Taxonomic Studies Research Articles

Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae)

BackgroundThe Bucephalidae is a large family of digenean trematodes but most previous analyses of its phylogenetic position have relied on a single mitochondrial gene or morphological features. Mitochondrial genomes (mitogenomes) remain unavailable for the entire family. To address this, we sequenced the complete mitogenome of Dollfustrema vaneyi and analyzed the phylogenetic relationships with other trematodes.ResultsThe circular genome of Dollfustrema vaneyi spanned 14,959 bp and contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a major non-coding region. We used concatenated amino acid and nucleotide sequences of all 36 genes for phylogenetic analyses, conducted using MrBayes, IQ-TREE and PhyloBayes. We identified pronounced topological instability across different analyses. The addition of recently sequenced two mitogenomes for the Aspidogastrea subclass along with the use of a site-heterogeneous model stabilized the topology, particularly the positions of Azygiidae and Bucephalidae. The stabilized results indicated that Azygiidae was the closest lineage to Bucephalidae in the available dataset, and together, they clustered at the base of the Plagiorchiida.ConclusionsOur study provides the first comprehensive description and annotation of the mitochondrial genome for the Bucephalidae family. The results indicate a close phylogenetic relationship between Azygiidae and Bucephalidae, and reveal their basal placement within the order Plagiorchiida. Furthermore, the inclusion of Aspidogastrea mitogenomes and the site-heterogeneous model significantly improved the topological stability. These data will provide key molecular resources for future taxonomic and phylogenetic studies of the family Bucephalidae.

Comparative characteristics of the lipidome of Cycas revoluta and C. rumphii (Cycadaceae)

A targeted lipidomics analysis of four classes of membrane glycerolipids was carried out in two species of Cycadaceae from the genus Cycas – C. revoluta and C. rumphii. The analysis of the molecular diversity of the main phospholipids, which are the components of extra-chloroplast membranes, has revealed archaic features, including a high level of molecular species containing C18:1 fatty acids (typical of Ginkgo biloba), increased relative content of molecular species with odd fatty acids C17:0 and C19:0 (typical of non-seed plants). At the same time, the analysis of the molecular diversity of the glycolipids which are the components of chloroplast membranes, did not find significant differences from most seed plants, which indicates a higher conservation of lipids of a photosynthetic apparatus. The identified features of the molecular composition of glycerolipids of two species of Cycas indicate the prospectiveness of using lipidomics for taxonomic and phylogenetic studies, with the data on the molecular composition of phosphatidylcholines, for which the greatest heterogeneity and species-specificity was demonstrated, deserving the most attention.

Understanding the role of bats as fungal vectors in the environment

Bats (Chiroptera), the second largest group of mammals, are known for their unique immune system and their ability to act as vectors for various zoonoses. Bats also act as important carriers of fungi, which include plant, animal, and human pathogens. Their roosting areas, foraging behaviors, and even migration routes make bats ideal vectors for fungi. We isolated 75 culturable fungal species from bats in Yunnan Province, China, with 36 species representing known pathogens of plants, animals, and humans, while 39 species are non-pathogenic fungi. Among these species, 77% (58 species) belonged to Ascomycota, 9% (seven species) belonged to Basidiomycota, and 13% (10 species) belonged to Mucoromycota. Even though several taxonomic studies on fungi associated with bats have been published, studies exploring the role of bats as fungal vectors are lacking. This study discusses the fungi host-specific traits and pathogenicity and the impact and ecological significance of bats as fungal vectors.

Additions to and revisions of the endemic and near-endemic Acanthaceae of Ethiopia

Taxonomic studies in the Acanthaceae of Ethiopia and neighbouring countries reveal the presence of several previously overlooked endemic and near-endemic taxa. The Isoglossa somalensis Lindau complex is revised, resulting in the description of a new species, Isoglossa recurva Hanny & I.Darbysh. from the forests of southwest Ethiopia, and a new variety of I. somalensis, var. glandulosa Hanny, G.Hoban & I.Darbysh. from montane southeast Ethiopia. Barleria induta C.B.Clarke from Ethiopia and Eritrea, treated as B. prionitis L. subsp. induta (C.B.Clarke) Brummitt & J.R.I.Wood in the Flora of Ethiopia and Eritrea (FEE), is reevaluated and found to represent two species, with B. praetermissa I.Darbysh. described from the Tigray region of northwest Ethiopia. Finally, Hypoestes microphylla Nees is resurrected as a good species, separate from the widespread H. triflora (Forssk.) Roem. & Schult. under which it was treated as a synonym in FEE. Descriptions, tables of comparison and notes on the habitat, ecology and extinction risk for these taxa are provided. The first record of I. gregorii (S.Moore) Lindau for Ethiopia is also noted and a revised key to Isoglossa in Ethiopia is presented. The endemic Acanthaceae of Ethiopia now stands at 21 species (23 taxa), whilst an additional 23 species (24 taxa) are considered to be range-restricted near-endemics.

Eplingiella sanoi sp. nov. (Hyptidinae-Lamiaceae): supports the urgent need for campos rupestres conservation in the Serra do Espinhaço Septentrional, Minas Gerais state, Brazil

A new species of Lamiaceae, Eplingiella sanoi, from the campo rupestre of an ecotone zone between the Cerrado and the Caatinga domains is described and illustrated. The new species expands the distribution of the genus to Southeast Brazil, previously restricted to Northeast Brazil. Eplingiella sanoi is compared to the three other species of the genus, especially E. cuniloides, the morphologically closest related species. We present an identification key for all the species of the genus, an occurrence map for Eplingiella sanoi, E. cuniloides and E. brightoniae and a formal conservation assessment for the new species. Eplingiella sanoi is endemic to the region between Pico da Formosa and Pico do Sucuruiú (Minas Gerais state, Serra do Espinhaço), an area under threat due to a planned wind farm installation. Recognizing this species emphasizes the imperative for more taxonomic studies and conservation of Serra do Espinhaço.

Protocolo de recolecta y tinción para el estudio taxonómico de los policládidos (Platyhelminthes: Polycladida)

The taxonomic study of polyclads (order Polycladida) dates back to the 19th century. The traditional taxonomy of these organisms requires a combination of the external and internal morphology of the body and the hermaphroditic reproductive system, where the histological techni que is an indispensable tool that plays a key role in this process. This protocol covers the collection processes up to the preparation of the specimens for histological analysis,adapting and improving techniques previously established by other authors for clear and precise visualization of the anatomical structures. Specimens are collected manually using fine paintbrush, photographed dorsally and ventrally, fixed in 10% frozen formalin neutralized with sodium borate and preserved in 70° ethanol. For taxonomic classification, complete mounts of the organisms and sagittal sections of the hermaphroditic reproductive system are used; a five-step histological protocol including hydration, staining, dehydration/differentiation, cleaning/transparency, and slide mounting is performed for each. This standardized technique complements morphological and taxonomic studies of the taxon.

Meristic co-evolution and genomic co-localization of lateral line scales and vertebrae in Central American cichlid fishes.

Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.

Taxonomic and Anatomic Studies on Some Ferns of District KOTLI, AZAD JAMMU and KASHMIR

Taxonomic and Anatomic Studies on Some Ferns of District KOTLI, AZAD JAMMU and KASHMIR

The Cretaceous Diatom Database: A tool for investigating early diatom evolution.

The Cretaceous period is the time of the first appearance of the diatoms in the fossil record. These fossils give us direct evidence of the age and early evolution of the diatom lineage. The fossil record, however, is incomplete and therefore often extrapolated through time-calibrated phylogenies. These two approaches offer different perspectives on the early evolution of diatoms, which is still poorly understood. We compiled the first comprehensive Cretaceous Diatom Database, a tool to investigate the taxonomy, diversity, and occurrence of the earliest known diatom lineages. To further aid the integration and use of the oldest diatom fossils in molecular clock analyses, we present a set of well-documented Cretaceous fossils that can be placed onto molecular phylogenetic trees of extant and extinct species, making them ideal candidates for the calibration of molecular clocks. The analysis of the fossil record and the Cretaceous Diatom Database revealed Cretaceous diversity is substantially greater than previously thought, yet considerable taxonomic work is still needed. The Cretaceous Diatom Database and the list of Cretaceous fossils for calibrating molecular clocks represent valuable resources for future evolutionary and taxonomic studies of modern and fossil diatoms.

A taxonomic study of the genus Antepipona de Saussure, 1855 (Hymenoptera: Vespidae: Eumeninae) from China, with two new species and three new records

A taxonomic study of the genus Antepipona de Saussure, 1855 (Hymenoptera: Vespidae: Eumeninae) from China, with two new species and three new records

Parasitoids of the black soldier fly (Hermetia illucens) – a minor problem or the tip of the iceberg?

Abstract An overview of parasitoid species found on the black soldier fly is presented. The future significance of these natural enemies remains uncertain. However, a thorough assessment of their impact on black soldier fly farms worldwide is essential. The initial step involves the taxonomic identification and study of the life cycles of the species involved.

Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes).

Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.

Miscellaneous nomenclatural notes on Andean Chrysochlamys (Clusiaceae: Clusieae)

Chrysochlamys (Clusiaceae) is a strictly Neotropical genus that comprises between 35 and 55 species. The taxonomy of the genus is poorly-known in South American region, especially in Andean countries. During the taxonomic revision of Chrysochlamys and related genera in Colombia we observed two mainly gaps: the unclear nomenclatural history of Andean Chrysochlamys and the necessity of lectotypification of some species published by Pax, Poeppig, Planchon and Triana. To solve both issues, we provide a Chrysochlamys nomenclatural history summary and reduce nomenclatural ambiguities on a few Andean flora. For this, we carried out an exhaustive analysis of Chrysochlamys and related genera type collections and protologues. We propose a new combination, Chrysochlamys microcarpa comb. nov., originally published in Tovomita, designated six lectotypes, propose a numbering for three Triana’s type collections, and discuss a case of inadvertent lectotypification. This paper provides relevant information about problematic or understudied Chrysochlamys species, which will be useful for subsequent taxonomic studies.

Three-dimensional reconstruction of Late Miocene Trapa from eastern Zhejiang Province, China: Insights into its phytogeography and evolution

Abundant plant fossils were found in the Upper Miocene Shengxian Formation, eastern Zhejiang Province, China, among which Trapa belongs to a dominant population. The fossil fruits of Trapa were well preserved with abundant details. However, due to compaction during fossilization, Trapa fruits were often flattened, leading to the loss of some characteristic features. Thereby, a bias in taxonomic and phylogenetic studies would occur when such studies were based on these fruit fossils. In this study, we present the first quantitative three-dimensional reconstruction of compressed Trapa fruit fossils to restore their original morphology prior to burial. This approach provides a novel perspective for the identification and classification of compressed fruit fossils. The three-dimensional reconstruction of Trapa fruit fossils enabled accurate comparisons with extant species. We subsequently identified it as a new species, named Traparadiatiformis L. Xiao sp. nov., revealing differences from previously known taxa of Trapa. Importantly, our comparison suggests that the long lower horns and residual stalk may represent inherent characteristics of early Trapa fruits. However, these traits gradually degenerated during fruit evolution, resulting in morphological simplification during geological time. T. radiatiformis with primitive features exhibits good resemblance to Trapanatans fruit characteristics, which means it may be an ancestor of T. natans. We summarize the palaeogeographic distribution of fossil Trapa using previously published literature and demonstrate that the genus was most prosperous in the Miocene and exhibited the same distribution as that at present. Additionally, through detailed morphological comparisons between Trapa and Hemitrapa fruits, along with phylogenetic analysis within the Primotrapa genus itself, we propose a homology between Trapa and Hemitrapa, suggesting that they could have a common ancestor.

Liomera schubarti, a new species of xanthid crab (Brachyura, Xanthidae) from the Persian Gulf, northwestern Indian Ocean

Abstract This taxonomic study describes Liomera schubarti n. sp., a newly discovered xanthid crab inhabiting live coral in the Persian Gulf. The new species shares a general resemblance with four other species of this genus, L. bella, L. margaritata, L. rugata and L. yaldwyni, particularly in carapace morphology, but it can be distinguished by the fusion of carapace areolets, specific pattern of granules on the outer surface of the chela and the unique structure of the male first gonopod. This contribution enriches our understanding of the xanthid crab diversity in the Persian Gulf.

Molecular phylogenetic reassessment of eastern Atlantic Callinectes (Brachyura, Portunidae)

Abstract Several species from the genus Callinectes are economically important, yet the number of species and their geographic distributions remain unclear. Recently, one of the American species, Callinectes larvatus, was synonymized with one of the African species, C. marginatus, making C. marginatus the only species of the genus regarded to be amphi-Atlantic in distribution. However, there was no formal taxonomic study to support this taxonomic change, which was in contradiction to earlier studies that had provided morphological characters to support the taxonomic separation of the eastern Atlantic species from those of western Atlantic distribution. Callinectes maracaiboensis has also been questionably resurrected. Here we present a molecular based analysis for all species of Callinectes, using the two common mitochondrial genes 16S and 12S. Our molecular data support the presence of three eastern Atlantic, three eastern Pacific, and nine western Atlantic species. Historically, it appears that the separation of Africa and South America with the opening of the Atlantic basin gave rise to sister species distributed on opposite sides of the Atlantic Ocean. In a second isolation event, the emergence of the Panamanian isthmus resulted in pairs of geminate species distributed in eastern Pacific and western Atlantic waters.

Two new members of the genus Sphingobacterium: Sphingobacterium zhuxiongii sp. nov. and Sphingobacterium luzhongxinii sp. nov.

Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5 % (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8 mol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8 % (19.0 and 21.6 % for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1 % (74.4 and 78.3 % for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6 % (25.7 %). The corresponding ANI value was 85.7 % (85.5 % for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1 %) and 82/190 (43.2 %) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).

Review of some Hystricosporites representatives from Bolivia

A taxonomic study of megaspores with bifurcate-tipped processes from the Devonian–Carboniferous transition of Bolivia was performed. Megaspore specimens were isolated from palynological samples of the Pando X1 and Manuripi X1 boreholes. Their morphological characteristics and wall structures were described and illustrated with transmitted optical light, ultraviolet fluorescence, and scanning electron microscopy. This megaspore assemblage comprised six fossil species of Hystricosporites (H. costatus, H. delectabilis, H. elongatus, H. expandus, H. furcatus and H. spiralis). The morphologic features of their sporoderms confirm that these megaspores with bifurcate-tipped processes could have had a botanical affinity related to lycopsids. Additional future studies of wall ultrastructure using transmission electron microscopy will provide more information about their phylogenetic relationships with fossil and extant lycopsids. Keywords: megaspores, lycopsids, Carboniferous, Devonian.

A new genus of Herpyllobiidae (Copepoda: Cyclopoida) from a deep-living annelid (Polychaeta: Sigalionidae).

A taxonomic study of deep-sea polychaetes collected at a depth of 2,805 m off the northern coast of California revealed a scaleworm of the family Sigalionidae with an attached parasitic copepod. The copepod represents an undescribed genus of the family Herpyllobiidae, comprising mesoparasitic copepods chiefly recorded from polychaetes of the family Polynoidae. Blakerius gen. nov. diverges from the other herpyllobiid genera by its possession of 1) a chalice-shaped ectosoma with several protuberances along the posterior margin and a long cylindrical shaft with a hyaline coating and integumental sculpturing, a short stalk with a small, anteriorly placed sclerotized ring, 2) a relatively large, discoid-shaped endosoma with digitiform process, and 3) attached male copepodids with 3-segmented antennules, containing limbless sac-like males. The new genus is compared with other herpyllobiids. This discovery increases the number of known herpyllobiid genera to six and is the first record of a herpyllobiid parasitizing a sigalionid polychaete.urn: lsid: zoobank.org:pub:5E31FEED-D3EB-460E-AEA4-02A9D3A778D6.

Two new taxa of Clematis subsection Pierotianae (Ranunculaceae) in Taiwan

Based on a taxonomic study of Clematis subsect. Pierotianae in Taiwan using morphological evidence, two new taxa are proposed: C. parviloba Gard. ex Champ. subsp. shengzhenii Y.H. Cheng & T.Y.A. Yang and C. pengii Y.H. Cheng & T.Y.A. Yang. Both taxa, endemic to Taiwan, are here described and illustrated and distribution maps of both taxa are presented. Morphological comparisons and a key for identification of the taxa of Clematis subsect. Pierotianae in Taiwan are also given.