Globally, the phylum Acidobacteriota is both extraordinarily widespread and abundant, playing indispensable roles in carbon, sulfur, and nutrient cycling. However, our comprehension is marked by a significant culture-based bias. Many of the newly reconstructed metagenome-assembled genomes (MAGs) represent uncultured lineages that remain substantially understudied, highlighting this gap. Concurrently, research on Acidobacteriota has been predominantly focused on soil environments, with a scarcity of studies in other environments. Here, we bridged this gap by compiling a genomic catalog of 4317 genomes. Protein content analysis, in conjunction with large-scale metabolic reconstructions, delineates seven genomic clusters of Acidobacteriota with unique metabolic profiles. Clusters 1 and 2 are soil-preferring, and clusters 3, 4, and 6 from various environments show diverse energy metabolism, including aerobic, facultatively anaerobic, anaerobic, and fermentative processes, and utilize a wide range of carbon substrates. Conversely, aquatic-preferring cluster 5 and cluster 7, derived from various environments, are strictly anaerobic, relying on nitrate/nitrite reduction or fermentation; also, cluster 5 has a limited carbon utilization range. Our analyses have also identified previously unrecognized roles in C1 metabolic pathways, the Calvin cycle, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification among the uncultured Acidobacteriota, indicating that Acidobacteriota represent overlooked important functions involved in methylotrophy, CO oxidation, carbon fixation, and nitrogen cycling. These findings provide new insights into the metabolic diversity of Acidobacteriota, emphasizing their functional importance across diverse taxa and environments, and significantly expanding our understanding of these dominant, yet understudied bacteria.

Crataegus L. (hawthorns) is a taxonomically challenging genus within the Rosaceae family, showing extensive morphological variation, frequent hybridization, and polyploidy. In China, about 18 species are currently recognized, but their subgeneric classification and species boundaries remain unresolved. To clarify these relationships, we analyzed 481 nuclear genes, 73 plastid coding sequences, and a comprehensive plastome dataset for 17 Chinese Crataegus species. Phylogenomic analyses of both nuclear and plastid data yielded well-supported trees that refine the taxonomy and elucidate evolutionary relationships within the genus. All Chinese species are resolved within two subgenera, Crataegus subg. Crataegus and Crataegus subg. Sanguineae, although most currently recognized species are not monophyletic, reflecting complex reticulate evolution involving hybridization and polyploidy. Integrating phylogenomic, morphological, and cytological evidence, we provide an updated taxonomic synopsis of Chinese Crataegus, describe one new species, propose five new combinations, and designate 31 lectotypes. This study establishes a robust framework for future systematic, conservation, and horticultural research on this ecologically and economically important lineage.

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.

The green odorous frog (Odorrana margaretae) represents an excellent model system for investigating the genetic basis of anuran skin secretions. Here, we report a chromosome-level genome assembly comprising 13 chromosomes with a total size of 6.20 Gb. Within this large genome, approximately 4.78 Gb (77.01%) consists of repetitive elements, with evidence of recent rapid expansions of DNA transposons and long terminal repeats (LTRs). Comparative gene family analyses identified 154 significantly expanded gene families in the green odorous frog, predominantly associated with innate immune functions. Targeted data mining revealed a diverse repertoire of antimicrobial peptides (AMPs), characterized by a massive expansion of histone-derived AMP copies organized into large tandem clusters. Additionally, the genome harbors an extensive array of olfaction-related genes, including 1035 functional olfactory receptor (OR) genes, with notable expansions in the α and γ subfamilies responsible for detecting airborne odors; transposable elements (TEs) are significantly enriched in the flanking regions of these OR genes. The species also shows a signature of tandem duplication in trace amine-associated receptor 2 (TAAR2) genes. Collectively, these findings suggest enhanced capabilities in odor detection and chemical communication, likely linked to its skin secretions. This high-quality reference genome provides a foundation for future studies on the genetic regulation of potent skin secretions in this species and other amphibians.

Orostachys is a small genus in the family Crassulaceae with about 16 species, the majority of which are biennial herbs. The taxonomic boundaries and phylogenetic relationships between Orostachys and its allied genera have been controversial, partly because of the absence of a robust phylogenetic framework. In the present study, we collected 30 samples, representing 27 species of Orostachys and related taxa. Using Hyb-seq and genome skimming methods, we obtained 750 single-copy orthologous nuclear genes and all plastid protein-coding genes. Both nuclear and plastid phylogenies revealed the polyphyly of Orostachys s.l., comprising three independent lineages corresponding to Kungia (=O. sect. Schoenlandia), the O. spinosa clade (=O. subsect. Appendiculatae), and the O. malacophylla clade (=O. subsect. Orostachys). These lineages each formed sister relationships with their respective allied taxa: Kungia with Sinocrassula, the O. malacophylla clade with Hylotelephium, and the O. spinosa clade with Meterostachys. Minimal gene flow was detected among the three lineages, and between each lineage and its sister group, indicating well-established reproductive isolation. Morphological character analyses corroborated these phylogenomic findings. Our results (i) support Fu′s taxonomic treatment of O. sect. Schoenlandia as the independent genus Kungia; (ii) do not support merging O. subsect. Orostachys (=the O. malacophylla clade) with Hylotelephium; and (iii) suggest that O. subsect. Orostachys should be taxonomically recognized as a new genus Amblystachys and make the relevant new combinations.

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.

The tribe Euphorbieae, the most species-rich lineage within the Euphorbiaceae family, comprises five genera across three subtribes (Anthosteminae, Neoguillauminiinae, and Euphorbiinae), with over 2000 species, predominantly in Euphorbia. While ecologically significant globally, critical gaps persist in resolving the species-level phylogeny of Euphorbieae and elucidating the biogeographic drivers of its global distribution. Among the total of 34 sampled species in Euphoroideae, 28 species were applied to represent all five genera in three subtribes of Euphorbieae, including 10 newly sequenced species representing 10 of the 11 extant species of Anthosteminae and Neoguillauminiinae, plus 18 representative Euphorbia (Euphorbiinae) species. Using plastome and nuclear ribosomal DNA (nrDNA) data sets, we reconstructed phylogenetic relationships, estimated the divergence times inferred ancestral areas, and analyzed diversification patterns. Our results strongly support Euphorbieae's monophyly and clarify sister relationships among subtribes. We present the first resolved species-level phylogeny for Euphorbieae (excluding the gigantic genus Euphorbia), revealing the tribe's evolutionary timeline, with instances of nuclear–plastid discordance suggestive of hybridization or incomplete lineage sorting. The crown age of Euphorbieae dates to approximately 62.11 million years ago (Ma) in the early Paleocene. Biogeographic analyses reveal the African origin at early Paleocene, followed by major dispersal events to Australasia, Asia, and the Neotropics. The combined plastome–nrDNA approach significantly enhanced phylogenetic resolution. These findings provide crucial insights into Euphorbieae's global “out of Africa” distribution pattern and contribute toward understanding the role of key innovations and climatic shifts in plant diversification.

Heliopora (subclass Octocorallia, order Scleralcyonacea, family Helioporidae), commonly known as the “blue coral,” represents the only reef-building lineage within Octocorallia. The genus shows diverse growth forms of branching, encrusting, and laminar types, which leads to ambiguities in traditional morphology-based taxonomy. Here, we investigated the diversity of Heliopora species in the South China Sea (SCS) and their phylogenetic relationships across the Indo–Pacific using integrated morphological and phylogenomic approaches. Whole-genome resequencing of 52 colonies from the SCS islands, combined with published data from 244 samples worldwide, revealed three distinct clades: H. coerulea, H. hiberniana, and a previously undescribed lineage. Morphological analyses characterized the new lineage with a blue skeleton, a short columnar to encrusting growth form, large autopores with 12–15 pseudosepta, absence of worm tubes, and elaborated coenchymal echinulations. These features contrast with the long-branching to lobate H. coerulea and the white-skeletoned H. hiberniana. Based on its unique morphology and distinct phylogenetic position, we describe this lineage as a new species: Heliopora chinensis sp. nov. It is distributed mainly in the SCS islands, Taiwan of China, and the Ryukyu Islands. Meanwhile, global research and citizen science records suggest that H. hiberniana is restricted to the lower latitudes of Indo–Pacific Ocean, whereas H. coerulea occurs broadly across the Indo–Pacific. Our findings highlight the effectiveness of integrating phylogenomics and morphology to resolve coral systematics, uncover cryptic species diversity, and provide new insights into speciation, diversification, and conservation of corals, thus providing a critical taxonomic basis for informing future conservation strategies for coral reef ecosystems.

Glaciers in High Mountain Asia, despite their vast extent, harbor poorly understood biodiversity compared to other mountain ranges. This study describes a new species of springtail, Desoria passui sp. n., and reports chironomid found as larva from the Passu Glacier in the Pakistani Karakoram. Phylogenetic analyses reveal that D. passui sp. n. is genetically distinct from known cryophilic springtails in European mountain ranges, indicating a local evolutionary lineage. Similarly, the chironomid larvae represent a potentially undescribed species within Metriocnemus that does not form a sister group but is instead affiliated also with other barcoded Eurasian species associated with glacial habitats. These findings suggest that the cryophilic arthropod diversity of the Karakoram remains largely undocumented and their evolutionary history is independent of other known mountain cryophilic species. Given the ongoing glacier retreat, documenting and understanding this hidden biodiversity are critical for informing conservation strategies and assessing ecosystem responses to climate change.

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.

The distribution patterns of plants in the Northern Hemisphere are closely linked to their evolutionary history. The genus Lonicera, commonly referred to as honeysuckle, is widely distributed across the northern temperate zone, making it an ideal model for exploring the distribution patterns and driving factors of plants in the Northern Hemisphere. This study, based on 108 globally distributed Lonicera samples (57 species), covered 22 of the 25 subsections of Lonicera recognized by Rehder (1903) and Nakai (1938), analyzed 485 orthologous loci and plastid genomes to investigate phylogenetic relationships, and observed phylogenetic incongruence. QuIBL and f-branch analyses revealed that incomplete lineage sorting (ILS) is the primary driver of phylogenetic discordance, accompanied by widespread but weak introgression, with only a small proportion of triplets showing strong support for introgression with relatively high mixture weights. Biogeographic and diversity distribution analyses suggest that Lonicera originated in the Qinghai–Xizang Plateau (QXP) and/or East Asia, spread to North America and Europe, and established diversity centers in East Asia, Central Europe, and western North America. Our results support the hypothesis that the uplift of the QXP and global climate shift of the Eocene–Oligocene transition (EOT) were both evolutionary drivers, with varied ecological adaptability among various Lonicera lineages. This study provides new insights into the phylogeny and biogeographic evolution of Lonicera, while also serving as a reference for studies on the evolutionary history of plant and animal lineages.

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.

Pollinators are key drivers of floral evolution and diversification. While floral traits often converge in response to shared pollinators, they may diverge following pollinator shifts. Here, we examine the evolution of floral traits in Brandisia, a hemiparasitic genus endemic to East and Southeast Asia that shows notable interspecific variation. We combined field observations, a literature survey of pollination systems across Orobanchaceae, measurements of 14 floral traits, and phylogenetically informed comparative analyses. Our results show that Brandisia species are primarily bird-pollinated, probably derived from the bee-pollinated condition predominant in Orobanchaceae. Their flowers show typical bird-pollination traits, including tubular corollas, exserted reproductive organs, and abundant dilute nectar. Several traits may also function to avoid antagonists through visual (e.g., red coloration inconspicuous to bees), morphological (e.g., reduced or recurved corolla lobes), or physiological (e.g., dilute nectar) barriers. Ancestral state reconstruction indicates that the common ancestor of Brandisia had moderately specialized floral traits, including solitary axillary flowers, orange-yellow coloration, short tubular corollas, and hexose-dominated nectar. From this ancestral condition, both more specialized and more generalized phenotypes evolved, involving 11 shifts across eight traits. Together, our findings indicate that Brandisia is predominantly bird-pollinated in the Asian flora. Rather than resulting from major pollinator shifts, floral trait variation in Brandisia reflects a continuum of adaptation to bird pollinators, potentially shaped by fine-scale niche partitioning. Some floral traits may also have evolved under additional selective pressures, such as avoiding bees. This study advances understanding of how bird pollinators shape floral diversification in angiosperm.

Taxonomic diversity (TD) and phylogenetic diversity (PD) are two important metrics of biodiversity, but they are often mismatched in many areas across the world. This geographic mismatch, typically identified through assessment of relative phylogenetic diversity (RPD), is associated with climatic conditions and is critical not only to understanding the origin and maintenance of biodiversity but also conservation planning. Here, using a comprehensive data set of butterflies across the world, we explore geographic patterns of RPD and its relationships with climatic factors. Butterfly species assemblages used in this study are species in 12 407 grid cells across the world. We use two different metrics to measure RPD: one directly relating PD to TD (PD_dev) and the other exploring variation on phylogenetic branch length (Mishler's RPD). We find that RPD is higher in humid subtropical and tropical regions, where butterflies originated and maintain many distinct phylogenetic lineages, and is lower in temperate and arid tropical regions as well as in geologically young mountains, where there are fewer major phylogenetic lineages and where regional radiations form clusters of closely related species. The patterns of PDdev and Mishler's RPD are largely similar, but PD_dev is more strongly related to temperature, whereas Mishler's RPD is more strongly related to precipitation, suggesting that these metrics capture different ways in which climate influences PD. Overall, areas with higher RPD likely hold higher evolutionary potential than areas with equivalent species richness but lower RPD, so that areas of high RPD would be of particular interest for biodiversity conservation.

Dolichopetalum is a monotypic liana genus of Apocynaceae and is restricted to subtropical montane forests in Asian subtropical karst areas. In this study, we used plastome data to examine the tribal position of Dolichopetalum within the family, and four plastid and three nuclear loci to further clarify its relationship and taxonomic status. We also estimated the time of origin of Dolichopetalum and modeled its range change by estimating the potential historic and current distributions. Our family-wide phylogenetic analysis confirms that Dolichopetalum belongs to the tribe Marsdenieae. Our subsequent analyses of Marsdenieae further suggest that Dolichopetalum is a distinct genus and has a distant relationship with Marsdenia s.str., challenging the traditional viewpoint. Dolichopetalum is probably allied to Campestigma, Cionura, Harmandiella, and Gongronema-Dischidanthus-Sarcolobus, and originated at about 11 Ma and rapidly diverged with its four allies over a period of less than three million years, which might be associated with the intensified East Asian monsoon in the early Late Miocene. The distributional range of Dolichopetalum may have undergone a dramatic contraction since the Last Glacial Maximum and will likely further shrink and undergo fragmentation in the future, possibly driven by global warming and desertification in Asian subtropical karst areas. This study provides new insights into the evolutionary history of Dolichopetalum and will have important conservation implications for the unique biodiversity of Asian subtropical karst areas under climate change scenarios.

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.

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.

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.

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

Understanding the genetic basis of phenotypic diversity is fundamental to evolutionary biology and selective breeding. The White Cloud Mountain minnow (Tanichthys albonubes) is a renowned ornamental fish, yet the genomic basis of its prized ornamental traits (e.g., golden body color and long-fin) remains poorly understood. Here, we present a high-quality chromosome-level genome assembly for T. albonubes, which has a size of 1067.12 Mb with contig and scaffold N50 values of 5.65 Mb and 41.71 Mb, respectively. A total of 1036.50 Mb (97.13%) was anchored into 25 pseudo-chromosomes. The genome is highly repetitive (53.48% repetitive sequences) and encodes 24 121 protein-coding genes. Based on this reference genome and whole genome resequencing data of 126 individuals from four populations (one wild population, one native hatchery population, golden strain and long-fin strain), we revealed that the golden strain originated directly from the native hatchery stock, while the long-fin strain was derived from a distinct wild lineage. By integrating window-based pairwise F_ST scans with GWAS analysis, we demonstrated that the golden body color is a monogenic trait, with chrna2b on chromosome 15 as a prime candidate. In contrast, we found fin elongation is a polygenic trait and identified four candidate genes (mosmob, tbx18, vwa8, wnt6b) and the hedgehog signaling pathway underpinned this long-fin phenotype. Our study provides fundamental genomic resources and unveils the genetic architecture underlying two striking ornamental traits of T. albonubes, offering crucial insights for its further selective breeding and conservation.

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.

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