Phylogenetic Position Research Articles

Phylogenetic position of Ancyrocephalus (sensu lato) curtus Achmerov, 1952 (Monopisthocotylea, Dactylogyridae), a parasite of fish Perccottus glenii Dybowski, 1877(Gobiiformes: Odontobutidae).

The genus Ancyrocephalus sensu lato is a large assemblage of species of dactylogyrid monopisthocotyleans without clear taxonomic boundaries. Despite an urgent need for revision, only three representatives of this taxon have been molecularly characterised so far. We found specimens of Ancyrocephalus curtus, a previously non-genotyped species, in gills of Perccottus glenii caught in the River Syumnyur, Amur Basin, Russia. The aim of this study was to assess the phylogenetic position of this parasite using partial sequences of 28S rRNA gene. In the phylogenetic tree, A. curtus appeared as a sister taxon to the dactylogyrine genus Gobioecetes. The new molecular evidence supports the hypothesis about the non-monophyletic status of Ancyrocephalus sensu lato.

A new species of Urocleidoides Mizelle & Price, 1964 from the gills of Schizodon nasutus Kner, 1858 (Characiformes, Anostomidae) in southeastern Brazil.

Based on an integrative approach, this study describes a new species of Urocleidoides infesting Schizodon nasutus in the Paranapanema River basin, Brazil. The new species can be distinguished from its congeners by specific morphological features, including the shape of the male copulatory organ and accessory piece, the ventral bar shape, and the shape and size of the hooks. Molecular analyses, particularly of the 28S rDNA gene, suggest a close relationship between the new species and Urocleidoides paradoxus. The phylogenetic and taxonomic arrangement of Urocleidoides is discussed, as the analyses of the 28S rDNA and COI mtDNA resolved the genus as non-monophyletic, with Diaphorocleidus, Rhinoxenus, and Cacatuocotyle nested within it. Additional morphological and molecular data of other congeneric species are required to investigate the phylogenetic position and classification of Urocleidoides. This study underscores the significance of using integrative approaches in understanding host-parasite associations and phylogenetic relationships, contributing to the description of the freshwater fish parasite biodiversity in South America, particularly in the Paranapanema river basin.

Arcyria and allied genera: taxonomic backbone and character evolution

Arcyria, one of the most diverse genera of bright-spored myxomycetes, has recently been identified as polyphyletic within the paraphyletic family Arcyriaceae sensu lato. However, due to the high variability and inconsistency of morphological traits in Trichiales, no taxonomic decision has yet been proposed to rectify this situation. A thorough revision of the genus is necessary. To address this, we present results of the extensive taxonomic and geographic sampling of the genus by incorporating sequences of two marker genes from 192 specimens of Arcyria spp. from 19 countries and six continents into the existing three gene phylogenetic backbone of Trichiales. Our phylogenies decisively confirm the polyphyletic nature of Arcyria, with a considerable part of the genus forming a sister clade to Hemitrichia. Consequently, we erect here the new family Hemitrichiaceae and resurrect the genus Heterotrichia to accommodate the second major branch of former Arcyria species. Additionally, we describe the new genus Spiromyxa with intermediate phylogenetic position and unique combination of morphological traits. Furthermore, we show that most of the Arcyria morphospecies included into this study are either species complexes or para- or polyphyletic taxa. Traits, previously thought to delimit the genus Arcyria, show little consistency with the phylogeny. In particular, the expanding, net-like capillitium, attached to the cup or stalk, appears to have been present in the ancestor of three families of Trichiales, afterwards mostly persisted in two of them and evolved into something else in the third. Such traits as ornamentation of capillitium, cup and spores retain their taxonomic value primarily at the species level. However, the colour of the spore mass in fresh condition partially aligns with our phylogenetic results: most of the yellow “Arcyria” species cluster within Heterotrichia, while red and grey species sort mostly into separate subclades within the clade incorporating the remaining species of the genus Arcyria.

Note on the phylogenetic position of Eptesicus species in the Vespertilionidae family (Chiroptera) using Brazilian bats and RAG2 sequences.

Note on the phylogenetic position of Eptesicus species in the Vespertilionidae family (Chiroptera) using Brazilian bats and RAG2 sequences.

Description and Phylogenetic Position of a New Genus and Species of Deep-Water Alpheid Shrimp Associated with Glass Sponges off New Caledonia (Decapoda: Caridea).

Batellopsis paula gen. et sp. nov., a new hexactinellid-associated alpheid shrimp, is described based on a single specimen collected at a depth of 477-503 m north of Île des Pins, New Caledonia. Batellopsis gen. nov. is part of a clade of four genera all containing hexactinellid-associated species, for which a molecular phylogeny is presented. The evolution of several morphological characters, including orbital teeth, a bulgefossa system on the fingers of the first pereiopod chela, and groups of microserrulate setae on the second pereiopod chela, is discussed in light of phylogenetic results.

The white grunt, Haemulon plumierii (Lacepède, 1801) as paratenic and definitive host of two acanthocephalan species, with the description of a new species of Dollfusentis (Palaeacanthocephala: Leptohynchoididae) from the Yucatán Peninsula, Mexico.

Acanthocephalans are a group of obligate endoparasites that alternate between vertebrates and invertebrates to complete their life cycles. Occasionally, the same individual host acts as a definitive or paratenic host for different acanthocephalan species. In this study, acanthocephalans were sampled in marine fish in three localities of the Yucatán Peninsula; adults and cystacanths were recovered from the intestine and body cavity, respectively, of Haemulon plumierii from off the coast of Sisal, Yucatán. Ribosomal DNA sequences (small and large subunits) were used to test the phylogenetic position of the species of the genus Dollfusentis, whereas the mtDNA gene cox 1 was used for assessing species delimitation. The cox 1 analysis revealed an independent genetic lineage, which is recognized herein as a new species, Dollfusentis mayae n. sp. The new species is morphologically distinguished from the other six congeners by having a cylindrical proboscis armed with 22-25 longitudinal rows bearing 12 hooks each. The cystacanths were morphologically identified as Gorgorhynchus medius by having a cylindrical trunk covered with tiny irregular spines on the anterior region, and a cylindrical proboscis armed with 17-18 longitudinal rows of 21 hooks each; small and large subunit phylogenetic analyses yielded G. medius within the family Isthomosacanthidae, suggesting that Gorgorhynchus should be transferred to this family from Rhadinorhynchidae where it is currently allocated.

Discovery and characterization of BRBV-sheep virus in nasal swabs from domestic sheep in China.

The escalating occurrence of infectious disease outbreaks in humans and animals necessitates innovative, effective, and integrated research to better comprehend their transmission and dynamics. Viral infection in livestock has led to profound economic losses globally. Pneumonia is the prevalent cause of death in sheep. However, very few studies exist regarding virus-related pathogens in sheep. Metagenomics sequencing technologies in livestock research hold significant potential to elucidate these contingencies and enhance our understanding. Therefore, this study aims to characterize respiratory viromes in paired nasal swabs from Inner Mongolian feedlot sheep in China using metaviromic sequencing. Through deep sequencing, de novo assembly, and similarity searches using translated protein sequences, several previously uncharacterized and known viruses were identified in this study. Among these discoveries, a novel Bovine Rhinitis B Virus (BRBV) (BRBV-sheep) strain was serendipitously detected in the nasal swabs of domestic sheep (Ovis aries). To facilitate further molecular epidemiological studies, the entire genome of BRBV-sheep was also determined. Owing to the unique sequence characteristics and phylogenetic position of BRBV-sheep, genetically distinct lineages of BRBV in sheep may exist. A TaqMan-based qRT-PCR assay targeting the 3D polymerase gene was developed and used to screen 592 clinical sheep specimens. The results showed that 44.59% of the samples (264/592) were positive. These findings suggest that BRBV sheep are widespread among Inner Mongolian herds. This discovery marks the initial identification of BRBV in sheep within Inner Mongolia, China. These findings contribute to our understanding of the epidemiology and genetic evolution of BRBV. Recognizing the presence of BRBV in sheep informs strategies for disease management and surveillance and the potential development of targeted interventions to control its spread.

Meristematic and meristematic-like fungi in Dothideomycetes

Meristematic fungi are mainly defined as having aggregates of thick-walled, melanised cells enlarging and reproducing by isodiametric division. Dothideomycetes black meristematic and meristematic-like fungi have been allied to Myriangiales, which currently has two accepted families, Myriangiaceae and Elsinoaceae, with fungi mainly regarded as pathogens, parasites, saprobes and epiphytes of different plant species. This study aimed to verify the phylogenetic position using four nuclear markers (SSU, LSU, ITS and RPB2) of the incertae sedis genera associated with Myriangiales, namely Endosporium, Gobabebomyces, Lembosiniella and Phaeosclera, and the new genus, Endophytium gen. nov. (including E. albocacti sp. nov. andE. cacti sp. nov.), established for endophytic fungi occurring in cacti in Brazil. Based on morphology, lifestyle and phylogenetic inferences, these black meristematic and meristematic-like fungi cannot be accommodated in Myriangiales. Combining these results, three new orders and two new families are introduced: Endophytiales ord. nov. (including Endophytiaceae fam. nov. for Endophytium gen. nov.), Endosporiales ord. nov. (including Endosporiaceae for Endosporium) and Phaeosclerales ord. nov. (including Phaeoscleraceae fam. nov. for Phaeosclera). Gobabebomyces and Lembosiniella remained incertae sedis due totheir disposition in the phylogenetic tree, that moved among clades accordingly with the gene analysed. Our results show thatthe inclusion of endophytic fungi obtained from plants in dry forests can contribute to the discovery of new taxa,clarify thephylogenetic position of allied taxa and confer information to the estimation of national and global fungal diversity.

A virus from Aspergillus cibarius with features of alpha- and betachrysoviruses.

From the ascomycete Aspergillus cibarius strain NW-FVA 2590, which was originally isolated from a root, associated with stem collar necrosis of Fraxinus excelsior L., a novel virus was isolated and characterized. Its genome is encoded on three monocistronic dsRNA segments ranging from 3683bp (dsRNA 1) over 3093 (dsRNA 2) to 2902bp (dsRNA 3), which are packed in isometric particles of around 35nm. While the viral RdRp (P1) is encoded on segment 1, protein sequencing showed that two more structural proteins are present which are translated from dsRNA 2 (P2) and dsRNA 3 (P3) and possibly form the viral capsid. Additionally, P2 and P3 may undergo posttranslational modifications since the detected proteins bands deviated from the calculated sizes. Due to its phylogenetic position, the novel virus was grouped in the family of Chrysoviridae and was tentatively denominated as Aspergillus cibarius chrysovirus 1 (AcCV1). Due to its composition, biological properties and phylogenetic position, distant from the genera Alphachrysovirus and Betachrysovirus, we suggest to position AcCV1 in a proposed genus "Gammachrysovirus".

Two new taxa and a new record of a rare species for the genus Cyathus (Nidulariaceae, Basidiomycota) from Brazilian Amazon Forest

Field investigation in different localities in the Brazilian Amazon Forest reveals two new species of Cyathus: C. pallidistipitatus and C. macauanensis. In addition, a second record for science and the first record for South America and Amazonia of C. tenuicorticalis is proposed. Based on morphological and molecular data, the new taxa were described, and the phylogenetic positioning of both new species was discussed. Comparative analyses with related taxa and a detailed discussion of the new record and the new species are provided.

First report of the genus Xerophorus from Asia with the description of Xerophorus pakistanicus (Callistosporiaceae), a new species from Southern Punjab, Pakistan

A novel species, Xerophorus pakistanicus, has been identified from Southern Punjab, Pakistan, based on morphological characters and molecular phylogenetic analyses. Xerophorus pakistanicus is characterized by a brown to dull orange, parabolic to campanulate pileus, a stipe turning light yellowish brown on handling, an absence of an annulus, amygdaliform to oblong basidiospores, utriform to pyriform caulocystidia, and the presence of clamp connections only in the stipitipellis. A phylogram, based on the combined nrITS-28S dataset, was constructed to assess the phylogenetic position of our strain, resulted Xerophorus pakistanicus sp. nov. within the genus Xerophorus. We present the new species with an illustrated morphological description and comparison with similar morphological or phylogenetically related species. This is the first record of the genus Xerophorus from Asia. A key to the known species of Xerophorus is also provided.

The effect of herbicides on arbuscular mycorrhizal fungi associated with annual invasive Asteroideae weeds

Invasive plants Galinsoga parviflora and Erigeron canadensis are common in crops and adjacent territories. One of the factors contributing to their spread is the community of arbuscular mycorrhizal fungi associated with these species. The nature of the symbiotic relationship between the host plant and AMF is determined by their phylogenetic position and place of growth. The aim of this work was to determine the level of mycorrhizal colonization of E. canadensis и G. parviflora growing in arable fields and along them. For plants at the flowering stage, high rates of frequency and intensity of mycorrhization were revealed. It has been shown that the level of mycorrhizal colonization of E. canadensis and G. parviflora is significantly influenced by the range of herbicides applied. The application of 2.4 D slightly reduced the intensity of colonization, but significantly stimulated the formation of arbuscules in plant roots. In turn, metribuzin prevented the formation of mycorrhiza. AMF associated with these plants formed a separate clade. This group, in our opinion, is responsible for more effective symbiosis with invasive plants of the Asteroideae subfamily and requires further closer study.

Floral structure and development in Nandina domestica and implications for systematic affinities in Berberidaceae and perianth evolution in Ranunculales

Abstract In Berberidaceae, the phylogenetic position and systematic affinities of the monotypic genus Nandina have long been debated and remain unclear. In addition, previous comparative studies have provided conflicting reports on the origin and development of its petals. Using scanning electron microscopy and microtome sections, we studied the structure and development of the flower and perianth in Nandina domestica to re-evaluate its affinities and homology of its petals. Our results confirm that N. domestica essentially shares the same Bauplan (organization) with other Berberidaceae and its petals are neither delayed in development nor much differentiated from sepals. However, we sometimes also observed the initiation of additional primordia that become confluent with the base of stamens of the outer whorl, but do not develop further and are no longer visible in later stages of development. Our study thus not only reconciles previous conflicting interpretations on the origin and development of petals in Nandina, but also confirms that it has a unique suite of vegetative and reproductive features supporting its position as a distinct member of the family. In addition, it suggests that the most recent common ancestors of both Berberidaceae and Ranunculales probably had two types of petaloid organs with distinct origin and development but still sharing a deep common genetic identity.

Two New Species of Aphyllon from Northeastern Mexico

Abstract— Plants originally identified as Aphyllon ludovicianum that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative A. multiflorum, or any other species of Aphyllon. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study, and georeferenced color photographs, we propose the new binomials Aphyllon spectabile for the plants from Nuevo Leon and Aphyllon gypsophilum for the plants from Coahuila, Mexico. These additions increase the taxonomic diversity of Aphyllon to 27 species plus ten additional subspecies. Gymnosperma glutinosum and two species of Xanthisma were reported for the first time as a host species for the genus Aphyllon. We also provide an updated key to Aphyllon in Mexico.

A New Species of Brachystele (Spiranthinae, Orchidaceae) with Nonresupinate Flowers from Central East Argentina

Abstract— Brachystele morronei, a new orchid species recently discovered in the central-eastern region of Argentina, is described and illustrated. It is the first known species with nonresupinate flowers of the Pelexia clade, constituting a very distinctive member of the group. The phylogenetic position of the new taxon was inferred from nuclear ribosomal DNA (ITS) and two plastid DNA regions (matK and trnLF). The combined nuclear and plastid data analyses using Bayesian and parsimony-based methods revealed that B. morronei is closely related to B. camporum. The geographic distribution and a conservation assessment of the new species are presented. Morphological differences among sympatric Brachystele species are described.

Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation.

Luisia, a genus of the subtribe Aeridinae of Orchidaceae, comprises ca. 40 species. Members of Luisia exhibit unique morphological characteristics and represent a valuable ornamental orchid genus. However, due to the scarcity of distinct morphological characters, species identification within this genus is ambiguous and controversial. In the present study, next-generation sequencing (NGS) methods were used to assemble the plastomes of five Luisia species and compare them with one publicly available Luisia plastid genome data. The plastomes of Luisia possessed a quadripartite structure, with sizes ranging from 146,243 bp to 147,430 bp. The plastomes of six Luisia species contained a total of 120 genes, comprising 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. Notably, all ndh genes were pseudogenized or lost. An analysis of codon usage bias showed that leucine (Leu) exhibited the highest frequency, while cysteine (Cys) exhibited the lowest frequency. A total of 57 to 64 SSRs and 42 to 49 long repeats were identified. Five regions and five coding sequences were identified for DNA barcodes, based on the nucleotide diversity (Pi) analysis. The species of Luisia constituted a monophyletic group and were sister to Paraphalaenopsis with strong support. Our study deepens the understanding of species identification, plastome evolution and the phylogenetic positions of Luisia.

Phylogenetic position of the Amazonian nurse frog Allobates gasconi (Morales 2002) revealed by topotypical data

Phylogenetic position of the Amazonian nurse frog Allobates gasconi (Morales 2002) revealed by topotypical data

Fast cycling culture of the annelid model Platynereis dumerilii.

Platynereis dumerilii, a marine annelid, is a model animal that has gained popularity in various fields such as developmental biology, biological rhythms, nervous system organization and physiology, behaviour, reproductive biology, and epigenetic regulation. The transparency of P. dumerilii tissues at all developmental stages makes it easy to perform live microscopic imaging of all cell types. In addition, the slow-evolving genome of P. dumerilii and its phylogenetic position as a representative of the vast branch of Lophotrochozoans add to its evolutionary significance. Although P. dumerilii is amenable to transgenesis and CRISPR-Cas9 knockouts, its relatively long and indefinite life cycle, as well as its semelparous reproduction have been hindrances to its adoption as a reverse genetics model. To overcome this limitation, an adapted culturing method has been developed allowing much faster life cycling, with median reproductive age at 13-14 weeks instead of 25-35 weeks using the traditional protocol. A low worm density in boxes and a strictly controlled feeding regime are important factors for the rapid growth and health of the worms. This culture method has several advantages, such as being much more compact, not requiring air bubbling or an artificial moonlight regime for synchronized sexual maturation and necessitating only limited water change. A full protocol for worm care and handling is provided.

Gemmata algarum, a Novel Planctomycete Isolated from an Algal Mat, Displays Antimicrobial Activity.

Axenic cultures of two strains, JC673T and JC717, both belonging to the phylum Planctomycetota, were isolated from distinct geographical locations in India. Strain JC673T was obtained from algal mats of a wetland situated in the state of Kerala, India, while strain JC717 originated from the Central Marine Fisheries Research Institute (CMFRI), state of Tamil Nadu, India. The two strains share 99.9% 16S rRNA gene sequence similarity and are most closely related to Gemmata obscuriglobus UQM 2246T (99.3% 16S rRNA gene sequence identity). The newly isolated strains are Gram-negative, grow aerobically and tolerate up to 4% (w/v) NaCl and a pH of up to 9.0. Cells are spherical and form pink-pigmented colonies. The respiratory quinone is MK-6. Major fatty acids are C18:0, C16:1ω5c and C16:0. Polar lipids include phosphatidylcholine, phosphatidylethanolamine, several unidentified amino lipids, unidentified phospholipids, additional unidentified lipids, and an unidentified choline lipid. The polyamine spermidine is produced by the two strains. The strains have a genome size of about 8.2 Mb with a DNA G+C content of 67.6%. Solvent-based culture extracts of the isolates showed antimicrobial activity against three bacterial test strains. Their phylogenetic position along with differences in morphological, physiological, and genomic features support the classification as a new species of the genus Gemmata, for which we propose the name Gemmata algarum sp. nov. Strain JC673T (=KCTC 72851T = NBRC 114340T) and JC717 are the type and non-type strain of the new species, respectively.

Characteristics of Stenotrophomonas rhizophila Lipopolysaccharide, a Representative of Antarctica

Characteristics of Stenotrophomonas rhizophila Lipopolysaccharide, a Representative of Antarctica