Coping with increasing global temperatures due to climate change may be especially challenging for trees with long generation times as changes might happen too quickly for successful adaptation. Juniperus przewalskii is an arid tolerant key species of forest ecosystems on the northeastern Qinghai-Tibet Plateau. Target capture sequencing was utilized to survey genetic variation and population structure, and to infer the evolutionary history of this species by analyzing 170 individuals from 23 populations. This approach provided valuable information on how local adaptation influences the genetic background of this species, as well as potential predictions regarding the species' response to global climate change. Our results revealed a new fine-scale genetic structure and high levels of genetic diversity as well as local adaptations despite gene flow. Redundancy analysis showed that climate contributed the most to the genetic variation of J. przewalskii. Analysis of gradient forest and risk of non-adaptedness indicated that, for the variables examined and the majority of locations sampled, it is improbable that J. przewalskii will need significant alterations in allele frequencies to endure the forecasted climate shifts. We also identified the most at-risk populations for preservation and numerous candidate genes that may be valuable for upcoming climate change. The significance of combining genetic and environmental information to forecast the resilience of a key tree species to global warming is underscored in our results, particularly in areas susceptible to climate fluctuations.

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

Understanding the factors contributing to genetic structure among closely related sympatric species is crucial for grasping adaptive divergence and speciation initiation. We focused on three dioecious fig trees (Ficus hispida, Ficus heterostyla, and Ficus squamosa) that constitute a clade of closely related species pollinated by closely related Ceratosolen wasps. Analyzing microsatellite data (64 sampling locations) and chemical volatiles for fig trees and inferring the phylogenetic relationships of their pollinating wasps, we show that despite sharing of a large proportion of volatile compounds and a few exchanges of pollinators, all species maintain genetic and morphological integrity. Admixture of F. heterostyla and F. hispida in F. squamosa is detected at its distribution margin. Two genetically distinct clusters of F. heterostyla, possibly indicating cryptic fig species pollinated by distinct pollinators, are highlighted. Ficus hispida is genetically homogeneous over its studied range but associated with at least three pollinator species. Life history traits of each Ficus species (fruiting mode, population density, flowering pattern, habitat preference) and seed dispersal mode (hydrochorous, zoochorous) are discussed together with elements on the morphology and biology of their pollinators to explain observed results. This study contributes to our understanding of how species in the fig–wasp mutualism diversify and coexist.

Viola philippica develops chasmogamous (CH) and cleistogamous (CL) flowers under different photoperiods, while Viola cornuta only forms CH flowers. Gene expression variations driven by photoperiods that contribute to the CH–CL transition remain largely unknown. Here, we performed comparative transcriptomics between V. philippica and V. cornuta during flower development and revealed differentially expressed genes (DEGs) between CL and CH flowers. Compared to CL flowers in V. philippica under 16-h daylight conditions, DEGs, including auxin response factor (ARF) genes and floral MADS-box genes, were identified in CH flowers under 12-h daylight conditions; however, their homologous genes in V. cornuta were equivalently expressed in CH flowers across both photoperiods. Genes in the modules most significantly correlated with floral types were DEGs between CH and CL flowers in V. philippica, but they were not altered in V. cornuta CH flowers under either photoperiod. Moreover, genes related to fatty acid, flavonoid, and anthocyanin biosynthesis were upregulated in CH flowers, whereas defense response genes were upregulated in CL flowers. Furthermore, the genes co-expressed with the floral B-class MADS-box gene APETALA3 included ARFs, CRABS CLAW, BIGPETALp, TCP14, and UGT87A, whose homologous genes are involved in nectary and floral organ development, including organ identity, size, and coloration. Thus, the putative coordination of genes involved in defense response and auxin signaling pathways, floral organ identity determination and growth, and fatty acid and flavonol biosynthesis in response to photoperiod might regulate CH–CL development in V. philippica, thus providing new insights into the evolution of dimorphic flower development in Viola.

Continent-wide disjunctions, where related taxa are distributed across isolated regions within the continent, are rare in grasses and remain poorly understood. The genus Trichoneura occurs in both the New World and the Old World, with no species occurring in both continents, and its distribution displays continental disjunctions. The current distribution of African Trichoneura is said to be a result of the formation of an African arid corridor, yet this remains understudied. Using complete chloroplast genomes and nuclear genes of seven newly sequenced Trichoneura species, we studied their phylogenetic relationships and divergence history, reconstructed their ancestral history, and modeled their ecological niche to understand their evolution and current distribution pattern. Our findings revealed that the plastomes of Trichoneura are generally conserved and range in length between 135 069 and 134 139 bp. Molecular results show that Trichoneura is monophyletic and diverged around 5.78 Ma. The Late Miocene origin of this genus correlates with the formation of the African arid corridor, which explains their fragmented distribution in Africa. Dispersal and vicariance are likely to have played pivotal roles in driving their divergence, leading to subsequent distribution toward Neotropical regions during the Pliocene period. Trichoneura mollis and Trichoneura lindleyana occurring in different regions displayed varying morphology, and we suggest further morphological and phylogenetic analysis to determine their taxonomic delimitation.

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

Inferring general biogeographic patterns in the sub-Antarctic region has been challenging due to the disparate geological origins of its islands and archipelagos—ranging from Gondwanan fragments to uplifted seafloor and more recently formed volcanic islands—and the remoteness of these island systems, spread around the austral continental landmasses. Here, we conduct phylogenetic reconstruction, divergence time estimation, and Bayesian Island Biogeographic analyses to reconstruct the spatio–temporal colonization histories of seven vascular plant lineages, which are either widespread across the sub-Antarctic region (Acaena magellanica, Austroblechnum penna-marina, Azorella selago, Notogrammitis crassior) or restricted to an extremely remote sub-Antarctic province (Colobanthus kerguelensis, Polystichum marionense, Pringlea antiscorbutica). Our results reveal high biological connectivity within the sub-Antarctic region, with southern landmasses (Australia, New Zealand, South America) as key sources of sub-Antarctic plant diversity since the Miocene, supporting long-distance dispersal as the primary colonization mechanism rather than tectonic vicariance. Despite the geographic isolation of the sub-Antarctic islands, eastward and westward colonization events have maintained this connectivity, likely facilitated by eastward-moving marine and wind currents, short-term weather systems, and/or dispersal by birds. Divergence time estimates indicate that most species diverged within the Plio–Pleistocene, with crown ages predating the Last Glacial Maximum, suggesting that sub-Antarctic archipelagos acted as refuges for biodiversity. Our findings highlight the role of one of the most remote sub-Antarctic archipelagos as both a refugium and a source of (re)colonization for continental regions. These results underscore the urgent need for establishing priority conservation plans in the sub-Antarctic, particularly in the face of climate change.

Angiosperm sexual systems are complex and diverse. Androdioecy, the co-occurrence of males and hermaphrodites, is rare and considered an intermediate evolutionary state between hermaphrodites and dioecy. However, the evolutionary factors that drive androdioecy remain unclear. Based on studies on Berchemia and Tapiscia life histories, it has been observed that species with long sexual reproductive cycles, in which flowers and fruits develop simultaneously, are typically androdioecious. Conversely, species with short sexual reproductive cycles in which the developmental periods of flowers and fruits do not overlap are typically hermaphroditic. Therefore, we hypothesized that a long reproductive cycle leads to the simultaneous development of flowers and fruits, creating a trade-off in reproductive resources. This trade-off ultimately drives evolution from hermaphroditism to androdioecy. To test this hypothesis, we conducted artificial experiments to remove fruits and defoliate representative species of Berchemia and Tapiscia to simulate resource release and shortage scenarios, respectively. Differences in the size and biomass of the flower parts between the treatment and control groups were compared. Our findings indicate that the simultaneous development of flowers and fruits leads to a tradeoff in reproductive resources, resulting in reduced investment in flowers. Additionally, limited resources are reallocated between female and male functions in bisexual flowers. Interestingly, when reproductive resources fluctuate, female functions are affected to a greater extent, whereas male functions are more resilient to resource changes. These results indicate that when reproductive resources are traded off, it leads to a bias toward male functions in hermaphrodites, promoting the emergence of male individuals and thus forming an androdioecious sexual system.

Species are distributed heterogeneously, and different regions have different numbers of species, producing species richness anomalies. More than 100 angiosperm genera demonstrate disjunct distributions in at least two of these regions: Europe, eastern North America, western North America, and East Asia, and commonly between East Asia and eastern North America. These regions have similar climates but usually exhibit species richness anomalies; however, the underlying causes of species richness anomalies in disjunct intercontinental regions remain poorly understood. In this study, we investigated the drivers of anomalies in ash tree (genus Fraxinus L.) species richness anomalies among disjunct intercontinental regions based on distribution data, macrofossil records, and corresponding evolutionary and environmental variables. Generalized linear regression and pathway model analyses incorporating environmental and evolutionary processes indicated that global cooling has contributed to the low species richness in Europe, whereas evolutionary divergence, shaped the distinct species distribution patterns in East Asia (which was identified as an evolutionary cradle) and North America (which was identified as an evolutionary museum). Environmental heterogenies and evolutionary divergence have resulted in a significant diversity anomaly between these regions. This study emphasizes the important role of evolution in the formation of species richness distribution patterns.

Dennstaedtiaceae, a heterogeneous family of ferns with 11 genera and about 270 species, has a global distribution. While substantial progress has been made in elucidating the intergeneric relationships within Dennstaedtiaceae, certain nodes, particularly within Hypolepidoideae, remain controversial. To date, no phylogenomic investigation of nuclear genes has been conducted for Dennstaedtiaceae, and the biological processes underlying its complex evolution remain largely unknown. In this study, we generated transcriptome sequences from nine species in Dennstaedtiaceae and combined them with publicly available data sets from 13 species and one outgroup. By utilizing the 23 transcriptomic data sets, representing nine out of the 11 genera in Dennstaedtiaceae, we successfully resolved the intergeneric relationships within the family and established a fundamental phylogenetic framework to investigate its evolutionary history. By combining the analyses of rate-adjusted K_s-based age distributions and phylogenetic reconciliation approaches, we found evidence of at least one round of whole-genome duplication (WGD) that is shared by all Dennstaedtiaceae species prior to their divergence. Extensive gene tree discordance was found across the backbone of Dennstaedtiaceae, with the most significant discordance within Hypolepidoideae. The results of incomplete lineage sorting (ILS) simulation revealed that ILS is a substantial contributor to these conflicts. Evidence from phylogenetic networks and introgression tests indicates the occurrence of gene flow among the clades of Paesia, Hiya, and Histiopteris, potentially explaining the observed cytonuclear discordance in Hypolepidoideae. Our phylotranscriptomic study of Dennstaedtiaceae provides novel insights into its complex reticulate evolutionary history, paving the way for future studies aimed at unraveling the mechanisms underlying its diversification and adaptation.

The Asteraceae capitulum, particularly a radiate capitulum with differing colors of ray and disc florets, resembles a solitary flower probably through adaption to animal pollination. A previous study found that the shape-color association in Chrysanthemum was due to co-option of the carotenoid-cleavage-dioxygenase gene CCD4a under regulation of the ray-floret identity CYC2g, a member of floral symmetry regulators CYCLOIDEA. Then questions arise: Is such a gene co-option specific to Chrysanthemum? Or did it originate earlier in the evolution of Chrysanthemum and allies? To answer these questions, we examined 11 species representing four color patterns of radiate capitula in the tribe Anthemideae, to which Chrysanthemum belongs. Comparative examinations of carotenoid content, expression patterns of CYC2-like and CCD-like genes along floret developments, and dual-luciferase assays showed that capitular color patterns were strongly correlated with patterns of carotenoid accumulation/degeneration. In the white-ray/yellow-disc species, both CYC2g and CCD4a were ray-specifically expressed and CYC2g can activate CCD4a; in the yellow-ray/yellow-disc species, CCD4a genes were either lost or repressed by CYC2g. The white discs of Achillea alpina must be due to other regulators activating CCD4a expression. The bicolor rays of Glebionis coronaria seemed to have complex color regulation probably due to redundant function of two CCD4a paralogs. In sum, the shape-color association of a radiate capitulum is evolutionarily conserved in the tribe Anthemideae, and the underpinning gene co-option of CCD4a into the floral symmetry regulation network probably arose before divergence of the tribes Anthemideae and Astereae as the divergence of CCD4 into CCD4a and CCD4b occurred at approximately that time.

Organisms exhibit diverse responses when exposed to novel environments, and successful adaptation depends on aligning evolutionary histories with these new conditions. Reusing standing genetic variation is a critical mechanism for this adaptation process. Using an extended Fisher's geometric model, we conducted simulations of evolving populations to investigate how evolutionary histories influence adaptation to novel environments. Our results highlight that distinct evolutionary histories produce varying patterns of genetic variance within populations. When organisms return to previously experienced environments, they exhibit enhanced performance and rapid adaptation. This supports the validity of the strategy commonly employed in ecological restoration to revert habitats to their original state. Moreover, small deviations of the greatest genetic variance direction from the optimum are beneficial for both fitness and fitness increase. A small genetic variance size is advantageous for fitness but impedes fitness increase. A short distance to the optimum and a sharp genetic variance shape are beneficial for fitness but have no significant effects on fitness increase. Our findings underscore the crucial role of evolutionary histories in shaping genetic variance and evolutionary potential when adapting to a new optimum. These results contribute to an evolutionary understanding of the factors underlying the disparate responses of phenotypically similar species to environmental change.

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

Geological and climatic events frequently represent the primary explanations to describe evolutionary processes among species. Freshwater fishes have been used previously 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 locus (cytb) and three nuclear loci (S7, RHO, and RAG1), were described in order to understand the evolutionary history of the species throughout its distributional range. Two well-defined and highly supported clades were recovered with all analyses and genes studied, with an 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, a phylogeographic structure in two genes was found within the widely distributed 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.

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

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 have 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 cytonuclear discordance briefly mentioned in previous studies remain unexplored. Through phylogenomic analyses utilizing data from both the nuclear genome and plastome of 42 species, we identified six major clades in Rhodiola and found extensive cytonuclear 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.

Plants exhibiting different growth 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, namely, the standardized 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 growth forms, providing valuable insights into the driving factors of species coexistence at various spatial scales.

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 data sets from GenBank for phylogenetic reconstruction using the supermatrix method. PyNCBIminer uses the 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 data sets, but it is also suitable for medium and small data sets. It 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 data sets encompassing several genetic markers of varying sizes for the angiosperm order Dipsacales. PyNCBIminer holds an advantage over similar programs 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.

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

Despite the importance of gamete production this topic has rarely been investigated in angiosperms using comparative approaches. Here, we investigated pollen and ovule numbers 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 resulted 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-styled and short-styled morphs (L-morph and S-morph, respectively), whereas ovule number was not influenced by elevation. Pollen production was significantly higher in the L-morph than in the S-morph, 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 emphasize the importance of considering pollen and ovule data separately.

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 analyzed the phylogeny, population structure, divergence time, demographic simulations, and ecological niche modeling 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 Ma. 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.

Taihangia rupestris Yu & Li, an early spring flowering plant of the Rosaceae family, is classified as a second-level protected species in China. Endemic to the cliff faces of the Taihang Mountains in central China, this rare species requires a comprehensive understanding and conservation approach. In this study, we analyzed population-level genetic variations in both chloroplast and nuclear genomes. Taihangia rupestris var. 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 Ma, T. rupestris diverged from its closely related species. Taihangia 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 Ma. Additionally, our study identified several chloroplast genes potentially involved in variety adaptive differentiation. These findings enhance our understanding of environmental adaptation and differentiation in the two T. rupestris varieties, providing valuable genetic insights for the conservation and utilization of this species.

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

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

Most species in the early divergent angiosperm family Annonaceae are apocarpous, with very diverse gynoecial morphologies. Although several Annonaceae genera with apocarpous flowers are known to possess an extragynoecial compitum (EGC) that enables intercarpellary pollen-tube growth to enhance fertilization success, the occurrence of EGC across the whole family remains obscure. Twenty Annonaceae species from all four subfamilies (Anaxagoreoideae, Ambavioideae, Annonoideae, and Malmeoideae) are examined here, with anatomical evidence revealing the occurrence of stigmatic exudate-mediated suprastylar EGC in all four subfamilies. Histological and ontogenetic studies furthermore indicate that trichomes in Cananga and Drepananthus form a confluent zone that connects adjacent stigmas, providing a structural premise for suprastylar EGC. Infrastylar EGC are reported in the Annonaceae for the first time in several genera, including Artabotrys, Annona, and Miliusa, associated with the opening on the ovary ventral groove and/or basal placentation. In addition to the sister genera Isolona and Monodora that are clearly syncarpous, flowers of the distantly related genus Cyathocalyx with a unicarpellate gynoecium have also been hypothesized to be syncarpous. Evidence of carpel vasculature and primordium development does not support that the solitary Cyathocalyx carpel is originated from carpel fusion, however, although the increased number of ovules renders it functionally similar to syncarpy. Gynoecial features, including the extensive occurrence of EGC and the increased number of ovules per carpel (consonant with reduction to a solitary carpel) in Cyathocalyx, may have evolved to overcome limitations associated with apocarpy and possibly contribute to the reproductive success and diversification of the family.

The earliest ovules or seeds widely reported from the Late Devonian (Famennian) are crucial for understanding the evolution of seed plants. Cosmosperma, the first Devonian seed documented in China and East Asia, is characterized by cupules with multiple segments enclosing a single ovule and covered by prickles. Two new Cosmosperma species, Cosmosperma dicrana sp. nov. and Cosmosperma lepta sp. nov., are now identified from the Upper Devonian (Wutong Formation) of Zhejiang and Anhui provinces, China, respectively. C. dicrana exhibits dichotomized fertile branches terminating in pairs of cupulate ovules, with centrifugally extending cupule segments at their distal portions. C. lepta displays slender cupulate ovules on pinnate fertile branches. Both species possess prickles on their cupules. A comparison with coeval seed plant taxa reveals differences in fertile branch types and suggests different evolutionary levels. The potentially weak dispersal ability of Cosmosperma is suggested by the absence of specialized structures for wind or water transport. Prickles on Cosmosperma cupules do not suggest adaptations for epizoochory but facilitate entanglement and friction. The adaptations for short-distance dispersal can be advantageous in a disturbed and heterogeneous environment. The presence of Late Devonian seed plant taxa with dispersal-adapted traits hints at habitat divergence, with some possibly inhabiting uplands or areas away from the coast. The prickles may also be an adaptation for maintaining stability in small- to medium-sized plants of the Late Devonian coastal communities.

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

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

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

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

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 (Fischer ex Trautv.) Makino 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 showed 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 identified 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.