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 lineage. 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 dataset 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 moss, whereas genome stability leads to the accumulation of large genomes in liverworts. Results of this study confirmed the distinct trends of genomic evolution in bryophytes.

The loss of biodiversity is one of the most serious environmental issues in the Anthropocene. Understanding the extinction risk of species is essential for preemptive conservation measures, but hampered by gaps in geographical and evolutionary knowledge, especially in areas/regions that are highly diverse in species. Combined with a 21,109-taxon angiosperm mega-phylogeny and comprehensive species distribution database, we evaluated the characteristics of angiosperm extinction risk at Sino-Himalaya and the Tibetan Plateau. Overall, our results show that there is a strong interaction between evolutionary and environmental factors on extinction risk, and both contribute spatially to threat processing in Sino-Himalaya and the Tibetan Plateau. The extinction risk of angiosperms in this region is spatially and phylogenetically clustered; the clades with low species richness are significantly more vulnerable to extinction than species-rich ones; the regions with the highest extinction risk are concentrated in the mountainous areas of southwest China. Integrated with the existing Red List, we further delineated more than 3,000 potentially threatened species and proposed practical conservation priorities for four types of species in Sino-Himalaya and the Tibetan Plateau. The extinction risk of angiosperms clarified both phylogenetically and spatially aggregate characteristics, serving as an important reference for predicting extinction trends and the formulation of targeted conservation strategies.

Plant miRNAs exhibit a dynamic and complex evolutionary landscape. Despite their rapid turnover, miRNAs play crucial roles in regulating key biological processes, underscoring their functional significance even when evolutionarily transient. This review explores the phenomenon of miRNA turnover through a comprehensive survey of miRNA conservation across land plants. We discuss how de novo miRNAs overcome challenges such as transcriptional activation, structural requirements for biogenesis, and functional integration into gene regulatory networks. Furthermore, we review the mechanisms of miRNA origination, including inverted duplication of target genes, derivation from retrotransposons or DNA transposons, spontaneous evolution, and a newly proposed mechanism through template switching mutations. Duplication of existing miRNAs plays a significant role in miRNA family expansion, driving the functional diversification and strengthening regulatory networks. While the phenomenon of miRNA loss has been preliminarily explored, its mechanisms remain insufficiently understood. To address this, we proposed three detailed steps to advance research into miRNA loss. This review provides an integrated perspective on the gain, expansion, and loss of plant miRNAs, offering insights into their evolutionary and biological significance.

Plants exhibiting different life forms possess different capabilities in adapting to their respective environments, consequently displaying distinct geographical patterns of phylogenetic relatedness across a broad environmental gradient. Here, we compare the geographical patterns of phylogenetic relatedness between woody and herbaceous angiosperms in China, based on three phylogenetic relatedness metrics, i.e., the standard effect sizes of phylogenetic diversity (PD_ses), mean pairwise distance (MPD_ses), and mean nearest taxon distance (MNTD_ses). Additionally, we explore the effects of three categories of environmental variables (current climate, historical climate change, and environmental heterogeneity) on the geographical patterns of phylogenetic relatedness of both plant groups. Our results indicate that the geographical patterns of phylogenetic relatedness of herbaceous and woody plants are inconsistent, and the deviations of phylogenetic relatedness between woody and herbaceous angiosperms have geographical patterns and vary along environmental gradients. Our study found that environmental variables have a greater influence on the phylogenetic relatedness of herbaceous plants than on that of woody plants, emphasizing that environmental variables, especially current climatic variables, are the primary drivers of the deviations of phylogenetic relatedness between woody and herbaceous angiosperms. In summary, we illustrate the distinct differences in phylogenetic relatedness among plants of different life forms, providing valuable insights into the driving factors of species coexistence at various spatial scales.

The Himalayas represent a complex mountain system housing some of the world's richest floras along with a high level of endemism. Among them, Lysionotus (Gesneriaceae) stands out as a small genus (~34 species) that is unexpectedly distributed across Southern to Eastern Asia. Within this genus, the mountain forests of the south Pan-Himalaya region emerge as a hotspot of diversity, hosting most of epiphytic and endemic Lysionotus species. To explore the origin, evolutionary history and development of the current distribution pattern of Lysionotus, we inferred a highly resolved phylogenetic framework using 649 nuclear genes sourced from transcriptomes for 27 species. We revealed three major clades within Lysionotus with strong support, corresponding to the genus's classification into three sections (sects. Didymocarpoides, Lysionotus, and Cyathocalyx) based on morphological characters. Molecular dating suggests that Lysionotus is likely to have originated in the karst regions of Northern Vietnam to Southwestern China during the middle Oligocene (28.18 Ma), and then migrated westwards to Southern Himalaya regions during the Miocene. The speciation rates of Lysionotus were likely positively linked to changes in East Asian monsoons and past temperatures. Notably, epiphytic species of sect. Lysionotus began colonizing the tropical and subtropical forests of the Pan-Himalaya around the mid-Miocene Climatic Optimum, coinciding with the transition to long seed appendages. Our findings support that the formation and development of forests in the Southern Himalaya, along with paleo-climate changes and morphological innovations, probably facilitated the evolution and expansion of the spatial distribution of Lysionotus.

Large phylogenies derived from publicly available genetic sequences are becoming a popular and indispensable tool in addressing core questions in ecology and evolution, as well as in tackling challenging conservation issues. Optimizing taxonomic coverage and data quality is essential for improving the precision and reliability of phylogenetic reconstructions and evolutionary inferences. Here we present PyNCBIminer, a user-friendly software that automates the assembly of large DNA datasets from GenBank for phylogenetic reconstruction using the supermatrix method. PyNCBIminer uses iterative BLAST procedure to retrieve genetic sequences accurately and efficiently from GenBank. The state-of-the-art strategies also serve to improve taxa coverage and the quality of target DNA markers. PyNCBIminer is designed to efficiently handle large datasets, but it is also suitable for medium and small datasets. PyNCBIminer is open source and freely available at GitHub (https://github.com/Xiaoting-Xu/PyNCBIminer) and Gitee (https://gitee.com/xiaotingxu/PyNCBIminer). Its utility and performance are demonstrated through the assembly of phylogenetic datasets encompassing several genetic markers of varying sizes for the angiosperm order Dipsacales. PyNCBIminer holds an advantage over similar program in that it performs the majority of computations on the NCBI server, eliminating the need for users to build and maintain large local databases and reducing the demands on their computers. In addition, it integrates other commonly used phylogenetic analysis software, providing users from various backgrounds with convenient options for retrieving and assembling GenBank sequence data, along with flexible features that allow for user-defined parameters and strategies.

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, likely due to rapid diversification. Our plastid genomic data support that Stimpsonia is sister to the remainder of the subfamily Primuloideae, in contrast to 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 likely 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.

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 partial still need to be resolved. Here, we collected samples from a total of 2,242 trees from 142 populations of three walnut species (Juglans regia L., J. sigillata Dode, and J. 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 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.

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 eleven species in East Asia and three in the Mediterranean region. Here we used target capture sequencing and obtained 1,991 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 Middle Eocene and then became continuously distributed across Eurasia. The East Asian-Tethyan disjunction arose when the Mediterranean and Himalayan-Hengduan Mountains clades diverged, likely 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, likely 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 on the origin of East Asian-Tethyan disjunction of organisms, especially gymnosperms.

Quaternary climate fluctuations and complex mountain systems had a prominent impact on the genetic diversification and speciation of montane organisms. However, the genetic imprints of the interplay between past climate events and rugged relief on montane species remain largely unresolved. Here, we analysed the phylogeny, population structure, divergence time, demographic simulations, and ecological niche modelling of the montane scorpionfly Cerapanorpa obtusa (Cheng) from 36 populations in the mountains of central China (MCC) using three mitochondrial and two nuclear genes to explore its evolutionary history. The results show that C. obtusa originated from the Minshan Mountains, and currently consists of six genetically fragmented lineages that diverged 1.25–0.52 million years ago (Mya). Four minor lineages (S1−S4) are confined to the topographically rugged Minshan Mountains, and two major lineages (NW and NE) are widely distributed in the northern MCC with relatively homogeneous landscapes. The Minshan Mountains are likely interglacial microrefugia for C. obtusa, and as spatial buffers in response to past climate changes. These findings provide some evidence that the interplay between climate changes and rugged relief may play a significant role in shaping the distinct phylogeographical pattern of cold-adapted montane insects. These results would also seem to suggest the importance of topographically rugged mountain systems in the conservation of evolutionary diversity and endemic species.

Understanding the Cenozoic vegetation history of what is now the Qinghai-Tibetan Plateau is crucial for elucidating the co-evolutionary dynamics between plateau development, its environment, and the organisms it hosts. In this study, we conduct a comprehensive analysis of phytoliths within the late Oligocene-Early Miocene lacustrine sedimentary section of the Lunpola Basin, central Qinghai-Tibetan Plateau. The diverse phytolith morphotype assemblages indicate that the vegetation of the central Tibetan region mainly comprised a mixed coniferous and broad-leaved forest. Grasses in the understory primarily consisted of Pooideae, distinguished by phytolith morphotypes such as rondel, crenate and Stipa-type bilobate forms. Combined with previous work, we infer that riparian vegetation of the central Tibetan region transitioned from a humid subtropical forest, dominated by broad-leaved woody plants during the middle Eocene, to a more seasonally arid open woodland containing abundant woody and herbaceous plants during the late Eocene, before developing into a cooler mixed coniferous and broad-leaved forest during the late Oligocene-Early Miocene. The growth of the central Tibetan region and retreat of the Tethys Ocean, together with the uplift of the Himalaya, contributed to this vegetation change. This study provides new evidence from the phytolith perspective for the evolutionary history of Qinghai-Tibetan Plateau vegetation being tied to plateau formation and regional climate change.

Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai-Tibet Plateau (QTP) and the mountainous region of southwestern China have long been regarded as biodiversity hotspots. However, despite considerable efforts, numerous plant species may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca. 58 perennial herb species, which has been used as an important traditional medicinal plant for centuries. Rampant exploitation has put some species at risk of extinction. Rhodiola has also been recognized as a promising model for investigating radiation speciation in the QTP. However, the phylogenetic relationships among major clades in the genus are still not well-resolved, and the underlying causes of cyto-nuclear discordance briefly mentioned in previous studies remain unexplored. Through phylogenomic analyses utilizing data from both nuclear genome and plastome of 42 species, we identified six major clades in Rhodiola and found extensive cyto-nuclear discordance, which was primarily attributed to hybridization and introgression occurring among clades or closely related species. In addition, the integration of morphological, phylogenomic, population genomic, and ecological evidence resulted in the identification and description of a new species of Rhodiola: R. renii sp. nov., and the reclassification of a previously Pseudosedum species merged into Rhodiola. Our results highlight the significant role of hybridization and introgression in the evolution of Rhodiola and probably other rapid-radiated groups in the QTP, and emphasize the need for increased species discovery efforts in biodiversity hotspots such as the QTP and its adjacent mountainous areas.

Taihangia rupestris Yu et 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. T. rupestris var. ciliate 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. ciliate were grouped into three distinct clusters. Approximately 29.82 million years ago, T. rupestris diverged from its closely related species. T. rupestris var. ciliate appeared first, followed by the differentiation of T. rupestris var. rupestris, which adapted to the climate of the southern Taihang Mountains, around 3.55 million years ago. 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.

Geological and climatic events frequently represent the primary explanations to describe evolutionary processes among species. Freshwater fishes previously have been used as models to uncover evolutionary and historical biogeographic patterns in central Mexico hydrologic systems and biotas. Xenotoca variata (Cyprinodontiformes: Goodeidae) is one of the most widely distributed species across central Mexico. The species represents a highly dimorphic and sexually selective species. In this study, the phylogenetic and phylogeographic patterns of populations of X. variata, using one mitochondrial (cytb) and three nuclear loci (S7, RHO and RAG1), were described in order to understand the evolutionary history of the species througout its distributional range. Two well-defined and highly supported clades were recovered with all analyses and genes studied, with estimated divergence time of ca. 2.42 Mya, corroborating the existence of an independent evolutionary unit in Cuitzeo Lake and its recognition as a putative new species. Also, phylogeographic structure in two genes was found within the widely distribute clades. The role played by climate change events and geological history, as well as the possible influence of reproductive traits in the phylogeographic pattern of the species, are discussed.

Despite the importance of gamete production this topic has rarely been investigated in angiosperms using comparative approaches. Here, we investigate pollen and ovule number per flower in 73 species and 99 populations of Primula comprising both distylous and homostylous reproductive systems. We investigated whether phylogenetic relationships influenced associations between variation in gamete production, floral traits and elevation, and whether the evolutionary breakdown of distyly to homostyly results in parallel changes to gamete production. We used a Bayesian approach facilitated by the MCMCglmm method to model pollen and ovule traits across species and determined whether they exhibited phylogenetic signals. We detected significant positive correlations between pollen number and elevation in both the long- and short-styled morphs (L-and S-morphs, respectively), whereas ovule number was not influenced by elevation. Pollen production was significantly higher in the L- than S-morphs, but there was no significant difference between morphs in ovule number. Pollen volume exhibited a positive correlation with the style length of compatible morphs. The transition from distyly to homostyly was associated with significant decreases in pollen production but not ovule number. Our findings demonstrate the importance of elevation on pollen production, perhaps because of selection to improve pollen transfer efficiency in uncertain pollinator environments. In contrast, ovule number variation appears to be more constrained by phylogenetic relationships. Our comparative analyses of a well-defined angiosperm lineage highlight the complex interactions between intrinsic and extrinsic factors influencing gamete production in plants and emphasizes the importance of considering pollen and ovule data separately.

Adaptive radiation is usually triggered by great in or ex-situ environmental changes. How an adaptive radiation occurs on lands, and how species richness relates to morphodisparity have been a major focus of evolutionary biology. Petrocodon, diversified in the southeastern Qinghai-Tibet Plateau (QTP), represents an ideal model to address these questions. To elucidate the dynamics of adaptive radiation of Petrocodon, we took an integrative approach, including phylogenetic, dating, disparity versus diversity, pollination, and gene expression analyses. Petrocodon with six clades has experienced radiation following the QTP uplift. Multiple modes of floral morphodisparity versus species diversity occur in the radiation process that are directly linked to their colonizing new environments and diversification with geographic expansion. Pollination and gene expression analyses suggest that accelerated emergence of de novo mutations might be relevant to the multiplex floral disparity and pollinator shifts in Petrocodon. For the first time in plants, we report that decreased genetic constraints on floral architecture triggered by QTP uplift might have generated abundant floral morphological variants, which were further targeted by selection for ecological divergence. The multiple modes of floral disparity versus species diversity may be attributed to accelerated mutations in colonizing new environments and repeatedly modifications of the already evolved traits in subsequent diversification and geographic expansion in Petrocodon. Our findings shed novel light on the interplay of ecological, developmental and evolutionary dynamics of disparity versus diversity in relation to trajectory changes of floral architecture in responses to environmental disturbance in a terrestrial plant group.

Toona fargesii, 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 chromosome-level genome. The Long Terminal Repeat (LTR) 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 (WGD) event occurred between 22.1 and 50.1 million years ago (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 (DEGs) between root sprouts (RS) and non-root sprouts (NRS) 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.

Gene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineage-specific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 exhibited a weak inhibiting effect on the ray-floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that demonstrated CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution.

The orchid Dactylorhiza cantabrica H.A. Pedersen is a narrow endemic occurring at western Cantabrian Mountains in NW Spain. Previous allozyme and morphological studies suggest that it might result from the hybridization of two widespread congeners: the triploid D. insularis and the diploid D. sambucina. However, this hypothesis has not been tested using multiple genetic markers, necessary to analyse phylogenies in complex genera such as Dactylorhiza. In this study, the Hyb-Seq technique is applied together with the universal Angiosperms353 probe kit to sequence multiple plastid and low-copy nuclear genes. The phylogenetic relationships between the three species, estimated based on 269 and 266 nuclear genes under concatenation and coalescent-based approaches, respectively, revealed highly-supported clades containing each putative parent, D. insularis and D. sambucina. The position of D. cantabrica was not well resolved, suggesting the existence of mixed inheritance, where different genes come from each parent. Phylogenetic networks, used for visualizing the conflict between nuclear gene trees, placed D. cantabrica between the two parents and revealed high levels of reticulation. In addition, nuclear genetic variation within and among species was explored with allele frequencies-based tools further supporting the intermediate position of D. cantabrica and the hypothesis of a recent hybrid origin. Finally, 75 plastid genes revealed that D. insularis might be the maternal donor. Altogether, our results point to the allopolyploid origin of D. cantabrica from D. insularis and D. sambucina, as well as to the clear genetic differentiation of the two parental species.

Aquilaria (Thymelaeaceae), a tropical and subtropical plant, is one of the main genera that can produce agarwood. Aquilaria sinensis and A. yunnanensis are native Chinese tree species, and A. sinensis is China's main agarwood source. Agarwood is a non-timber forest product with high economic and medicinal value. First-grade agarwood is sold as much as $100,000 per kilogram. There has been little research on the saprobic fungi associated with Aquilaria, with only eleven records having been reported. In the present study, ten terrestrial saprobic fungi associated with A. sinensis and A. yunnanensis were collected in China. Based on morphological and phylogenetic studies, these ten collections are introduced herein as one new genus (Aquilariomyces), nine new species—Aquilariomyces aquilariae, Corynespora aquilariae, Melomastia maomingensis, Nigrograna aquilariae, Parathyridariella aquilariae, Peroneutypa maomingensis, Phaeoseptum aquilariae, Pseudothyridariella aquilariae, and Triangularia aquilariae, and one known species (Camarographium clematisidis). Descriptions, illustrations of morphological characteristics, photo plates, phylogenetic trees, and the results of a pairwise homoplasy index test (PHI) test results are provided.

During the Cretaceous period, the lacewing superfamily Mantispoidea, with an assemblage of species possessing raptorial forelegs, have undergone a rapid species radiation, characterized by abundant species richness and high morphological plasticity. Nevertheless, the morphology and early evolution of the specialized predatory organ around the time of its origin in raptorial Mantispoidea have been poorly documented due to the rarity of fossil evidence, especially for the pre-Cretaceous fossils. Herein, a new genus and new species, i.e. Archarhachiberotha longitarsa J. Wang, Ren et Y. Wang gen. et sp. nov., was described from the Middle Jurassic Jiulongshan Formation of northeastern China. This new genus was characterized by the remarkable raptorial forelegs, i.e. typically elongated coxa, relatively less-swollen femur and rudimentary small femoral spines, and well-developed tarsi. Considering the peculiar morphological combination and antiquity of the new genus, it was assigned to be a stem-group lineage of Mantispoidea. Besides, the detailed analyses of morphology and biological functions of raptorial forelegs were made to conclude that the new genus evolved into an unknown but primitive raptorial type that was distinctly different from the extant morphological features and raptorial mechanisms. In addition, the evolutionary tendency of raptorial Mantispoidea herein summarized highlights morphological diversity and disparity between fossil and extant representatives, and provides a rare case to explore the entire evolutionary history of a specialized structure in one lineage. 

Eucalypt fossils were widely reported from the Cenozoic deposits across the Southern Hemisphere (Australia, New Zealand, and Argentina). However, no attached reproductive and vegetative fossil remains of this myrtaceous clade have been discovered till now. We report and describe for the first time a fossil eucalypt twig with attached foliage, flower buds, and mature flowers from the early Eocene (~55–52 Ma) sediments (Palana Formation) of Rajasthan, western India. As both vegetative and reproductive organs are in organic connection, they clearly represent the same species. In addition, here we also introduce fossil materials of isolated leaves, flower buds, inflorescence, and flowers recovered from the same stratigraphic level. Morphological similarities that relate our Eocene fossils to extant members of the eucalypt clade include robust, thick petiolate lanceolate-shaped leaves with intramarginal secondary veins; operculate flower buds consisting of imbricate petals with discernable margins; solitary inflorescence with 3 flowers per umbellaster, epigynous and bisexual flowers. Based upon combined characteristics of leaf, flower, and bud morphology, these fossils conform to the Eucalypt clade and are recognized as a new fossil genus and species Hindeucalyptus eocenicus Patel, R.F. Almeida, Ali et Khan, gen. nov. et sp. nov. We also compare it with extant and extinct eucalypts using morphological phylogeny and character mapping analyses. In addition, we briefly discuss its phytogeographic and paleoclimatic implications regarding the distribution and habitat of fossil and modern eucalypts.

The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a dataset of more than 569,990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole-genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different datasets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a non-monophyletic group, consisting of Erotyloidea, Nitiduloidea and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early-diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.

Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, D. floribunda, D. yunnanensis and D. elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population-level genomic data (RAD-SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis-D. floribunda group, but with cyto-nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil-calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD-SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai-Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid- Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome-scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.

The two invasive Reynoutria species, R. japonica var. japonica, R. sachalinensis and their hybrid R. x bohemica are often misidentified by managers and non-specialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations, in terms of morphology, genetic diversity and ploidy level. We resolved the identity of North-Eastern French invasive populations using 4,582 SNPs from a RADseq analysis, DNA contents estimated by flow cytometry and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of R. x bohemica represented by one genotype each. Estimation of genome size using DAPI-staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base and apex shape, and the extrafloral nectaries on the node.

Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenge. Here we identify the spatial distribution of diversity and endemism in Astragalus, using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.

Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai-Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China, P. pseudoglanca and P. wuana are classified into sect. Leucoides and sect. Tacamahaca, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections. Through identification based on morphology and habitats, we confirmed that the “P. pseudoglanca” recorded in the Flora of Sichuan is not true P. pseudoglanca, while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole-genome re-sequencing of 150 individuals from the 31 taxa, we derived 2.28 million SNPs. Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca, and they all originate through the natural hybridization between P. ciliata in sect. Leucoides and P. curviserrata in sect. Tacamahaca. Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.

The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time-calibrated phylogeny for 749 species representing c. 80% of the genera of this clade using nrDNA ITS, plastid matK, and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade’s temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil-calibrated dating analysis showed a nearly simultaneous divergence of the stem node [c. 62 million years ago (Ma)] and the crown node (c. 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c. 10 Ma. Possible explanations for the present-day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra- and intercontinental long-distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid-Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.

Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of LTR contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with diseases tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in root, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.

Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 non-redundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast-to-nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.

The most significant driver of adaptive radiation in the New World leaf-nosed bats (Phyllostomidae) is their remarkably diverse feeding habits, yet there remains a notable scarcity of studies addressing the genetic underpinnings of dietary diversification in this family. In this study, we have assembled a new genome for a representative species of phyllostomid bat, the fringe-lipped bat (Trachops cirrhosis), and integrated it with eight published phyllostomid genomes, along with an additional 10 genomes of other bat species. Comparative genomic analysis across 10,200 orthologus genes has unveiled that those genes subject to divergent selection within the Phyllostomidae clade are notably enriched in metabolism-related pathways. Furthermore, we identified molecular signatures of divergent selection in the bitter receptor gene Tas2r1, as well as 14 genes involved in digesting key nutrients such as carbohydrates, proteins, and fats. In addition, our cell-based functional assays conducted on Tas2r1 showed a broader spectrum of perception for bitter compounds in phyllostomids compared to non-phyllostomid bats, suggesting functional diversification of bitter taste in Phyllostomidae. Together, our genomic and functional analyses lead us to propose that divergent selection of genes associated with taste, digestion and absorption, and metabolism assumes a pivotal role in steering the extreme dietary diversification in Phyllostomidae. This study not only illuminates the genetic mechanisms underlying dietary adaptations in Phyllostomidae bats but also enhances our understanding of their extraordinary adaptive radiation.

The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anti-carcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β-tubulin), and RNA polymerase II second largest subunit (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and phylogenetic relationships with their close relatives. This taxonomic revision significantly contributes to our understanding the diversity of Xylaria in China and enriches the knowledge of fungal biodiversity worldwide.

Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity, paleogeographic and paleoclimate events and information from studies that introduce the temporal dimension. The Carthamus-Carduncellus complex (Cardueae, Compositae) constitutes a good case study to investigate the biogeographic history of this region because it evolved throughout the basin. We performed molecular dating, ancestral area estimation and diversification analyses based on previous phylogenetic studies of a nearly complete taxon sampling of the complex. The main aims were to determine the role of tectonic and climatic events in the disjunction of the complex and the expansion route of the two main lineages, Carduncellus s.l. and Carthamus. Our results suggest that the main lineages in the complex originated during the Miocene. Later, all main paleogeographic and paleoclimatic events during the Neogene and Pleistocene in the Mediterranean basin had an important imprint on the evolutionary history of the complex. The Messinian Salinity Crisis facilitated the dispersion of the genus Carduncellus from North Africa to the Iberian Peninsula and the split of the genera Phonus and Femeniasia from the Carduncellus lineage. The onset of the Mediterranean climate in the Pliocene together with some orogenic processes could be the main causes of the diversification of the genus Carduncellus. In contrast, Pleistocene glaciations played a key role in the species diversification of Carthamus. In addition, we emphasize the problems derived from secondary dating and the existing differences between two previous dating analyses of the tribe Cardueae.

Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node-dating (ND) based on plastomes of all eight extant species and tip-dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% HPD: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant events without fossils, but as many as to six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via Bering Land Bridge during the early Oligocene and the early Miocene. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except P. fraxinifolia and P. stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.

The Sui people living in Guizhou province have a unique ethnic culture and population history due to their long-time isolation from other populations. To investigate the genetic structure of Sui populations in different regions of Guizhou, we genotyped 89 individuals from 4 Sui populations using genome-wide SNP arrays. We analyzed the data using principal component analysis (PCA), ADMIXTURE analysis, f-statistics, qpWave/qpAdm, TreeMix analysis, fineSTRUCTURE, and GLOBETROTTER. We found that Sui populations in Guizhou were genetically homogeneous and had a close genetic affinity with Tai-Kadai-speaking populations, Hmong-Mien-speaking Hmong, and some ancient populations from southern China. The Sui populations could be modeled as an admixture of 33.5%-37.9% of Yellow River Basin farmer-related ancestry and 62.1%-66.5% of Southeast Asian-related ancestry, indicating that the southward expansion of northern East Asian-related ancestry influenced the formation of the Tai-Kadai-speaking Sui people. Future publications of more ancient genomics in southern China could effectively provide further insight into the demographic history and population structure of the Sui people.

The geodiversity of rocky ecosystems includes diverse plant communities with specific names, but their continental-scale floristic identity and the knowledge on the role of macroclimate remain patchy. Here we assessed the identity of plant communities in eastern Brazil across multiple types of rocky landscapes and evaluated the relative importance of climatic variables in constraining floristic differentiation. We provided lists of diagnostic species and an assessment of the conservation status of the identified floristic groups. We compiled a dataset of 151 sites (4,498 species) from rocky ecosystems, including campos rupestres, campos de altitude, granitic-gneiss lowland inselbergs and limestone outcrops. We used unsupervised clustering analysis followed by ANOSIM to assess floristic groups among sites. We performed a random forest variable selection to test whether the identified floristic groups occupy distinct climatic spaces. Six groups (lithobiomes) segregated floristically according to lithology and climate. Alongside campos de altitude and limestone outcrops, inselbergs were divided according to the biome in which they occur (Atlantic Forest or Caatinga) and campos rupestres were largely segregated according to their lithological matrix (ironstone or quartzitic). Plant communities of Caatinga inselbergs were more similar to limestone outcrops, while Atlantic Forest inselbergs communities resembled campos de altitude. The composition of plant communities on outcrops seems to be largely constrained by lithology, but climatic factors are also meaningful for sites with similar lithology. The current network of protected areas does not cover these unique ecosystems and their floristic heterogeneity, with protection least adequate for Caatinga inselbergs, ironstone campos rupestres and limestone outcrops.

The general dynamic model of oceanic island biogeography (GDM) views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, Cyrtandra, and inferred directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of Cyrtandra in the Southeast Asian grade showed early bursts followed by a plateau which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by its wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model, wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step towards a framework for investigating diversification dynamics as predicted by GDM in highly successful insular taxa.

Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromeae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromeae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological dataset increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution which can facilitate the search for agronomically relevant traits.

The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1438 to 1870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla-Oaxaca, Sonora-Sinaloan and Jalisco) and three centers of diversity from South America (Southern central Andes, Caatinga and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus Opuntia are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees and other insects. Climate variability, whether natural or human induced, threaten global crop production including high temperatures, salinity, drought, flood, changes in soil pH and urbanization. Cacti have several adaptations that are important for coping with abiotic stresses, such as crassulacean acid metabolism (CAM photosynthesis), as well as modifications to root and stem physiological pathways. This review aims to provide a comprehensive view of the fruit crops in Cactaceae, including the evolution, worldwide distribution, and the environmental factors impacting cultivation.

Islands in the tropical Pacific Ocean are renowned for high biodiversity and endemism despite having relatively small landmasses. However, our knowledge of how this biodiversity formed remains limited. The taxon cycle, where well-dispersed, earlier colonizers become displaced from coastal to inland habitats by new waves of colonizers, producing isolated, range-restricted species, has been proposed to explain current biodiversity patterns. Here, we integrate the outcomes of phylogenetic studies in the region to investigate the sources, age, number of colonizations, and diversification for 16 archipelagos in the tropical and subtropical South Pacific. We then evaluate whether results support the taxon cycle as a plausible mechanism for these observations. We find that most species in the Pacific arrived within the last 5 million years from geographically close sources, suggesting that colonization by new taxa is a frequent and ongoing process. Therefore, our findings are broadly consistent with the theory of the Taxon Cycle, which posits that ongoing colonization results in the gradual displacement of established lineages. Only the oldest archipelagos, New Caledonia and Fiji, do not conform to this trend, having proportionally less recent colonization events, suggesting that the taxon cycle may slow on older islands. This conclusion is further validated by New Caledonia having lower diversification rate estimates than younger islands. We found that diversification rates across archipelagos are negatively correlated with area and age. Therefore, a taxon cycle that slows with island age appears to be a suitable concept to understand the dynamic nature and biodiversity patterns of Pacific Islands.