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 environment 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.

Recent phylogenomic studies have confirmed that Scirtidae is one of the earliest-diverging groups of polyphagan beetles. Cretaceous scirtid fossils and genome-scale data have shown promise in elucidating the evolutionary history of Scirtidae. However, knowledge about the Mesozoic diversity of scirtids remains limited, and a recent phylogenomic study of Australasian Scirtinae failed to consider among-site compositional heterogeneity. In this study, we present a refined phylogeny of Scirtinae using data from ultraconserved elements under the better-fitting site-heterogeneous CAT-GTR+G4 model. A new scirtine fossil, Serracyphon philipsi gen. et sp. nov., is reported from mid-Cretaceous Kachin amber. This fossil is characterized by serrate antennae, uncarinated antennomere 1, absence of subocular carinae, and absence of a buttonhole on subgenal ridges. The placement of Serracyphon is evaluated within our updated phylogenomic framework for scirtine evolution. Additionally, we critically reevaluate the taxonomy of the “Scirtes” fossils previously described from the Eocene of the Isle of Wight.

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.

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 datasets from 69,680 to 400,330 aa in length for phylogenomic reconstructions. Using these datasets, 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 newly revealed some 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.

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.

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, F. heterostyla, F. 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 V. 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.

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.

Carex sect. Paniceaesensu 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 (ETS, ITS) and three plastid (matK, trnL-F, and rpl32-trnL^UAG) regions, along with 474 nuclear loci from high-throughput sequencing (HybSeq). Dating analysis and ancestral area reconstruction were employed to investigate the evolutionary and biogeographic history of sect. Paniceae s.l. A broader circumscription of sect. Paniceae s.l., incorporating sects. Bicolores and Laxiflora, 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 Asian–Eastern North America pattern of disjunction.

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 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 modelled their ecological niche to understand their evolution and current distribution pattern. Our findings reveal that the plastomes of Trichoneura are generally conserved and range in length between 135,069 bp to 134,139 bp. Molecular results show that Trichoneura is monophyletic and diverged around 5.78 mya. 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 likely played pivotal roles in driving their divergence, leading to subsequent distribution towards neotropical regions during the Pliocene period. T. mollis and T. lindleyana occurring in different regions displayed varying morphology, and we suggest further morphological and phylogenetic analysis to determine their taxonomic delimitation.