Karst area are well known as their extremely biodiversity and the investigation of plants adaptation in these unique environments is one of research hotspots. Previous studies primarily focused on the genomic adaptation of karst endemic species, but the special adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas, serves as a valuable model for understanding the genomic mechanisms of this issue. Here, the genome of H. subcapitata was sequenced using the PacBio and Illumina platforms and de novo assembled with contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events likely facilitated the expansion of stress-responsive gene families, which in turn influenced functional pathway regulation. Especially, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared to the karst-endemic Primulina tabacum, H. subcapitata showed upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation was the unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.

Ectomycorrhizal (ECM) fungi form symbiotic relationships with woody plants, completing their life cycles through mutualistic associations. The evolution of this symbiosis involves genomic adaptations including gene gain and loss. However, how these genomic characteristics reflect speciation and adaptation throughout the evolutionary history of ECM fungi remains unclear. In the present study, we explored speciation and host adaptation in Tricholoma species, an ecologically relevant clade of ECM basidiomycetes. We compared the genomes of three species, Tricholoma matsutake, T. populinum, and T. bakamatsutake, which despite their close phylogenetic relationships, have different tree hosts. A phylogenetic tree constructed using single-copy orthologous genes estimated the divergence time of T. populinum to be approximately 28.48 Mya, coinciding with the diversification of subg. Eupopulus in East Asia. The split between T. matsutake and T. bakamatsutake was estimated at around 8.08 Mya, corresponding to the diversification period of evergreen broadleaved forests in East Asia. In this study, we identified 19, 13, and 13 positively selected genes in the genomes of T. bakamatsutake, T. matsutake, and T. populinum, respectively. Additionally, 2983, 2783, and 1548 genes have undergone rapid evolution in their genomes. GO enrichment analysis revealed the functions of these rapidly evolving genes, including those associated with cell cycle, cytoplasmic components, and GTPase mediation. Gene flow analysis indicated unidirectional migration from the ancestor of T. populinum to T. matsutake and T. bakamatsutake, whereas bidirectional gene flow was observed in the ancestors of T. matsutake and T. bakamatsutake. This study suggested that host-induced immigrant unviability in symbiotic fungi is the primary cause of prezygotic isolation. The combination of ecology-based genomic evidence and gene flow analysis offers new insight into the speciation and evolutionary mechanisms of symbiotic fungi.

The tribe Cunonieae comprises five genera and 214 species of shrubs and trees currently distributed in the Southern Hemisphere and the tropics, exhibiting an amphi-pacific disjunct distribution shared with Araucariaceae, Myrtaceae, Nothofagaceae, Podocarpaceae, and Proteaceae, among others. To address the central question of how historical geological forces have shaped the distribution of plant diversity in the southern hemisphere, we aimed to provide evidence from the biogeographical history of Cunonieae. We generated the most densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, based on 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL-F, rpl16, and ITS). We included 184 samples of Rosids to estimate divergence times using fossil calibration points. For biogeographic inference, we employed a time-stratified model including fossils as tips. Cunonia and Pterophylla were paraphyletic in the ITS tree, and Cunonia was paraphyletic in the plastid tree. Pancheria, Vesselowskya, and Weinmannia were monophyletic, the latter with conflicting nuclear and plastid phylogenies. The crown group Cunonieae was dated at ~56 Mya and its ancestral areas were Antarctica and Patagonia. Antarctica acted as a bridge between Australia and South America before the consolidation of the Antarctic Ice Sheet, and the extinction of the lineage in Antarctica from Oligocene to Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated further burst in diversification along the Andes, in Madagascar, and New Caledonia where at least three colonization events occurred.

Neotropical catfishes of the genus Rhamdia are divided into cis- and trans-Andean/Middle American reciprocally monophyletic components, the latter notable for its considerable cave-dwelling diversity. Despite previous research, uncertainties remain regarding the systematics and historical biogeography of the Middle American clade. To test previous phylogenetic hypotheses and improve our understanding of the evolutionary history of this group of Middle American freshwater fishes, we generated and analyzed comparative mitogenome-wide data from most valid species and known cave-dwelling forms. Our results corroborate this clade as divided into two reciprocally monophyletic groups (split dated at ~9 Ma): a clade representing the species Rhamdia guatemalensis (crown group dated at ~2.8 Ma) and a clade consisting of the remaining Middle American species (i.e., the Rhamdia laticauda species group; crown group dated at ~4 Ma). Our results also confirm the notion that R. laticauda is deeply paraphyletic and that phylogenetically scattered geographic lineages of this taxon could represent different species. Our divergence time estimates coupled with present-day distribution patterns support the biogeographic scenario in which northward dispersal and colonization of Central America and southern North America by Rhamdia was catalyzed by the emergence of the Panamanian Isthmus land bridge and stream captures across Lower Central America. Cave colonization in Middle American Rhamdia is widespread, convergent, relatively recent (dating from the Pleistocene), and most likely opportunistic, with established cave-dwelling populations possibly representing “evolutionary dead ends”.

The 26 genera of aurantioids and the 28 species of one genus, Citrus, are mapped. The distributions are explained, not by using fossil-calibrated clade ages and ancestral-area algorithms, but by focusing on the geometry of the clade distributions and the tectonic history at the break-zones (nodes). Allopatry is attributed to vicariance, overlap to normal dispersal. Subfamily Aurantioideae is allopatric with its sister groups in Eurasia and the Americas. In contrast, the seven main clades within Aurantioideae show a high level of overlap. But within each of these seven main clades, there is again a high level of allopatry. The pattern is explained by vicariance events at the first and third levels. The overlap at the second level can be accounted for if vicariance (now obscured) generated the clades and subsequent dispersal caused secondary overlap of the clades. This latter phase of mobilism can be explained by the migration of coastlines and maritime flora far inland during marine transgressions, especially in the mid-Cretaceous. Many aurantioids inhabit mangrove-associate vegetation, beach thicket, limestone substrate, and areas with high levels of disturbance. Within Citrus, the five main clades overlap in south-central China (Nanling Mountains) and are allopatric elsewhere. The overlap-zone has been interpreted as a centre of origin, but it is explained here as a break-zone, the site of vicariance in a widespread ancestor, where localised, secondary overlap has developed later. The zone coincides with a belt of mid-Cretaceous deformation manifested in voluminous magmatism, subsidence, rifting, back-arc extension, and the opening of the East China sea.

Pinaceae are one of the most economically and ecologically important tree families and play a key role in boreal, temperate and montane forests of the Northern Hemisphere. The family have a rich fossil record with the earliest occurrence of the Pinaceae crown group probably from the Late Jurassic, and diverse seed cones, woods, leaves and pollen grains from the Early Cretaceous of the Northern Hemisphere. However, the origin and early evolutionary history of Pinaceae is not well understood, in part because of uncertainty about the phylogenetic position of early fossils. In this paper we describe a new woody stem of Pinaceae based on well-preserved material from the Early Cretaceous Huolinhe Formation in Jarud Banner, eastern Inner Mongolia, Northeast China. Piceoxylon jarudense sp. nov. has distinct growth rings with secondary xylem composed of tracheids, ray tracheids, ray parenchyma cells, axial parenchyma cells, and axial and radial resin canals. Pitting on radial walls of tracheids is abietinean; cross-field pitting is piceoid and taxodioid with 2–6 pits arranged in 1–2 rows per cross-field. Axial and radial resin canals are lined by thick-walled epithelial cells. Piceoxylon has been considered to include species with wood anatomy comparable to extant Larix, Pseudotsuga, Picea and Cathaya. Comparisons of wood anatomy and constrained phylogenetic analyses of Piceoxylon jarudense, one of the earliest records of Piceoxylon, both suggest that P. jarudense is most likely allied with Larix and Pseudotsuga within the pinoid clade suggesting divergence of the Larix-Pseudotsuga clade before ~125.6 Ma.

Understanding how East Asian subtropical evergreen broad-leaved forests (EBLFs) evolved over time is not only vital for biodiversity conservation but also facilitates predictive modeling of ecosystem services under global change scenarios. During recent decades, numerous studies have been devoted to investigating evolution of EBLFs. However, there are often contradictory interpretations of the different taxa associated with different geological events and environmental backgrounds. Here, we synthesize several key aspects of the spatiotemporal evolution of EBLFs. Firstly, the EBLFs emerged concomitantly with the development of Asian monsoon systems, occurring no earlier than the Eocene. While the southernmost region was inhabited by tropical elements, EBLFs are not the direct relic of boreotropical flora because the presence of a broad arid belt at that time. Rather, they represent a unique assemblage including boreotropical relics, tropical floras and deciduous broad-leaved forests. Secondly, the evolution of EBLFs should not be contextualized within an enclave, the adjacent vegetation systems to elucidate the potential connections between EBLFs and other biomes should be considered to avoid an isolated phenomenon. Thirdly, the adaptive response of EBLFs to environmental changes caused by anthropogenic disturbance in subtropical regions remains understudied. Such a knowledge gap must be addressed to develop effective conservation strategies to sustain the ecosystem amidst the dual pressure of climate change and human activity in future. Finally, current researches have predominantly focused on the dominant tree species in EBLFs, whereas comprehensive understanding requires expanding the investigation of associated flora, including understory trees and herbaceous plants. This review not only consolidates contemporary perspectives on the evolution of EBLFs but also proposes a framework to navigate the Anthropocene challenges. By bridging historical patterns with future projections, we aim to catalyze transformative research on EBLFs resilience and sustainable management, fostering further research and development regarding the resurgence.

The rodent family Platacanthomyidae encompasses both the Malabar spiny tree mouse (genus Platacanthomys) and the soft-furred tree mice (genus Typhlomys). This family represents a typical relict group of ancient origin, and its evolutionary history and dynamics warrant further investigation. A critical scientific question concerns whether the evolutionary trajectory of this ancient taxon has been shaped by environmental perturbations, such as the periodic climatic oscillations of the Quaternary glacial periods. This study aims to elucidate the evolutionary trajectory of the Platacanthomyidae by examining fossil records alongside extant species. Molecular dating revealed that the most speciose genus Typhlomys within this family began diverging approximately 21.15 million years ago (Mya). The speciation rate and net diversification rate of the Platacanthomyidae was notably high around 20 Mya, but it has shown a continuous decline since then, while the extinction rate of this taxa has remained stable. The current dataset indicates that the evolutionary trajectory of this family appears to have remained unaffected by late Cenozoic climatic fluctuations and subsequent anthropogenic influences associated with societal development. The ancestral distribution reconstruction has not yielded conclusive evidence regarding the origin of this family, thereby positioning it among the most enigmatic taxa within Rodentia. Moreover, the evolutionary mechanisms underlying the divergence of these ancestral species and their subsequent ecological adaptations to paleoenvironmental changes require future studies.

Apomixis can confer fertility upon spontaneous hybrids and allopolyploids, both of which have played a pivotal role in the evolutionary trajectory and diversification of flowering plants. We hypothesized that an unusual morphotype of Elatostema represents a viable hybrid species between E. scabrum and E. hirticaule, as opposed to a sterile F1 hybrid. To test this, we employed phylogenomic, flow cytometry, cytological, and morphological analyses. A two-step phylogenomic approach was used. Genome skimming was performed on one E. longpingii population, three populations of each parent (E. scabrum, E. hirticaule), and ten Elatostema and one Pilea species. Population genetic analyses were then conducted using RAD sequencing data from the type population of hybrid and parent species. Phylogenomic analyses using genome skimming and RAD sequencing data consistently supported a hybrid origin, placing E. longpingii close to or nested within E. scabrum and distant from E. hirticaule. Chromosome counts revealed pentaploid, triploid, and tetraploid ploidy levels in E. longpingii, E. scabrum, and E. hirticaule, respectively. Flow cytometry suggested apomixis in E. longpingii and E. scabrum, while E. hirticaule exhibited sexual reproduction. Morphological studies indicated that E. longpingii shares traits from both parents. Our findings demonstrate a novel reproductively viable hybrid species in Elatostema, likely originated through a natural hybridization event involving heteroploidy, coupled with the inheritance of an apomictic reproductive pathway from its maternal parent. These results provide compelling evidence that hybridization and apomixis have played pivotal roles in driving reticulate evolution and promoting diversification within the Elatostema.

This study conducted phylogenomic analyses of the higher-level phylogeny and evolution of mitogenomes and characteristics of Lycosidae Sundevall, 1833 (wolf spiders) utilizing 56 complete mitogenomes. In comparison to analyses based on target-genes, the mitogenomic phylogenies revealed Tricassinae as sister to Hippasinae and positioned Tricassinae + Hippasinae as sister to Lycosinae + Pardosinae. The findings did not support Evippinae as sister to Sosippinae and indicated uncertain phylogenetic relationships among genera (Lycosa, Trochosa, Ovia and Alopecosa) within Lycosinae. The study proposes the validation of Wadicosinae, revisions of three species Pardosa multivaga Simon, 1880, Arctosa ningboensis Yin, Bao & Zhang, 1996 and Alopecosa cinnameopilosa (Schenkel, 1963), and recommends placing Halocosa hatanensis (Urita, Tang & Song, 1993) into Evippinae. Contrary to previous findings, the initial diversification of wolf spiders occurred during the Earliest Oligocene Glacial Maximum, with rapid diversification during the Miocene, both interpreted as responses to significant climate changes and grassland expansion during these periods. Within Lycosidae, mitochondrial gene rearrangements (seven patterns) were observed only in Piratula of Zoicinae and P. multivaga, primarily resulting from tRNA transportation and loss. Ancestral state reconstruction analyses did not support web building as the ancestral trait of lycosid prey-capture strategies, instead suggesting an evolutionary progression from vagrant hunting to web building and burrowing, with shifts to web building or burrowing occurring independently multiple times.

East Asia has been hypothesized to be separated into distinct northern and southern regions by a climatic barrier, which is an east−west-oriented arid zone at approximately 40° N in eastern China. However, the impacts of climate change and local environmental selection on widespread species in this area are still poorly understood. In this study, we generated extensive genomic data for the crop pest Aelia fieberi (Hemiptera: Pentatomidae), which was sampled across its entire distribution in China, and we used these data in combination with niche analyses to investigate its phylogeographic pattern and examine the impact of climate change on its population structure and demographic history. We found that A. fieberi comprised two genetic lineages (southern and northern) that diverged during the middle Pleistocene, leading to a distinct "south−north" genetic pattern; this divergence was probably triggered by Pleistocene climate change in the arid belt. The two lineages of A. fieberi both experienced population expansion after the Last Interglacial (LIG) until the Last Glacial Maximum (LGM) and experienced secondary contact in the late Pleistocene. Local environmental adaptation may play an important role in maintaining and/or reinforcing the south−north divergence. Our study provides a detailed example of how climatic barriers and local environmental selection collaborate to facilitate adaptation to heterogeneous landscapes in East Asia from a phylogeographic perspective.

Grylloblattids are an ancient insect lineage crucial for understanding insect evolution and phylogeny. Systematic and in-depth studies of this taxon are still needed. This investigation advances grylloblattid systematics through three principal contributions: taxonomic revision of extant Grylloblattidae with redesigned diagnostic keys, description of a new species Grylloblattella aletaiensis sp. nov., and geometric morphometrics analyses to quantify interspecific differentiation in the first tergum morphology across all genera of extant Grylloblattidae. We further sequenced and assembled the first complete mitochondrial genome (16,625 bp) from an Asian-lineage grylloblattid, revealing conserved gene arrangement and structural conservation shared with polyneopteran lineages. Phylogenetic delineation of basal lineages within Grylloblattidae was conducted using concatenated mitochondrial and nuclear loci, coupled with divergence time estimation analyses to reconstruct historical biogeographic dynamics. This multidisciplinary operational framework synthesizes molecular phylogenetics and temporal biogeography, establishing a robust empirical foundation for interdisciplinary research in paleoentomology, evolutionary developmental biology, and evidence-based conservation prioritization for relict insect lineages. The evolutionary history of grylloblattids is closely coupled with global geo-climate changes since the Mesozoic Era, serving as a model system for investigating the macroevolution of insects.