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.

Multimedia representations of phylogenies can only broaden the audience experiencing results of the field. I developed a bioinformatics pipeline for representation of phylogenies as audio and video, optimized to enable conversion of an extremely wide range of phylogeny structures (from tens to tens of thousands of terminals). I also compiled and standardized a set of contemporary phylogenetics results comprising only ones that were provisioned in analyzable form supplementary to a publication and that had been assigned a Creative Commons license by the authors. Fifty-six such phylogenies each were audified and the resultant media files made easily accessible. This work provisionally addresses a problematic gap in public information on phylogenetics for non-visual modalities, and exemplifies how evolutionary biologists might better respond to obligations in widening participation.

Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus’ distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro-Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro-Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro-Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro-Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.

Evanioidea, as a poorly known group of Hymenoptera, exhibited remarkable species diversity during the Cretaceous, especially within the basal fossil family †Praeaulacidae. Here, we describe a new genus and species, †Coronaulacus cancan gen. et sp. nov., from Cretaceous Kachin amber. Based on its unique morphological characteristics and phylogenetic analysis, we place the new genus into †Praeaulacidae. This new genus is significantly distinct from other genera of the family; it is characterized by a ring of tubercles around the median ocellus, fore wing vein 3r-m absent, an unusually enlarged terminal tarsomere of the midleg, and extremely elongated hind legs. The ring of tubercles indicate that the new taxon was a parasitoid on wood-living insects. We discuss the morphology and function of the mid legs and hind legs. We suggest that the males of this genus might have exhibited behavior similar to dance flies (Diptera: Empididae) or hangingflies (Mecoptera: Bittacidae). During mating, the males possibly used their mid legs with the expanded distal tarsus to effectively grasp and restrain the females and their elongate hind legs to suspend themselves and their mate from the vegetation, providing support and stability during copulation.

Burmoniscus Collinge, 1916, the most species-rich genus within the family Philosciidae, presents significant taxonomic challenges due to interspecific morphological convergences and intraspecific variations. This study employs an integrative taxonomic framework combining morphological examination with molecular phylogenetic analyses and species delimitations based on the sequence data of a mitochondrial COI gene and three nuclear genes (18S rRNA, 28S rRNA and NaK) to classify Burmoniscus species. Our results reveal 21 species Burmoniscus from China, including 12 new species (Burmoniscus acutatus Li & Jiang, sp. nov., B. obscurus Li & Jiang, sp. nov., B. cuneatus Li & Jiang, sp. nov., B. rectangulatus Li & Jiang, sp. nov., B. solus Li & Jiang, sp. nov., B. spinellosus Li & Jiang, sp. nov., B. cordatus Li & Jiang, sp. nov., B. trispinatus Li & Jiang, sp. nov., B. rotundus Li & Jiang, sp. nov., B. simplicissimus Li & Jiang, sp. nov., B. rubustus Li & Jiang, sp. nov. and B. variatus Li & Jiang, sp. nov.) and firstly report two species, B. schultzi Taiti, Ferrara & Kwon, 1992 and B. comtus (Budde-Lund, 1894) from China. This work highlights the critical role of integrative taxonomy in clarifying species boundaries and uncovering hidden diversity in terrestrial isopods.

Allopolyploidy, involving whole genome duplication (WGD) of interspecific hybrids, is a driving force in the evolution of angiosperms, and has provided favored substrates for the domestication of major agricultural crops. This suggests allopolyploidy is a rich source of genetic variation amenable to natural and artificial selection. While allopolyploidy-induced chromosomal variation is common, its immediate phenotypic effects are challenging to delineate due to the confounding influence of post-polyploidy evolution. Newly constructed allopolyploids, having not yet undergone evolution, present suitable systems to address this issue. In this study, we synthesized five sets of allotetraploids, each with a unique genome constitution of S*S*DD, comprising a common paternal (DD) but distinct maternal (S*S*) parental diploid species of Aegilops. We observed that, except for one sterile synthetic allotetraploid, the remaining four allotetraploids exhibited high fertility, enabling the establishment of sexual lineages through selfing. Chromosomal variation in both number and structure occurred extensively, demonstrating moderate (though variable) effects on key morphological traits related to growth, development, and reproductive fitness of the nascent allotetraploids. All four sets of fertile allotetraploids can be crossed with bread wheat to generate pentaploid F₁ hybrids, which as maternal parents can be further backcrossed to bread wheat. This approach promises a feasible strategy for the concomitant introgression of the vast repertoire of genetic variation from the D- and each of the four S* genome-containing species to bread wheat.

Cicadomorpha, the most diverse infraorder of hemipteran insects, is a group of plant sap-sucking insects consisting of three monophyletic superfamilies: Cercopoidea, Cicadoidea, and Membracoidea. This study aims to resolve the controversy surrounding the phylogenetic relationships between these superfamilies, specifically whether Cercopoidea is more closely related to Cicadoidea (topology H1) or Membracoidea (topology H2). To tackle this issue, we assembled four matrices, including three amino acid datasets and one nucleotide dataset, and performed comprehensive phylogenomic analyses using both coalescent and concatenation methods. Our results showed that the amino acid matrix with low ratio of missing data-based analyses strongly supported topology H2, indicating that Cercopoidea is sister to Membracoidea. However, the other three matrices yielded conflicting results. Interestingly, when site-heterogeneous models were used, the results flipped, and the datasets that previously supported topology H1 supported topology H2. Further analyses, including model comparisons, tree topology tests, and phylogenetic analyses without an outgroup, also supported the conclusion that Cercopoidea is more closely related to Membracoidea. The study highlights the importance of modelling among site compositional heterogeneity in phylogenomic analyses to mitigate systematic errors. Additionally, we noted that datasets with high missing data ratios may lead to conflicting phylogenetic relationships. Our study provides strong evidence that Cercopoidea is sister to Membracoidea and highlights the importance of careful methodological considerations in phylogenetic analyses.

The genus Phaeolus holds significant economic and ecological value as an important pathogen of conifer trees. Although species diversity within this genus has been described in recent years, there were limited studies of its origin, evolution, and biogeography. In this study, we collected new specimens from China and USA, and reconstructed the phylogeny, divergence times, and biogeography of Phaeolus based on ITS and nLSU sequences. Phylogenetic analyses identified two new species, Phaeolus himalayanus and Phaeolus occidentiamericanus, one new combination, Phaeolus hispidoides, one synonym, Phaeolus fragilis (treated as P. schweinitzii), and one new record from China, Phaeolus sharmae. Phaeolus himalayanus is characterized by pileate, imbricate basidiomata, round to irregular pores of 2-3 per mm, abundant gloeoplerous hyphae, mango-shaped to ellipsoid basidiospores (5.5-7 × 4-4.5 µm), and distribution in Xizang of China. Phaeolus occidentiamericanus is characterized by pileate, imbricate basidiomata, round to irregular pores 2-3 of per mm, mango-shaped to ellipsoid basidiospores (6.5-7.8 × 4-5 µm), and distribution in the western USA. Molecular clock analyses indicated that the genus Phaeolus likely originated in the Late Cretaceous, with species divergence occurring between 9-71 Mya. Ancestral state reconstruction suggested that the genus originated in the Himalaya-Hengduan Mountains region and subsequently dispersed to Europe and North America. The earliest host trees of Phaeolus were probably Abies and Pinus, with all known species capable of growing on Pinus, demonstrating a strong host trees preference. Additionally, a key of the genus Phaeolus is added. This study provides a crucial foundation in pathogen control and ecological conservation of this genus in the future.

Due to the high cost of whole-genome and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multi-genomic datasets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene datasets and organellar genomes derived from next-generation sequencing were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asian Bupleurum, in which two clades are strongly supported and all intersectional relationships are resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at approximately 50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The East Asian lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both East Asian groups. Combined with geological events and gene-environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with SCO tree. The arid event in Central Asia may have driven the adaptation of East Asian Bupleurum (especially in East Asian Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in East Asia, offering valuable insights into the interplay between genetic and ecological factors in plant diversification.