Monophyletic Research Articles

Nuclear DNA-based phylogenetic analysis of Neocinnamomum species

AbstractNeocinnamomum plants are evergreen shrubs or small trees belonging to the Neocinnamomeae tribe of the Lauraceae family. Their seeds are rich in fatty acids, and their leaves are often used in traditional Chinese medicine. Presently, only a few studies have been performed on Neocinnamomum plants; therefore, the genome-based phylogeny among Neocinnamomum species has not been determined, which limits the germplasm innovation of this genus. In this study, by the Illumina (next-generation sequencing) and third-generation sequencing technologies, the whole genomes of seven Neocinnamomum species samples were sequenced, their nuclear DNA (nrDNA) sequences were assembled and characterized, and their phylogeny was reconstructed. The results revealed four hypervariable regions (i.e. transcribed spacer regions) in the nrDNA sequences, among which the highest degree of variation was observed in the external transcribed spacer (ETS) region localized behind the 26S gene. A total of 27 insertions/deletions and 184 single-nucleotide polymorphisms, both localized mainly in the ETS and internal transcribed spacer regions, were identified. Phylogenetic trees were constructed based on the nrDNA sequences using the maximum likelihood (ML) and Bayesian inference (BI) methods with Caryodaphnopsis henryi as the outgroup. The ML tree divided the seven Neocinnamomum species into four clades. Clade I consisted of Neocinnamomum caudatum var. macrocarpum and Neocinnamomum caudatum, clade II included Neocinnamomum delavayi and Neocinnamomum mekongense, clade III included Neocinnamomum fargesii and a branch species of N. delavayi and clade IV included Neocinnamomum lecomtei, constituting a monophyletic and basal group. The BI tree shared the same topological structure as the ML tree, and all the support values of the BI tree were one except for that of one Neocinnamomum species (0.98). The results of this study provide new evidence regarding the phylogenetic evolution of the Neocinnamomum plants.

Host range, severity and trans boundary transmission of Orf virus (ORFV).

Contagious ecthyma in small ruminants is a zoonotic disease caused by Orf virus (ORFV) in the genus Parapoxvirus that can be deadly to its natural hosts. It causes significant losses worldwide, and commonly infects humans. However, the literature about its comparative severity in sheep and goat hosts is misleading; and while contagious ecthyma has been shown to occur in camels and transmit to humans, there is confusion as to whether ORFV is responsible. Camels are important from a 'One Health' perspective as they have been implicated as a reservoir host for the virus causing Middle East Respiratory Syndrome (MERS), which has a case fatality rate of 35% in humans. We compared ORFV gene sequences and mortality data from the West Bank in Palestine, where ORFV has not been reported previously, with data from the region. Surprisingly, we found that infections of camels that had been attributed to ORFV were more closely related to a different member of the genus Parapoxvirus. Two Middle East ORFVs isolated from humans were unrelated and sat alongside sheep and goat derived sequences on two distinct ORFV lineages of a maximum likelihood B2L gene tree. One of the viral lineages bifurcated to produce a monophyletic group of goat-derived ORFVs characterized uniquely by a glycine at amino acid reside 249. We found that serine is the ancestral allele shared between ORFV infections of sheep and also two closely related Parapoxviruses (PCPV and CCEV), indicating that the glycine allele represents a more recent shift in virus host range adaptation to goats. Furthermore, and contrary to some reports that ORFV is more severe in goats than in sheep, we observed median mortality of up to 24.5% in sheep, but none in goats. We also identified trans-boundary spread of ORFV between the West Bank and Israel.

First complete Niobe yangtzeensis Lu, 1975 (Asaphidae, Trilobita) from the Middle Ordovician of South China, and its systematic and palaeogeographic implications

Since Niobe yangtzeensis was erected in 1975, due to no complete or even cephalic specimens, the generic assignment of Niobe yangtzeensis remains controversial. Based on the new discovery of a complete specimen of Niobe yangtzeensis in Yichang of South China, this species is redescribed and its generic position assignment is clarified and confirmed. A phylogenetic analysis of Niobinae shows that each of the four genera of this subfamily (Niobe, Niobella, Proxiniobe and Gog) forms a monophyletic group, and that among which Niobe yangtzeensis belongs to the genus Niobe. The palaeogeographical distribution and environmental analysis of Niobinae, suggest that Niobella, Proxiniobe and Gog lived in a relatively deeper-water (the outer-shelf or slope) environment, while Niobe preferred a shallower water environment, such as the inner shelf.

Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex

As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.

Classification and phylogeny of Amaryllidaceae, the modern synthesis and the road ahead: a review

The classification and phylogenetic history of the Amaryllidaceae is reviewed since the dawn of molecular systematics in the 1990’s. The family is now recognized as comprising three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, of which the latter is the largest. The family likely had a Gondwanaland origin in what is now Africa. Agapanthoideae is monotypic, endemic to South Africa, and the first branch in the family tree of life; Allioidieae is sister to Amaryllidoideae. Four tribes are recognized in Allioideae: Allieae (monotypic, with nearly 1000 species of Allium across the Northern Hemisphere), Gilliesieae (5–7 genera in southern South America), Leucocoryneae (six genera mostly in southern South America), and Tulbaghieae (monotypic, with ca. 30 species endemic to South Africa). Amaryllidoideae is cosmopolitan, but mostly pantropical, consisting of 13 tribes. Centers of diversity occur in South Africa, South America and the Mediterranean region. The American clade is sister to the Eurasian clade (tribes Galantheae, Lycorideae, Narcisseae and Pancratieae) of the subfamily. The American Amaryllidoideae resolves as two monophyletic groups, 1) the hippeastroid clade (tribes Griffineae and Hippeastreae) and 2) the Andean tetraploid clade (tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae). Molecular analyses are reviewed for each main clade of the family, along with the resultant taxonomic changes. Directions for future studies are briefly discussed.

A reinvestigation of multiple independent evolution and Triassic-Jurassic origin of multicellular Volvocine algae.

The evolution of multicellular organisms is considered to be a major evolutionary transition, profoundly affecting the ecology and evolution of nearly all life on earth. The volvocine algae, a unique clade of chlorophytes with diverse cell morphology, provide an appealing model for investigating the evolution of multicellularity and development. However, the phylogenetic relationship and timescale of the volvocine algae are not fully resolved. Here, we use extensive taxon and gene sampling to reconstruct the phylogeny of the volvocine algae. Our results support that the colonial volvocine algae are not monophyletic group, and multicellularity independently evolve at least twice in the volvocine algae, once in Tetrabaenaceae and another in the Goniaceae + Volvocaceae. The simulation analyses suggest that incomplete lineage sorting is a major factor for the tree topology discrepancy, which imply that the multispecies coalescent model better fits the data used in this study. The coalescent-based species tree supports that the Goniaceae is monophyletic, and Crucicarteria is the earliest diverging lineage, followed by Hafniomonas and Radicarteria within the Volvocales. By considering the multiple uncertainties in divergence time estimation, the dating analyses indicate that the volvocine algae occurred during the Cryogenian to Ediacaran (696.6-551.1 Ma), and multicellularity in the volvocine algae originated from the Triassic to Jurassic. Our phylogeny and timeline provide an evolutionary framework for studying the evolution of key traits and the origin of multicellularity in the volvocine algae.

Genetic characterization and prevalence of Pseudomonas syringae strains from sweet cherry orchards in New Zealand

AbstractBacterial canker of cherry, caused by Pseudomonas syringae pathovars, is a major constraint to cherry growing in New Zealand. The prevalence of strains from cherry orchards in Central Otago, the main growing area for cherries in New Zealand, was studied, to better understand the epidemiology of the disease. Pseudomonas spp. isolates were collected from symptomatic and asymptomatic cherry tissue from 23 commercial cherry orchards in 2015. Isolates were classified into strains belonging to three different taxonomic groups by determining their phylogeny using the gltA gene sequence for all the strains and multilocus sequence analysis (MLSA) of four housekeeping genes for 35 strains. Pathogenicity of all Central Otago strains was tested on immature cherry fruit to support the phylogenetic classification. The two main taxonomic groups were P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1), in Phylogroup 2 (PG2) and Phylogroup 3 (PG3), respectively. The third group comprised nonpathogenic strains classified as Pseudomonas spp. Strains of Psm1 formed a monophyletic group, representing an almost clonal population. There was more variation detected within strains of Pss, although they were restricted to group PG2d. Nonpathogenic Pseudomonas spp. and pathogenic Pss and Psm1 strains coexisted in the same orchard. It was concluded that Pss is the predominant pathovar in Central Otago. This is the first detailed study of the P. syringae species complex in cherry orchards in New Zealand and provides the basis for future epidemiology studies.

Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity.

The tribe Paullinieae has the highest diversity of vascular variants among the seed plants. The developmental diversity is better understood in the species-rich genera Paullinia and Serjania; however, the phylogeny and diversity of vascular variants in the smaller genera of Paullinieae remain understudied. Here we investigate the evolution of development of stem vasculatures in the small genus Urvillea. We generate the first molecular phylogeny of Urvillea derived from 11 markers using a maximum likelihood and Bayesian approach. In combination with phylogenetic reconstruction, stochastic character mapping is used to assess evolutionary changes in stem ontogenies, determined from developmental anatomy of stems collected in the field or from herbarium and wood collections. Urvillea is supported as a monophyletic group and sister to Serjania. There are five stem ontogenies in Urvillea, including typical growth and four different vascular variants. Most stem ontogenies initiate with lobed stems in primary growth. Lobed stems in secondary growth are ancestral in Urvillea, but this ontogeny was lost multiple times. A reversal to typical growth occurred in non-climbing species. Phloem wedges, fissured stems, and ectopic cambia each evolved once independently. Phloem wedges is an intermediate developmental stage in the formation of fissured stems, which is characterized by a continuous fragmentation of vascular tissues. Lobed stems may generate constriction zones and lobes may split or not. Urvillea is the third most diverse genus (after Serjania and Paullinia) with respect to the number of vascular variants within Paullinieae. One ontogeny (fissured stems) is exclusive to the genus. Differential cambial activity and ectopic cambia are the main ontogenetic processes generating stem diversity. The evolutionary history of vascular variants demonstrates the large developmental plasticity of the cambium in such a small genus and further demonstrates that complex anatomies have repeatedly evolved within Paullinieae lianas.

Evidence of novel Treponema phylotypes implicated in contagious ovine digital dermatitis and association of treponemes with major lameness causing foot pathogens

In this study 269 swabs collected from 254 ovine foot lesions and 15 apparently healthy ovine feet were screened by PCR for the presence of major lameness causing foot pathogens viz. Treponema species, D. nodosus, F. necrophorum and T. pyogenes with the presumption that ovine foot lesion positive for Treponema species alone or in association with other three pathogens were categorized as contagious ovine digital dermatitis (CODD). While samples positive for D. nodosus alone or its combination with F. necrophorum and T. pyogenes were considered as footrot (FR) and samples in which F. necrophorum or T. pyogenes was found either alone or in combination were considered as interdigital dermatitis (ID). The overall occurrence of Treponema sp. in ovine foot lesions was 48.0%, and ranged from 33 to 58%. In Treponema positive samples D. nodosus, F. necrophorum and T. pyogenes were present in 34 (27.4%), 66 (54.4%) and 84 (68.5%) in contrast to Treponema negative samples in which these were present in 15 (11.1%), 20 (14.12%) and 17 (12.6%) samples, respectively. The data signifies that Treponema sp. are significantly associated with these foot pathogens and their different combinations with Treponema sp. influence the severity of CODD lesion. The identification of Treponema phylotypes was done by sequencing the 16S rRNA gene fragment of ten representative samples. Out of ten sequences, four (Trep-2, Trep-4, Trep-7 and Trep-10) were identical to Treponema sp. phylotype 1 (PT1) that belongs to phylogroup T. refringens-like, one sequence (Trep-1) was genetically close (90% sequence homology) to Treponema brennaborense while five sequences (Trep-3, Trep-5, Trep-6, Trep-8 and Trep-9) matched with uncultured bacterium clones of treponemes forming separate monophyletic group in phylogenetic tree and could represent new digital dermatitis phylogroup presently containing five ovine specific phylotypes. This is the first report on the presence of Treponema phylotypes other than three digital dermatitis (DD) Treponema phylogroups viz. T. phagedenis-like, T. medium/T. vincentii–like, and T. pedis-like that are frequently detected in CODD lesions. Metagenomic analysis of two representative samples revealed the abundance of genus Treponema in CODD lesion while this genus was absent in swab collected from clinically healthy foot suggesting that it might play primary role in producing CODD. These findings may further aid in understanding the etiopathogenesis of CODD and could help to develop appropriate treatment and mitigation strategies to combat the disease.

Molecular phylogeny and systematics of the South Asian freshwater‐fish genus Puntius (Teleostei: Cyprinidae)

AbstractDuring the past decade, the ca 120 species of small, colourful tropical Asian freshwater fishes previously referred to the cyprinid genus Puntius have been shown to consist of multiple morphologically distinct evolutionary lineages that resolve as monophyletic groups in molecular studies. Many of these clades have been allocated to new genera such as Dawkinsia, Desmopuntius, Haludaria, Oliotius, Pethia, Puntigrus, Sahyadria, Striuntius and Waikhomia. Others have been assigned to existing but previously poorly delineated genera such as Barbodes and Systomus, while some 40 species remain in Puntius. The divergent morphology of several species retained in Puntius suggests, however, that the systematics of this group requires further attention. Here, based on a phylogeny incorporating newly generated data from the mitochondrial cytochrome b (cytb), mitochondrial cytochrome c oxidase subunit 1 (cox1), nuclear recombination activating protein 1 (rag1), and interphotoreceptor retinoid‐binding protein (irbp) gene markers, we investigate the interrelationships of the species of Puntius in Sri Lanka in the wider context of their Indian and Southeast Asian congeners. We identify three well‐supported monophyletic groups that warrant recognition as new genera: Rohanella (type species Puntius titteya), Plesiopuntius (type species Gnathopogon bimaculatus) and Bhava (type species Puntius vittatus). The first of these is endemic to rainforest streams in Sri Lanka's perhumid southwestern wet zone, whereas the latter two are widely distributed in both Sri Lanka and southern India, including the Western Ghats. Our study highlights the presence of distinct evolutionary lineages among several widespread species.

Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method

The family Alloherpesviridae contains herpesviruses of fish and amphibians. Due to the significant economic losses to aquaculture that herpesviruses can cause, the primary areas of research interest are concerning their pathogenesis and prevention. Despite alloherpesvirus genomic sequences becoming more widely accessible, methods regarding their genus/species classification are still relatively unexplored. In the present study, the phylogenetic relationships between 40 completely sequenced alloherpesviruses were illustrated by the viral proteomic tree (ViPTree), which was divided into three monophyletic groups, namely Cyprinivirus, Ictalurivirus and Batrachovirus. Additionally, average nucleotide identity (ANI) and average amino acid identity (AAI) analyses were performed across all available sequences and clearly displayed species boundaries with the threshold value of ANI/AAI set at 90%. Subsequently, core-pan analysis uncovered 809 orthogroups and 11 core genes shared by all 40 alloherpesvirus genome sequences. For the former, a 15 percent identity depicts a clear genus boundary; for the latter, 8 of them may be qualified for phylogenetic analysis based on amino acid or nucleic acid sequences after being verified using maximum likelihood (ML) or neighbor-joining (NJ) phylogenetic trees. Finally, although the dot plot analysis was valid for the members within Ictalurivirus, it was unsuccessful for Cyprinivirus and Batrachovirus. Taken together, the comparison of individual methodologies provides a wide range of alternatives for alloherpesviruses classification under various circumstances.

Associative Genetic Diversity of Sarcocystis levinei Isolates across the Globe

Bubaline sarcocystosis, caused by Sarcocystis levinei, is worldwide in distribution. Yet, very limited reports are available across the globe on the phylogenetic aspects of this particular Sarcocystis spp. Virtually no literature is available on its molecular aspects from India. Thus, the present study was designed to phylogenetically characterize the various isolates of S. levinei based on 18S rRNA and cox 1 mitochondrial genes. A total of 11 isolates of S. levinei from Northern India were characterized for 18S rRNA (MG957189-MG957199) and cox 1 (MH255771-MH255781) genes. PCR products were cloned, sequenced, and compared with other sequences across the world. A phylogenetic tree was constructed based on the maximum likelihood (ML) method. Phylogenetic analysis placed S. levinei and S. cruzi into two monophyletic sister groups. An appreciable amount of genetic variability was noticed between various S. levinei sequences for both the gene loci. A total of three haplotypes were noticed for each gene. The generated sequences showed 99.8–100.0% and 99.7–100.0% nucleotide homologies within themselves with regard to the 18S rRNA and cox 1 genes, respectively. Few of the studied sequences showed marked similarity and closeness with the Egyptian sequences than their Indian counterparts. This is the first report of molecular characterization and sequence phylogenetic study of S. levinei from India.

Analysis of the Genomic Features and Evolutionary History of Pithovirus-Like Isolates Reveals Two Major Divergent Groups of Viruses.

New representatives of the phylum Nucleocytoviricota have been rapidly described in the last decade. Despite this, not all viruses of this phylum are allocated to recognized taxonomic families, as is the case for orpheovirus, pithovirus, and cedratvirus, which form the proposed family Pithoviridae. In this study, we performed comprehensive comparative genomic analyses of 8 pithovirus-like isolates, aiming to understand their common traits and evolutionary history. Structural and functional genome annotation was performed de novo for all the viruses, which served as a reference for pangenome construction. The synteny analysis showed substantial differences in genome organization between these viruses, with very few and short syntenic blocks shared between orpheovirus and its relatives. It was possible to observe an open pangenome with a significant increase in the slope when orpheovirus was added, alongside a decrease in the core genome. Network analysis placed orpheovirus as a distant and major hub with a large fraction of unique clusters of orthologs, indicating a distant relationship between this virus and its relatives, with only a few shared genes. Additionally, phylogenetic analyses of strict core genes shared with other viruses of the phylum reinforced the divergence of orpheovirus from pithoviruses and cedratviruses. Altogether, our results indicate that although pithovirus-like isolates share common features, this group of ovoid-shaped giant viruses presents substantial differences in gene contents, genomic architectures, and the phylogenetic history of several core genes. Our data indicate that orpheovirus is an evolutionarily divergent viral entity, suggesting its allocation to a different viral family, Orpheoviridae. IMPORTANCE Giant viruses that infect amoebae form a monophyletic group named the phylum Nucleocytoviricota. Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established. With advances in isolation techniques, the speed at which new giant viruses are described has increased, escalating the need to establish criteria to define the emerging viral taxa. In this work, we performed a comparative genomic analysis of representatives of the putative family Pithoviridae. Based on the dissimilarity of orpheovirus from the other viruses of this putative family, we propose that orpheovirus be considered a member of an independent family, Orpheoviridae, and suggest criteria to demarcate families consisting of ovoid-shaped giant viruses.

First report of leaf spot on pecan caused by Choanephora cucurbitarum in China.

Pecan (Carya illinoinensis K. Koch) is an important and widely planted nut tree species in Jiangsu Province, China (Mo et al. 2018). In July 2020, leaf spot symptoms were frequently observed on pecan in Jurong, Jiangsu Province (119°15'36"E, 32°1'6"N). Disease incidences ranged from 40 to 65% among 150 mature pecan trees from three nurseries. The disease severity index (DSI, Jiang et al. 2019) reached 58.4. Symptoms began as small brown spots scattered on leaves that gradually expanded to large, circular to irregular black and brown necrotic lesions. In severe cases, lesions developed on large portions of a single leaf, and eventually the dead leaves fell from the trees. Three monoconidial isolates (Chen2346, Chen2347, Chen2348) were isolated from lesion margins and cultured on potato dextrose agar (PDA) medium. Colonies on PDA were white and cottony, later becoming light gray with abundant reproductive structures. Sporangiophores were aseptate, hyaline, unbranched, and apically dilated to form a clavate vesicle, which produced sporangia. Sporangia were globular to ellipsoid, brown to dark brown, 103 to 128 µm in length, and 88 to 114 µm in width (n = 30). Sporangiola were brown, ellipsoid to ovoid, with longitudinal striae, and measured 13.9 to 18.8 × 7.9 to 10.8 μm (n = 60). The morphological characteristics of these isolates agreed with descriptions of Choanephora cucurbitarum (Kirk 1984). Genomic DNA of these three monoconidial isolates was extracted, and the partial sequences of the internal transcribed spacer (ITS) and large subunit (LSU) of rDNA were amplified using primer pairs ITS1/ITS4 (White et al. 1990) and LR0R/LR7 (Vilgalys and Hester 1990), respectively. The consensus sequences (GenBank accession nos.: OP315248 to OP315250 for ITS and OP315251 to OP315253 for LSU) were aligned using BLASTn and showed100% identity with the sequences from C. cucurbitarum found in GenBank (accession nos.: MF942131 for ITS and ON025788 for LSU). To further confirm the identity, a phylogenetic analysis was performed with MEGA (v.7.0) and MrBayes (v.3.1.2) software, using the maximum likelihood and Bayesian inference methods, respectively. The multigene phylogeny revealed that the three isolates in this study, as well as, C. cucurbitarum specimen, clustered as a strongly supported monophyletic group (99 bootstrap value; 0.95 posterior probabilities). Based on the morphological and molecular data, the isolates were identified as C. cucurbitarum. To confirm pathogenicity, healthy pecan seedlings (2 years old) were each inoculated with a mycelial block (3 × 3 mm) excised from the margin of a colony on the vein of each leaf. Seedlings treated with non-colonized PDA blocks were used as controls. The inoculated seedlings were maintained in sterile plastic boxes with moistened sheets of filter paper at 25 ± 1°C and a 12-h photoperiod. Fifteen leaves per isolate were tested for each treatment. The experiment was repeated twice. Three days after inoculation, symptoms similar to those in the field appeared, whereas the control leaves remained symptomless. Subsequently, C. cucurbitarum was reisolated from the lesions and morphologically identified, confirming Koch's postulates. To the best of our knowledge, this is the first report of C. cucurbitarum causing leaf spot on C. illinoinensis in China. This study provides the foundation to further investigate the biology, epidemiology, and management of this disease.

Phylogenetic analysis and morphology of Ganoderma multipileum, a Ganoderma species associated with dieback of the metropolitan woody plant Delonix regia (Boj. ex Hook.) Raf. in Vietnam.

Ganoderma multipileum, a wood decay mushroom, was initially discovered and classified in Taiwan through the analysis of its morphology and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. In this study, we identified a mushroom associated with the dieback of Delonix regia (Boj. ex Hook.) Raf., a woody ornamental street tree in Vietnam, as Ganoderma multipileum. This classification was based on phylogenetic analysis of ITS, RPB2, and TEF1 sequences, as well as morphology assessment and scanning electron microscope observation of basidiospores. The phylogenetic analysis revealed that the specimens collected in Vietnam formed a monophyletic group of Ganoderma multipileum with a high bootstrap value and posterior probability (100%/1.00). Furthermore, the morphological features consistent with laccate Ganoderma, including a thin pileipellis composed of enlarged and bulbous hyphae, and the basidiomes exhibited two different phenotypes. Notably, scanning electron microscopy of the basidiospores revealed ovoid spores with numerous echinules, providing the first documented evidence of this characteristic for Ganoderma multipileum. This research represents the first recorded instance of Ganoderma multipileum in Vietnam associated with the dieback of Delonix regia.

A fifty-locus phylogenetic analysis provides deep insights into the phylogeny of Tricholoma (Tricholomataceae, Agaricales).

As an ectomycorrhizal fungal genus that contains matsutake and other edible mushrooms, Tricholoma has great economic and ecological significance. However, the phylogenetic relationships within the genus remain unsettled. To clarify the infrageneric relationships of Tricholoma, including the identification of monophyletic subgenera and sections, three phylogenetic analyses were conducted employing single-locus (ITS), five-locus (ITS/ RPB2/EF-1α/MCM7/mtSSU) and 50-locus (45 single-copy orthologous genes plus the aforementioned ones) DNA nucleotide sequences. Our data indicated that ITS sequences could serve the species delimitation of Tricholoma in most cases and monophyletic groups recognition in some cases, and the five-locus dataset could resolve a section-level phylogeny of this genus, while the 50-locus dataset could clarify the delimitation of subgenera and settle the relationships among sections within this genus. A fifty-locus dataset was firstly employed to construct a robust phylogeny of Tricholoma. Based on this, a new infrageneric arrangement for the genus Tricholoma, with four subgenera, of which two are in accordance with the previous subgenera Pardinicutis and Sericeicutis, and eleven sections, is suggested. Subgenus Pardinicutis, occupying the basal position, only harbors sect. Pardinicutis, while the subg. Sericeicutis comprises sects. Lasciva and Sericella located at the sub-basal position with good support. Subgenus Terrea is newly erected here and consists of sect. Terrea, sect. Atrosquamosa and two as yet unnamed phylogenetic lineages. Besides an unnamed section-level lineage, subg. Tricholoma consists of sects. Genuina, Muscaria, Rigida, Tricholoma, Fucata and Matsutake, of which the two latter are newly proposed. The previously defined subg. Contextocutis is clustered within subg. Tricholoma and is a synonym of the latter. Tricholoma colossus, T. acerbum and their allies, which used to be allocated in sect. Megatricholoma (or genus Megatricholoma), are relocated to sect. Genuina since they form a strongly supported monophyletic group and share rusty or black spots on lamellae with other species in this section. Taxonomic descriptions of the new infrageneric taxa and a key to subgenera and sections of the genus Tricholoma are presented. Citation: Ding XX, Xu X, Cui YY, et al. 2023. A fifty-locus phylogenetic analysis provides deep insights into the phylogeny of Tricholoma (Tricholomataceae, Agaricales). Persoonia 50: 1-26. https://doi.org/10.3767/persoonia.2023.50.01.

A phylogenetic analysis of the Korean endemic species <i>Paraphlomis koreana</i> (Lamiaceae) inferred from nuclear and plastid DNA sequences

<i>Paraphlomis koreana</i> (Lamiaceae) was newly named and added to Korean flora in 2014. <i>Paraphlomis</i> belongs to the tribe Paraphlomideae, along with <i>Ajugoides</i> and <i>Matsumurella</i>. However, a recent study has suggested that <i>P. koreana</i> is morphologically similar to <i>Matsumurella chinensis</i>, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of <i>P. koreana</i> within the tribe and compare its genetic relationship with <i>M. chinensis</i>. We sequenced an additional complete plastid genome for an individual of <i>P. koreana</i> and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of <i>P. koreana</i>. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (<i>rpl16</i> intron, <i>rpl32</i>-trnL, <i>rps16</i> intron, and <i>trnL-F</i>) covering 13 <i>Paraphlomis</i> species and <i>M. chinensis</i> were conducted. Phylogenetic analyses concordantly supported that <i>P. koreana</i> forms a monophyletic group with <i>M. chinensis</i>. Moreover, our study revealed that <i>P. koreana</i> includes nrDNA sequences of <i>M. chinensis</i> as minor intraindividual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of <i>P. koreana</i> within <i>Paraphlomis</i> should be reconsidered.

Untangling the threads: phylogenetic relationships of threadfins (Percomorphacea: Perciformes: Polynemidae)

AbstractThreadfins are primarily marine bony fishes that have part of the pectoral fin modified into specialized sensitive filaments. They compose the Polynemidae, a family with eight genera and 42 extant species. The internal relationships and phylogenetic position of Polynemidae within Percomorphacea are controversial, with highly conflicting hypotheses proposed by both molecular and phenotypic analyses. We performed a cladistic analysis of threadfins based on the most comprehensive sampling of morphological data ever done. The final dataset included 197 characters from external morphology, the laterosensory system, osteology, myology and neurology in representatives of all valid polynemid genera. More than half of the characters are reported here for the first time, notably the myological ones. A sensitivity analysis of 11 different weighting schemes (equal weighting and extended implied weighting parsimony) resulted in a fully resolved tree. Sciaenidae, not Pleuronectiformes, is recovered as sister to Polynemidae. All polynemid genera are resolved as monophyletic except Polydactylus, which is polyphyletic. Filimanus, Pentanemus and Polydactylus s.s. appear as successive sister taxa of all remaining threadfins. Leptomelanosoma, Parapolynemus and Polynemus form a monophyletic group. Eleutheronema and Galeoides appear intercalated with other species of Polydactylus in the apical portions of the polynemid tree.

In the Dawn of an Early Invasion: No Genetic Diversity of Angiostrongylus cantonensis in Ecuador?

The nematode Angiostrongylus cantonensis has been reported worldwide. However, some basic questions remain unanswered about A. cantonensis in Ecuador: (1) Was the invasion of A. cantonensis in Ecuador unique, or did it occur in different waves? (2) Was this invasion as recent as historical records suggest? (3) Did this invasion come from other regions of South America or elsewhere? To address these issues, we assessed the genetic diversity of MT-CO1 gene sequences from isolates obtained in 11 of Ecuador's 24 provinces. Our Bayesian inference phylogenetic tree recovered A. cantonensis as a well-supported monophyletic group. All 11 sequences from Ecuador were identical and identified as AC17a. The haplotype AC17a, found in Ecuador and the USA, formed a cluster with AC17b (USA), AC13 (Thailand), and AC12a-b (Cambodia). Notably, all the samples obtained in Ecuadorian provinces' different geographic and climatic regions had no genetic difference. Despite the lack of genetic information on A. cantonensis in Latin America, except in Brazil, our finding differs from previous studies by its absence of gene diversity in Ecuador. We concluded that the invasion of A. cantonensis in Ecuador may have occurred: (1) as a one-time event, (2) recently, and (3) from Asia via the USA. Further research should include samples from countries neighboring Ecuador to delve deeper into this.

A billion years arms-race between viruses, virophages, and eukaryotes

Bamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses, Mavericks and Polinton-like viruses. Two main hypotheses for their origins have been proposed: the ‘nuclear-escape’ and ‘virophage-first’ hypotheses. The nuclear-escape hypothesis proposes an endogenous, Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis proposes that NCLDVs coevolved with protovirophages; Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and that Mavericks and Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (family Lavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.