Understanding how East Asian subtropical evergreen broad-leaved forests (EBLFs) have 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 the 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. First, 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 of 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. Second, 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. Third, 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 amid the dual pressure of climate change and human activity in the future. Finally, current research has 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.

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.

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.

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.

Recent phylogenomic studies have confirmed that Scirtidae is one of the earliest-diverging groups of polyphagan beetles. Cretaceous 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 by analyzing ultraconserved element data 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.

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.

Due to the high cost of whole-genome sequencing 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 multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum, in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The EA 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 EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA 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 EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.

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.

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.

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.

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 modeling 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.

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 transfer RNA 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.

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.

Gene loss is a widespread phenomenon in species evolution, yet the evolutionary significance of large-scale gene loss—whether arising through neutral processes or adaptive evolution—remains a subject of ongoing debate. Agaricus bisporus, a globally distributed macrofungus, serves as an ideal model to investigate this phenomenon. Utilizing the “map-to-pan” method, we constructed a high-resolution pangenome comprising 30 793 genes and 143 Mb of additional sequences, including 21 370 genes absent in the reference genome. Phylogenetic and admixture analyses identified four genetic lineages: the globally distributed MIX and region-specific European, America, and Highland lineages. Core gene analyses revealed a substantially lower genetic load in MIX lineage, accompanied by a marked reduction in the frequency of deleterious mutations compared with other lineages. Presence–absence variation (PAV) analyses further demonstrated extensive gene loss in MIX lineage, with functional enrichment analyses associating these PAVs with DNA damage repair pathways. This finding suggests that gene loss could enhance tolerance to DNA damage, thereby mitigating mutation accumulation. A significantly higher proportion of lost PAVs in MIX lineage was under selective pressure, supporting gene loss as an adaptive strategy. Our findings highlight two key mechanisms facilitating the MIX lineage's broad distribution: (1) the reduction of deleterious mutations, thereby lowering genetic load, and (2) the selective loss of redundant, non-essential genes, enhancing adaptability across diverse environments. This study not only underscores the adaptive significance of large-scale gene loss in the evolution of A. bisporus but also offers a broader framework for understanding how gene loss events shape the evolutionary trajectories of other fungal species.

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.

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 postpolyploidy 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.

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.

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 regarding the systematics and historical biogeography of the Middle American clade remain. 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 genus Phaeolus holds significant economic and ecological value as an important pathogen of coniferous 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 the United States, and reconstructed the phylogeny, divergence times, and biogeography of Phaeolus based on internal transcribed spacers (ITS) and nuclear large ribosomal subunit (nLSU) sequences. Phylogenetic analyses identified two new species, Phaeolus himalayanus and Phaeolus occidentiamericanus, one new combination, Phaeolus hispidoides, one synonym, Phaeolus fragilis (treated as Phaeolus schweinitzii), and one new record from China, Phaeolus sharmae. Phaeolus himalayanus is characterized by pileate, imbricate basidiomata, round to irregular pores of two to three per millimeter, 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 of two to three per millimeter, mango-shaped to ellipsoid basidiospores (6.5–7.8 × 4–5 µm), and distribution in the western United States. Molecular clock analyses indicated that the genus Phaeolus likely originated in the Late Cretaceous, with species divergence occurring between 9–71 Ma. 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.

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.

Investigating the evolutionary history and species diversification patterns in hyperdiverse lineages is essential for understanding how species diversity accumulates and how floras assemble historically across diverse regions. A large angiosperm family, Apocynaceae, exhibited remarkable diversity in functional traits including growth form, fruit types, and pollen aggregation, which may have a substantial impact on species diversification rates. However, the lack of a robust and well dated phylogeny has hindered our understanding of Apocynaceae diversification. To address this gap, we reconstructed a robust phylogeny covering 22 of 25 tribes using plastome sequences, then employed this framework to estimate divergence times, analyze diversification patterns, and investigate associations between species diversification and functional traits. The plastome phylogenies received strong nodal support across most branches. Among higher taxonomic groupings, three subfamilies (Asclepiadoideae, Secamonoideae, and Periplocoideae) were monophyletic. At the tribal levels, 19 tribes were strongly supported as monophyletic except Melodineae, Willughbeieae, and Vinceae. Additionally, five genera (Vincetoxicum, Cynanchum, Hoya, Marsdenia, and Aganosma) were identified as nonmonophyletic. Our analyses revealed that Apocynaceae originated in the paleotropics during the middle Late Cretaceous. Integrating binary state speciation and extinction (BiSSE), hidden state speciation and extinction (HiSSE), and fast, intuitive state-dependent speciation-extinction (FiSSE) analyses, we found that species with pollinia had a higher speciation rate than those without. Dry-fruited species had a higher speciation rate than those with fleshy fruits. Furthermore, Bayesian analysis of macro-evolutionary mixtures (BAMM) detected a diversification rate increase coinciding with the evolution of pollinia with clip-type attachment mechanisms in the subfamily Asclepiadoideae. Herbs had the highest speciation rate, followed by climbers and self-supporting species. Our findings contribute to understanding the historical assembly of floras in tropical and subtropical Asia.

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, forewing vein 3r-m absent, an unusually enlarged terminal tarsomere of the midleg, and extremely elongated hindlegs. The ring of tubercles indicate that the new taxon was a parasitoid on wood-living insects. We discuss the morphology and function of the midlegs and hindlegs. 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 hindlegs to suspend themselves and their mate from the vegetation, providing support and stability during copulation.

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.

Carpesium (Asteraceae) represents the largest Asian genus within the subtribe Inulinae of the tribe Inuleae, exhibiting maximum species diversity in China. This study presents the first comprehensive phylogenetic analysis of Carpesium, utilizing nuclear ribosomal internal transcribed spacer (ITS), specific chloroplast DNA sequences (rps16-trnQ, rpl32-trnL, and ndhF-rpl32), whole chloroplast genomes and chloroplast coding sequence (CDS). The results demonstrate that Carpesium, excluding C. abrotanoides, constitutes a monophyletic group. The Carpesium s.str. clade contains two well-supported lineages with distinct morphological characteristics. Based on morphological analyses, molecular phylogenetic evidence, and karyotypic studies, this research establishes Cladocarpesium gen. nov. to accommodate C. abrotanoides. The comprehensive sampling approach has facilitated a thorough phylogenetic reconstruction of the Inula complex, establishing a robust systematic framework that clarifies previously uncertain relationships among constituent species. This multilocus methodology provides essential insights for reassessing infrageneric classifications within this taxonomically complex group.

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 were audified and the resultant media files were made easily accessible. This work provisionally addresses a problematic gap in public information on phylogenetics for nonvisual modalities, and exemplifies how evolutionary biologists might better respond to obligations in widening participation.

Understanding the genetic diversity and genetic load of endangered species is essential for developing effective conservation strategies, particularly in ecologically sensitive regions such as the Himalayas. Cupressus austrotibetica, a rare conifer and the tallest recorded tree in Asia, reaching up to 102.3 m, faces substantial anthropogenic and environmental threats. To evaluate its genetic status, we sequenced transcriptomes of 54 individuals sampled across its restricted range and compared them with 96 individuals of C. gigantea, a closely related endangered species with broader distribution at higher elevations. Our analysis reveals that C. austrotibetica exhibits higher genetic diversity (π = 0.0091) compared to C. gigantea (π = 0.0042). Demographic analyses identified three historical bottleneck events in C. austrotibetica and two in C. gigantea, with two of these events coinciding with Quaternary climatic oscillations. Despite its relatively high genetic diversity, C. austrotibetica has a smaller effective population size based on Stairway Plot 2 (N_e ≈ 7200) than C. gigantea (N_e ≈ 17 600). Furthermore, C. austrotibetica harbors a higher proportion of severe deleterious mutations, while C. gigantea retains more moderate deleterious variants. These findings indicate that a recent anthropogenic bottleneck event has likely driven the reduced population size and increased genetic load in C. austrotibetica, emphasizing the urgent need for conservation priorities for this imperiled species.

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.

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 aimed 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 Agrostisas 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, orabsent. Core (species with congruent alignment using ITS and plastid data) phylogenetic analysis of Agrostis reveals 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, that is, 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. aemulus (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. suspicatus Willd., and Vilfa muricata J. Presl.

We present a phylogenetic analysis of benthic ctenophores of the order Platyctenida, sampling all but one genus. Using complete mitochondrial genomes and nuclear ribosomal data and a reassessment of anatomy, our integrated analysis uncovers an unexpectedly close relationship between two unusual members of the Coeloplanidae: Coeloplana (Benthoplana) meteoris and Vallicula multiformis. These two species form a well-supported clade, deriving at or near the base of the tree of Platyctenida, distantly related to other Coeloplana, rendering Coeloplana and Coeloplanidae non-monophyletic. A unique mitochondrial gene order and a tentacle bulb with four extensions are newly identified synapomorphies of this lineage. We elevate the subgenus Benthoplana to the generic level, erect the new family Benthoplanidae for Benthoplana and Vallicula, and provide diagnoses for these taxa and their accepted species. We also show that planktonic Ctenoplana (Diploctena) neritica is the early life stage of Benthoplana meteoris, and suggest that the remaining Ctenoplanidae likely represent early life history stages of Coeloplanidae and perhaps other platyctenes. While both the nuclear ribosomal (18S and 28S) and mitochondrial protein-coding genes suggest a deep phylogenetic divergence between Benthoplanidae and Coeloplanidae, we detect conflicting phylogenetic signal between these markers, suggesting nuclear-mitochondrial discordance, leaving the placement of Tjalfiellidae and Lyroctenidae uncertain.

Geographical range size is a fundamental ecological characteristic of a species, and the product of complex interactions of many factors in its history. Here, we investigate the causes of range size variation among 43 species of the woody plant genus Betula (birches), which each occupy areas of between one and 20 million square kilometers in the northern hemisphere. We find their distributions are more affected by temperature variables than by precipitation variables. The climatic niche breadth, median latitude, width of seed wings, degree of bark peeling, and ploidy of species all have significant impacts on range size variation, but number of leaf veins and life form do not. Many of these attributes, and range size itself, have a phylogenetic component and, once phylogeny is accounted for, ploidy no longer has a significant effect on range size, and climatic niche breadth is clearly the most important factor. Our results therefore support the niche-breadth hypothesis for range size variation and to a lesser extent also support the dispersal-ability hypothesis and Rapoport's rule that range size decreases toward the tropics. The climatic niche breadth of Betula species is likely to be a key attribute in their ability to avoid decline or extinction under climate change.

The genetic structure and population history of ethno-linguistically diverse populations from the Yunnan–Guizhou Plateau remain underrepresented in human genomic research. We analyzed genome-wide data from 239 individuals in Guizhou, combined with modern and ancient datasets, to investigate their fine-scale genetic structure, demographic events, and functional consequences of adaptive genomic signatures. Our findings revealed three genetically distinct groups corresponding to linguistic categories, shaped by differential gene flow from ancient millet farmers and southern Chinese populations. We identified population-specific adaptive candidate genomic regions associated with immune, metabolic, and hematological functions. Additionally, we detected clinically relevant variants with implications for disease risk prediction and precision medicine. These findings underscore the importance of genetic diversity in understanding human adaptation and health disparities, offering a framework for equitable genomic research in underrepresented populations.

Weasels represent the most widely distributed and diverse lineage within the family Mustelidae. They have experienced adaptive radiation and have long been the subject of significant taxonomic debates. This study undertakes a comprehensive study of this group, employing morphological measurements, mitochondrial genomes, nuclear genes, and single copy orthologs extracted from whole genome data. Based on the outcomes of phylogenetic tree construction using orthologous genes, it is ultimately verified that the genera Mustela and Neogale are independent genera, thereby resolving the controversy regarding the species they encompass. Through molecular systematics and morphological studies, a putative Mustela species collected from Mabian Dafengding National Nature Reserve in Sichuan is confirmed as a new species, designated Mustela mopbie sp. nov. This new species exhibits molecular phylogenetic affinity with M. altaica and M. nivalis, yet shares morphological similarities with M. kathiah, M. nivalis and M. aistoodonnivalis. Notably, it is considerably smaller than these species and possesses distinctive body coloration and tail morphology. This study provides a detailed description of this new species and demonstrates that larger datasets yield more robust phylogenetic signal. Furthermore, we observed substantial incongruence between mitochondrial and nuclear gene trees, suggesting potential genomic introgression between this new species and its closely related congeners (M. altaica and M. nivalis).

Karst areas are well known for their extreme biodiversity and the investigation of plant adaptation in these unique environments is a research hotspot. Previous studies have primarily focused on the genomic adaptation of karst endemic species, but the specific 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 these genomic mechanisms. Here, the H. subcapitata genome was sequenced using the PacBio and Illumina platforms and de novo assembled with a 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% of sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: the 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 probably facilitate the expansion of stress-responsive gene families, which in turn influence functional pathway regulation. In particular, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared with the karst endemic Primulina tabacum, H. subcapitata showed the 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 is a unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.

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 themost densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, basedon 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL‐F, rpl16, and internal transcribed spacer (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 Ma, 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 the Oligocene to the Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated a further burst in diversification along the Andes, in Madagascar, and in New Caledonia, where at least three colonization events occurred.

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.

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 Ma. The speciation rate and net diversification rate of the Platacanthomyidae was notably high around 20 Ma, 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.

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.

Ectomycorrhizal (ECM) fungi form symbiotic relationships with woody plants, completing their life cyclesthrough mutualistic associations. The evolution of this symbiosis involves genomic adaptations including gene gain andloss. However, how these genomic characteristics reflect speciation and adaptation throughout the evolutionaryhistory 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. Gene ontology 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 causeof prezygotic isolation. The combination of ecology‐based genomic evidence and gene flow analysis offers new insightinto the speciation and evolutionary mechanisms of symbiotic fungi.

Fossil Ericales pollen from late Oligocene to Early Miocene sediments of the Ban Pa Kha Subbasin, Li Basin, northern Thailand, were examined using the single-grain method. A total of 24 different ericalean pollen types belonging to Ebenaceae (Diospyros), Ericaceae (Cassiope, Vaccinium, and Rhododendron), Pentaphylacaceae (Adinandra), Sapotaceae, Styracaceae (Rehderodendron and Styrax), and Symplocaceae (Symplocos) were identified. All the fossil pollen, except that of Sapotaceae, represent families/genera that are described for the first time from the Cenozoic of Thailand. By considering present terrestrial biome occupancy, Köppen–Geiger climate profiles, and vertical distributions of potential modern analogs of the parent plants producing the fossil pollen, the phytosociological and paleoecological preferences of the fossil taxa were assessed. Our results demonstrate that modern analogs of most of the ericalean taxa have wide ecological and climatic amplitudes with a broad zone of convergence in warm and cold temperate humid or seasonally dry climates. Exceptions are Sapotaceae, which rarely occur outside lowland tropical forests, and Cassiope, which at present occurs at high elevations and, besides Rehderodendron, is one of two modern analogs absent from the modern flora of Thailand. Along with a review of phytosociological studies in montane forests of northern Thailand and neighboring regions, this suggests that the assemblage of dispersed ericalean pollen of the Ban Pa Kha Subbasin likely derives from more than one vegetation type and possibly from different vertical zones.

The tribe Trichosporeae is the most species-rich, systemically complex, and morphologically diverse tribe in the Old World Gesneriaceae. It has long been a focal point and a challenge in the phylogeny of Trichosporeae, with frequent unclear relationships and delimitations among a lot of genera. Here, we conducted a molecular phylogenetic analysis by employing nine DNA fragments with a high sampling coverage for key clades in the tribe Trichosporeae. Meanwhile, we carried out a comprehensive morphological and anatomical investigation on vegetative and floral organs in related genera and species, and try to uncover morphological synapomorphies associated with molecular clades. Our results demonstrated a well-supported phylogeny of major clades in the tribe, strongly corroborated by morphological data. We find that some genera, such as Raphiocarpus, Briggsia, and Boeica, are not monophyletic. Based on molecular phylogenetic and morphological analyses, we established five new genera and revived a genus in the tribe Trichosporeae, including Neoraphiocarpus, Anisophyllaea, Hispidopalata, Pseudobriggsia, and Kaiyua with revival of Boeicopsis. We further redefined the genera Raphiocarpus and Briggsiopsis. Our results would deepen our understanding about the phylogeny of the Old World Gesneriaceae.