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

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

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

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

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

Species are distributed heterogeneously, and different regions have contrasting 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 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.

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.

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.

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.

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.

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.

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.

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.