Molecular Phylogenetic Studies Research Articles

Rice bran oil supports robust growth of the commensal fungus Malassezia

Malassezia are lipophilic budding yeasts that thrive on natural lipid sources. They are found on the skin, scalp, and upper back of humans and other warm-blooded animals, due to the high sebaceous gland activity in these regions that support their growth. They generally thrive as commensals and, upon certain not-so-well-defined conditions, transform into pathogenic states, giving rise to dermatological diseases and, at times, systemic infections. The studies for identifying the role of Malassezia in causing disease are severely hampered due to the lack of suitable growth media. Because of the challenges associated with isolation, there have been cases reported of undetectable fungal sepsis and often misdiagnosis for the same reason. The media routinely used for culturing yeast is supplemented with lipids. This study aimed to show that an inexpensive oil supplement like rice bran can support the growth of Malassezia, and SDA media supplemented with rice bran oil gave commendable growth of the budding yeast, better than the traditionally used olive oil-supplemented media. Therefore, rice bran oil can be used as a lipid supplement in the culture medium for the isolation, and maintenance of lipophilic yeasts. Our study again signifies the importance of media in microbiological research and stresses the need to develop better growth substrates for difficult-to-culture organisms like Malassezia and this will aid in molecular taxonomy, species characterization and phylogenetic studies.

Chlorohiptage (Tetrapteroids, Malpighiaceae), a distinct new genus endemic to Vietnam based on morphological and molecular data

Background and aims – Vietnam is one of the leading diversity centres for Asian Malpighiaceae, comprising 24 accepted species and three native genera (i.e. Aspidopterys, Hiptage, and Tristellateia). During recent fieldwork towards completing the taxonomic revision of Malpighiaceae for the Flora of Vietnam, we have collected specimens from two populations that could not be placed in any of the three native genera of this family. We performed morphological and molecular phylogenetic studies to test the generic placement of those specimens. Material and methods – We sampled 27 genera (including the Asian Acridocarpus, Aspidopterys, Brachylophon, Hiptage, Stigmaphyllon, and Tristellateia, out of a total of 75) of Malpighiaceae representing all phylogenetic clades comprising paleotropical lineages (i.e. acridocarpoids, bunchosioids, tetrapteroids, malpighioids, and stigmaphylloids), the unusual specimen recently collected in Vietnam, and the two genera of Elatinaceae as outgroups. Maximum Likelihood analysis was carried out based on a molecular matrix alignment of the internal transcribed spacer marker (ITS). Comprehensive morphological analyses were also carried out based on the collected specimens and additional herbarium specimens. Key results – Our molecular phylogeny strongly supported the unusual specimen from Vietnam placed as sister to Hiptage in the tetrapteroid clade. Key morphological traits differing these Vietnamese specimens from Hiptage were identified related to the floral bud imbrication, shape, colour, posture of sepals and petals, length of stamen filaments, number of styles, and shape of mericarps, allowing the proposition of a new monospecific genus. Conclusions – Chlorohiptage vietnamensis is proposed as a new monospecific genus closely related to Hiptage but differing in several key morphological traits. A complete morphological description is provided alongside photographic illustrations and notes on its conservation, distribution, ecology, etymology, and taxonomy. Additionally, an updated identification key to the genera of the tetrapteroid clade is provided.

Ektaphelenchoides factum n. sp. in Pinus taeda from the USA and E. pini in Pinus koraiensis from China

Summary The genus Ektaphelenchoides is a diverse group of nematodes; they are either inhabitants of trees or present in the rhizosphere of economical plants. Members of the genus have ecological relevance in terms of being associated with insects and predators of other nematodes. In the present study, a new Ektaphelenchoides species, E. factum n. sp., is described and illustrated. The new species was isolated from a log sample of Pinus taeda imported from the USA. It is characterised by the lateral field with three incisures, stylet distinctly tripartite. Females having a vulval flap, the anus and rectum indistinct, and the tail (posterior part of body) filiform. Males having arcuate and 21.5 (19.4-22.9) μm long spicules, the lamina of the spicule is smoothly curved to distal end, condylus well developed with a broadly rounded tip, rostrum triangular with finely rounded tip and cucullus absent, tail arcuate and conical with terminus bearing a sharply pointed mucron. The new species is different from other Ektaphelenchoides species in having a vulval flap. Molecular characterisation and phylogenetic studies also supported its unique status. In addition, a Chinese native population of E. pini, detected in Pinus koraiensis branches from Liaoning province, P.R. China, is described.

Molecular phylogeny and taxonomy of Phlomoides (Lamiaceae subfamily Lamioideae) in China: Insights from molecular and morphological data

Phlomoides, with 150–170 species, is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae (Lamiaceae). With about 60 species, China is one of three major biodiversity centers of Phlomoides. Although some Phlomoides species from China have been included in previous molecular phylogenetic studies, a robust and broad phylogeny of this lineage has yet to be completed. Moreover, given the myriad new additions to the genus, the existing infrageneric classification needs to be evaluated and revised. Here, we combine molecular and morphological data to investigate relationships within Phlomoides, with a focus on Chinese species. We observed that plastid DNA sequences can resolve relationships within Phlomoides better than nuclear ribosomal internal and external transcribed spacer regions (nrITS and nrETS). Molecular phylogenetic analyses confirm the monophyly of Phlomoides, but most previously defined infrageneric groups are not monophyletic. In addition, morphological analysis demonstrates the significant taxonomic value of eight characters to the genus. Based on our molecular phylogenetic analyses and morphological data, we establish a novel section Notochaete within Phlomoides, and propose three new combinations as well as three new synonyms. This study presents the first molecular phylogenetic analyses of Phlomoides in which taxa representative of the entire genus are included, and highlights the phylogenetic and taxonomic value of several morphological characters from species of Phlomoides from China. Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future.

Species clarification of fairy inkcap (“Coprinellus disseminatus”) in China

ABSTRACT Coprinellus disseminatus and other morphologically similar species are widely dispersed worldwide and are commonly referred to as “fairy inkcap”. Based on the molecular phylogenetic study and morphological observation, a thorough investigation was carried out utilising 74 collections of related species that were gathered from seventeen provinces and five Chinese fungaria between 1998 and 2023 and revealed 11 lineages of “fairy inkcap”, nine of which were found in China, and which belonged to the two genera Coprinellus and Tulosesus. In sect. Disseminati, genetic diversities (π), and fixation index (Fst) amongst lineages were computed, and a haplotype-based network was established to ascertain the relationships amongst each clade. A new section of Coprinellus, sect. Aureodisseminati, were discovered. In addition, four new species (C. aureodisseminatus, C. austrodisseminatus, C. parcus, and C. velutipes), a new subspecies of C. disseminatus, a new combination (Tulosesus pseudodisseminatus), the first discovery of epigamous type of C. magnoliae and a new record to China (T. subdisseminatus) were also identified and thoroughly described with accompanying illustrations. Their differences in macro- and micro-features, as well as their character sequence, were discussed.

Bunium serdengectii (Apiaceae), a new species from South Anatolia, Turkey

A new species, Bunium serdengectii (Apiaceae), is described from South Anatolia, Turkey. It grows in open Pinus brutia forests and in macchia formation of the Taurus Mountains in the district of Akseki (Antalya province). The taxonomic affinities of the new species were determined by analyzing morphological data and a molecular phylogenetic study of nrITS. Bunium serdengectii belongs to the section Elegantia, and is related to B. pinnatifolium, but morphologically is more related to B. sayae. The anatomical structure of the fruit is given in detail. The diagnostic morphological characters of B. serdengectii are discussed. In addition, the geographical distribution of the new species and the morphologically related species is mapped.

Novel Pestalotiopsis that causes gray spot disease of Polygonatum cyrtonema Hua in Hunan Province of China.

Polygonatum cyrtonema Hua is a perennial herb of the Asparagaceae family that is used for both dietary and medicinal purposes in China. In September 2019, a new leaf spot disease on Po. cyrtonema was detected which is currently widespread in Huaihua, Hunan Province, China. Pathogenic fungi were isolated and purified from samples of diseased tissue that were collected for morphological and molecular phylogenetic studies. The pathogen was identified using multi-locus (ITS, TEF-1, TUB2) phylogenies, as well as morphological characters, and was found to be clustered but separately divergent from species of Pestalotiopsis. However, there were significant morphological differences between the pathogen and similar species. The pathogen was finally identified as a new species that was designated Pestalotiopsis xuefengensis. This is the first report of P. xuefengensis serving as the causal agent of gray leaf spot on Po. cyrtonema. This study will provide useful information for the diagnosis and management of this disease.

Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes

Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae. It is widely distributed and grows in a variety of environments, including plains, mountains, deserts, forests, grasslands, and even waters where almost all legumes can be found. It is one of the most important sources of starch, protein and oil in the food of mankind and also an important source of high-quality forage material for animals, which has important economic significance. In our study, the codon usage patterns and variation sources of the chloroplast genome of nine important forage legumes were systematically analyzed. Meanwhile, we also constructed a phylogenetic tree based on the whole chloroplast genomes and protein coding sequences of these nine forage legumes. Our results showed that the chloroplast genomes of nine forage legumes end with A/T bases, and seven identical high-frequency (HF) codons were detected among the nine forage legumes. ENC-GC3s mapping, PR2 analysis, and neutral analysis showed that the codon bias of nine forage legumes was influenced by many factors, among which natural selection was the main influencing factor. The codon usage frequency showed that the Nicotiana tabacum and Saccharomyces cerevisiae can be considered as receptors for the exogenous expression of chloroplast genes of these nine forage legumes. The phylogenetic relationships of the chloroplast genomes and protein coding genes were highly similar, and the nine forage legumes were divided into three major clades. Among the clades Melilotus officinalis was more closely related to Medicago sativa, and Galega officinalis was more closely related to Galega orientalis. This study provides a scientific basis for the molecular markers research, species identification and phylogenetic studies of forage legumes.

Morphological and phylogenetic analyses reveal a new species of Anthracophyllum (Omphalotaceae, Agaricales) in Zhejiang Province, China.

During the investigations of macrofungi resources in Zhejiang Province, China, an interesting wood rot fungus was collected. Based on morphological and molecular phylogenetic studies, it is described as a new species, Anthracophyllum sinense. A. sinense is characterized by its sessile, charcoal black and pleurotoid pileus, sparse lamellae occasionally branching, clavate basidia with long sterigmata [(3-)6-7(-8) μm], and non-heteromorphous cystidia. A. sinense establishes a separate lineage close to A. archeri and A. lateritium in the phylogenetic tree.

Molecular phylogeny of Boesenbergia (Zingiberaceae) reveals shared characters and infrageneric division

The classification of Boesenbergia (Zingiberaceae) has long been a challenge, and recent insights from molecular phylogenetic studies have both raised and resolved a number of questions. Combined morphological and molecular revisions resulted in the description of new species as well as merging of Haplochorema and Jirawongsea into Boesenbergia. This study uses the most complete set of Boesenbergia accessions and sister genera to investigate the evolutionary relationships of the genus in a phylogenetic framework. This framework confirms the previously identified clades and the placement of the included accessions within those clades. These clades share being single-flowered and having a basipetalous flowering sequence, characters uniting all taxa in Boesenbergia, but also have unique or mostly unique characters that are clade specific. In addition, the phylogeny identifies two species, B. purpureorubra and B. siamensis, that are hard to place within these clades based on both molecular and morphological data, while the morphological data points to a stronger affiliation with the clade including the type of the genus.

An integrative taxonomic approach to the Atlantic Hansarsia (formerly Nematoscelis) yields new krill taxa (Crustacea: Euphausiidae)

A recent molecular phylogenetic and biogeographic study on the krill genus Hansarsia revealed undescribed cryptic diversity in the Atlantic. Each of four species analysed encompassed robust molecular clades that were linked to dimorphic males in H. microps, H. atlantica and H. tenella. We tested the robustness and divergence of the observed clades using an integrative approach including (1) three independent species delimitation methods for the mitochondrial COI gene (ASAP, GMYC, bPTP), (2) variability of two nuclear genes (H3 and ITS1) and (3) morphological analysis (MDS and PCA) with a dataset of 22 characters scored for 131 specimens. Both molecular and morphological analyses resulted in at least six distinct clades within the Atlantic Hansarsia. The strongest divergence was revealed between the two clades of H. tenella, one of which we diagnosed as a new species. Two clades of H. megalops also showed significant divergence but in the absence of males, we were reluctant to designate new species. Different clades linked to male forms in H. microps and H. atlantica are suggested as an incipient species. We also hypothesise an unusual trend in the evolution of euphausiids, in which visual recognition enhances tactile interaction during mating. Our results show that analyses of ostensibly well studied groups may yet yield taxonomic surprises. ZooBank: urn:lsid:zoobank.org:pub:AE045636-50EF-450A-B9B3-9231E8B91522

Taxonomic and phylogenetic study of the subgenus Tricercandra in the genus Chloranthus</o> (Chloranthaceae)

The genus Chloranthus consists of 17 taxa with the two subgenera Chloranthus and Tricercandra. These two subgenera can be distinguished by the morphology of the androecium. In South Korea, C. japonicus and C. fortunei of the subgenus Tricercandra are distributed. Although C. fortunei is typically not branched, a variant that branches from the stem has recently been discovered. Here, we conducted morphological and molecular phylogenetic analyses to elucidate the interspecific relationships within the subgenus Tricercandra and to evaluate the taxonomic position of the variant of C. fortunei. Morphological analyses revealed distinct differences among C. angustifolius, C. japonicus, C. fortunei, and the variant of C. fortunei. However, distinguishing between C. holostegius and C. nervosus was challenging. A principal component analysis also showed that while C. angustifolius, C. japonicus, C. fortunei, and the corresponding variant clustered independently, C. holostegius and C. nervosus overlapped, rendering them indistinguishable. Molecular phylogenetic studies using nuclear ribosomal internal transcribed spacer (nrITS) regions and three plastid regions, rbcL, rpl20-rps12, and trnL-F, revealed that the subgenus Tricercandra was monophyletic. Within the subgenus Tricercandra, C. angustifolius formed a sister clade with C. fortunei in the combined three plastid gene tree, while C. japonicus displayed different phylogenetic relationships between the nrITS and plastid gene trees. In addition, neither C. holostegius nor C. nervosus was monophyletic, consistent with the morphological analyses. The variant of C. fortunei formed an independent subclade on the nrITS tree but was not distinguished from other C. fortunei on the plastid gene tree. Our study elucidated clear species delimitation among C. angustifolius, C. japonicus, and C. fortunei and suggested key morphological characters useful for distinguishing them. Furthermore, our findings highlighted the ambiguous species delimitation and phylogenetic uncertainty between C. holostegius and C. nervosus. While we demonstrated morphological differences between the typical C. fortunei and its variant, the limited molecular phylogenetic evidence implies a need for further study.

Molecular Identification and Phylogenetic Study Based on the Fusion Gene of Newcastle Disease Virus Isolated from Broiler Poultry Farms in Markazi Province, Iran

Newcastle disease (ND) is an economically significant and extremely spreadable viral illness affecting a wide variety of avian species. ND can rapidly spread within poultry farms and result in considerable economic losses for the global poultry industry. This disease is endemic in Iran, and despite intensive vaccination efforts in the poultry industry, outbreaks of ND occur unexpectedly. This study aimed to isolate the Newcastle disease virus (NDV) from poultry farms with breathing problems in Markazi province, Iran, and investigate the evolutionary relationship and molecular characteristics of the isolates during 2017-2019. To this end, tissue samples (lung, brain, and trachea) were taken from 42 broiler farms exhibiting respiratory symptoms. The samples were inoculated into 9-11-day-old embryonated eggs, and the virus was isolated from 20 (47.6%) of the 42 farms. Subsequently, RT-PCR was used to amplify partial fusion gene sequences from the new isolates. The amplified products were sequenced and compared phylogenetically to the standard pilot dataset (125 selected sequences) generated by the NDV consortium. As determined by phylogenetic analysis, all nine isolates belonged to subgenotype VII.1.1 of genotype VII and were highly similar to isolates from other parts of Iran and China. Moreover, all isolates possessed a polybasic cleavage site motif (112RRQKRF117), characteristic of virulent strains. Furthermore, the present isolates shared a high nucleotide identity (96%) with viruses previously isolated from other provinces of Iran, as determined by BLAST searches and multiple alignments. In addition, they shared a high degree of sequence similarity but were distinct from the existing NDV vaccines. Therefore, the genetic dissimilarity between current vaccine strains and circulating NDVs must be considered in vaccination programs.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

A new species and new records of Hymenopellis and Xerula (Agaricales, Physalacriaceae) from China.

Hymenopellis is the genus that exhibits the highest number of species within the Xerula/Oudemansiella complex. Numerous species of Hymenopellis demonstrate edibility, and some of these species have been domesticated and cultivated. During an extensive survey carried out in Henan and Jilin Provinces, China, a substantial quantity of Hymenopellis specimens was gathered as a component of the macrofungal resource inventory. Based on the findings of morphological and molecular phylogenetic studies, a new species, Hymenopellis biyangensis, has been identified. A new record species, Hymenopellis altissima, has been discovered in China. Additionally, two new record species, Hymenopellis raphanipes and Xerula strigosa, have been found in Henan Province. Internal transcribed spacer (ITS) and large subunit ribosomal (nrLSU) were used to establish a phylogeny for species identification. Detailed descriptions, field habitat maps and line drawings of these species are presented. The discussion focuses on the relationships between newly discovered species and other related taxa. Additionally, this study provides and a key to the documented species of Hymenopellis and Xerula found in China.

Phylogenetic analysis of the Cladophora coelothrix complex, including the description of the new genus Leliaertia (Cladophorales, Ulvophyceae)

ABSTRACT Molecular phylogenetic studies have revealed the polyphyletic nature of Cladophora as traditionally circumscribed, which is separated into four main clades: Cladophoraceae, Siphonocladus, Pithophoraceae and Pseudocladophoraceae. Several taxonomic proposals have recently been made to resolve its polyphyletic nature. The present work focuses on the cryptic diversity of Cladophora coelothrix, within the Siphonocladus clade. Based on new collections from northeastern Brazil and phylogenetic analyses of partial SSU and LSU rDNA sequence alignments, we propose the new genus and species Leliaertia repens to accommodate one of the cryptic species hitherto included in C. coelothrix, occurring in the tropical Atlantic, Indian and Pacific Oceans. Leliaertia repens was recovered in the Siphonocladus clade and is phylogenetic distinct from the genuine Cladophora species in the Cladophoraceae. The new species occurs in marine and estuarine environments and forms conspicuous mats of semi-prostrate filaments. It represents a cryptic species and genus since morphological features, including the diameter and length:diameter ratio of the apical cell, show high levels of overlap with other species, including C. socialis. Our phylogenetic data indicate that L. repens, C. coelothrix and C. socialis represent a complex of cryptic species with at least four lineages, some of which co-occur in tropical seas.

Phylogenomic data reveal three new families of poorly studied Solifugae (camel spiders)

The systematics of the arachnid order Solifugae have been an enigma, owing to challenges in interpreting morphology, a paucity of molecular phylogenetic studies sampling across the group, and a dearth of taxonomic attention for many lineages. Recent work has suggested that solifuge families largely exhibit contiguous distributions and reflect patterns of vicariance, with the exception of three families: Melanoblossidae, Daesiidae and Gylippidae. Morphological studies have cast doubt on their existing circumscriptions and the present composition of these taxa renders their distributions as disjunct. We leveraged ultraconserved elements (UCEs) to test the phylogenetic placement of three key lineages of Solifugae that cause these anomalous distributions: Dinorhax rostrumpsittaci (putative melanoblossid), Namibesia (putative daesiid), and Trichotoma (putative gylippid). Phylogenetic placement of these three genera based on UCEs rendered the families that harbor them as para- or polyphyletic, recovering instead relationships that better accord with a biogeographic history driven by vicariance. Toward a stable and phylogenetically informed classification of Solifugae, we establish three new families, Dinorhaxidae new rank, Namibesiidae new rank and Lipophagidae new rank.

Molecular phylogenetic studies of some species of the genera Campanula and Mzymtella (Campanulaceae)

A molecular phylogenetic study of some species of the Campanulaceae family has been carried out using marker sequences of the ITS1 gene 5.8S rDNA-ITS2. The results of Sanger sequencing revealed a separate clade of some species with a large level of differences among themselves. For Mzymtella sclerophylla Kolak., the presence of a unique ribotype was shown.

Recent contributions of molecular population genetic and phylogenetic studies to classic biological control of weeds

Recent contributions of molecular population genetic and phylogenetic studies to classic biological control of weeds

Revision of the Chinese freshwater crab genus Tenuipotamon Dai, 1990 (Decapoda: Brachyura: Potamidae), with the description of a new genus from southwestern China

Abstract The taxonomy of the potamiscine freshwater crab genus Tenuipotamon Dai, 1990, which contains seven species, is revised. According to a concurrent molecular phylogenetic study, Tenuipotamon is paraphyletic, and is composed of two lineages. In this study, Tenuipotamon sensu stricto is restricted to its type species, T. purpura Dai, 1990, while a new genus, Pusillamongen. nov., is established to accommodate the remaining six species placed previously in Tenuipotamon sensu stricto (T. baishuiense Chen, 1993, T. huaningense Dai & Bo, 1994, T. panxiense Chen, 1993, T. tonghaiense Chen, 1993, T. xinpingense Chen, 1993, and T. yuxiense Chen, 1993). Diagnoses are provided for the two genera, which are both endemic to the topographically complex Hengduan Mountains Region of southwestern China.