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While metopids (Armophorea: Metopida) represent the most species‐rich group of free‐living anaerobic ciliates thriving in hypoxic environments, our understanding of their true diversity remains incomplete. Most metopid species are still characterized only morphologically. Particularly, the so‐called IAC clade (named in the past after some of the taxa included, Idiometopus, Atopospira, and Clevelandellida), comprising free‐living members as well as the endosymbiotic ones (order Clevelandellida), is in serious need of revision. In our study, we establish a new free‐living genus in the IAC clade, Pidimetopus n. gen., with descriptions of two new species, P. nanus n. sp., and P. permonicus n. sp., using up‐to‐date molecular and morphologic methods. The genus is characterized by small cells (up to 75 μm long), not more than 10 adoral membranelles and eight somatic kineties, and usually, four long caudal cilia that can stiffen. In addition to morphologic and molecular characterizations, we also conducted a statistical morphotype analysis of the polymorphic species P. nanus n. sp. We discuss the relevance of the earlier morphologically described species Metopus minor as a putative collective taxon for several small metopids less than 50 μm long. [ABSTRACT FROM AUTHOR]

Metacommunity theory predicts that the relative importance of regional and local processes structuring communities will change over ecological succession. Determining effects of these processes on taxonomic and evolutionary diversity in spatially structured freshwater habitats of different successional stages may greatly improve understanding of the maintenance of diversity across temporal and spatial scales. In this study, we evaluated crayfish diversity at local and regional scales in pond metacommunities undergoing secondary succession from beaver (Castor canadensis) disturbance. Following theoretical predictions from metacommunity ecology of the increasing importance of local processes over succession, we hypothesised a decline in crayfish local and β diversity over succession from stronger local structuring as the older ponds may provide less suitable habitat than streams.Crayfish species and phylogenetic diversity were evaluated in beaver pond metacommunities and reference headwater streams located in three catchment regions. DNA sequences from the mitochondrial cytochrome oxidase I gene were used to assign crayfish to species for community and phylogenetic diversity tests. Local and β diversity were contrasted across beaver ponds ranging in age from 24 to 70 years and as a function of metacommunity processes.Counter to predictions, local species diversity among streams and the successional stages of ponds categorised by age class (24–39 years; 42–57 years; 60–70 years) did not differ, but community and phylogenetic convergence occurred in the oldest pond ecosystems. Crayfish community composition differed between the youngest and oldest ponds, resulting from higher abundance in the youngest ponds and community convergence in the oldest ponds. The association between community composition and the environment was strongest in streams and decoupled with pond age. In contrast, the correlation between intraspecific haplotype composition and the environment increased over succession. Among the three metacommunities, the regional crayfish species diversity arose from a combination of the temporal and environmental drivers from beaver‐constructed ecosystems and dispersal limitation within catchments.This study represents the first investigation of the taxonomic and phylogenetic diversity response to the successional stages of beaver pond metacommunities. The detection of differential crayfish composition and haplotype sorting to pond age suggests a role for local structuring and further indicates that future studies should acknowledge succession in shaping species diversity at local and regional scales. Dispersal limitation within catchment regions probably contributes to the evolution of crayfish species diversity in metacommunities and the overall maintenance of biodiversity.The results support a transition in community and freshwater ecology from a recent emphasis on spatial processes towards the integration of temporal drivers to better identify regulators of taxonomic and phylogenetic diversity across scales. [ABSTRACT FROM AUTHOR]

Russula is the largest genus in the Russulales and is widespread throughout the world. Almost all Russula species are known to be ectomycorrhizal with high ecological and edible values, and some are lethal poisonous. In this study, four new species belonging to the subgenus Russula crown clade are identified based on morphological and phylogenetic evidence from the Xizang Autonomous Region and other provinces of China. Morphologically, Russula paragraveolens (sect. Polychromae, subsect. Xerampelinae) is mainly characterised by a cherry red to blood red pileus centre, a reddish orange pileus margin; R. pseudograveolens (sect. Polychromae, subsect. Xerampelinae) is characterised by a violet brown to brownish red pileus centre, a pale red to pastel red pileus margin and short basidia; R. shigatseensis (sect. Flavisiccantes, subsect. Lepidinae) is characterised by a brownish orange to madder red pileus centre, pinkish red pileus margin, and having lateral branches or branches of hyphal terminations in pileipellis; R. yadongensis (sect. Tenellae, subsect. Laricinae) is characterised by a dark purplish red pileus centre with brownish purple tints and having isolated to clustered spines of spore ornamentations. Their distinct taxonomic status is confirmed by the positions of the four new species in both the ITS and 4-locus (nucLSU, mtSSU, rpb2, tef1) phylogenetic trees. [ABSTRACT FROM AUTHOR]

The study sample was collected during a field survey done in the year 2019 from Darjeeling hills, India. A detailed morphological description along with field images and internal transcribed spacer (ITS) sequence analyses suggested that the collected specimen is Gerhardtia foliicola. It is well characterized by its reddish brown and hygrophanous pileus, densely crowded lamellae, irregular ellipsoid basidiospores and its occurrence on leaf litter and humus in broadleaf or coniferous forests. [ABSTRACT FROM AUTHOR]

Seventy-eight Rhizoctonia isolates were obtained from brassicas in five Brazilian states between 2015 and 2017. The isolates were identified by phylogenetic analysis of the rDNA internal transcribed spacer region (ITS) and tested for pathogenicity and aggressiveness. Sixty-eight isolates were identified as R. solani and 10 isolates as binucleate Rhizoctonia. The most prevalent anastomosis group (AG) was AG-4 HG-I (83.3% of isolates), followed by AG-A (7.7%), AG-1 IB (2.6%), AG-G (2.6%), AG-R (2.6%) and AG-2-2 IIIB (1.3%). AG-4 HG-I isolates were widely distributed and recovered from all Brazilian states sampled, including 12 brassicas-growing fields. All isolates were pathogenic to broccoli, cauliflower and kale, causing necrotic lesions on subterraneous stems. There was no significant difference in aggressiveness among the different AGs in broccoli, but AG-1 IB isolates were more aggressive to cauliflower and AG-4 HG-I isolates were more aggressive to kale. This study is the first report of AG-4 HG-I, AG-2-2 IIIB, AG-A, AG-G and AG-R infecting brassica plants in Brazil. To our knowledge, this is the first detailed research of the AG composition of Rhizoctonia populations causing brassica diseases in Brazil. [ABSTRACT FROM AUTHOR]

Background and Aims Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. Methods Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. Key Results The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. Conclusions The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study. [ABSTRACT FROM AUTHOR]

Summary: Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited.Using exome capture sequencing and a fossil‐calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic.We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species.Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages. [ABSTRACT FROM AUTHOR]

Summary: Understanding the capacity of temperate trees to acclimate to limited soil water has become essential in the face of increasing drought risk due to climate change. We documented seasonal – or phenological – patterns in acclimation to water deficit stress in stems and leaves of tree species spanning the angiosperm phylogeny.Over 3 yr of field observations carried out in two US arboreta, we measured stem vulnerability to embolism (36 individuals of 7 Species) and turgor loss point (119 individuals of 27 species) over the growing season. We also conducted a growth chamber experiment on 20 individuals of one species to assess the mechanistic relationship between soil water restriction and acclimation.In three‐quarters of species measured, plants became less vulnerable to embolism and/or loss of turgor over the growing season. We were able to stimulate this acclimatory effect by withholding water in the growth chamber experiment.Temperate angiosperms are capable of acclimation to soil water deficit stress, showing maximum vulnerability to soil water deficits following budbreak and becoming more resilient to damage over the course of the growing season or in response to simulated drought. The species‐specific tempo and extent of this acclimatory potential constitutes preadaptive climate change resilience. [ABSTRACT FROM AUTHOR]

Summary: Across temperate forests, many tree species produce flowers before their leaves emerge. This flower–leaf phenological sequence, known as hysteranthy, is generally described as an adaptation for wind pollination. However, this explanation does not address why hysteranthy is also common in biotically pollinated taxa.We quantified flower–leaf sequence variation in the American plums (Prunus, subg. Prunus sect. Prunocerasus), a clade of insect‐pollinated trees, using herbaria specimens and Bayesian hierarchical modeling. We tested two common, but rarely interrogated hypotheses – that hysteranthy confers aridity tolerance and/or pollinator visibility – by modeling the associations between hysteranthy and related traits. To understand how these phenology–trait associations were sensitive to taxonomic scale and flower–leaf sequence classification, we then extended these analyses to all Prunus species in North America.Our findings across two taxonomic levels support the hypotheses that hysteranthy may help temporally partition hydraulic demand to reduce water stress and increase pollinator visibility – thereby reducing selective pressure on inflorescence size.Our results provide foundational insights into the evolution of flower–leaf sequences in the genus Prunus, with implications for understanding these patterns in biotically pollinated plants in general. Our approach suggests a path to advance these hypotheses to other clades, but teasing out drivers fully will require new experiments. [ABSTRACT FROM AUTHOR]

Aim: Understanding the historical biogeography of the Earth's oldest terrestrial lineages provides insights into lineage diversification in relation to plate tectonics, climate change and biome shifts at maximum timescales. We investigate the biogeography of an ancient arachnid family, dragon pseudoscorpions, which are found today in mesic (mostly temperate) forests on all continents except Antarctica and Europe, have potential origins on Pangea and comprise species with extremely limited dispersal capacities. We evaluate the respective role of continental vicariance (abiotic) and biome shifts (biotic) deep in time and unravel the evolutionary history of this ancient group. Location: Global. Taxon: Pseudotyrannochthoniidae (Arachnida: Pseudoscorpiones). Methods: Five loci were sequenced for 75 Pseudotyrannochthoniidae samples collected across the globe. A matrix was compiled comprising 106 terminals and ~8800 bp, and phylogenetic analyses were performed to uncover relationships. Divergence time and ancestral range estimation analyses were used to reconstruct historical biogeography. Results: Pseudotyrannochthoniidae was monophyletic with high support but relationships among genera did not reflect current taxonomy and instead showed geographical structuring. Pseudotyrannochthoniidae originated in East Asia during the Middle Triassic and began diversifying in the Early Cretaceous. Main Conclusions: Diversity and distributional patterns of dragon pseudoscorpions can be explained by the interplay of continental vicariance through Pangaean breakup, and biome shifts via the spread of temperate habitats in the Cretaceous and their ongoing distributional fluctuations. Pseudotyrannochthoniidae diversification began in the Early Cretaceous as they dispersed with temperate forests across the Northern Hemisphere. Cretaceous vicariance, followed by widespread Holarctic extinction in the Late Tertiary–Quaternary, created their disjunct distribution at northern latitudes. Northern and Southern Hemisphere lineages diverged as Gondwana and Laurasia rifted, and Gondwanan breakup resulted in Afrotropical/Indomalayan and Austral clades. Austral lineages spread with temperate forests, however, cooling caused their disappearance from Antarctica and led to disjunct distributions at low latitudes. [ABSTRACT FROM AUTHOR]

Aim: This study aimed to illustrate the changing diversity patterns of native freshwater fish in the past two centuries and to identify priority locations for native fish conservation to counter future degradation. Location: Japanese archipelago. Methods: We used the published native fish fauna data in 39 lakes across Japan, analysing historical and current diversity and projecting future distribution patterns based on the Japanese Red List. We assessed fish assemblages' taxonomic, phylogenetic, and functional alpha and beta diversity across different periods. Additionally, we proposed a cumulative diversity index that incorporated taxonomic, phylogenetic and functional facets, and then examined its relationship with the latitudinal positioning of the lakes across periods. Results: We observed a significant decrease in the richness of native freshwater fish since historical periods. Accompanying this decline were significant reductions in both phylogenetic relatedness and functional redundancy. Fish beta diversity increased from the past to the present and is predicted to decline drastically, indicating an ongoing homogenization process. Using the cumulative diversity index, we identified Hokkaido and Kyushu as crucial habitats for endemic fishes. These islands, with unique biogeographical backgrounds, contributed substantially to the national dissimilarity patterns of native fish assemblages in the historical period. However, the contribution is diminishing due to the ongoing decline in fish endemism. Main Conclusions: The conservation priority of native freshwater fish in Japan should be assigned to Hokkaido and Kyushu due to the inhabited endemic species. The proposed framework for assessing the cumulative diversity of biotic communities presented the potential to aid macroecological explorations that underpin biodiversity conservation. [ABSTRACT FROM AUTHOR]

New Zealand is home to 16 endemic species of Lepidium (Brassicaceae), including two species considered to have become extinct since European colonisation and an additional species shared with Australia. Previous meiotic chromosome counts suggest at least some are high polyploids. A hybrid origin has been proposed for several of them, with African and American species implicated as parents. We generated amplicon sequence data for 15 genes derived from targeted enrichment data from a selection of species endemic to New Zealand, and of African, American, and Australian origin naturalised in New Zealand. These were analysed, along with publicly available genomic data from other Lepidium species. Our results are consistent with earlier work in supporting two main groups of endemic New Zealand Lepidium, corresponding to different dominant nrDNA sequences. Our data suggest that these two groups differ in ploidy (one octoploid, the ploidy of the other uncertain). The octoploid species combine four distinguishable subgenomes and the other species may be the products of allopolyploidisation between octoploid species and a diploid species closely related to, if not, L. africanum. Previously proposed links to American Lepidium are also supported, with at least two Australasian Lepidium subgenomes related to subgenomes present in American polyploid species. The affinities of two further subgenomes present in Australasian Lepidium remain to be determined, but they may also be of American origin. One New Zealand endemic species, L. naufragorum, displays sequences broadly consistent with it being the octodecaploid product of hybridisation between octoploid and decaploid New Zealand groups. [ABSTRACT FROM AUTHOR]

We used entire mitochondrial (mt) genome sequences (14.5–15 kbp) to resolve the phylogeny of the four main lineages of the Haematobothrion ticks: Alloceraea, Archaeocroton, Bothriocroton and Haemaphysalis. In our phylogenetic trees, Alloceraea was the sister to Archaeocroton sphenodonti, a tick of an archetypal reptile, the tuatara, from New Zealand, to the exclusion of the rest of the species of Haemaphysalis. The mt genomes of all four of the Alloceraea species that have been sequenced so far had a substantial insert, 132–312 bp, between the tRNA‐Glu (E) gene and the nad1 gene in their mt genomes. This insert was not found in any of the other eight subgenera of Haemaphysalis. The mt genomes of 13 species of Haemaphysalis from NCBI GenBank were added to the most recent data set on Haemaphysalis and its close relatives to help resolve the phylogeny of Haemaphysalis, including five new subgenera of Haemaphysalis not previously considered by other authors: Allophysalis (structurally primitive), Aboimisalis (structurally primitive), Herpetobia (structurally intermediate), Ornithophysalis (structurally advanced) and Segalia (structurally advanced). We elevated Alloceraea Schulze, 1919 to the status of genus because Alloceraea Schulze, 1919 is phylogenetically distinct from the other subgenera of Haemaphysalis. Moreover, we propose that the subgenus Allophysalis is the sister to the rest of the Haemaphysalis (14 subgenera) and that the 'structurally primitive' subgenera Hoogstraal and Kim comprise early diverging lineages. Our matrices of the pairwise genetic difference (percent) of mt genomes and partial 16S rRNA sequences indicated that the mt genome sequence of Al. kitaokai (gb# OM368280) may not be Al. kitaokai Hoogstraal, 1969 but rather another species of Alloceraea. In a similar way, the mt genome sequence of H. (Herpetobia) nepalensis Hoogstraal, 1962 (gb# NC_064124) was only 2% genetically different to that of H. (Allophysalis) tibetensis Hoogstraal, 1965 (gb# OM368293): this indicates to us that they are the same species. Alloceraea cretacea may be better placed in a genus other than Alloceraea Schulze, 1919. Reptiles may have been the host to the most recent common ancestor of Archaeocroton and Alloceraea. [ABSTRACT FROM AUTHOR]

The genus Gracilinanus ranges from savannas to dense forests in South America, yet its systematics have never been thoroughly investigated across its wide distributional range. We assessed Gracilinanus phylogenetic relationships, species boundaries, and geographical limits using mtDNA sequences. Our analysis confirmed the distinctiveness of the six recognized species (G. aceramarcae, G. agilis, G. emiliae, G. marica, G. microtarsus, and G. peruanus), with a mean p-distance for interspecific nucleotide sequence divergences ranging from 13–16.2% and robust phylogenetic support (BPP > 0.95; BS > 75%). Refined species delimitation approaches (GMYC, PTP, ASAP) revealed potential cryptic diversity, suggesting up to 20 candidate species. Three geographically structured and divergent lineages (4.1–4.8% sequence divergence) were identified within G. agilis, extending its Cerrado range. Within G. emiliae, we found divergence values ranging from 4.7–5.7% and the first known record for the northeastern Atlantic Forest. Three divergent clades were recovered within G. microtarsus (9.0–9.8% sequence divergence), including a new lineage for the northern Atlantic Forest. For G. peruanus, we found two divergent lineages (7.2%) and the first documented occurrence for Amazonian lowland forest. This comprehensive sampling revealed greater genetic diversity in Gracilinanus, extending its geographic limits. Here we propose nine putative new species, emphasizing a hidden diversity that warrants formal description and further increases the taxonomic diversity of this genus. These newly identified lineages underscore the urgency of inventorying and conserving the threatened ecosystems of the Cerrado and Atlantic Forest hotspots. [ABSTRACT FROM AUTHOR]

We report the first North American origin class I avian orthoavulavirus 1 (AOAV-1) isolated from a faecal dropping of wild Eurasian teal (Anas crecca) in South Korea. Whole genome sequencing and comparative phylogenetic analysis revealed that the AOAV-1/Eurasian teal/South Korea/KU1405-3/2017 virus belongs to the sub-genotype 1.2 of class I AOAV-1. Phylogenetic analysis suggested multiple introductions of the North American sub-genotype 1.2 viruses into Asia and its establishment in the wild bird population in East Asia since May 2011. These results provide information on the epidemiology of AOAV-1, particularly the role of migratory wild birds in exchanging viruses between the Eurasian and North American continents. Enhanced genomic surveillance is required to improve our understanding on the evolution and transmission dynamics of AOAV-1 in wild birds. [ABSTRACT FROM AUTHOR]

The genus Indotyphlops has a widespread distribution in the Indian landmass and Southeast Asia, with 20 reported species. The current classification within the genus is based on morphology. In this study, we sampled all the reported Indotyphlops species from subcontinental India, to resolve relationships within this genus and to understand biogeographic patterns that resulted in the widespread distribution. We generated sequences for five nuclear markers which were used in the global typhlopoid phylogeny and built phylogenetic trees of the superfamily Typhlopoidea. We also carried out divergence time analysis and biogeographic analysis to understand the time and modes of dispersal and diversification of these species. The results show Indotyphlops sensu lato to be polyphyletic, with the clade consisting of I. porrectus and I. exiguus sister to a clade consisting of the southeast Asian typhlopid genera Ramphotyphlops, Anilios, Malayotyphlops, Acutotyphlops, Sundatyphlops, and Indotyphlops sensu stricto. The other clade consists of I. pammeces and I. braminus from the Indian subcontinent and I. albiceps from Southeast Asia. Biogeographical analysis suggests two dispersals from Asia to the Indian landmass—an earlier dispersal from Eurasia into India led to the lineage consisting of I. porrectus and I. exiguus, followed by a later dispersal that evolved into I. pammeces and I. braminus. These results necessitate a taxonomic revision. We propose the genus Pseudoindotyphlops gen. nov. for the clade currently consisting of the most recent common ancestor (MRCA) of I. porrectus and I. exiguus, and all descendants thereof. [ABSTRACT FROM AUTHOR]

This article aimed to detect the existence of barley-specific Nikita and Sukkula retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposon-amplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese × Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for Nikita and 0–73% in all samples for Sukkula. In addition, intrapopulation genetic polymorphism rates were also 0–15% in Chinese × Embden crossbred, 0–25% in Turkish White, 0–25% in Turkish Multicolor for Nikita; while 0–27% in Chinese × Embden, and 0–50% in Turkish Multicolor for Sukkula. There was no polymorphism for Sukkula among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In silico analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements. [ABSTRACT FROM AUTHOR]

Aim Location Taxon Methods Results Main Conclusions The efficiency of animal‐mediated seed dispersal is threatened by the decline of animal populations, especially in tropical forests. We hypothesise that large‐seeded plants with animal‐mediated dispersal tend to have limited geographic ranges and face an increased risk of extinction due to the potential decline in seed dispersal by large‐bodied fruit‐eating and seed‐dispersing animals (frugivores).Atlantic Forest, Brazil, South America.Angiosperms.First, we collected dispersal‐related traits (dispersal syndrome, fruit size, and seed size), growth form (tree, climber, and other) and preferred vegetation type (open and closed) data for 1052 Atlantic Forest plant species. Next, we integrated these with occurrence records, extinction risk assessments, and phylogenetic trees. Finally, we performed phylogenetic generalised least squares regressions to test the direct and interactive effects of dispersal‐related traits and vegetation type on geographical range size.Large‐seeded species had smaller range sizes than small‐seeded species, but only for species with animal‐mediated dispersal, not for those dispersed by abiotic mechanisms. However, plants with abiotic dispersal had overall smaller range sizes than plants with animal‐mediated dispersal. Furthermore, we found that species restricted to forests had smaller ranges than those occurring in open or mixed vegetation. Finally, at least 29% of the Atlantic Forest flora is threatened by extinction, but this was not related to plant dispersal syndromes.Large‐seeded plants with animal‐mediated dispersal may be suffering from dispersal limitation, potentially due to past and ongoing defaunation of large‐bodied frugivores, leading to small range sizes. Other factors, such as deforestation and fragmentation, will probably modulate the effects of dispersal on range size, and ultimately extinction. Our study sheds light on the relationship between plant traits, mutualistic interactions, and distribution that are key to the functioning of tropical forests. [ABSTRACT FROM AUTHOR]

True mangroves and mangrove associates are salt‐tolerant trees and shrubs that serve a critical role in preserving the ecological balance of tropical and subtropical estuarine environments. However, they are not immune to the damage caused by fungal pathogens. In this study, leaves exhibiting leaf spot symptoms were gathered from mangrove estuary and forests in Prachuap Khiri Khan, Thailand. Through morphological and multilocus phylogenetic analyses (LSU, ITS, RPB2 and TUB2) along with genealogical concordance phylogenetic species recognition, we identified Allophoma acanthi sp. nov. from Acanthus ilicifolius. Additionally, A. minor was identified as the causative agent of leaf spots in true mangrove and mangrove associate species, namely, Acanthus ilicifolius, Combretum sp., Hibiscus tiliaceus, Intsia bijuga, Lumnitzera racemosa and Sonneratia alba. We also provide evidence to support the synonymization of A. thunbergiae with A. minor. All eight isolates of Allophoma species in this study demonstrated pathogenicity to their original hosts with varied virulence, confirming Koch's postulates. Our findings contribute to the understanding of fungal pathogens affecting true mangroves and mangrove associates. [ABSTRACT FROM AUTHOR]

Aim Location Methods Results Main Conclusions Understanding how species' traits mediate environmental responses provides a mechanistic perspective on community assembly processes. Although traits that influence the response of multicellular organisms to environments have been studied, the identification of such traits in unicellular organisms, like ciliates, is underexplored. Since ciliates are dominant animals in coastal sandy sediments and contribute significantly to interstitial community respiration, identifying links between their occurrence and sandy‐coast characteristics is crucial for conserving biodiversity and protecting coastal habitats.Coasts of China.We used Hierarchical Modelling of Species Communities, a trait‐based joint species distribution model, to analyse ciliate community data collected from 344 sites belonging to 31 beaches across the Chinese coastline.We found that physical variables play the most important role in determining ciliate occurrence. The beach index combines the tidal range, sediment grain size and beach slope of beach‐selected species based on body size as well as feeding type, while sediment grain size constrained different mobility types, with swimming species favouring fine sandy sediments. The significant contribution of phylogeny in explaining the residual variation among species responses indicates that there are phylogenetically conserved but unmeasured traits too that influence species' responses. Species richness of benthic ciliates was higher in dissipative beaches with high primary productivity.Based on our research, ciliate occurrence in coastal beaches is mediated by their traits which are filtered by local environmental variables. The beach index is essential in predicting distribution patterns and species richness of benthic ciliates. Nevertheless, further research is needed to identify additional traits that will enhance the accuracy of predicting ciliate niches. Our study provides insights into the mechanisms driving ciliate community assembly processes and has implications for the conservation of biodiversity in sandy coastal habitats. [ABSTRACT FROM AUTHOR]

Background: Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. Result: Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. Conclusion: Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution. [ABSTRACT FROM AUTHOR]

Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225–146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses. [ABSTRACT FROM AUTHOR]

Random forests have emerged as a promising tool in comparative metagenomics because they can predict environmental characteristics based on microbial composition in datasets where β-diversity metrics fall short of revealing meaningful relationships between samples. Nevertheless, despite this efficacy, they lack biological insight in tandem with their predictions, potentially hindering scientific advancement. To overcome this limitation, we leverage a geometric characterization of random forests to introduce a data-driven phylogenetic β-diversity metric, the adaptive Haar-like distance. This new metric assigns a weight to each internal node (i.e., split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial composition. Alongside this, a weighted nearest-neighbors classifier, constructed using the adaptive metric, can be used as a proxy for the random forest while maintaining accuracy on par with that of the original forest and another state-of-the-art classifier, CoDaCoRe. As shown in datasets from diverse microbial environments, however, the new metric and classifier significantly enhance the biological interpretability and visualization of high-dimensional metagenomic samples. Author summary: Traditional phylogenetic β-diversity metrics, particularly weighted and unweighted UniFrac, have had great success in comparing and visualizing high-dimensional metagenomic samples. Nonetheless, these metrics rely upon pre-established biological assumptions that might not capture key microbial players or relationships between some samples. On the contrary, supervised machine learning algorithms, such as random forests, can often capture intricate relationships between microbial samples; however, unveiling these relationships is often challenging due to the intricate inner mechanisms inherent to these algorithms. The adaptive Haar-like distance integrates the merits of β-diversity metrics and random forests, allowing for precise, intuitive, and visual comparison of metagenomic samples, offering valuable scientific insight into the distinctions and associations among microbial environments. [ABSTRACT FROM AUTHOR]

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants. [ABSTRACT FROM AUTHOR]

Rare species are often considered inferior competitors due to occupancy of small ranges, specific habitats, and small local populations. However, the phylogenetic relatedness and rarity level (level 1–7 and common) of interacting species in plant-plant interactions are not often considered when predicting the response of rare plants in a biotic context. We used a common garden of 25 species of Tasmanian Eucalyptus, to differentiate non-additive patterns in the biomass of rare versus common species when grown in mixtures varying in phylogenetic relatedness and rarity. We demonstrate that rare species maintain progressively positive non-additive responses in biomass when interacting with phylogenetically intermediate, less rare and common species. This trend is not reflected in common species that out-performed in monocultures compared to mixtures. These results offer predictability as to how rare species' productivity will respond within various plant-plant interactions. However, species-specific interactions, such as those involving E. globulus, yielded a 97% increase in biomass compared to other species-specific interaction outcomes. These results are important because they suggest that plant rarity may also be shaped by biotic interactions, in addition to the known environmental and population factors normally used to describe rarity. Rare species may utilize potentially facilitative interactions with phylogenetically intermediate and common species to escape the effects of limiting similarity. Biotically mediated increases in rare plant biomass may have subsequent effects on the competitive ability and geographic occurrence of rare species, allowing rare species to persist at low abundance across plant communities. Through the consideration of species rarity and evolutionary history, we can more accurately predict plant-plant interaction dynamics to preserve unique ecosystem functions and fundamentally challenge what it means to be "rare". [ABSTRACT FROM AUTHOR]

Summary The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity. [ABSTRACT FROM AUTHOR]

Simple Summary: Many resources exist to analyze cancer RNA data, but many of the algorithms and programs can appear as black boxes to non-bioinformaticians. To make RNA data more accessible, we here present modular barcoding, an approach predicated on the idea that cancer type-specific modules derived from high-quality, "gold standard" datasets will also be of high quality. Key to the use of these modules is their direct visualization, which can be done in spreadsheet programs in a color-coded way, essentially creating interactive heatmaps and visual gene set enrichments. We illustrate a variety of uses, including cancer subtype analyses, novel gene–gene and gene–clinical relationships, the inference of novel gene functions, and single-cell RNAseq analysis. Finally, we provide the tools for users to create their own modules, which will further improve their quality over time as single-cell RNAseq resolution advances. Modular barcoding is a user-friendly, tractable, yet powerful approach to make novel transcriptomic discoveries. A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses. [ABSTRACT FROM AUTHOR]

Background Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. Methods We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. Results Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P <.001). Conclusions IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission. [ABSTRACT FROM AUTHOR]

IntroductionMethodsKey results and conclusionsDicranum Hedw. is one of the most taxonomically challenging genera of mosses, having 93 accepted species worldwide. Although recent integrative taxonomic revisions have clarified the delimitation of most species within this genus, the circumscriptions of some Dicranum species remain unsolved. During our recent survey of Dicranum in China, an intriguing species with an unknown combination of morphological traits was discovered in the Shennongjia National Nature Reserve, Central China. We carried out a study to provide morphological and phylogenetic evidence with which to determine the taxonomic status of this Chinese species.The phylogenetic evidence was obtained through the combined analysis of five loci (rps4–trnT, trnL–trnF, trnH–psbA, rps19–rpl2 and rpoB) and one nuclear region (nrITS1–5.8S–ITS2). Morphological characteristics were investigated by microscopic examination of specimens.A new moss species, Dicranum shennongjiaense W.Z.Huang & R.L.Zhu, is described and illustrated based on molecular and morphological evidence. This new species is characterised by its falcate leaves, rectangular and elongated laminal cells with strongly protruding upper angles on the dorsal side in the upper leaf portion, irregularly bistratose laminal cells above the midleaf, one layer of guide cells in the costa, and sharp serrations on the dorsal side of the costa in the upper leaf portion. Additionally, D. baicalense Tubanova, previously known only from Russia, is newly reported for China. A key for identification of the Chinese species of Dicranum sect. Dicranum is provided. [ABSTRACT FROM AUTHOR]

Background: Woody bamboos are the only diverse large perennial grasses in mesic-wet forests and are widely distributed in the understory and canopy. The functional trait variations and trade-offs in this taxon remain unclear due to woody bamboo syndromes (represented by lignified culm of composed internodes and nodes). Here, we examined the effects of heritable legacy and occurrence site climates on functional trait variations in leaf and culm across 77 woody bamboo species in a common garden. We explored the trade-offs among leaf functional traits, the connection between leaf nitrogen (N), phosphorus (P) concentrations and functional niche traits, and the correlation of functional traits between leaves and culms. Results: The Bayesian mixed models reveal that the combined effects of heritable legacy (phylogenetic distances and other evolutionary processes) and occurrence site climates accounted for 55.10–90.89% of the total variation among species for each studied trait. The standardized major axis analysis identified trade-offs among leaf functional traits in woody bamboo consistent with the global leaf economics spectrum; however, compared to non-bamboo species, the woody bamboo exhibited lower leaf mass per area but higher N, P concentrations and assimilation, dark respiration rates. The canonical correlation analysis demonstrated a positive correlation (ρ = 0.57, P-value < 0.001) between leaf N, P concentrations and morphophysiology traits. The phylogenetic principal components and trait network analyses indicated that leaf and culm traits were clustered separately, with leaf assimilation and respiration rates associated with culm ground diameter. Conclusion: Our study confirms the applicability of the leaf economics spectrum and the biogeochemical niche in woody bamboo taxa, improves the understanding of woody bamboo leaf and culm functional trait variations and trade-offs, and broadens the taxonomic units considered in plant functional trait studies, which contributes to our comprehensive understanding of terrestrial forest ecosystems. [ABSTRACT FROM AUTHOR]

The majority of pigeon paramyxovirus type 1 (PPMV-1) strains are generally non-pathogenic to chickens; however, they can induce severe illness and high mortality rates in pigeons, leading to substantial economic repercussions. The genomes of 11 PPMV-1 isolates from deceased pigeons on meat pigeon farms during passive monitoring from 2009 to 2012 were sequenced and analyzed using polymerase chain reaction and phylogenetic analysis. The complete genome lengths of 11 isolates were approximately 15,192 nucleotides, displaying a consistent gene order of 3′-NP-P-M-F-HN-L-5′. ALL isolates exhibited the characteristic motif of 112RRQKRF117 at the fusion protein cleavage site, which is characteristic of velogenic Newcastle disease virus. Moreover, multiple mutations have been identified within the functional domains of the F and HN proteins, encompassing the fusion peptide, heptad repeat region, transmembrane domains, and neutralizing epitopes. Phylogenetic analysis based on sequences of the F gene unveiled that all isolates clustered within genotype VI in class II. Further classification identified at least two distinct sub-genotypes, with seven isolates classified as sub-genotype VI.2.1.1.2.2, whereas the others were classified as sub-genotype VI.2.1.1.2.1. This study suggests that both sub-genotypes were implicated in severe disease manifestation among meat pigeons, with sub-genotype VI.2.1.1.2.2 displaying an increasing prevalence among Shanghai's meat pigeon population since 2011. These results emphasize the value of developing pigeon-specific vaccines and molecular diagnostic tools for monitoring and proactively managing potential PPMV-1 outbreaks. [ABSTRACT FROM AUTHOR]

A new species of Pristionchus was isolated from a soil-dwelling bee, Halictus (Seladonia) aerarius, collected from Sugadaira, Nagano, Japan. The nematode was successfully cultured on nematode growth medium agar previously inoculated with the Escherichia coli strain OP50; however, it did not propagate well. Typologically, the new species is similar to other Pristionchus belonging to the maupasi, pacificus and lheritieri groups in the stomatal structure of stenostomatous form. However, the species is characterised by the relatively short, conical tail of the female and the arrangement of male genital papillae in which the second- and third-paired papillae are almost at the same level and one of these two are directed laterally. Phylogenetically, the nematode belongs to the maupasi group, the ‘American clade’ within the genus, and is separable from the other species in the group. Biologically, the species has several interesting characters: it is seemingly native to Japan, regardless of its phylogenetic group; it is in tight and specific phoretic association with a eusocial bee; it lacks a eurystomatous form (or this form occurs rarely) under cultured conditions; and it shows characteristic clumping behaviour on culture media. The new species is taxonomically described herein as Pristionchus seladoniae n. sp. [ABSTRACT FROM AUTHOR]

The walnut industry in Argentina has grown in recent years, especially in northern Patagonia. However, this expansion has also brought new challenges, including the emergence of diseases threatening the health and productivity of walnut plantations. One of the most important diseases affecting walnut crops worldwide is ‘ink disease’ or ‘walnut dieback'. The aim of this study was to characterize ink disease, identify the aetiological agents, and estimate its incidence in walnut orchards of northern Patagonia, Argentina. Symptomatic trees were observed in the seven surveyed walnut orchards, showing a range of symptoms, including chlorosis and wilting, stem cankers and desiccation. In vivo assay and molecular analyses revealed that not only Phytophthora (P.) but also Phytopythium (Ph.) species are the causal agents of the disease, with P. drechsleri, Ph. mercuriale and Ph. vexans  being the most virulent over the commonly used rootstock Juglans hindsii. Notably, Ph. vexans was the most frequently isolated pathogen, suggesting its prevalence and potential impact on the regional walnut industry. Overall, this study provides critical insights into the prevalence and impact of Phytophthora and Phytopythium species on walnut health in northern Patagonia. The presence of multiple pathogenic oomycete species raises concerns about the health of walnut orchards, as well as the potential risk of pathogen transmission to other fruit crops in the region. The findings will help growers to develop better cultural practices and implement measures to guarantee the sustainability of the walnut industry in Patagonia. [ABSTRACT FROM AUTHOR]

Background: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. Results: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12–36 Mb) and gene-sparse (~ 2300–5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70–90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. Conclusions: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites. [ABSTRACT FROM AUTHOR]

Despite the high biological and ecological diversity of the South China Sea, limited research has been conducted on the deep‐sea species diversity of caridean shrimps. Based on the collections from three scientific expeditions conducted in the South China Sea, 31 caridean species, belonging to nine families, were reported, including the identification of two species not previously documented in this region, namely Janicella spinicauda (A. Milne‐Edwards, 1883) and Systellaspis curvispina Crosnier, 1988. In addition to morphological features, the COI and 16S gene sequences of these species were analyzed to assess their evolutionary relationships within each family. Phylogenetic analyses, with highest species coverage to date, indicated that similarity in morphological characteristics does not always lead to closer phylogenetic relationships and some defining characteristics for specific taxa are not always synapomorphies but may be the result of convergent evolution. Our results establish reliable evolutionary relationships within specific taxa and highlight the necessity for further taxonomic revisions within these taxa. [ABSTRACT FROM AUTHOR]

The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein‐coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T‐rich region. The gene organization and arrangement were similar to those of all other known Satyrinae mitogenomes. All PCGs were initiated with the canonical codon pattern ATN, except for the cox1 gene, which used an atypical CGA codon. Nine PCGs used the complete stop codon TAA, while the remaining PCGs (cox1, cox2, nad4, and nad5) were terminated with a single T nucleotide. The canonical cloverleaf secondary structures were found in all tRNAs, except for trnS1 which lacked a dihydrouridine arm. The 448 bp A + T‐rich region was located between rrnS and trnM, and it included the motif ATAGA followed by a 19‐bp poly‐T stretch and a microsatellite‐like (TA)6 element preceded by the ATTTA motif. The phylogenetic tree, inferred using Bayesian inference and maximum likelihood methods, generated similar tree topologies, revealing well‐supported monophyletic groups at the tribe level and recovering the relationship ((Satyrini + Melanitini) + ((Amathusiini + Elymniini) + Zetherini)). The close relationship between Satyrina and Melanargiina within the Satyrini was widely accepted. Additionally, Lethina, Parargina, and Mycalesina were closely related and collectively formed a sister group to Coenonymphina. Moreover, A. merlina was closely related to Oeneis buddha within the Satyrina. These findings will provide valuable information for future studies aiming to elucidate the phylogenetic relationships of Satyrinae. [ABSTRACT FROM AUTHOR]

The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site‐heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms. [ABSTRACT FROM AUTHOR]

Meconopsis biluoensis, a new species of Papaveraceae in an alpine meadow from Yunnan, Southwest China, is described and illustrated. Morphologically, it resembles Meconopsis georgei, while it is distinct in acaulescent and hispid with clearly expanded bases on the leaves. A genus‐level molecular phylogenetic analysis supported the closest relationship between M. biluoensis and M. georgei. In a finer population‐level molecular phylogenetic analysis using ribosomal DNA (rDNA) and the chloroplast genome, individuals from M. biluoensis and M. georgei were clearly separated, and the extremely short branch length indicated that the two species had a very short differentiation time. The species has currently been assessed as "endangered" (EN) due to its small‐sized population and narrow distribution following the IUCN categories and criteria. [ABSTRACT FROM AUTHOR]

Trees growing outside their native geographic ranges often exhibit exceptional growth and survival due in part to the lack of co‐evolved natural enemies that may limit their spread and suppress population growth. While most non‐native trees tend to accumulate natural enemies over time, it remains uncertain which host and insect characteristics affect these novel associations and whether novel associations follow patterns of assembly similar to those of native hosts. Here, we used a dataset of insect–host tree associations in Europe to model which native insect species are paired with which native tree species, and then tested the model on its ability to predict which native insects are paired with which non‐native trees. We show that native and non‐native tree species closely related to known hosts are more likely to be hosts themselves, but that native host geographic range size, insect feeding guild, and sampling effort similarly affect insect associations. Our model had a strong ability to predict which insect species utilize non‐native trees as hosts, but evolutionarily isolated tree species posed the greatest challenge to the model. These results demonstrate that insect–host associations can be reliably predicted, regardless of whether insect and host trees have co‐evolved, and provide a framework for predicting future pest threats using a select number of easily attainable tree and insect characteristics. [ABSTRACT FROM AUTHOR]

RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein–protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication. [ABSTRACT FROM AUTHOR]

Simple Summary: The interspecific limits within the Charipinae subfamily are still not clear, although many improvements have been made to the taxonomy of this group. Three genes (mitochondrial COI and 16S rDNA, and nuclear ITS2 rDNA) have been sequenced from five different species: Alloxysta brevis (Thomson, 1862), A. castanea (Hartig, 1841), A. ramulifera (Thomson, 1862), A. victrix (Westwood, 1833), and Phaenoglyphis villosa (Hartig, 1841). The phylogeny resulting from concatenating the three genes confirms that these molecular markers can be used to separate Charipinae species and also shows the close relationship between the genera Alloxysta and Phaenoglyphis. The genetic distances of these species are presented. The hymenopteran subfamily Charipinae (Cynipoidea: Figitidae) consist of a group of parasitic wasps that are exclusive hyperparasitoids of Hemipteran. The species boundaries in Charipinae have historically been unclear. While diagnostic morphological features have been established for the stepwise separation of species, it is recommended to confirm those limits using molecular data. Here, we focus on the genera Alloxysta Förster, 1869 and Phaenoglyphis Förster, 1869, both of which contain species that are hyperparasitoids of aphids. We sequenced three genes (mitochondrial COI and 16S rDNA, and nuclear ITS2 rDNA) from specimens that were identified as belonging to five species: Alloxysta brevis (Thomson, 1862), A. castanea (Hartig, 1841), A. ramulifera (Thomson, 1862), A. victrix (Westwood, 1833), and Phaenoglyphis villosa (Hartig, 1841). The phylogeny resulting from concatenating these genes supported the species status of the five morphologically identified taxa, with P. villosa nested within Alloxysta. Our study thus indicates that these molecular markers can successfully distinguish charipine species, and also indicates that the genera Alloxysta and Phaenoglyphis may be more closely related than previously hypothesized. We also present the first estimates of genetic distances for these species. Future studies that include more species, loci, and/or genomic data will complement our research and help determine species relationships within the Charipinae subfamily. [ABSTRACT FROM AUTHOR]

Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC—psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others. [ABSTRACT FROM AUTHOR]

Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships and evolutionary history of the genus remain unresolved. In this study, we newly sequenced three plastomes of S. oblongicarpa and compared them with those of the other congeneric species to explore the taxonomic delimitation of the species and the evolutionary history of the genus. The plastome structure of Sinojackia species was extremely conserved in terms of number of genes, sequence length, and GC content. The codon usage patterns revealed that natural selection may be the main factor shaping codon usage bias. Our phylogenetic tree shows that Sinojackia is monophyletic and can be divided into two clades. Sinojackia oblongicarpa as a distinct species is supported for it is distantly related to S. sarcocarpa. The evolutionary analysis of morphological features indicates that the woody mesocarp is an ancestral feature. Sinojackia originated in central Southeast China during the early Miocene. In this period, it experienced elevated diversification and migrated from central Southeast China to the Hunan Province and the Sichuan Province with the development of the Asian monsoon and East Asian flora. Glacial–interglacial interactions with the monsoon climate may provide favorable expansion conditions for Sinojackia on a small scale. [ABSTRACT FROM AUTHOR]

Two new species from China, Hymenogaster pseudoniveus and H. zunhuaensis, are described and illustrated based on morphological and molecular evidence. Hymenogaster pseudoniveus is distinguished from other species of the genus based on the color of peridium, which is snow white to white when unexcavated but then turns yellowish to earth yellow, and the basidiospores, which are ornamented with nearly longitudinally arranged ridges up to 2 μm high. H. zunhuaensis is diagnosed by its dirty white to pale yellow peridium, yellow brown to brown gleba, and the smaller (Lm × Wm = 11.7 μm × 9.8 μm) broadly ellipsoidal to subglobose basidiospores (Q = 1.1–1.3). ITS/LSU-based phylogenetic analysis supports the erection of the two new species, each placed in distinct clades with strong statistical support, suggesting that they represent two distinct species novel to science. Based on the morphological and molecular evidence, we have published two new species of Hymenogaster. A key for Hymenogaster species from China is provided. [ABSTRACT FROM AUTHOR]

Two rod-shaped, non-spore-forming, Gram-negative bacteria, strain KR3-3T isolated from fresh soil in Korea and strain VNH31T obtained from soil samples from motorbike repair workshop floors in Vietnam, were identified. Phylogenetic analysis utilizing 16S rRNA gene sequences revealed their affiliation with the family Sphingobacteriaceae and their relation to the genus Pedobacter, exhibiting 16S rRNA gene sequence similarities lower than 98.00% with all known species within the genus Pedobacter. Growth of VNH31T and KR3-3T was impeded by NaCl concentrations exceeding >0.5% and 1.5%, respectively, while they both thrived optimally at temperatures ranging between 25 and 30 °C. Notably, neither strain reduced nitrate to nitrite nor produced indole. Negative results were observed for the acidification of D-glucose and hydrolysis of urea, gelatin, casein, and starch. VNH31T exhibited growth on β-galactosidase, sodium acetate, L-serine, and L-proline, whereas KR 3-3T demonstrated growth on D-glucose, D-mannose, D-maltose, N-acetyl-glucosamine, sucrose, sodium acetate, L-serine, 4-Hydroxybenzoic acid, and L-proline. Core genome-based phylogenetic analysis revealed that the two isolates formed distinct clusters within the genus Pedobacter. The DNA G+C contents of KR3-3T and VNH31T were determined to be 44.12 mol% and 32.96 mol%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values (67.19–74.19% and 17.6–23.6%, respectively) between the Pedobacter isolates and the closely related type strains fell below the threshold values utilized for species delineation. Following comprehensive genomic, chemotaxonomic, phenotypic, and phylogenetic analyses, the isolated strains are proposed as two novel species within the genus Pedobacter, named Pedobacter albus sp. nov. (type strain KR3-3T = KACC 23486T = NBRC 116682T) and Pedobacter flavus sp. nov. (type strain VNH31T = KACC 23297T = CCTCC AB 2023109T). [ABSTRACT FROM AUTHOR]

There are many species of Lepidoptera, but few complete mitochondrial genomes of Lepidoptera have been included in databases. Here, the complete mitochondrial genome sequence of Salassa thespis was isolated and characterized. It was 15,302 bp in length and contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. Among the 13 PCGs, the initiation codon of cytochrome c oxidase subunit 1 (cox1) was CGA, and the rest were ATN. The cox1 and cox2 genes had an incomplete stop codon T, while the rest terminated with TAA. Codon usage analysis showed that Phe, Ile, Leu and Asn were the most frequent amino acids, while Trp was the least. Like other Lepidopterans, some conserved motifs were found in the A + T-rich region, including a 17 bp poly-T guided by ATAGA, the AT-rich area and a poly-A element. Bayesian inference and maximum likelihood phylogenetic tree analysis based on 13 PCGs of S. thespis confirmed that it belonged to the Saturniidae family and showed the following relationship: (S. thespis + (Rhodinia fugax + Samia canningi)). The enrichment of mitochondrial DNA provides reference information for the study of the evolution and diversity of Lepidoptera insects. [ABSTRACT FROM AUTHOR]

Based on morphological, chemical and molecular studies, two new species of the lichen genus Letrouitia are newly described from China. Letrouitia arcuata is distinguished by its arcuate ascospores [8–10(–12)-locular, (28–)33–50(–62.5) × (8–)10–14.5 µm] and L. sinuosa by its ascomata with wavy margins and ascospores with lens-shaped locules [6–8-locular, (18–)19.5–32(–34) × (6.5–)8–14 μm]. In addition, L. magenta is reported for the first time as a new record in China, characterized by small and round ascomata. The descriptions, distribution and phylogenetic analysis of the respective species have been actualized and a key to the Letrouitia species known from China is provided. [ABSTRACT FROM AUTHOR]

Calmodulin (Calm), a crucial Ca2+ sensor, plays an important role in calcium-dependent signal transduction cascades. However, the expression and the relevance of Calm in stress and immune response have not been characterized in Megalobrama amblycephala. In this study, we identified the full-length cDNA of Calm (termed MaCalm) in blunt snout bream M. amblycephala, and analyzed MaCalm expression patterns in response to cadmium and Aeromonas hydrophila challenges. MaCalm was 1603 bp long, including a 5′-terminal untranslated region (UTR) of 97 bp, a 3′-terminal UTR of 1056 bp and an open reading frame (ORF) of 450 bp encoding a polypeptide of 149 amino acids with a calculated molecular weight (MW) of 16.84 kDa and an isoelectric point (pI) of 4.09. Usually, MaCalm contains four conservative EF hand motifs. The phylogenetic tree analysis indicated that the nucleotide sequence of MaCalm specifically clustered with Ctenopharyngodon idella with high identity (98.33%). Tissue distribution analysis demonstrated that the ubiquitous expression of MaCalm mRNA was found in all tested tissues, with the highest expression in the brain and the lowest expression in muscle. MaCalm showed significant upregulation at 14 d and 28 d post exposure to varying concentrations of cadmium in the liver; HSP70 transcripts in the liver significantly upregulated at 14 d post exposure to different concentrations of cadmium. Moreover, in response to the A. hydrophila challenge in vivo, MaCalm transcripts in the liver first increased and then decreased, but MaCalm transcripts in the kidney declined gradually with prolonged infection. After the A. hydrophila challenge, the expression level of HSP70 was significantly downregulated at 24 h in the liver and its expression level was notably downregulated at 12 h and at 24 h in the kidney. Collectively, our results suggest that MaCalm possesses vital roles in stress and immune response in M. amblycephala. [ABSTRACT FROM AUTHOR]

Despite its ubiquitous infectivity to mammals with strong host specificity, our current knowledge about Pneumocystis has originated from studies of merely 4% of extant mammalian species. Further studies of Pneumocystis epidemiology across a broader range of animal species require the use of assays with high sensitivity and specificity. To this end, we have developed multiple universal Pneumocystis primers targeting different genetic loci with high amplification efficiency. Application of these primers to PCR investigation of Pneumocystis in free-living hares (Lepus townsendii, n = 130) and rabbits (Oryctolagus cuniculus, n = 8) in Canada revealed a prevalence of 81% (105/130) and 25% (2/8), respectively. Genotyping analysis identified five and two variants of Pneumocystis from hares and rabbits, respectively, with significant sequence divergence between the variants from hares. Based on phylogenetic analysis using nearly full-length sequences of the mitochondrial genome, nuclear rRNA operon and dihydropteroate synthase gene for the two most common variants, Pneumocystis in hares and rabbits are more closely related to each other than either are to Pneumocystis in other mammals. Furthermore, Pneumocystis in both hares and rabbits are more closely related to Pneumocystis in primates and dogs than to Pneumocystis in rodents. The high prevalence of Pneumocystis in hares (P. sp. 'townsendii') suggests its widespread transmissibility in the natural environment, similar to P. oryctolagi in rabbits. The presence of multiple distinct Pneumocystis populations in hares contrasts with the lack of apparent intra-species heterogeneity in P. oryctolagi, implying a unique evolution history of P. sp. 'townsendii' in hares. [ABSTRACT FROM AUTHOR]

Penicillium species are ubiquitous in the environment and are of substantial importance, especially in industrial and medical aspects. During our investigation of the biodiversity of Penicillium, three new species were discovered in soil samples collected from East and Northeast China. They were determined as new to science based on morphological comparisons and phylogenetic analyses, and were found to belong to the subgenus Penicillium section Robsamsonia and subgenus Aspergilloides sections Aspergilloides and Citrina. Descriptions and illustrations of these species are provided, and their geographic distributions are also discussed. [ABSTRACT FROM AUTHOR]