific diversification have interacted to generate pantropical biodiversity.