Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

New treasures in Cordycipitaceae: Fungicolous fungi associated with Pseudocercospora fijiensis and P. musae in Brazil, including Matutinistella gen. nov

Cordycipitaceae is a large family belonging to the order Hypocreales, including cosmopolitan species found on different substrates. This family includes species with different lifestyles such as entomopathogenic, endophytic, and mycoparasitic fungi. Some mycoparasitic species in this family attack phytopathogenic fungi. We identified species of Cordycipitaceae found during a survey of fungicolous fungi associated with Pseudocercospora fijiensis and P. musae in Brazil. Based on morphological characters combined with phylogenetic analysis of ITS, LSU, SSU, RPB1, RPB2, and TEF1-α, we propose a new genus in Cordycipitaceae, namely Matutinistella, with its type species M. brasiliensis, and a new species of the genus Simplicillium, namely S. pseudocercosporicola. Furthermore, we report P. fijiensis as a new host of the mycoparasitic fungus Simplicillium lanosoniveum. In this study we newly report fungicolous fungi of Cordycipitaceae associated with the causal agents of Black Sigatoka and Yellow Sigatoka on banana crops. We provide relevant information for future work involving control measures for these diseases that cause major losses in banana crops. Citation: Custódio FA, Pereira OL (2025). New treasures in Cordycipitaceae: Fungicolous fungi associated with Pseudocercospora fijiensis and P. musae in Brazil, including Matutinistella gen. nov. Fungal Systematics and Evolution 15: 133-152. doi: 10.3114/fuse.2025.15.06.

Morphological data, phylogenomics and recalcitrant nodes

In this paper we examine the relative contribution of information to nodes in a phylogenomic analysis combined with morphological datasets. We examine the behaviour of branch support metrics using the partitioned Bremer support (PBS) and its likelihood counterpart partitioned likelihood support (PLS). These metrics measure the contribution of a data partition to a node in question, and can be easily computed for likelihood and parsimony. Specifically, we assess the ratios of support values for morphological data to molecular data at this recalcitrant node. We find that there is a strong linear correlation between this ratio with the weight of the weaker partition where a flip (the flip weight) in topology ensues. This linear relationship allows us to estimate the amount of morphological data it will take to flip a phylogenomic hypothesis. For the datasets we use in this study flip weights are surprisingly small.

Morpho-phylogenetic evidence reveals four novel species of Coniella (Diaporthales, Schizoparmaceae) from southern China

Coniella species are distributed worldwide and have been reported as plant pathogens, endophytes, or saprobes. In our ongoing survey of terrestrial plant fungi in southern China, we obtained Coniella isolates from diseased plant leaf tissues in Fujian, Hainan, and Yunnan provinces. Maximum likelihood and Bayesian inference based on four loci (ITS, LSU, rpb2, and tef1-α) were used to clarify the taxonomic placement of the species. We confirmed that they represent four new species, namely Conielladiaoluoshanensis, C.dongshanlingensis, C.grossedentatae, and C.veri based on both morphology and phylogeny support. The new species are compared with other Coniella species, comprehensive descriptions and micrographs are provided.

Somnuekiaflaviflora (Malvaceae, Brownlowioideae), a new genus and species from Thailand

Somnuekia is described as a new genus of Malvaceae, currently known only from a few locations in the upper part of Tenasserim in northern and peninsular Thailand. Morphological and molecular phylogenetic analyses, based on plastid DNA sequence regions, support the recognition of this new genus within the Brownlowioideae (Malvaceae). Its distinct phylogenetic position, along with a distinct set of morphological and palynological characteristics, strongly support the recognition of Somnuekia as a new genus. A formal description of Somnuekiaflaviflora is provided along with illustrations, photographs, a distribution map and conservation notes. Furthermore, this new genus is compared to other Asian genera within the subfamily.

Phylogenetic minimum description length: an optimality criterion based on algorithmic complexity

Phylogenetic minimum description length (PMDL) is proposed as an optimality criterion for phylogenetic analysis. PMDL is based on algorithmic (Kolmogorov) information and the minimum description length principle. This criterion generates natural weighting functions (i.e. not being externally specified) for a diversity of phylogenetic graph, data and model types. PMDL is a generalized criterion that converges on existing forms of inference (i.e. parsimony, likelihood, Bayesian) in specific circumstances. Furthermore, as opposed to existing criteria, PMDL includes graph complexity allowing for the competition of hypotheses with myriad types of phylogenetic graphs (e.g. trees, networks, forests). Owing to its compound nature, PMDL allows for analytical model choice along with phylogenetic graph hypothesis while avoiding over-parameterization. Although uncomputable, heuristic methods are presented for the calculation of upper bounds on the algorithmic information content of a phylogenetic hypothesis. Examples are presented demonstrating the approach.

Fungi from Malus in Qujing, China: two new species, three new records, and insights into potential host jumping and lifestyle switching

Apple trees [Malus domestica Borkh. (Rosaceae)] are one of the important temperate fruit crops in China. In comparison to other temperate fruits, such as grapes and pears, fungal studies (in Yunnan) associated with M. domestica are fewer in number. In the present study, we investigated fungi associated with M. domestica in Qujing City, Yunnan Province, China. Samples were collected from apple gardens in different locations. Single spore isolation was carried out to isolate saprobic fungi, while the surface sterilization method was carried out to isolate endophytic fungi. Molecular analyses were carried out to determine the phylogenetic placement of the new collections. Based on the combined methods of morphology and phylogeny, Cytospora qujingensis sp. nov. and Hypoxylon malongense sp. nov. are introduced as novel saprobic and endophytic taxa, respectively. Moreover, Aureobasidium pullulans and Cytospora schulzeri are reported as new geological records from southwestern China. Allocryptovalsa castaneae is reported on M. domestica in China for the first time. The checklist of fungi associated with M. domestica in China is presented.

Psychrophilic fungi from the world's roof, II: Species delimitation within an integrative taxonomic framework

Southeast Qinghai-Tibet Plateau, which harbors large numbers of marine glaciers and spans across two worldwide "biodiversity hotspots," is facing massive habitat loss in the context of global warming, and the biodiversity of coldadapted fungi in this unique area is also suffering drastic reduction. In this study, we selected 23 fungal isolates that represented the most commonly encountered psychrophilic taxa isolated from soil or water samples of marine glaciers in the southeast Qinghai-Tibet Plateau for detailed taxonomic studies. Incorporating morphological characteristics, multilocus phylogenetic analyses, and the results of four widely used molecular species delimitation methods, including two distance-based: Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), and two tree-based: Bayesian Poisson Tree Processes (bPTP) and generalized mixed Yule coalescent model (GMYC), seven Gelida (formerly Psychrophila) species, including six new species, and two Tetracladium species, including one new species, were described. As the genus name Psychrophila is an illegitimate later homonym of a plant genus, we proposed the new name Gelida as a replacement for Psychrophila and transferred four illegitimate Psychrophila species to Gelida as new combinations. Our study provides a valuable perspective on how to delimit robust and accurate species boundaries within an integrative taxonomic framework, which is especially important for efficient biodiversity assessment and conservation of the fungal groups that are facing serious habitat loss.

Phytophthora heterospora is the causal agent of black rot disease on the orchid Cattleya leopoldii in Brazil

Widely produced and marketed worldwide, orchids suffers from several diseases that have a negative effect on production. Black rot disease is among the most common and severe disease, characterized by black spots of rot on leaves, pseudobulbs and roots, which usually lead to the plant death. The world literature lists some Phytophthora species as causal agents of the disease, but there is no advanced study on the etiology of this disease in Brazil, which makes it difficult to determine an efficient control method. This work aims to contribute to the study of the etiology of black rot on Cattleya leopoldii in Brazil. Severely diseased C. leopoldii plants with typical symptoms of black rot, collected from a commercial orchid farm in Brazil, were taken to the laboratory and used to isolate the pathogen. Based on morphological characters analysis combined with molecular data, the isolates were identified as belonging to the species Phytophthora heterospora. This is the first worldwide report of P. heterospora causing black rot disease on orchids.

Efficiency of mycorrhizal fungi for seed germination and protocorms development of commercial Cattleya species (Orchidaceae)

Orchidaceae is one of the largest plant families and stands out for its wide variety of flowers with ornamental and environmental importance. Cattleya is one of the main commercial genera, presenting a great diversity of species and hybrids that attract the attention of collectors, orchid enthusiasts, and consumers. In their natural environment, orchids associate with mycorrhizal fungi, which are responsible for providing carbon and other nutrients during seed germination. This study investigated the potential of mycorrhizal fungi isolated from the genus Cattleya for in vitro symbiotic germination of seeds from three contrasting Cattleya species, comparing them with non-symbiotic germination in a commercially used culture medium for orchid propagation. The isolated fungi were molecularly identified through phylogenetic analyses of DNA sequences using the ITS (Internal Transcribed Spacer) region. Three isolates obtained were identified as Tulasnella amonilioides, and through microscopic evaluations, the formation of monilioid cells was observed, a morphological characteristic previously unknown for this species. The T. amonilioides isolates were efficient in promoting seed germination of Cattleya bicolor, Cattleya walkeriana and Cattleya jongheana and accelerated the germination process when compared with the non-symbiotic commercial medium, showing to be promised for commercial seed production of these orchids species.

Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference

Viral phylodynamics focuses on using sequence data to make inferences about the population dynamics of viral diseases. These inferences commonly include estimation of growth rates, reproduction numbers and times of most recent common ancestor. With few exceptions, existing phylodynamic inference approaches assume that all observed and ancestral viral genetic variation is fitness-neutral. This assumption is commonly violated, with a large body of analyses indicating that fitness varies substantially among genotypes circulating in viral populations. Here, we focus on fitness variation arising from deleterious mutations, asking whether incomplete purifying selection of deleterious mutations has the potential to bias phylodynamic inference. We use simulations of an exponentially growing population to explore how incomplete purifying selection distorts tree shape and shifts the distribution of mutations over trees. We find that incomplete purifying selection strongly shapes the distribution of mutations while only weakly impacting tree shape. Despite incomplete purifying selection shifting the distribution of deleterious mutations, we find little discernible bias in estimates of viral growth rates and times of the most recent common ancestor. Our results reassuringly indicate that existing phylodynamic inference approaches that assume neutrality may nevertheless yield accurate epidemiological estimates in the face of incomplete purifying selection. More work is needed to assess the robustness of these findings to alternative epidemiological parametrizations.This article is part of the theme issue ''"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Reading tree leaves: inferring speciation anfd extinction processes using phylogenies

The birth-death process (BDP) is widely used in evolutionary biology as a model for generating phylogenetic trees of species. The generalized birth-death process (GBDP) allows rate variation over time, with speciation and extinction rates to be arbitrary functions of time. Here we review the probability theory underpinning the GBDP as a model of cladogenesis and recent findings concerning its identifiability. The GBDP with arbitrary continuous rate functions has been shown to be non-identifiable from lineage-through-time data: even with species phylogenies of infinite size the parameters cannot be estimated. However, a restricted class of BDPs with piecewise-constant rates has been shown to be identifiable. We review and illustrate these results using simple examples and discuss their implications for biologists interested in inferring the past tempo and mode of evolution using reconstructed phylogenetic trees.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Morpho-phylogenetic evidence reveals Pseudolomaanthathailandica gen. et sp. nov. and Submultiguttulisporamultiseptata gen. et sp. nov. in Chaetosphaeriaceae

Anamorphic chaetosphaeriaceous fungi exhibit high morphological variability and are distributed worldwide across terrestrial and aquatic habitats. During an ongoing taxonomic study of microfungi, two intriguing chaetosphaeriaceous hyphomycetes were collected from dead wood and dead bamboo stems in China and Thailand. A polyphasic approach, combining morphological characteristics and phylogenetic analysis of LSU and ITS sequence data, revealed that these fungi represent two new genera within Chaetosphaeriaceae. Pseudolomaantha and Submultiguttulispora are proposed for these new genera, and they exhibit non-phialidic and phialidic asexual morphs, respectively. Pseudolomaanthathailandica gen. et sp. nov. is characterized by a sporidesmium-like asexual morph with macronematous, mononematous conidiophores; monoblastic conidiogenous cells, and pyriform to obclavate, rostrate conidia bearing an apical appendage. Submultiguttulisporamultiseptata gen. et sp. nov. is distinguished by macronematous, mononematous conidiophores, mono- to polyphialidic conidiogenous cells, and fusiform or ellipsoidal-fusiform, pale brown to olive green to brown conidia with filiform, hyaline appendages at both ends. Detailed descriptions, illustrations, and notes on the new collections are provided, along with a key to non-phialidic hyphomycetous genera in Chaetosphaeriaceae.

Two novel hyphomycetes associated with ferns from China

During an ongoing investigation of fungi associated with ferns in southwestern China, three hyphomycetes were discovered on the dead rachises of Angiopterisfokiensis and an unidentified fern. Based on morphology and multi-gene phylogenetic analyses, Arthrobotrysangiopteridis and Corynesporaseptata are introduced as new species. Arthrobotrysangiopteridis is a nematode-trapping fungus characterized by macronematous, mononematous, hyaline conidiophores, conidiogenous cells with polyblastic denticles at each node, and 0-1-septate, clavate to elongate pyriform, hyaline conidia. Corynesporaseptata features macronematous, mononematous, pale brown to dark brown conidiophores, integrated, monotretic conidiogenous cells and up to 7-distoseptate with one true septum, subcylindrical to obclavate, hyaline to pale brown conidia. Detailed descriptions and illustrations of these two new species are provided, along with morphological comparisons of the new taxa with closely related species.

A novel genotype of Babesia microti-like group in Ixodes montoyanus ticks parasitizing the Andean bear (Tremarctos ornatus) in Ecuador

Babesia species (Piroplasmida) are hemoparasites that infect erythrocytes of mammals and birds and are mainly transmitted by hard ticks (Acari: Ixodidae). These hemoparasites are known to be the second most common parasites infecting mammals, after trypanosomes, and some species may cause malaria-like disease in humans. Diagnosis and understanding of Babesia diversity increasingly rely on genetic data obtained through molecular techniques. Among hard ticks, several Ixodes species are known vectors of Babesia microti-like species in the Northern Hemisphere. Recently, Ixodes and Amblyomma ticks have been recorded parasitizing the Andean bear (Tremarctos ornatus) in Ecuador. Previous reports have suggested babesiosis in a fatal case of this threatened bear species in that country. This study aimed to detect Piroplasmida DNA in hard ticks collected from Andean bears at two sites in Ecuador. This species plays a critical role as an ecological engineer and a seed disperses, contributing significantly to the maintenance and health of Andean ecosystems. Twelve ticks screened with conventional PCR and Piroplasmida DNA was amplified from one Ixodes montoyanus tick collected from a free-living female Andean bear at Llanganates National Park. Two Babesia sequences were characterized: one for the 18 S ribosomal rRNA gene and another for the cytochrome c oxidase 1 gene. Phylogenetic analyses for both loci placed these sequences within the B. microti-like clade. This study reports a novel B. microti-like genotype identified in an I. montoyanus parasitizing a female Andean bear, contributing to the knowledge of the diversity of this group in South America. Given their conservation status, future epidemiological surveillance of Babesia and other tick-borne infectious agents in Andean bears is needed.

Ectophoma salviniae sp. nov., Neottiosporina mihintaleensis sp. nov. and four other endophytes associated with aquatic plants from Sri Lanka and their extracellular enzymatic potential

Endophytic fungi associated with selected aquatic plants, Eichhornia crassipes, Nymphaea nouchali, Salvinia minima and S. molesta were evaluated. Ectophoma salviniae sp. nov. and Neottiosporina mihintaleensis sp. nov. are introduced as novel taxa from Salvinia spp. from Sri Lanka. Chaetomella raphigera is reported as a new geographical record, Colletotrichum siamense and C. truncatum are reported as novel host records in aquatic plants, while Phyllosticta capitalensis has been identified on the same host (Nymphaea nouchali) in the North-Central Province of Sri Lanka. Identification of the fungi was based on morphological characteristics and multi-locus phylogenetic analyses using ITS, LSU, SSU, ACT, CHS-1, GAPDH, tub2, rpb2, and tef1-α molecular markers. The identified fungi were analysed for extracellular enzymatic properties. According to the qualitative analysis, Ectophoma salviniae sp. nov. exhibited the highest amylase production, Chaetomella raphigera exhibited the highest cellulase enzyme production, and Neottiosporina mihintaleensis sp. nov. exhibited the highest laccase production. The results demonstrate the aquatic fungal diversity in this region and their extracellular enzymatic potentials, providing valuable insights for future biotechnological approaches.

Diversity of Lignicolous Freshwater Fungi from Yuanjiang River in Yunnan (China), with the Description of Four New Species

Yuanjiang River (Red River) is one of the six major water systems in Yunnan Province, which originates from western Yunnan Province. This river system features numerous tributaries, complex terrain, and abundant natural resources. During the investigation on the diversity of lignicolous freshwater fungi in the Yuanjiang River, nine species were collected and identified, five belonging to Dothideomycetes and four to Sordariomycetes. Based on morphology and multigene phylogenetic analyses, four species, namely, Aquadictyospora aquatica, Dictyosporium fluminicola, Myrmecridium submersum, and Neomyrmecridium fusiforme, are described as new species. Dictyocheirospora aquadulcis is reported as a new national record, and Myrmecridium hydei is reported as a new habitat record. Dictyocheirospora rotunda, Halobyssothecium aquifusiforme, and Pseudohalonectria lutea were known earlier from freshwater habitats, but we described them in detail in this paper. This study contributes significantly to the understanding of the diversity of lignicolous freshwater fungi in southwestern China.

Multigene phylogeny, taxonomy, and potential biological properties of Pseudoroussoella and Neoroussoella species (Roussoellaceae, Dothideomycetes) from Asteraceae weeds in northern Thailand

In our study, dead stems of two Asteraceae species (weeds) were collected from northern Thailand. Both morphology and multigene phylogeny were used to determine the identity of the taxa. Maximum likelihood and Bayesian inference analyses of combined LSU, SSU, ITS, tef1-α and rpb2 data revealed two new species Pseudoroussoellabidenticola, and Neoroussoellachromolaenae with one new host record of N.entadae. Preliminary investigation into antibacterial properties revealed that our three isolates inhibited the growth of Bacillussubtilis, Escherichiacoli, and Staphylococcusaureus. Additionally, we present updated phylogenetic trees for Roussoellaceae, accompanied by detailed descriptions and illustrations of the three identified species.

Five new species, two new sexual morph reports, and one new geographical record of Apiospora (Amphisphaeriales, Sordariomycetes) isolated from bamboo in Yunnan, China

Apiospora is an important genus in the Apiosporaceae family with a worldwide distribution. They exhibit different lifestyles including pathogenic, saprophytic, and endophytic. In this study, we aimed to explore the Apiospora associated with bamboo and collected 14 apiospora-like taxa from the forests of Yunnan Province, China. Morphological and phylogenetic analyses (combined ITS, LSU, tef1-α, and tub2 sequence data) confirmed that these collections belong to Apiospora s. str. and reports five new species (viz., Ap. dehongensis, Ap. jinghongensis, Ap. shangrilaensis, Ap. zhaotongensis, and Ap. zhenxiongensis). New sexual morphs of asexually typified Ap. globose and Ap. guangdongensis species, and a new geographical record of Ap. subglobosa are also reported. The findings of this study not only enhance the diversity of bambusicolous fungi in the region of Yunnan, but also geographical distribution of some known Apiospora species.

Melomastia (Dothideomycetes, Ascomycota) species associated with Chinese Aquilaria spp

This study is based on three terrestrial saprobic fungi associated with Aquilaria in Guangdong and Yunnan provinces in China. All isolated species matched with generic concepts of Melomastia. Detailed morphological characteristics and combined multigene phylogeny of LSU, SSU, and TEF revealed that the new isolates represent two new species (Melomastiaguangdongensis and M.yunnanensis), and one new host and geographical record (M.sinensis). Melomastiaguangdongensis is distinct from the phylogenetically closest species in having semi-immersed to immersed, globose to subglobose ascomata, and two strata of the peridium. Melomastiayunnanensis differs from the phylogenetically closest species in having immersed ascomata, conical ostiolar canals, and branched pseudoparaphyses. The discovery of these two new species and one new record collected expands the number of saprobic species associated with Aquilaria from 28 to 31. Descriptions, photo plates, and phylogenetic analyses of taxa are provided.

Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota)

The Diaporthales includes 32 families, many of which are important plant pathogens, endophytes and saprobes, e.g., members of the families Pseudoplagiostomataceae, Pyrisporaceae and Schizoparmaceae. Nucleotide sequences derived from five genetic loci including: ITS, LSU, TEF1-α, TUB2 and RPB2 were used for Bayesian evolutionary analysis to determine divergence times and evolutionary relationships within the Schizoparmaceae. Molecular clock analyses revealed that the ancestor of Schizoparmaceae split during the Upper Cretaceous period approximately 75.7 Mya (95 % highest posterior density of 60.3-91.3 Mya). Reconstructing ancestral state in phylogenies (RASP) with using the Bayesian Binary Markov chain Monte Carlo (BBM) Method to reconstruct the historical biogeography for the family Schizoparmaceae indicated its most likely origin in Africa. Based on taxonomic and phylogenetic analyses, the Pseudoplagiostomataceae and Pyrisporaceae relationships were clarified and a total of four species described herein. For Pseudoplagiostomataceae, three new species and one known species that include, Pseudoplagiostoma fafuense sp. nov., Ps. ilicis sp. nov., Ps. sanmingense sp. nov. and Ps. bambusae are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered Pseudoplagiostoma castaneae to be a synonym of Pyrispora castaneae. In addition, a new species of Schizoparmaceae, Coniella fujianensis sp. nov. is described and illustrated.

Constructing phylogenetic trees for microbiome data analysis: A mini-review

As next-generation sequencing technologies advance rapidly and the cost of metagenomic sequencing continues to decrease, researchers now face an unprecedented volume of microbiome data. This surge has stimulated the development of scalable microbiome data analysis methods and necessitated the incorporation of phylogenetic information into microbiome analysis for improved accuracy. Tools for constructing phylogenetic trees from 16S rRNA sequencing data are well-established, as the highly conserved regions of the 16S gene are limited, simplifying the identification of marker genes. In contrast, metagenomic and whole genome shotgun (WGS) sequencing involve sequencing from random fragments of the entire gene, making identification of consistent marker genes challenging owing to the vast diversity of genomic regions, resulting in a scarcity of robust tools for constructing phylogenetic trees. Although bacterial sequence tree construction tools exist for upstream bioinformatics, many downstream researchers-those integrating these trees into statistical models or machine learning-are either unaware of these tools or find them difficult to use due to the steep learning curve of processing raw sequences. This is compounded by the fact that public datasets often lack phylogenetic trees, providing only abundance tables and taxonomic classifications. To address this, we present a comprehensive review of phylogenetic tree construction techniques for microbiome data (16S rRNA or whole-genome shotgun sequencing). We outline the strengths and limitations of current methods, offering expert insights and step-by-step guidance to make these tools more accessible and widely applicable in quantitative microbiome data analysis.

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

Phylogenetics has been widely used in molecular biology to infer the evolutionary relationships among species. With the rapid development of sequencing technology, genomic data with thousands of sites become increasingly common in phylogenetic analysis, while heterogeneity among sites arises as one of the major challenges. A single homogeneous model is not sufficient to describe the evolution of all sites and partitioned models are often employed to model the evolution of heterogeneous sites by partitioning them into distinct groups and utilizing distinct evolutionary models for each group. It is crucial to determine the best partitioning, which greatly affects the reconstruction correctness of phylogeny. However, the best partitioning is usually intractable to obtain in practice. Traditional partitioning methods rely on heuristic algorithms or greedy search to determine the best ones in their solution space, are usually time consuming, and with no guarantee of optimality. In this study, we propose a novel partitioning approach, termed PsiPartition, based on the parameterized sorting indices of sites and Bayesian optimization. We apply our method to empirical datasets, and it performs significantly better compared to existing methods, in terms of Bayesian information criterion (BIC) and the corrected Akaike information criterion (AICc). We test PsiPartition on the simulated datasets with different site heterogeneity, alignment lengths, and number of loci. It is demonstrated that PsiPartition evidently and stably outperforms other methods in terms of the Robinson-Foulds (RF) distance between the true simulated trees and the reconstructed trees, especially on the data with more site heterogeneity. More importantly, our proposed Bayesian optimization-based method, for the first time, provides a new general framework to efficiently determine the optimal number of partitions. The corresponding reproducible source code and data are available at http://github.com/xu-shi-jie/PsiPartition .

Cytospora: an important genus of canker pathogens

Cytospora species have commonly been reported as important plant pathogenic fungi with wide host ranges and geographic distributions. With the increase in the number of cryptic species being described, a comprehensive global taxonomic revision of the genus Cytospora is required. The present study includes 399 isolates from 32 countries. These isolates were subjected to DNA sequence analysis for five genomic loci (ITS, act1, rpb2, tef1-α and tub2). Based on these data, it could be confirmed that Cytospora, Leucostoma, Valsa, Valsella and Valseutypella are congeneric. Furthermore, 111 species of Cytospora could also be reassessed, 44 species and four combinations newly introduced, and new typifications proposed for a further three species. Three asexual morphological groups (including 13 asexual morphological types) and three sexual morphological groups (including eight sexual morphological types) were designated. The present study explored the species diversity of Cytospora and re-evaluated the identity of all cultures in the Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands) that were deposited as either Cytospora or as one of its related genera. This is the most comprehensive phylogenetic analysis thus far conducted on Cytospora and the results contribute to an increased understanding of the taxonomy of these important fungi. It is also hoped that the findings will lead to improved management strategies for diseases associated Cytospora species. Taxonomic novelties: New species: Cytospora acericola X.L. Fan & C.M. Tian, C. adamsii Jami, Crous & M.J. Wingf., C. beijingensis L. Lin & X.L. Fan, C. betulae Jami, Crous & M.J. Wingf., C. brabeji Jami, Crous & M.J. Wingf., C. castaneicola L. Lin & X.L. Fan, C. cerebriformis L. Lin & X.L. Fan, C. conceptaculata L. Lin & X.L. Fan, C. crataegina X.L. Fan & C.M. Tian, C. deqinensis L. Lin & X.L. Fan, C. diqingensis L. Lin & X.L. Fan, C. eastringensis L. Lin & X.L. Fan, C. elaeagnina L. Lin & X.L. Fan, C. fraxinea X.L. Fan & C.M. Tian, C. guyuanensis L. Lin & X.L. Fan, C. jiufengensis L. Lin & X.L. Fan, C. lauricola L. Lin & X.L. Fan, C. lhasaensis L. Lin & X.L. Fan, C. lijiangensis L. Lin & X.L. Fan, C. lvxinensis L. Lin & X.L. Fan, C. malvicolor X.L. Fan & C.M. Tian, C. multiseriata L. Lin & X.L. Fan, C. nanyangensis X.L. Fan & C.M. Tian, C. polyspora X.L. Fan & C.M. Tian, C. pseudochrysosperma L. Lin & X.L. Fan, C. qinghaiensis L. Lin & X.L. Fan, C. qingshuiensis L. Lin & X.L. Fan, C. sanbaensis L. Lin & X.L. Fan, C. shaanxiensis L. Lin & X.L. Fan, C. shangrilaensis L. Lin & X.L. Fan, C. sidaohensis L. Lin & X.L. Fan, C. sinensis L. Lin & X.L. Fan, C. songshanensis L. Lin & X.L. Fan, C. suecica Jami, Crous & M.J. Wingf., C. syringina L. Lin & X.L. Fan, C. tenebrica L. Lin & X.L. Fan, C. tetraspora L. Lin & X.L. Fan, C. tongzhouensis X.L. Fan & C.M. Tian, C. uniloculata L. Lin & X.L. Fan, C. washingtonensis Jami, Crous & M.J. Wingf., C. xiaolongmenensis L. Lin & X.L. Fan, C. yinchuanensis L. Lin & X.L. Fan, C. yuduensis L. Lin & X.L. Fan, C. yulinensis L. Lin & X.L. Fan. New combinations: Cytospora auerswaldii (Nitschke) L. Lin & X.L. Fan, C. multicollis (Checa et al.) L. Lin, X.L. Fan & Crous, C. tristicha (De Not.) L. Lin, X.L. Fan & Crous, C. weiriana (Petr.) X.L. Fan & Crous. New replacement names: Cytospora desmazieri L. Lin, X.L. Fan & Crous, C. fuckeliana L. Lin, X.L. Fan & Crous, C. hoffmannii L. Lin, X.L. Fan & Crous, C. massarii L. Lin, X.L. Fan & Crous, C. nitschkeana L. Lin, X.L. Fan & Crous, C. saccardoi L. Lin, X.L. Fan & Crous. New synonyms: Cytospora ampulliformis Norph., Bulgakov, T.C. Wen & K.D. Hyde, C. brevispora (G.C. Adams & Jol. Roux) G.C. Adams & Rossman, C. cenisia Sacc., C. ceratospermopsis C.M. Tian & X.L. Fan, C. cotini Norph., Bulgakov & K.D. Hyde, C. ershadii Zafari & Hanifeh, C. erumpens Norph., Bulgakov, T.C. Wen & K.D. Hyde, C. fraxinigena Senan., Camporesi & K.D. Hyde, C. galegicola Q.J. Shang, E. Camporesi & K.D. Hyde, C. granati D.P. Lawr., L.A. Holland & Trouillas, C. hippophaicola Spetik, Eichmeier, Gramaje, Stuskova & Berraf-Tebbal, C. massariana Sacc., C. nivea (Hoffm.) Sacc., C. parakantschavelii Norph., Bulgakov, T.C. Wen & K.D. Hyde, C. parasitica Norph., Bulgakov & K.D. Hyde, C. paratranslucens Norph., Bulgakov, T.C. Wen & K.D. Hyde, C. pini Desm., C. populicola D.P. Lawr., L.A. Holland & Trouillas, C. predappioensis Q.J. Shang, Norph., Camporesi & K.D. Hyde, C. quercicola Senan., Camporesi & K.D. Hyde, C. rosae Senan., Camporesi & K.D. Hyde, C. salicella Sacc., C. vinacea D.P. Lawr., Travadon & Pouzoulet, Valsa germanica Nitschke, V. massariana De Not., V. nivea (Hoffm.) Fr., Valsella salicis Fuckel, Sphaeria nivea Hoffm. Typification: Lecto- and epitypifications (basionyms): Sphaeria chrysosperma Pers., Valsa eucalypti Cooke & Harkn., Valsella salicis Fuckel. Citation: Lin L, Fan XL, Groenewald JZ, Jami F, Wingfield MJ, Voglmayr H, Jaklitsch W, Castlebury LA, Tian CM, Crous PW (2024). Cytospora: an important genus of canker pathogens. Studies in Mycology 109: 323-401. doi: 10.3114/sim.2024.109.05.

Pseudoplagiostoma Causing Leaf Spot Disease in Key Tropical Fruit Crops in Thailand

Fruit crops have a pivotal role in Thailand's economy. Continuous evaluation of 13 potential and emerging diseases in fruit crops is important. Necrotic and discolored leaf spots were observed in Persea americana (avocado) and Mangifera indica (mango). The isolated fungi from the leaf spot were identified through multi-loci phylogenetic analyses using a concatenated matrix of ITS, LSU, tef1α, and tub2. The fungal isolates from Pe. americana were identified as Pseudoplagiostoma perseae, and isolates from Mangifera indica were identified as Ps. mangiferae. The pathogenicity assays confirmed that Ps. perseae causes leaf spots of Pe. americana, while Ps. mangiferae causes leaf blotch of M. indica. The pathogenicity of Ps. perseae and Ps. mangiferae has been reported in China and Taiwan. Hence, this study provides a report of the novel geographical distribution of Ps. perseae and Ps. mangiferae. Moreover, the cross-inoculation tests of Ps. perseae and Ps. mangiferae on M. indica and Pe. americana were conducted, respectively. Both pathogens showed host specificity, as suggested by the phylogenetic relationship and the host plants. In addition, disease control with carbendazim, trifloxystrobin, mancozeb, and prochloraz was assayed. All fungicides equally inhibited the mycelial growth of both pathogens.

The Meaning and Measure of Concordance Factors in Phylogenomics

As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci and therefore less sampling variance. While we can more accurately measure the mean signal in these datasets, lower sampling variance is often reflected in uniformly high measures of branch support-such as the bootstrap and posterior probability-limiting their utility. Larger datasets have also revealed substantial biological variation in the topologies found across individual loci, such that the single species tree inferred by most phylogenetic methods represents a limited summary of the data for many purposes. In contrast to measures of statistical support, the degree of underlying topological variation among loci should be approximately constant regardless of the size of the dataset. "Concordance factors" (CFs) and similar statistics have therefore become increasingly important tools in phylogenetics. In this review, we explain why CFs should be thought of as descriptors of topological variation rather than as measures of statistical support, and argue that they provide important information about the predictive power of the species tree not contained in measures of support. We review a growing suite of statistics for measuring concordance, compare them in a common framework that reveals their interrelationships, and demonstrate how to calculate them using an example from birds. We also discuss how measures of topological variation might change in the future as we move beyond estimating a single "tree of life" toward estimating the myriad evolutionary histories underlying genomic variation.

Sequential Bayesian Phylogenetic Inference

The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from a given analysis is used as input for the next analysis (e.g., a single multiple sequence alignment is used to estimate a gene tree). In this framework, uncertainty is not propagated from step to step, which can lead to inaccurate or spuriously confident results. Here, we formally develop and test a sequential inference approach for Bayesian phylogenetic inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior distribution produced in the previous step. Our sequential inference approach presented here not only accounts for uncertainty between analysis steps but also allows for greater flexibility in software choice (and hence model availability) and can be computationally more efficient than the traditional joint inference approach when multiple models are being tested. We show that our sequential inference approach is identical in practice to the joint inference approach only if sufficient information in the data is present (a narrow posterior distribution) and/or sufficiently many important samples are used. Conversely, we show that the common practice of using a single point estimate can be biased, for example, a single phylogeny estimate can transform an unrooted phylogeny into a time-calibrated phylogeny. We demonstrate the theory of sequential Bayesian inference using both a toy example and an empirical case study of divergence-time estimation in insects using a relaxed clock model from transcriptome data. In the empirical example, we estimate 3 posterior distributions of branch lengths from the same data (DNA character matrix with a GTR+Γ+I substitution model, an amino acid data matrix with empirical substitution models, and an amino acid data matrix with the PhyloBayes CAT-GTR model). Finally, we apply 3 different node-calibration strategies and show that divergence time estimates are affected by both the data source and underlying substitution process to estimate branch lengths as well as the node-calibration strategies. Thus, our new sequential Bayesian phylogenetic inference provides the opportunity to efficiently test different approaches for divergence time estimation, including branch-length estimation from other software.

Morpho-phylogenetic evidence reveals novel species and new records of Nigrograna (Nigrogranaceae) associated with medicinal plants in Southwestern China

During a survey of saprobic fungal niches in Southwestern China, eighteen ascomycetous collections of Nigrograna (Nigrogranaceae, Pleosporales, Dothideomycetes) were found on dead branches of medicinal plants. These taxa were characterized and identified based on morphological and culture characteristics, and phylogenetic analyses of a combined the internal transcribed spacer region of rDNA (ITS), nuclear large subunit rDNA (28S, LSU), RNA polymerase second-largest subunit (rpb2), nuclear small subunit rDNA (18S, SSU), and translation elongation factor 1-alpha (tef1-α) sequence dataset also confirmed their placement. As a result, four novel species, namely Nigrogranacamelliae, N.guttulata, N.longiorostiolata and N.neriicola were described. Additionally, four new host records of N.acericola, N.magnoliae, N.oleae and N.thymi were introduced. Furthermore, this study addresses the taxonomic status of N.trachycarpi, proposing its synonymy under N.oleae. Detailed illustrations, descriptions and informative notes for each newly identified taxon and novel host record are provided in this study.

The coevolution of fungus-ant agriculture

Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276 ants. We found that fungus-ant agriculture originated ~66 million years ago when the end-of-Cretaceous asteroid impact temporarily interrupted photosynthesis, causing global mass extinctions but favoring the proliferation of fungi. Subsequently, ~27 million years ago, one ancestral fungal cultivar population became domesticated, i.e., obligately mutualistic, when seasonally dry habitats expanded in South America, likely isolating the cultivar population from its free-living, wet forest-dwelling conspecifics. By revealing these and other major transitions in fungus-ant coevolution, our results clarify the historical processes that shaped a model system for nonhuman agriculture.

Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies. We discuss the various approaches to modeling rate evolution, provide a comprehensive list of available software, and examine the challenges and advancements of the prevalent Bayesian framework, contrasting them to faster non-Bayesian methods. Lastly, we offer insights into potential advancements in the field in the era of big data.

Three new species of the genus Clavulina (Hydnaceae, Cantharellales) from North China based on morphological and phylogenetic analysis

Clavulina possesses important ecological and economic value and has attracted extensive attention from mycologists. Macrofungal diversity is high in China, but Clavulina species have not been thoroughly studied. In this study, based on morphological evidence and phylogenetic analyses of the nucleotide sequences of three loci (nrITS, nrLSU, and rpb2), three new species of Clavulina from North China were identified. Morphologically, Clavulinachengdeensis is characterized by its white to dirty white basidiomata with somewhat pale orange tips and somewhat wrinkled hymenium. Clavulinagriseoviolacea is characterized by its gray to dark grayish violet basidiomata, with a sometimes-white stipe base, monopodial or irregularly polychotomous toward branch apices. Clavulinapallida is characterized by its white to pale cream white basidiomata with somewhat orange tips. Phylogenetically, the three new species form three independent branches with high support values in the phylogenetic tree.

Unveiling fungi associated with Castanopsis woody litter in Yunnan Province, China: Insights into Pleosporales (Dothideomycetes) species

During a survey of the diversity of lignicolous fungi in Yunnan Province, China, we collected and identified five microfungi species from dead woody litters of Castanopsis trees in terrestrial habitats. Through both morphological comparisons and phylogenetic analyses of multi-gene sequences, we identified two taxa as new species and three collections as new host records within Pleosporales. Pseudolophiostomalincangense sp. nov. is introduced as a sexual morph in Lophiostomataceae, Pleopunctumbaoshanense sp. nov. is introduced as a hyphomycetous fungi in Phaeoseptaceae, and Paraphomaaquatica as a first report of sexual morph in Paraphoma. In addition, Occultibambusakunmingensis and Pleopunctummegalosporum were isolated for the first time from the dead twigs of Castanopsisdelavayi and C.calathiformis, respectively. Comprehensive morphological descriptions, illustrations, and phylogenetic analysis results are provided for the above-mentioned species.

Morphological and Phylogenetic Analyses Reveal Three Novel Species of Sanguinoderma (Ganodermataceae, Basidiomycota) from Yunnan Province, China

Sanguinoderma (Ganodermataceae) is recognized as a valuable medicinal resource in Taiwan, China. Additionally, it serves as a traditional folk medicine for treating neurotic epilepsy in Malaysia. This study involved the collection of six specimens of Sanguinoderma from Yunnan Province, China. Employing multigene phylogenetic analysis of DNA sequences, including internal transcribed spacer (ITS), nuclear large subunit (LSU), RNA polymerase II second largest subunit (rpb2), translation elongation factor 1-alpha (tef1-α), mitochondrial small subunit (mtSSU), nuclear small subunit (nSSU) and morphological examinations, three new species, viz. Sanguinoderma concentricum, S. dehongense and S. ovisporum, are introduced. Sanguinoderma concentricum is characterized by a central stipe basidiomata, an orbicular to suborbicular pileus, a grayish-yellow surface with alternating concentric zones and wavy margin-like petals and regular pileipellis cells (4-8 × 17-28 μm). Sanguinoderma dehongense is characterized by a long stipe and flabelliform basidiomata, a dark-grayish yellow-to-dark-yellow pileus surface, irregular pileipellis cells and wavy margin and ellipsoid basidia (8-11 × 9-13 μm). Sanguinoderma ovisporum is characterized by a reniform basidiomata, a heterogeneous context and ovoid basidiospores (7.5-8.6 × 5.5-7.2 µm). A detailed description and illustrations of these new species are provided, as well as a morphological comparison with similar taxa.

Diversity and Pathogenicity of Six Diaporthe Species from Juglans regia in China

Walnut (Juglans regia L.) is cultivated extensively in China for its substantial economic potential as a woody oil species. However, many diseases caused by Diaporthe greatly affect the health of Juglans regia trees. The present study revealed the presence of Diaporthe species from Juglans regia. A total of six species of Diaporthe were isolated from twigs of Juglans regia in three provinces in China, including two known species (Diaporthe gammata and D. tibetensis) and four novel species (D. chaotianensis, D. olivacea, D. shangluoensis and D. shangrilaensis). Phylogenetic relationships of the new species were determined by multilocus phylogenetic analyses based on partial sequences of the internal transcribed spacer (ITS) region, calmodulin (cal) gene, histone H3 (his3) gene, translation elongation factor 1-α (tef1-α) gene and β-tubulin (tub2) gene. Pathogenicity tests indicated that all Diaporthe species obtained in this study were confirmed as pathogens of Juglans regia. This study deepens the understanding of species associated with several disease symptoms in Juglans regia and provides useful information for effective disease control.

Characterization of Colletotrichum species obtained from citrus in northern Thailand and introducing a new host record for C. plurivorum

Citrus trees are affected by many plant‐pathogenic fungi. The present study aimed to characterize Colletotrichum species on citrus showing anthracnose symptoms, leaf and fruit spot and wither tip in northern Thailand using multilocus data and assay their pathogenicity. The surveys were carried out from December 2021 to January 2022 and 73 isolates were obtained from infected tissues. The fungal strains were identified based on morphological traits and were confirmed via amplification and sequencing of ITS, ACT, CHS‐1, GAPDH and TUB2. In all, 41 isolates were subjected to multilocus phylogeny. Forty of these isolates of Colletotrichum species belonged to the C. gloeosporioides species complex and one isolate belonged to the C. orchidearum species complex. Colletotrichum siamense, comprising 19 isolates, was the most dominant species associated with symptomatic citrus, followed by C. gloeosporioides (17 isolates), C. fructicola (three isolates), C. endophytica (one isolate) and C. plurivorum (one isolate). C. plurivorum is reported for the first time from citrus in the world. These isolates were obtained from mandarin (Citrus reticulata), pomelo (C. maxima), Persian lime (C. latifolia), Thai lime (C. hystrix) and acid lime (C. aurantifolia). The pathogenicity of the isolated fungi was tested through inoculation on branch, fruit and leaf using the detached method on mandarin, pomelo and Persian lime hosts, confirming Koch's postulate. In terms of disease severity, C. gloeosporioides and C. siamense were observed to be the most pathogenic species. This is the first pathogenic and molecular study of Colletotrichum species infecting citrus in northern Thailand.

New Species and Records of Pleurotheciaceae from Karst Landscapes in Yunnan Province, China

Pleurotheciaceae is a genera-rich and highly diverse family of fungi with a worldwide distribution in aquatic and terrestrial habitats. During the investigation of lignicolous freshwater fungi from karst landscapes in Yunnan Province, China, 15 fresh strains were obtained from submerged decaying wood. Based on the morphology and phylogenetic analysis of a combined LSU, ITS, SSU, and rpb2 sequence dataset, Obliquifusoideum triseptatum, Phaeoisaria obovata, Pleurotheciella brachyspora, Pl. longidenticulata, and Pl. obliqua were introduced as new species, P. synnematica and Rhexoacrodictys melanospora were reported as new habitat records, and P. sedimenticola and Pl. hyalospora were reported as new collections. In addition, based on morphological comparisons and phylogenetic analysis, we accepted Obliquifusoideum into in the family Pleurotheciaceae (Pleurotheciales, Savoryellomycetidae). Freshwater habitats are the primary habitats of Pleurotheciaceae species, and Yunnan Province has the highest concentration and species diversity of Pleurotheciaceae in China.

New species and records of Botryosphaeriales (Dothideomycetes) associated with tree dieback in Beijing, China

Botryosphaeriales species are important pathogens that have worldwide distribution. In this study, 23 Botryosphaeriales strains were isolated from 13 host species during a dieback disease survey in Beijing, China. Based on morphological and phylogenetic analyses, six Botryosphaeriales species were identified, including two new species named Dothiorellahortiarborum sp. nov. and Phaeobotryonfraxini sp. nov., and four new host records: Aplosporellaginkgonis from Cotinuscoggygriavar.cinereus, A.javeedii from Acermiyabei, Acertruncatum, Forsythiasuspensa, Lagerstroemiaindica, Sambucuswilliamsii, Syringavulgaris, Ulmuspumila, Xanthocerassorbifolium, A.yanqingensis from Acertruncatum, and Do.acericola from Forsythiasuspensa, Ginkgobiloba, and Syringaoblata. This study enriches the species diversity associated with tree dieback in Beijing, China, and contributes to the further study of the taxonomy of this order.

Three novel woody litter inhabiting fungi in Didymosphaeriaceae, Phaeoseptaceae and Synnemasporellaceae from Zhujiangyuan Nature Reserve, Yunnan Province, P.R. China

Zhujiangyuan Nature Reserve, located in Qujing City, Yunnan Province, China, is reported with high fauna and floral diversity, while the fungal diversity of the region is poorly documented. During the summer season in 2023, decaying wood-inhabiting microfungi were collected from different microhabitats. The novel species were identified based on morphological characteristics and phylogenetic analyses (based on combined datasets of ITS, LSU, SSU, tef1-α, and rpb2 regions). Two species belong to Dothideomycetes (viz., Spegazziniazhujiangyuanensis sp. nov. and Phaeoseptumzhujiangyuanense sp. nov. in Pleosporales) while the other one resides in Sordariomycetes (Synnemasporellafanii sp. nov. in Diaporthales). The results are in conformity with the earlier studies that predicted higher fungal diversity in this region.

Two new species of Ganoderma (Ganodermataceae, Basidiomycota) from Southwest China

Ganoderma is a large and diverse genus containing fungi that cause white rot to infect a number of plant families. This study describes G.phyllanthicola and G.suae as new species from Southwest China, based on morphological and molecular evidence. Ganodermaphyllanthicola is characterized by dark brown to purplish black pileus surface with dense concentric furrows, pale yellow margin, irregular pileipellis cells, small pores (5-7 per mm) and ellipsoid to sub-globose basidiospores (8.5-10.0 × 6.0-7.5 µm). Ganodermasuae is characterized by reddish brown to oxblood red pileus surface and lead gray to greyish-white pore surface, heterogeneous context, wavy margin and almond-shaped to narrow ellipsoid basidiospores (8.0-10.5 × 5.0-7.0 μm). The phylogeny of Ganoderma is reconstructed with multi-gene sequences: the internal transcribed spacer region (ITS), the large subunit (nrLSU), translation elongation factor 1-α gene (TEF-1α) and the second subunit of RNA polymerase II (RPB2). The results show that G.suae and G.phyllanthicola formed two distinct line-ages within Ganoderma. Descriptions, illustrations and phylogenetic analyses results of the two new species are presented.

Isolation and molecular characterization of a novel relapsing fever group Borrelia from the white-eared opossum Didelphis albiventris in Brazil

This study aimed to detect, isolate and to characterize by molecular methods a relapsing fever group (RFG) Borrelia in white-eared opossums (Didelphis albiventris) from Brazil. During 2015-2018, when opossums (Didelphis spp.) were captured in six municipalities of the state of São Paulo, Brazil, molecular analyses revealed the presence of a novel RFG Borrelia sp. in the blood of seven opossums (Didelphis albiventris), out of 142 sampled opossums (4.9% infection rate). All seven infected opossums were from a single location (Ribeirão Preto municipality). In a subsequent field study in Ribeirão Preto during 2021, two new opossums (D. albiventris) were captured, of which one contained borrelial DNA in its blood. Macerated tissues from this infected opossum were inoculated into laboratory animals (rodents and rabbits) and two big-eared opossums (Didelphis aurita), which had blood samples examined daily via dark-field microscopy. No spirochetes were visualized in the blood of the laboratory animals. Contrastingly, spirochetes were visualized in the blood of the two D. aurita opossums between 12 and 25 days after inoculation. Blood samples from these opossums were used for a multi-locus sequencing typing (MLST) based on six borrelial loci. Phylogenies inferred from MLST genes positioned the sequenced Borrelia genotype into the RFG borreliae clade basally to borreliae of the Asian-African group, forming a monophyletic group with another Brazilian isolate, "Candidatus B. caatinga". Based on this concatenated phylogenetic analysis, which supports that the new borrelial isolate corresponds to a putative new species, we propose the name "Candidatus Borrelia mimona".

Two novel species and a new host record of Alternaria (Pleosporales, Pleosporaceae) from sunflower (Compositae) in Myanmar

Sunflower (Helianthusannuus L.) is a widely cultivated, fast-growing crop known for its seeds and oil, with substantial ecological and economic importance globally. However, it faces challenges from leaf diseases caused by Alternaria species, which threaten its yield. Three small-spored Alternaria species were isolated from leaf spot and blight symptoms on sunflower in Myanmar. All the species were determined based on morphological characterization and a multi-locus phylogenetic assessment of seven genes, including the internal transcribed spacer of rDNA region (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2), translation elongation factor 1-α (TEF1), Alternaria major allergen gene (Alt a 1), endopolygalacturonase gene (EndoPG), and an anonymous gene region (OPA10-2). The results introduced two new Alternaria species, A.myanmarensis sp. nov. and A.yamethinensis sp. nov., and a known species of A.burnsii, firstly reported from sunflower.

Amphichorda monjolensis sp. nov., a new fungal species isolated from a Brazilian limestone cave, with an update on acremonium-like species in Bionectriaceae

Caves are unique environments characterized by spatial limitations, partial or total absence of direct light, and scarcity of organic carbon and nutrients. Caves are shelters for a variety of adapted animals and microorganisms such as fungi, many of which are still unknown. Amphichorda is a fungal genus belonging to the family Bionectriaceae, which includes cave-dwelling and entomopathogenic species with biotechnological applications. In this study, a new fungal species was identified using morphological and multi-locus phylogenetic analyses of the ITS, LSU, and TEF loci, in the Gruta Velha Nova limestone cave located in the Southern Espinhaço Range, Monjolos, Minas Gerais, Brazil. During the exposure of potato dextrose agar plates to the cave environment, an insect from the family Rhaphidophoridae passed by and fed on the culture medium, resulting in three fungal isolates. Phylogenetic analyses showed that these isolates formed a clade distinct from all known species, leading us to introduce a new species, Amphichorda monjolensis, which may be associated with this insect. Here, we also proposed two new combinations for species of acremonium-like fungi in the Bionectriaceae: Bulbithecium globosisporum (synonym: Acremonium globosisporum) and Hapsidospora curva (synonym: Acremonium curvum). The discovery of A. monjolensis highlights the potential of caves as shelters for new species with significant biotechnological importance.

Genetic Variability Among U.S.-Sentinel Cotton Plot Cotton Leafroll Dwarf Virus and Globally Available Reference Isolates Based on ORF0 Diversity

The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America, has been identified in commercial cotton plantings in the United States. Here, the CLRDV intraspecific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South American lineages. Principal component analysis (PCA) identified seven statistically supported intraspecific populations. The Bayesian phylogeny and PCA dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia and eastern Texas. The Alabama-Georgia founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central United States. Based on the geographically restricted distribution, spread of another extant Texas population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).

Common Methods for Phylogenetic Tree Construction and Their Implementation in R

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.

New insights into the systematics of the afrotropical Amblyomma marmoreum complex (Acari: Ixodidae) and the genome of a novel Rickettsia africae strain using morphological and metagenomic approaches

The Amblyomma marmoreum complex includes afrotropical species, such as Amblyomma sparsum, a three-host tick that parasitizes reptiles, birds, and mammals, and is a recognized vector of Ehrlichia ruminantium. However, the lack of morphological, genetic and ecological data on A. sparsum has caused considerable confusion in its identification. In this study, we used microscopy and metagenomic approaches to analyze A. sparsum ticks collected from a puff adder snake (Bitis arietans) in southwest Senegal (an endemic rickettsioses area) in order to supplement previous morphological descriptions, provide novel genomic data for the A. marmoreum complex, and describe the genome of a novel spotted fever group Rickettsia strain. Based on stereoscope and scanning electron microscopy (SEM) morphological evaluations, we provide high-quality images and new insights about punctation and enameling in the adult male of A. sparsum to facilitate identification for future studies. The metagenomic approach allowed us assembly the complete mitochondrial genome of A. sparsum, as well as the nearly entire chromosome and complete plasmid sequences of a novel Rickettsia africae strain. Phylogenomic analyses demonstrated a close relationship between A. sparsum and Amblyomma nuttalli for the first time and confirmed the position of A. sparsum within the A. marmoreum complex. Our results provide new insights into the systematics of A. sparsum and A. marmoreum complex, as well as the genetic diversity of R. africae in the Afrotropical region. Future studies should consider the possibility that A. sparsum may be a vector for R. africae.

Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification

Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.

New Insights into Tetraplosphaeriaceae Based on Taxonomic Investigations of Bambusicolous Fungi and Freshwater Fungi

Species within Tetraplosphaeriaceae have been frequently documented in recent years with the extensive investigations of microfungi along a latitudinal gradient from north to south in the Asian/Australian region. Both bamboo substrates and freshwater habitats serve as extensive reservoirs, hosting a rich diversity of fungi that exhibit broad geographical distributions. The most common fungi in these two environments are generally distributed in distinct families. However, our statistics have revealed an intriguingly distinct preference of Tetraplosphaeriaceae species for inhabiting both bamboo substrates and freshwater habitats. The genera Pseudotetraploa (100%) and Triplosphaeria (100%) exhibit a strong preference, followed by Shrungabeeja (71%) and Quadricrura (67%). Our taxonomic and phylogenetic study of microfungi in southern China have identified four additional novel species, viz., Aquatisphaeria bambusae sp. nov., Pseudotetraploa phyllostachydis sp. nov., Pseudotetraploa yangjiangensis sp. nov., and Tetraploa submersa sp. nov. from bamboo substrates and freshwater habitats. In addition, Aquatisphaeria thailandica has previously been documented from freshwater habitats in Thailand; however, we have once again isolated this species from decaying bamboo substrates in Guangdong, China. The new findings substantiate our hypothesis that the preference of Tetraplosphaeriaceae species for colonizing bamboo substrates and freshwater habitats will be more evident through more extensive investigations conducted in such environments.

Insights into the molecular phylogeny and morphology of three novel Dothiora species, along with a worldwide checklist of Dothiora

Most species of Dothiora are known from the dead parts of various host plants as saprobic fungi in terrestrial habitats occurring in tropical and temperate regions. In the present study, samples of Dothiora were collected from dead twigs and branches of Capparis spinosa, Rhaponticum repens, and an unknown angiosperm plant from the Tashkent and Jizzakh regions of Uzbekistan. Multi-gene phylogenetic analyses based on a combined ITS, LSU, SSU, TEF1, and TUB2 sequence data revealed their taxonomic positions within the Dothideaceae. Three new species of Dothiora, namely, Dothiora capparis, Dothiora rhapontici, and Dothiora uzbekistanica were proposed by molecular and morphological data. Likewise, the phylogenetic relationship and morphology of Dothiora are discussed. In addition, we provide a list of accepted Dothiora species, including host information, distribution, morphology descriptions, and availability of sequence data, to enhance the current knowledge of the diversity within Dothiora.

Paramphibambusabambusicola gen. et. sp. nov., Arecophilaxishuangbannaensis and A.zhaotongensis spp. nov. in Cainiaceae from Yunnan, China

Morphological comparisons and multi locus phylogenetic analyses (base on the combined genes of ITS, LSU, rpb2 and tub) demonstrated that three new saprobic taxa isolated from bamboo belong to Cainiaceae. These taxa comprise a novel genus Paramphibambusa (P.bambusicolasp. nov.) and two new species, Arecophilaxishuangbannaensis and A.zhaotongensis. The three new taxa belong to Cainiaceae (Xylariales, Sordariomycetes) a poorly studied family, which now comprises eight genera. Paramphibambusa can be distinguished from other Cainiaceae genera in having ascomata with a neck and ascospores lacking longitudinal striation, germ slits or germ pores. The two new Arecophila species clustered in a clade with Arecophila sp. and A.bambusae. Detailed morphological descriptions, illustrations, and an updated phylogenetic tree are provided for the new taxa.

Three Novel Cheiroid Hyphomycetes in Dictyocheirospora and Dictyosporium (Dictyosporiaceae) from Freshwater Habitats in Guangdong and Guizhou Provinces, China

Over the past two decades, numerous novel species have been identified within Dictyosporiaceae, primarily in Dictyocheirospora and Dictyosporium. A recent monograph has revealed that these two genera exhibit a distinct preference for freshwater habitats, particularly in southern China. However, further investigation into the distribution and diversity of the two genera in Guangdong and Guizhou Provinces remains insufficient. In this study, we conducted an analysis of four intriguing cheiroid hyphomycetes collected from flowing rivers in these two regions. Through morphological and phylogenetic analyses incorporating combined LSU, SSU, ITS, and tef1-α sequence data, we have identified them as a novel species in Dictyocheirospora (Dictyoc. submersa sp. nov.), two novel species in Dictyosporium (Dictyos. guangdongense sp. nov. and Dictyos. variabilisporum sp. nov.), and one previously documented species (Dictyos. digitatum). Specifically, the identification of Dictyos. guangdongense is primarily based on its distinct morphology, characterized by complanate, cheiroid, and brown to dark brown conidia, with a hyaline, short, and atrophied appendage arising from the apical cell of the outer row. In addition, the morphological distinctions between Dictyocheirospora and Dictyosporium are further clarified based on our new data. This study also highlights a few phylogenetic matters regarding Dictyosporiaceae.

New insights into the molecular phylogeny, biogeographical history, and diversification of Amblyomma ticks (Acari: Ixodidae) based on mitogenomes and nuclear sequences

BACKGROUND

Amblyomma is the third most diversified genus of Ixodidae that is distributed across the Indomalayan, Afrotropical, Australasian (IAA), Nearctic and Neotropical biogeographic ecoregions, reaching in the Neotropic its highest diversity. There have been hints in previously published phylogenetic trees from mitochondrial genome, nuclear rRNA, from combinations of both and morphology that the Australasian Amblyomma or the Australasian Amblyomma plus the Amblyomma species from the southern cone of South America, might be sister-group to the Amblyomma of the rest of the world. However, a stable phylogenetic framework of Amblyomma for a better understanding of the biogeographic patterns underpinning its diversification is lacking.

METHODS

We used genomic techniques to sequence complete and nearly complete mitochondrial genomes -ca. 15 kbp- as well as the nuclear ribosomal cluster -ca. 8 kbp- for 17 Amblyomma ticks in order to study the phylogeny and biogeographic pattern of the genus Amblyomma, with particular emphasis on the Neotropical region. The new genomic information generated here together with genomic information available on 43 ticks (22 other Amblyomma species and 21 other hard ticks-as outgroup-) were used to perform probabilistic methods of phylogenetic and biogeographic inferences and time-tree estimation using biogeographic dates.

RESULTS

In the present paper, we present the strongest evidence yet that Australasian Amblyomma may indeed be the sister-group to the Amblyomma of the rest of the world (species that occur mainly in the Neotropical and Afrotropical zoogeographic regions). Our results showed that all Amblyomma subgenera (Cernyomma, Anastosiella, Xiphiastor, Adenopleura, Aponomma and Dermiomma) are not monophyletic, except for Walkeriana and Amblyomma. Likewise, our best biogeographic scenario supports the origin of Amblyomma and its posterior diversification in the southern hemisphere at 47.8 and 36.8 Mya, respectively. This diversification could be associated with the end of the connection of Australasia and Neotropical ecoregions by the Antarctic land bridge. Also, the biogeographic analyses let us see the colonization patterns of some neotropical Amblyomma species to the Nearctic.

CONCLUSIONS

We found strong evidence that the main theater of diversification of Amblyomma was the southern hemisphere, potentially driven by the Antarctic Bridge's intermittent connection in the late Eocene. In addition, the subgeneric classification of Amblyomma lacks evolutionary support. Future studies using denser taxonomic sampling may lead to new findings on the phylogenetic relationships and biogeographic history of Amblyomma genus.