Maximum Likelihood Analyses Research Articles

Notes on the Ecology and Distribution of Species of the Genera of Bondarzewiaceae (Russulales and Basidiomycota) with an Emphasis on Amylosporus.

The family Bondarzewiaceae is an important and diverse group of macrofungi associated with wood as white rotting fungi, and some species are forest tree pathogens. Currently, there are nine genera and approximately 89 species in the family, distributed in tropical, subtropical, and temperate climates. To address the phylogenetic relationships among the genera, a combined ITS-28S dataset was subjected to maximum likelihood (ML), Bayesian inference (BI), and time divergence analyses using the BEAST package. Both ML and BI analyses revealed two major clades, where one major clade consisted of Amylosporus, Stecchericium, and Wrightoporia austrosinensisa. The second major clade is composed of Bondarzewia, Heterobasidion, Gloiodon, Laurilia, Lauriliella, and Wrightoporia, indicating that these genera are phylogenetically similar. Wrightoporia austrosinensisa recovered outside of Wrightoporia, indicating that this species is phylogenetically different from the rest of the species of the genus. Similarly, time divergence analyses suggest that Bondarzewiaceae diversified around 114 million years ago (mya), possibly during the Early Cretaceous Epoch. The genus Amylosporus is well resolved within the family, with an estimated stem age of divergent around 62 mya, possibly during the Eocene Epoch. Further, the species of the genus are recovered in two sister clades. One sister clade consists of species with pileate basidiomata and generative hyphae with clamp connections, corresponding to the proposed section Amylosporus sect. Amylosporus. The other consists of species having resupinate basidiomata and generative hyphae without clamps, which is treated here as Amylosporus sect. Resupinati. We provided the key taxonomic characters, known distribution, number of species, and stem age of diversification of each section. Furthermore, we also described a new species, Amylosporus wadinaheezicus, from Oman, based on morphological characters of basidiomata and multigene sequence data of ITS, 28S, and Tef1-α. With pileate basidiomata and phylogenetic placement, the new species is classified under the proposed A. sect. Amylosporus. An identification key to the known species of Amylosporus is presented. Ecology and distribution of species of the genera in the family are discussed.

Assessing Species-Level Identification of Some Cryptic Frog Species of Bangladesh Using 16s and 12s Rrna Genes

In recent years, a number of new and undescribed anuran species are being discovered at a very fast rate in South and Southeast Asia. With the revelation of more and more species that were previously considered to be some other species, accurate identification of these morphologically cryptic anurans based on morphology alone have become difficult. In this study, we attempted specieslevel identification of 15 frog specimens belonging to the families Dicroglossidae and Microhylidae of Bangladesh by analyzing their 16S and 12S rRNA gene sequences. The collected specimens were successfully identified to be belonging to eight different species, namely Fejervarya dhaka, F. asmati, F. pierri and F. orissaensis; Euphlyctis kalasgramensis and Euphlyctis sp.; Microhyla berdmorei and M. mymensinghensis using BLAST and maximum likelihood analyses. In some cases the frog samples showed morphological resemblance but after molecular analysis they were found to be different and in another case morphologically distant samples were found to be molecularly similar. For example, two of the specimens (ESP 01, ESP 02) turned out to be E. kalasgramensis at molecular analysis, however, did not match with the morphological and morphometric descriptions (specially snout-vent length) described previously. Moreover, a species is suspected to be still undescribed and another species namely M. berdmorei was thought to be absent in Bangladesh which has been recorded in our study. Thus, morphological ambiguity strengthens the urge for molecular analysis for proper identification. Dhaka Univ. J. Biol. Sci. 33(2): 27-52, 2024 (July)

The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

ABSTRACT The leopard shark Triakis semifasciata (family Triakidae) is threatened by habitat loss and targeted by recreational and commercial fishermen in the Eastern Pacific Ocean, from Oregon, USA, to the Gulf of California, Mexico. Despite environmental issues, there are few genetic and genomic resources available for this species. This study assembled the complete mitochondrial genome of T. semifasciata from a skin metagenomic sample and described it in detail. The phylogenetic position of T. semifasciata amongst closely related species was also examined using mitochondrial protein-coding genes (PCGs). The mitochondrial genome of T. semifasciata is 16,613 bp in length and consists of 13 PCGs, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. A 30 bp long region was identified as the origin of replication for the light strand (OL) between the trnN and trnC genes, and a 974 bp long putative control region (CR) contains the origin of replication for the heavy strand (OH). The gene order in T. semifasciata is identical to that of cofamilial species. An analysis of Ka/Ks ratios for all PCGs yielded values < 1, indicating that all PCGs experience strong purifying selection. All tRNAs exhibit a canonical ‘cloverleaf’ secondary structure except for tRNA-Ser1 which lacks the stem of the dihydrouridine (DHU) arm and in place possesses a simple loop. A phylomitogenomic maximum likelihood (ML) analysis did not support the monophyly of the family Trakidae and placed T. semifasciata in a sister position to Hemitriakis japanica. However, the aforementioned sister position was poorly supported by ML bootstrap values. This study represents a new genomic resource for this commercially and recreationally important species and confirms that mitochondrial genomes can be assembled from skin metagenomic samples as shown before in an unrelated shark species.

Morphological and Molecular Analyses of Aponurus laguncula Looss, 1907 (Digenea: Lecithasteridae) Parasitic in Atlantic Spadefish Chaetodipterus faber (Broussonet, 1782) (Acanthuriformes: Ephippidae) from Brazilian Coastal Zone.

An integrative taxonomic description of Aponurus laguncula (Lecithasteridae), a digenean parasitic species of Chaetodipterus faber (Acanthuriformes) from Brazilian Southeast, is provided. Morphological techniques, as whole mounted slides, histology and scanning electron microscopy, and molecular analyses supported that integrative description. Fifteen digenean specimens were stained in hydrochloric carmine and mounted on permanent slides. Two specimens were stained in hematoxylin and eosin following histological routine processing. Four parasites were dehydrated through a graded ethanol series, critical point dried with carbon dioxide and coated with gold to scanning electron microscopy analysis. Sequence of the large ribosomal subunit (28S rDNA) gene was generated and used to construct a phylogeny based on maximum likelihood and Bayesian inference analyses. Morphological description and morphometric data obtained in present study were in accordance with previous studies of the species. Use of another morphological techniques, as scanning electron microscopy and histology, corroborated the observed features of whole mounted slides. Also, they provided a better observation of previous reported characteristics and new features reporting, such as an elongated hermaphroditic duct, a smooth tegument and cells that compose the prostatic gland. The molecular sequence obtained in the present study formed a robust clade with available sequences of species of Aponurus. The integrative taxonomic approach successfully combined morphological observations, including both previously reported features and new descriptions from histological and electron microscopy analyses, with molecular data to identify these specimens as A. laguncula. Moreover, the detailed characterization of structures, such as the gonads in A. laguncula, that would be challenging to analyze using a single technique, was possible. Further molecular studies with less conserved genetic markers should be conducted to understand phylogenetic relationships between Aponurus species.

Generalist species exhibit more genetic structure in comparison to a habitat specialist: Evidence from a phylogeographic study of two freshwater crabs (Decapoda: Potamonautidae: Potamonautes), implications for habitat conservation.

During the present study, the phylogeography of the wetland specialist, freshwater crab, Potamonautes flavusjo, was investigated and compared to that of the ubiquitous, generalist, P. sidneyi, using DNA sequence data from the mitochondrial cytochrome oxidase subunit one (COI). We inferred the evolutionary history of each species and compared their population-level genetic structure by constructing haplotype networks and using an analysis of molecular variation. Additionally, we explored the evolutionary relationship between southern African lentic and lotic freshwater crab species by examining the usefulness of carapace attributes in relation to genetic indices and a species' assumed dispersal capacity. In the lentic species, P. flavusjo, a single interconnected haplocluster characterized by shared haplotypes was observed, suggesting marked maternal dispersal, a result corroborated by the low F ST values. In contrast, for the lotic species, P. sidneyi two distinct haploclusters and marked genetic differentiation was observed indicating the absence of maternal dispersal, a result corroborated by the high F ST values. The phylogenetic relationship in P. sidneyi was further investigated using a maximum likelihood and Bayesian inference analyses with the addition of sequence data from the mitochondrial 16S rRNA locus to estimate divergence times. Three species delimitation methods (ASAP, PTP, and bGMYC) were used to explore the presence of distinct lineages in P. sidneyi. The phylogenetic results indicated that within P. sidneyi two clades were present, while divergence time estimates suggest cladogenesis during the middle to late Pleistocene. The species delimitation methods used showed moderate congruence, however all oversplit the number of putative lineages. Our results indicated that P. sidneyi is a species complex comprised of two cryptic lineages, occurring in sympatry contemporarily possibly alluding to secondary contact. Carapace height was found to have no discernible influence on the genetic indices and presumed dispersal capabilities of mainland southern African freshwater crab species. The importance of our results are discussed in terms of conservation of freshwater habitats.

Intra- and interspecific variation of Amblyomma ticks from southern Africa

BackgroundAmblyomma spp. ticks, known for their long mouthparts, bright ornate appearance and aggressive hunting behaviour, are vectors of a number of important pathogens. In southern Africa, 17 Amblyomma spp. are currently documented. Of these species, Amblyomma hebraeum and Amblyomma variegatum have been well studied due to their wide geographical range and their status as competent vectors of pathogens that are of veterinary and medical importance. Studies on other Amblyomma spp. in southern Africa have been neglected, fostering ongoing debates on the validity of certain species such as Amblyomma pomposum. This study investigated the inter- and intra-species variation of Amblyomma ticks collected in southern Africa, focusing on resolving the dispute about A. pomposum and A. variegatum being distinct species.MethodsFour Amblyomma tick species were collected from Angola, Mozambique, South Africa, Zambia and Zimbabwe, and were identified morphologically as Amblyomma eburneum (208), A. hebraeum (4758), A. pomposum (191) and A. variegatum (2577) using identification keys. Gene amplification targeting the 12S and 16S rRNA, cytochrome oxidase I, cytochrome B and internal transcribed spacer-2 genes was conducted for 204 ticks, for which varying success was achieved during amplification for each of the markers. Maximum likelihood analyses were performed in IQ-TREE.ResultsThe phylogenetic topologies and ABGD analyses of each individual gene clustered A. pomposum within the A. variegatum clade, while clearly separating A. eburneum and A. hebraeum from all other species. None of the genetic markers indicated intraspecific structuring on the basis of geographical origin, despite great distances between sampling sites.ConclusionOur study concludes that there is insufficient molecular evidence to differentiate A. pomposum and A. variegatum from each other. We highlight the need for whole mitochondrial genome sequencing of these two species to resolve the ongoing controversies. Furthermore, we propose mating and hybrid viability studies between the two species to confirm their reproductive isolation.Graphical

Resolving the Taxonomy of Mountain Syrphidae (Diptera) in the Iberian Peninsula: The Species Group of Cheilosia melanura Becker, 1894.

The largest genus of Palaearctic Syrphidae, Cheilosia Meigen, 1822 (Syrphidae: Rhingiini), is currently under revision in the Ibero-Balearic region (Iberian Peninsula + Balearic Islands). Prior to this study, various species groups with putative phylogenetic support were defined for this genus of complex taxonomy. The group of Cheilosia melanura Becker, 1894 includes species distributed all over Europe, with some of these species being similar each other in both morphology and genetics. After recent fieldwork in different Iberian localities and consultation of entomological collections, a new species from Sierra Nevada (Granada, Spain) was uncovered, described, and illustrated. Data on diagnostic characters, intraspecific variability, and adult biology were also provided. Maximum likelihood analyses of the fragment "C" of the 5' end of the cytochrome c oxydase subunit I (COI-5') and complete COI-5' were performed to explore and support morphological species concepts within the group. The Spanish-endemic Cheilosia andalusiaca Torp Pedersen, 1971 is recognised here to be part of the C. melanura group based both on morphological and molecular evidence. Cheilosia carbonaria Egger, 1860 and Cheilosia cynocephala Loew, 1840 from the Iberian Peninsula are reported for the first time based on specimens originating in the Spanish Pyrenees. An identification key for the Iberian species of the C. melanura group is provided.

Multi-gene phylogeny and morphological characters reveal seven new species of Micropsalliota (Agaricales, Agaricaceae) from southern China, with an updated key for the species distributed in China

ABSTRACT Species of Micropsalliota generally grow in the tropics and are characterised by small, slender basidiomes, brown basidiospores, and cheilocystidia that vary in shape with capitate or subcapitate apex, and pigmented pileipellis. Based on morphological characters and molecular evidence, here we describe seven new species from southern China, viz. Micropsalliota ferruginea, M. fimbriata, M. gigaspora, M. longicystis, M. nana, M. squarrosa, and M. umbonata. Micropsalliota appendiculata, a species recently described from Vietnam, was first recorded in China. The Maximum likelihood and Bayesian analyses based on multi-locus sequence datasets (the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, nrITS; the D1–D2 domains of nuc 28S rDNA, LSU; partial sequences of the most variable region of the second-largest subunit of RNA polymerase II, rpb2, and a portion of the translation-elongation factor 1-α, tef1) shows that the genus is separated into 11 major clades and subclades. To aid in diagnosis, a key to 32 species of Micropsalliota in China is provided.

Paronatrema davidbowiei n. sp. (Trematoda: Syncoeliidae), a new parasite of the pelagic thresher (Alopias pelagicus) and its phylogenetic relationships within the suborder Hemiurata Skrjabin & Guschanskaja, 1954

A new species of hemiurid trematode found on the gills and in the aorta of the pelagic thresher Alopias pelagicus from the eastern Pacific, off Costa Rica, is described based on an integrative taxonomic approach that includes the use of light and scanning electron microscopy, and 28S rDNA sequencing. Phylogenetic analysis was also performed to explore, for the first time, the relationships of a member of the subfamily Otiotrematinae within the suborder Hemiurata. Paronatrema davidbowiei n. sp. can be distinguished from the congeners by having tegumental spines on the dorsal surface of the forebody, papillae on the oral sucker, and different morphology or number of testicular follicles. BLAST analysis revealed that sequences of Paronatrema davidbowiei n. sp. had the highest degree of similarity with Hirudinella spp. (Hirudinellidae). Results from Maximum Likelihood and Bayesian phylogenetic analyses, returning trees with the exact same topology and strong branch support, distinguished between the two superfamilies included in the suborder Hemiurata: Azygioidea and Hemiuroidea. Our analysis placed the new species in a clade with Copiatestes filiferus, the only existing sequence of the family Syncoeliidae.

Phylogeny, niche modelling and morphology unveil a new lianescent species of Sigmoidotropis (Leguminosae, Papilionoideae) across rainforest enclaves within Brazilian dry vegetation

AbstractThe small Neotropical papilionoid legume genus Sigmoidotropis (nine species) has been described only relatively recently as the result of the taxonomic rearrangement of the genus Vigna (subtribe Phaseolinae), based on phylogenetic analyses of DNA sequence data. Here, we formally propose a new lianescent species of Sigmoidotropis that occurs disjunctly in enclaves of moist forest of mountainous regions surrounded by dry vegetation at three different localities in the Brazilian states of Bahia and Minas Gerais. Its phylogenetic position and morphological affinities with other genera of Phaseolinae were evaluated by Bayesian inference and maximum likelihood analyses, using sequence data from the nuclear ITS/5.8S and plastid trnK/matK. To better understand this new species’ widely disjunct distribution and a possible connection between its populations in the past, an environmental niche modelling (ENM) analysis was performed. The phylogenetic analyses revealed that Sigmoidotropis appears closest to the genera Ancistrotropis and Delgadoana, together forming the Sigmoid‐keel clade. The new species proposed here is strongly recovered within Sigmoidotropis, being most closely related to S. ekmaniana, S. elegans, and S. megatyla. The ENM indicated changes in the potential distribution of the new species over different climatic periods, with expansion during colder periods and contraction during warmer periods, leading to possible relictual populations in moist forest enclaves. A description of the new species Sigmoidotropis maculata is presented, along with illustrations, a distribution map, taxonomic comments, and conservation status assessment.

Characterization of the complete mitochondrial genome of a newly discovered torrent catfish, Liobagrus geumgangensis, and their phylogenetic relationships.

A new Liobagrus fish was reported from the Korean Peninsula, but research on this taxon is lacking. Moreover, existing research on the mitogenome of the genus Liobagrus in Korea is very limited, and no studies have been conducted on structural characteristics of transfer RNA (tRNA) or gene order comparisons between taxa; instead, research has been restricted to basic phylogeny. The complete mitochondrial genome of Liobagrus geumgangensis was analyzed for the first time. We then aimed to reconstruct the phylogenetic relationships of the genus Liobagrus and estimate the divergence time of speciation events. We used a dissected fin clip from an adult of Liobagrus geumgangensis. Genomic DNA was extracted and analyzed with whole genome sequencing (WGS) and assembled by the NOVOPlasty method. The mitogenome sequence was annotated, and a genome map, tRNA structure, and phylogenetic tree were constructed using maximum likelihood analysis. In addition, divergence time was estimated. The mitochondrial genome was 16,522bp in length and comprised 37 genes. The overall base composition was 30.5% A, 25.5% T, 28.4% C, and 15.7% G. Most tRNAs exhibited the typical clover leaf shape, except trnS1. Phylogenetic analysis revealed that Liobagrus geumgangensis clustered within a clade with four other Liobagrus species exclusive to the southern region of the Korean Peninsula. Its divergence was estimated to have occurred during the late Miocene. Characteristics of Liobagrus geumgangensis mitogenome were consistent with those of other torrent catfish species. Time scale estimation revealed distinct groupings, with some distributed across mainland Asia and others in the southern region of the Korean Peninsula. Notably, the Korean Peninsula group was identified as its own lineage, comprising entirely endemic species.

First Report of Root Rot of Cathaya argyrophylla caused by Fusarium oxysporum in China.

Cathaya argyrophylla [Chun & Kuang.] is an ancient relict plant and its embryonic development is similar to that of Pinus species. This has important scientific value for studying the phylogeny of Pinaceae (Wu et al. 2023). In July 2022, root rot was detected in the seedling cultivation base of C. argyrophylla in Daozhen County, Guizhou Province, China (28.89 °N, 107.6 °E). The incidence of the disease was 30% (n = 100); the susceptible plants wilted, leaves withered, and roots showed brown-to-black lesions and rot. Ten root tissues were randomly collected from the edges of the lesions of six symptomatic susceptible plants. The tissues were sterilized with 75% alcohol for 30 seconds, followed by 2-minute immersion in 3% sodium hypochlorite. After washing with sterile water, the tissues were incubated on potato dextrose agar (PDA; BoWei, Shanghai) at 28 ℃ for five days. Four single-spore cultures were obtained using a single-spore isolation method (Gong et al., 2010). Single-spore cultures grew rapidly on PDA. After five days of incubation, the colonies were white and pink, indicating a large amount of aerial mycelia. Microconidia were ovate or ellipsoid, measuring 5.0-10.0 × 1.5-3.0 μm (n = 50); Macroconidia were falcate, slightly curved or straight, measuring 19.5-28.5 × 2.0-6.0 μm (n = 50). Based on morphological features, the pathogen was considered to be Fusarium spp. (Leslie and Summerell 2006). Three representative strains, GF5, GF6, and GF7, were selected for molecular identification, and genomic DNA was extracted to confirm morphological diagnosis. The internal transcribed spacer (ITS) (White et al. 1990) was amplified using primers ITS1/ITS4, and the β-tubulin gene (Varga et al. 2011) was amplified using primers Bt2a/Bt2b. The ITS and β-tubulin sequences were aligned with GenBank, and amplification of the genes from the three isolates was consistent. The ITS (OP482273) and β-tubulin (OR825353) sequences of GF5 were stored in GenBank, and their homology with Fusarium oxysporum HC131(accession numbers MW600442 and MW670451) was 99 to 100%. Maximum likelihood analysis using MEGA 11.0 showed that isolate GF5 belongs to F. oxysporum. The reconstructed phylogenetic tree confirmed the phylogenetic position of the isolate GF5. The pathogenicity test was carried out using GF5 and GF6 isolates. The taproots of ten 3-year-old C. argyrophylla plants were washed, and then the roots were immersed in a 2 × 106/mL conidial suspension for one hour. Ten plants with sterile water were used as controls. After planting in pots (30 × 25 cm) with sterilized forest soil, the plants were cultured in a greenhouse (25 ℃ and 12-hour photoperiod). Thirty days after inoculation, all plants inoculated with the isolated pathogen showed wilting symptoms, and the roots showed typical root rot symptoms, whereas the control group showed no symptoms. The pathogens re-isolated from all inoculated plants were morphologically identical and had ITS sequences identical to F. oxysporum, validating Koch's hypothesis. The pathogenicity test was repeated twice and similar results were obtained. Although this fungus has been previously reported to cause root diseases in hosts, such as Musa nana Lour. and Pinus massoniana Lamb. (He et al. 2010; Luo et al. 2020), to our knowledge, this is the first report of F. oxysporum causing root rot in C. argyrophylla. These findings provide a basis for the development of management strategies for C. argyrophylla infection.

Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies.

Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s. African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny. Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species. Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.

The complete mitochondrial genome and phylogenetic analysis of Cyanopterus ninghais (Hymenoptera: Braconidae)

Cyanopterus ninghais is an important gregarious ectoparasitoid during the larval stage of Monochamus alternatus, a key vector for pine wilt disease in Asia. In this study, the complete mitochondrial genome of C. ninghais was sequenced and analyzed. The mitochondrial genome of C. ninghais is 15,386 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The nucleotide composition is 41.32% A, 8.29% G, 6.06% C, and 44.33% T. Phylogenetic trees of Braconidae were constructed using 13 PCG sequences via Bayesian inference (BI) and maximum likelihood (ML) analyses to determine their phylogenetic position. Both ML and BI analyses revealed that C. ninghais is closely related to Euurobracon yokahamae, Virgulibracon endoxylaphagus, and Habrobracon hebetor.

The mitochondrial genome of a social wasp, Vespula rufa (Linnaeus, 1758) (Hymenoptera: Vespidae)

For an ongoing systematic study of Korean Vespidae, we analyzed the complete mitochondrial genome of a social wasp, Vespula rufa (Linnaeus 1758), from the South Korea. The mitogenome is 17,521 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The nucleotide composition is 40.5% adenines, 43.0% thymines, 6.0% guanines, and 10.5% cytosines. The GC content is 16.5%. A maximum-likelihood analysis was conducted to understand phylogenetic relationships, based on 13 complete mitogenome sequences of Vespinae species. We recognized that V. rufa is being placed basal within the genus Vespula. The complete mitochondrial genome of V. rufa provides useful genetic information for further studies.

The chloroplast genome structure of Turpinia affinis (Staphyleaceae)

The species Turpinia affinis Merr. et Perry 1941 is widely distributed throughout southwestern China. In folk medicine, this species is often used as a substitute for the Chinese medicine Turpiniae Folium, whose legal origin is T. arguta (Lindl.) Seem. In order to ascertain the relationship between these two species, the chloroplast genome of T. affinis was aequenced and assembled, resulting in a typical quadripartite molecule with a length of 160,769 base pairs and an overall GC content of 37.3%. Additionally, 131 genes were annotated, comprising 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A maximum likelihood analysis demonstrated that the Turpinia species form a monophyletic clade, with T. affinis positioned as the sister taxon to the clade comprising the remaining species within the genus. This outcome enhances the genomic data for the genus Turpinia and will contribute to further investigations into phylogenetics, evolution, and sustainable resource utilization.

Vicariant speciation resulting from biogeographic barriers in the Australian tropics: The case of the red-cheeked dunnart (Sminthopsis virginiae).

Global biodiversity loss continues unabated, and in Australia, the rate of recent mammal extinctions is among the worst in the world. Meanwhile, the diversity among and within many endemic mammal species remains undescribed. This information is crucial to delineate species boundaries and thus inform decision-making for conservation. Sminthopsis virginiae (the red-cheeked dunnart) is a small, dasyurid marsupial found in four disjunct populations around the northern coast of Australia and New Guinea. There are three currently recognized subspecies, each occupying a distinct geographic location. Sminthopsis v. virginiae occurs in Queensland, S. v. rufigenis is distributed across New Guinea and the Aru Islands, and S. v. nitela has populations in the Top End of the Northern Territory and the Kimberley region of Western Australia. Previous molecular work has suggested the current subspecies definitions are not aligned with DNA sequence data, though the sampling was limited. We undertook a comprehensive genetic and morphological review of S. virginiae to clarify relationships within the species. This included mitochondrial (CR, 12S, and cytb) and nuclear (omega-globin, IRBP, and bfib7) loci, and morphometric analysis of skulls and whole wet-preserved specimens held in museums. Maximum Likelihood and Bayesian phylogenetic analyses resolved samples into two distinct clades, demarcated by the Gulf of Carpentaria in Australia's north. Sminthopsis. v. nitela was consistently separated from S. v. virginiae and S. v. rufigenis, based on the overall body and skull size and craniodental features, while S. v. virginiae and S. v. rufigenis were more difficult to distinguish from each other. Thus, we redescribed S. virginiae, recognizing two species, S. nitela (raised from subspecies) and S. virginiae (now comprising the subspecies S. v. virginiae and S. v. rufigenis). This study highlights the importance of recognizing cryptic mammal fauna to help address the gap in our knowledge about diagnosing diversity during a time of conservation crisis.

NEW INSIGHTS BASED ON MORPHOLOGICAL AND MOLECULAR DATA REVEAL THE TAXONOMIC STATUS OF HALIOTREMA PTEROISI (MONOGENOIDEA: DACTYLOGYRIDAE) INFECTING DEVIL FIREFISH PTEROIS MILES (PERCIFORMES: SCORPAENOIDEI: SCORPAENIDAE) IN THE RED SEA OFF EGYPT.

Paperna, 1972 (Monogenoidea: Dactylogyridae) was found parasitizing the gill lamellae of devil firefish, Pterois miles (Bennet) (Perciformes: Scorpaenidae), in the Red Sea off Safaga (26°44'N, 33°56'E), Egypt. The parasite species was described based on morphological features of available specimens and transferred to PlatycephalotremaKritsky and Nitta, 2019 (Dactylogyridae) as Platycephalotrema pteroisi (Paperna, 1972) n. comb. The occurrence of Pl. pteroisi off Safaga, Egypt, represented a range extension for the helminth of about 160 km to the southwest of the southern end of the Gulf of Aqaba. The transfer of the species to Platycephalotrema based on an evaluation of morphological features was supported by an analysis of molecular sequences of the 28S rDNA gene of Pl. pteroisi and 49 other dactylogyrid species. Maximum-likelihood, Bayesian inference, and maximum parsimony analyses of this dactylogyrid sequence data revealed H. pteroisi to nest with significant support within the clade of Platycephalotrema spp. During the literature review of dactylogyrid species infecting scorpionfishes, it was determined that Ancyrocephalus sp. of Dyer et al. from luna lion fish Pterois lunulata Temminck and Schlegel collected off Okinawa-jima, Japan represented an undescribed species of Platycephalotrema.

Schistura sonarengaensis, a new species of cave-dwelling loach (Teleostei: Nemacheilidae) from Meghalaya, northeast India.

A new species of nemacheilid loach, Schistura sonarengaensis sp. nov., is described from three cave-dwelling populations (Barak-Surma-Meghna drainage) in the South Garo Hills district of Meghalaya, India. The new species possesses prominent eyes but is easily distinguished from all the congeners of the genus Schistura from Barak-Surma-Meghna and adjacent rivers drainages of northeast Indian (except S. syngkai) in having 13-26 vertically elongated to circular mid-lateral black blotches (brownish in life) overlayered on a grayish-black mid-lateral stripe on a dull white or pale-beige (golden brown in life) body. However, it can be easily distinguished from S. syngkai in having a complete (vs. incomplete) lateral line with more 72-89 (vs. 19-42) lateral-line pored scales, greater pre-dorsal length (48.5-53.1 vs. 41.9-44.1 %SL), a wider body at dorsal-fin origin (11.3-16.7 vs. 9.4-10.3 %SL), greater dorsal (18.1-21.1 vs. 15.1-17.0 %SL) and lateral (20.9-24.1 vs. 17.4-18.9 %SL) head length, a wider head (14.5-18.5 vs. 11.6-13.3 %SL), and moderately forked (vs. emarginated) caudal fin. Further, molecular analysis confirms the distinctiveness of S. sonarengaensis sp. nov. from its congeners found in northeast India by significant divergences with uncorrected genetic distance ranging from 3.7% to 17.3% in the mitochondrial cytochrome c oxidase subunit I (COI) gene dataset. The phylogenetic position of the new species with its sister species was evaluated using maximum likelihood and Bayesian analysis. The species delimitation approaches assemble species by automatic partitioning (ASAP) and Poisson tree processes (PTP) utilized for testing species assignments consistently identified our test group as a distinct species from its sister species. Although the new species lacks typical morphological adaptations usually associated with a subterranean life, such as complete absence (or vestigial presence) of eyes and pigmentation, it exhibits a reduction of pigmentation when compared to the epigean congeners.

Neoscytalidium dimidiatum causing stem canker on Hylocereus megalanthus in China.

Hylocereus megalanthus (syn. Selenecereus megalanthus), commonly known as Yanwo fruit (bird's nest fruit), is an important tropical fruit, which is popular and widely planted due to its high nutritional and economic value in southern China. In September 2022, a serious stem and fruit canker was observed on Ecuadorian variety of Yanwo fruit plant in a 0.2 ha orchard in Guangdong (N21°19'1.24" E110°7'28.49"). Almost all plants were infected and disease incidence of fruits and stems was about 80% and 90% respectively. Symptoms on the stem and fruits were small, circular or irregular, sunken, orangish brown spots that developed into cankers (Fig 1 A, B and C). Black pycnidia were embedded under the surface of the cankers at the initial stage, subsequently they became erumpent from the surface, and the infected parts rotted. Five symptomatic stems from five plants were collected, 0.2 cm2 tissues adjacent to cankers were surface sterilized and placed on potato dextrose agar (PDA) to incubate at 25 to 28 ℃. Fungal isolates each with similar morphology grew from 100% of the tissues. Colonies covered with aerial mycelium were grayish white, and then gradually turned to grayish black. Septate hyphae were hyaline to brown and constricted into arthroconidial chains. The arthroconidia were variously shaped and colored, orbicular to rectangular, hyaline to dark brown, thick-walled, and zero- to one- septate, averaging 7.7 × 3.6 μm (n>50) (Fig 1 D, E, F and G). To identify the fungus, the internal transcribed spacer region (ITS), translation elongation factor 1-alpha (tef1), beta-tubulin (tub2), histone H3 (his3) and chitin synthase (chs) gene of isolate ACCC 35488 and ACCC 35489 (Agricultural Culture Collection of China) were amplified and sequenced with primer pairs: ITS1/ITS4 (White et al. 1990), EF1-728F/EF2-rd (Carbone & Kohn 1999; O'Donnell et al.1998), TUB2Fd/ TUB4Rd（Aveskamp et al 2009）, CYLH3F/H3-1b (Crous et al. 2004) and CHS-79F/CHS-345R (Carbone & Kohn 1999) (ITS: OQ381102 and PP488350; tef1: OQ408545 and PP510454; tub2: OQ408546 and PP510455; his3: OQ408544 and PP510453; chs: OQ408543 and PP510452). Sequence Blastn results showed above 99% identical with those of Neoscytalidium dimidiatum ex-type strain CPC38666. Phylogenetic tree inferred from Maximum Likelihood analysis of the combined ITS, tub2 and tef1 sequences revealed two isolates clustered with N. dimidiatum (Fig 2). Pathogenicity was tested on healthy one-year-old cuttings and fruits of Ecuadorian variety at room temperature. Six sites were pin-pricked on each stem and fruit. Both wounded stems and fruits were inoculated with spore suspensions (106 spore/ml) and 6-mm fungal plugs respectively. Sterile water and agar were used as control. The test was repeated twice. Stems and fruits were enclosed in plastic boxes with 80% relative humidity. Symptoms described above were observed on inoculated stems and fruits at five days post inoculation (Fig 1 H and I). No symptoms developed on the controls. Neoscytaliudium dimidiatum was reisolated from the cankers with a frequency of 100% via morphological and molecular analysis. This is first report of stem and fruit canker caused by N. dimidiatum on H. megalanthus in China and this disease represents a serious risk of Yanwo fruit yield losses. This fungus is widespread occurring throughout the world causing diseases on a wide variety of plants. The finding will be helpful for its prevention and control.