Taxonomic Placement Research Articles

Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

Lichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

Studies on Neotropical crickets: The continental Otteiini taxa (Orthoptera: Phalangopsidae), those cave crickets are not confined to the West Indies.

The tribe Otteiini is a group of cave crickets, that were believed only to inhabit the Greater Antilles (Cuba, Cayman Islands, and Hispaniola). However, when reviewing and studying similar cave crickets in Mexico, their relationship was proven with island taxa, expanding their distribution to the continental area, from the Yucatan Peninsula to the Gulf and Northeast of Mexico. Herein, the genus Paracophus is divided, and three additional genera are described: Hubbellcophus n. gen., Venegascophus n. gen. and Hortacophus n. gen. Also, two additional species for Paracophus are described (P. victoriensis n. sp. and P. velazquezi n. sp.). Diagnoses for all genera and dichotomous keys for genera and species are provided. Finally, the taxonomic relationships between the insular and continental taxa of the tribe are discussed, and the different taxonomic placements they had over time, with some genera located in Phalangopsinae and Luzarinae (Phalangopsidae) and Pentacentrinae (Gryllidae).

Taxonomic reassessment and phylogenetic placement of Cyrtodactylus phuketensis (Reptilia, Gekkonidae) based on morphological and molecular evidence.

The taxonomy and phylogeny of the Cyrtodactylus pulchellus complex along the Thai-Malay Peninsular region has been the focus of many recent studies and has resulted in the recognition of 17 species. However, the majority of these studies were focused on Peninsular and insular Malaysia where there were specimens and genetic vouchers. The taxonomic status and phylogenetic relationships of the Thai species in this complex remain unresolved, due to the lack of genetic material of some species, especially C. phuketensis and C. macrotuberculatus from Thai populations. In this study, we investigated the phylogenetic relationship between C. phuketensis and its closely related species C. macrotuberculatus, using both morphometric and molecular data. Phylogenetic analyses of mitochondrial NADH dehydrogenase subunit 2 (ND2) gene revealed that C. phuketensis is embedded within a C. macrotuberculatus clade with 1.45–4.20% (mean 2.63%) uncorrected pairwise sequence divergences. Morphological comparisons showed nearly identical measurements of C. phuketensis and C. macrotuberculatus and overlapping ranges in meristic characters. Based on these data, C. phuketensis is considered to be a variant of C. macrotuberculatus, thus rendering C. phuketensis a junior synonym of C. macrotuberculatus.

Molecular phylogeny and morphology of Pseudobaeospora cyanea

Pseudobaeospora cyanea, a rare basidiomycete belonging to an underinvestigated genus, is currently recorded from only three localities of the Iberian Peninsula. Moreover, to date no sequences of this rare species have been deposited in GenBank. In this paper a new collection from NW Italy is reported with detailed morphological descriptions and iconography. The first ITS and LSU sequences for the species are provided and uploaded to GenBank, and the taxonomic placement of P. cyanea within the genus is discussed.

Sequences of Previously Unknown Rhabdoviruses Detected in Bat Samples from the Republic of the Congo.

The family Rhabdoviridae contains diverse viruses, including vector-borne and nonvector-borne viruses, some that are human pathogens, including rabies virus and also nonpathogenic viruses. Bats, which are a known reservoir of viruses with zoonotic potential including coronaviruses, also carry multiple rhabdoviruses such as but not limited to lyssaviruses. We collected samples from 193 insectivorous and frugivorous bats in the Republic of the Congo and tested them for rhabdovirus RNA. Four samples were found positive for viral RNA representing sequences of four different, not previously described rhabdoviruses. Although phylogenetic and taxonomic placement of the novel sequences is uncertain, similarities with previously detected rhabdovirus sequences in bats suggest that these could represent vertebrate viruses. Considering the pathogenic risks some rhabdoviruses pose for humans, these results highlight the need for more research and surveillance regarding rhabdoviruses and bats.

Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae)

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps—a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia—using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.

Phylogenetic placement of the enigmatic longhorned beetle Vesperoctenus flohri Bates (Vesperidae) and a first description of its female internal structures

Taxonomic placement of the enigmatic monotypic Mexican longhorned beetle genusVesperoctenusBates is examined through inclusion in and reanalysis of the dataset of Haddad et al. (2018,Systematic Entomology43: 68–89). We describe and discuss the phylogenetic significance of the internal structures of a recently collectedV. flohrifemale from the Sierra de la Laguna mountain range in Mexico, the same specimen from which phylogenomic data was generated. Our phylogenomic analyses (469 genes) recoveredVesperoctenuswith maximal statistical support within the cerambyciform family Vesperidae, sister toVesperusDejean (Vesperinae).Vesperus+Vesperoctenuswere recovered sister to Philinae, and collectively form a clade sister to Anoplodermatinae. Thus, we placeV. flohriwithin Vesperidae: Vesperinae: Vesperoctenini based on analyses of large-scale phylogenomic data. Finally, we propose that the conservation status ofV. flohrimerits assessment.

Multi-gene phylogenetic evidence indicates that Pleurodesmospora belongs in Cordycipitaceae (Hypocreales, Hypocreomycetidae) and Pleurodesmospora lepidopterorum sp. nov. on pupa from China.

A new species, Pleurodesmospora lepidopterorum, isolated from a pupa, is introduced. Morphological comparisons and phylogenetic analyses based on multigene datasets (ITS+RPB1+RPB2+TEF) support the establishment of the new species. Pleurodesmospora lepidopterorum is distinguished from P. coccorum by its longer conidiogenous pegs located in the terminal or lateral conidiophores, and smaller subglobose or ellipsoidal conidia. A combined dataset of RPB1, RPB2, and TEF confirmed the taxonomic placement of Pleurodesmospora in Cordycipitaceae for the first time.

A Virus Infecting Hibiscus rosa-sinensis Represents an Evolutionary Link Between Cileviruses and Higreviruses.

Hibiscus (Hibiscus spp.) are popular ornamental and landscape plants in Hawaii which are susceptible to foliar diseases caused by viruses belonging to the genera Cilevirus and Higrevirus (family Kitaviridae). In this study, a virus infecting H. rosa-sinensis plants displaying foliar symptoms consistent with infection by a kitavirus, including yellow chlorotic blotches with a green perimeter, was characterized. The genome consisted of two RNAs 8.4 and 4.4 kb in length, and was organized most similarly to cileviruses, but with important distinctions. These included the location of the p29 homolog as the 3′-terminal open reading frame (ORF) of RNA2 instead of its typical locus at the 3′-end of RNA1; the absence of a p15 homolog on RNA2 and the adjacent intergenic region which also harbors small putative ORFs of unknown function; and the presence of an ORF encoding a 10 kDa protein at the 3′-terminal end of RNA1 that was also found to be present in the hibiscus green spot virus 2 genome. Spherical particles approximately 55–65 nm in diameter were observed in infected leaf tissue, and viral RNA was detected by reverse-transcription PCR in individual mites collected from symptomatic plants tentatively identified as Brevipalpus yothersi. Although phylogenetic analyses placed this virus between the higrevirus and cilevirus clades, we propose the tentative taxonomic placement of this virus, designated hibiscus yellow blotch virus (HYBV), within the genus Cilevirus.

Phylogenetic assessment and taxonomic revision of Halobyssothecium and Lentithecium (Lentitheciaceae, Pleosporales)

Our studies on lignicolous aquatic fungi in Thailand, Sweden, and the UK resulted in the collection of three new Halobyssothecium species (H. bambusicola, H. phragmitis, H. versicolor) assigned to Lentitheciaceae (Pleosporales, Dothideomycetes). Multi-loci phylogenetic analyses of the combined large subunit, small subunit, internal transcribed spacers of ribosomal DNA, and the translation elongation factor 1-alpha sequence data enabled a revision of the taxa assigned to Lentithecium and the transfer of L. cangshanense, L. carbonneanum, L. kunmingense, L. unicellulare, and L. voraginesporum to Halobyssothecium. Collection of an asexual morph of L. lineare and phylogenetic analysis confirmed its taxonomic placement in Keissleriella. Detailed descriptions and illustrations of H. bambusicola, H. phragmitis, and H. versicolor are provided.

Morphological–phylogenetic analysis of the late Cenozoic Chlamydini von Teppner (Bivalvia, Pectinidae) of southern South America

AbstractThe tribe Chlamydini was highly diversified in the marine Neogene of southern South America, reaching its maximum taxonomic diversity during the Miocene. However, the evolutionary relationships of South American taxa remain uncertain. This is the first phylogenetic analysis based on a large morphological matrix on Pectinidae, which focuses on South American taxa and species related to Chlamys s.s. The phylogenetic analysis is based on a matrix composed of 145 shell‐characters scored for 48 species, and multiple searches were conducted using equal and implied weighting. Two new monophyletic clades are defined, Multiplicata and Pauciplicata. The first includes Dietotenhosen, Ckaraosippur, Zygochlamys, Moirechlamys (South America), the North‐West Pacific Azumapecten, and the North‐East Pacific Chlamys hastata. Pauciplicata is represented by Chokekenia (Patagonia, Argentina), Laevichlamys (tropical Atlantic and Indo‐Pacific), Semipallium (Indo‐Pacific), Swiftopecten (South America and North Pacific), and Jorgechlamys + Reticulochlamys (Patagonia, Argentina). All of these genera are monophyletic except for the paraphyletic Jorgechlamys. The oldest documented occurrence of the tribe is Semipallium foulcheri from the lower Oligocene, a derived taxon that pushes the divergence time of basal genera to the Eocene–Oligocene boundary, generating ghost lineages in all clades, except Jorgechlamys + Reticulochlamys. Pauciplicata and Multiplicata diverge in the early history of the tribe, at the Eocene–Oligocene boundary. Future analyses are necessary to gain a better understanding of the taxonomic arrangement of this poorly understood tribe. Further insights into the relationships of its deepest nodes may well resolve many ghost lineages.

Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach

BackgroundIn zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner.ResultsUsing the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories.ConclusionsUsing high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.

Diversity of marine fungi associated with wood baits in the estuary Ria de Aveiro, with descriptions of Paralulworthia halima, comb. nov., Remispora submersa, sp. nov., and Zalerion pseudomaritima, sp. nov.

ABSTRACT Lignicolous marine fungi are a particular group of microorganisms that are typically found in mangroves, salt marshes, and estuaries, normally associated with driftwood or submerged wood. During investigations of lignicolous fungi occurring in the estuary Ria de Aveiro, Portugal, wood baits were submerged in a marina for 1 year. Seventeen distinct marine fungal species were identified, with the most abundant taxa belonging to the family Lulworthiaceae. Through single- and multilocus phylogenies based on sequences of the internal transcribed spacer (ITS) region and large subunit (28S) and small subunit (18S) of the ribosomal RNA gene cluster in combination with morphological and physiological data, we describe Remispora submersa, sp. nov., and Zalerion pseudomaritima, sp. nov., as novel species. Additionally, we propose that Papulaspora halima, a species whose taxonomic placement has been somehow confusing, be transferred to the genus Paralulworthia as Paralulworthia halima.

A new species, a new combination, and a new record of Crossotarsus Chapuis, 1865 (Coleoptera, Curculionidae, Platypodinae) from China.

This study describes a new species, Crossotarsus beaveri Lai & Wang, sp. nov., designates a new combination, C. brevis (Browne, 1975, comb. nov. from Platypus Herbst, 1793), and notes a new record, C. emorsus Beeson, 1937, from China. Genetic data from four genes indicate that the new species and C. brevis form a clade clustered with other Crossotarsus species. Molecular phylogeny and morphological characters support their taxonomic placement.

Encyonopsis indonesica sp. nov. (Bacillariophyceae, Cymbellales), a new diatom from the ancient lake Matano (Sulawesi, Indonesia).

A new species, Encyonopsis indonesica, is described from the ancient lake Matano, Sulawesi island, Indonesia. The morphology of this species was studied by means of light and scanning electron microscopy. E. indonesica has a remarkable valve ultrastructure. The valve surface is ornamented with numerous longitudinal siliceous ribs and siliceous verrucae. Valve face delineated from the mantle by a thickened marginal ridge. Raised sterna border the raphe branches. Raphe is distinctly undulate with distal ends hooked strongly to the ventral side. The only similar species to E. indonesica is Amphora dissimilis described from New Caledonia. Comparison of both taxa is given and A. dissimilis is transferred to Encyonopsis. The taxonomic placement of both taxa is evaluated, and the phenomenon of external siliceous ornamentation is discussed.

Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae.

The genus Sirolpidium (Sirolpidiaceae) of the Oomycota includes several species of holocarpic obligate aquatic parasites. These organisms are widely occurring in marine and freshwater habitats, mostly infecting filamentous green algae. Presently, all species are only known from their morphology and descriptive life cycle traits. None of the seven species classified in Sirolpidium, including the type species, S. bryopsidis, has been rediscovered and studied for their molecular phylogeny, so far. Originally, the genus was established to accommodate all parasites of filamentous marine green algae. In the past few decades, however, Sirolpidium has undergone multiple taxonomic revisions and several species parasitic in other host groups were added to the genus. While the phylogeny of the marine rhodophyte- and phaeophyte-infecting genera Pontisma and Eurychasma, respectively, has only been resolved recently, the taxonomic placement of the chlorophyte-infecting genus Sirolpidium remained unresolved. In the present study, we report the phylogenetic placement of Sirolpidium bryopsidis infecting the filamentous marine green algae Capsosiphon fulvescens sampled from Skagaströnd in Northwest Iceland. Phylogenetic reconstructions revealed that S. bryopsidis is either conspecific or at least very closely related to the type species of Pontisma, Po. lagenidioides. Consequently, the type species of genus Sirolpidium, S. bryopsidis, is reclassified to Pontisma. Further infection trials are needed to determine if Po. bryopsidis and Po. lagenidioides are conspecific or closely related. In either case, the apparently recent host jump from red to green algae is remarkable, as it opens the possibility for radiation in a largely divergent eukaryotic lineage. Citation: Buaya AT, Scholz B, Thines M (2021). Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae. Fungal Systematics and Evolution 7: 223-231. doi: 10.3114/fuse.2021.07.11.

Investigating species boundaries in Colletotrichum

Colletotrichum is one of the most important plant pathogenic genera that is responsible for numerous diseases which can have a profound impact on the agricultural sector. Species delineation is difficult due to a lack of distinctive phenotypic variation. Therefore, in this study three different genomic approaches based on phylogenetic, evolutionary and coalescent-based methods are applied to establish robust species boundaries. The reliability of five different DNA barcodes was also assessed to provide further insights into species delineation. The ITS region can resolve the placement of taxa up to the species complex level. The GAPDH and TUB2 markers are determined to be the most informative for most complexes. However, no single marker could discriminate between species in all complexes, therefore different molecular approaches based on multi-locus datasets are recommended. This is the first study to provide an estimated divergence time for all species complexes in Colletotrichum. The estimated divergence time for species complexes ranged between 4.8 to 32.2 MYA. Based on the high level of congruent results obtained from the different molecular approaches, a new species complex, the Colletotrichum agaves complex is introduced. This complex consists of five taxa which are characterised by the presence of straight or slightly curved conidia with obtuse apices. This study shows that coalescent approaches and multi-locus phylogeny are crucial to establish species boundaries in Colletotrichum. The taxonomic placement of three singleton taxa Colletotrichum axonopodi, C. cariniferi and C. parallelophorum is revised. We accept 248 species and provide recommendations regarding species boundaries in the graminicola–caudatum complex.

The Taxonomic Position and Lectotypification of Frullania diversitexta Steph. (Frullaniaceae, Marchantiophyta) and Its Synonyms, with Notes on the Placement of F. ignatovii Sofronova, Mamontov & Potemkin

Frullania diversitexta Steph. currently occupies its own subgenus, subg. Diversitextae (Kamim.) S.Hatt., although its taxonomic placement is somewhat enigmatic. The habit of the species, as well as the position and shape of the lobules, are morphologically comparable to species in subg. Diastaloba Spruce and subg. Frullania Spruce, whereas its tuberculate perianth ornamentation is reminiscent of species in subg. Trachycolea Spruce. Here, molecular sequence data resolves F. diversitexta within subg. Trachycolea in a relationship with F. plana Sull. (sect. Planae R.M.Schust.). Frullania diversitexta and F. plana have a similar branching pattern, leaf lobe shape, leaf cell areolation, stylus, lobule position, underleaf shape and primary branch appendages that often have two saccate lobules. Differences in their lobule shape, sexuality, position of the gynoecia and perianth ornamentation, however, decidedly warrant the placement of F. diversitexta in its own section, sect. Diversitextae (Kamim.) J.J.Atwood, Vilnet & Mamontov, stat. nov. Lectotypes are designated for F. diversitexta and its three synonyms: F. abducens Steph., F. sendaica Steph. and F. tosana Horik. (replaced synonym of F. tenella Steph., hom. illeg.). Frullania ignatovii Sofronova, Mamontov & Potemkin, having obovoid, skull shaped lobules with an unusual bilabiate mouth, is also resolved within subg. Trachycolea, in a sister relationship with F. davurica Hampe and F. jackii Gottsche.

Phylogenetic relationships of the poorly known treefrog Boana hobbsi (Cochran amp; Goin, 1970) (Anura: Hylidae), systematic implications and remarks on morphological variations and geographic distribution.

Boana hobbsi is a poorly known hylid frog currently placed within the Boana punctata group. Yet, morphological, ecological and bioacoustic traits do not support this placement, with no molecular data being available to date to test this hypothesis. Based on newly collected mitochondrial DNA sequences, morphological data review and field observations, we provide new insight into the phylogenetic relationships, morphological variations and geographic distribution of B. hobbsi. Our findings reveal that B. hobbsi is nested (with strong support) within the Boana benitezi group, recovering once more a polyphyletic Boana punctata group. Supported by this new genetic, morphological and ecological evidence, we propose a new taxonomic arrangement which includes B. hobbsi as a member of the Boana benitezi group. Furthermore, we emphasize the importance of conducting biological inventories in remote Amazonian areas, where many taxonomic and geographic knowledge gaps persist with regards to Amphibian diversity.

The skeletal remains of the euryhaline sclerorhynchoid †Onchopristis(Elasmobranchii) from the ‘Mid’-Cretaceous and their palaeontological implications

AbstractWe present the first known cranial remains of the fossil batoid †Onchopristis numidus. Based on two exceptionally well-preserved specimens collected from the ‘Kem Kem Beds’ (Albian–Cenomanian), south-east Morocco, an almost complete description of the rostral and cranial portions of the genus †Onchopristis is provided, together with new observations regarding the development and arrangement of the rostral denticle series for this genus. The comparison between the rostrum length of the specimens of †O. numidus with those of extant pristids, reveals a relatively large batoid species with an estimated total length between two and four metres. Overall, the cranial morphology of †Onchopristis resembles that of other sclerorhynchoids. Its robust hypertrophied rostrum, with the characteristic wood-like mineralization covering the inner layer of tessellate cartilage at the centre of the rostrum, in addition to the thick lateral layers of densely porous cartilage on the sides of the rostral cartilages, resembles that observed in †Ischyrhiza and †Schizorhiza, and differentiates †Onchopristis from other sclerorhynchoids (e.g. †Libanopristis, †Micropristis and †Sclerorhynchus). Aiming to determinate the phylogenetic relations of †Onchopristis within sclerorhynchoids, a cladistic analysis was carried out based on the remains described here; its results suggest a new taxonomic arrangement within the sclerorhynchoids.