Molecular Phylogenetic Research Articles

Multigene phylogenetics of Sargassum (Phaeophyceae) revealed low molecular diversity in contrast to high morphological variability in the NE Atlantic Ocean.

Sargassum species play a key role in habitat formation in tropical and subtropical regions; however, species identification has been hampered by the phenological plasticity exhibited in response to environmental conditions and life history. Molecular phylogenetics has challenged taxa circumscriptions and proven critical in delimiting species in this genus. Yet, the Atlantic species of Sargassum remain poorly understood, and recent studies have shown low molecular diversity between the species in the NW Atlantic. Here, we expand the taxon sampling to the NE Atlantic to assess the diversity of Sargassum in the Atlantic basin, based on a comprehensive morphological and multigene approach. We selected genes commonly used in delineating species in this genus (ITS2, rbcLS, cox3, mtsp) and explored additional markers (cox2, nad6, psbC, clpC, atpB) to infer the phylogenetic relationships between the morphospecies observed in the NE Atlantic. Phylogenetic analyses using single-gene and multigene alignments including 185 new sequences confirmed the low molecular diversity and supported the distinction of a single clade in Sargassum section Sargassum of N Atlantic benthic species. In contrast, morphological analysis resulted in the identification of 10 species and three new morphospecies that we described here but opt not to equate to species until further molecular evidence is available. Our results were congruent with previous findings from the NW Atlantic and highlight the morphological and ecological diversity of Sargassum in the Atlantic. These results suggest a recent colonization and incipient speciation of Sargassum in the Atlantic basin and showcase the need of further high-throughput analyses.

Biofertilizer based on <i>Agrobacterium </i>as a key to food security

Background: The concept of food security is contingent upon the fulfillment of two fundamental requirements: physiological and socioeconomic. The former comprises providing sustenance that is both safeguarded and enhanced in line with people’s nutritional needs and priorities, whereas the latter includes the mechanisms by which these needs are supplied. The objective is to ensure a state of robust and healthy well-being. As a sustainable solution, biofertilizers play a pivotal role in addressing the challenges of food security. Biofertilizers represent a cost-effective and environmentally friendly solution, with the potential to enhance soil productivity through nitrogen fixation. They also enhance crop yield by increasing the concentration of nutrients. Access to functional foods derived from biofertilizer-enhanced yields may contribute to improved dietary diversification and overall well-being. Objective: The objective is to isolate and screen the most active nitrogen-fixing bacterium as a basis to a new biofertilizer. Methods: The isolation of nitrogen-fixing bacteria was conducted using the soil sowing technique. The selection of nitrogen-fixing bacteria was based on their morphophysiological characteristics. Bacterial growth was evaluated by viable cell count. Cultivation of the selected bacterium occurred in both flasks (on a shaker) and a bioreactor to compare growth conditions. The stimulatory effect of the selected bacterium on seed germination was assessed based on the final germination rate. The selected bacterium identified through molecular taxonomy. Results: A total of 100 pure cultures were isolated, from which nitrogen-fixing bacteria were selected. The cultivation conditions for these bacteria were optimized regarding pH, temperature and process duration in a flask on a shaker. Strain NB4 exhibited the most favorable development under optimal settings. Additionally, cultivation parameters for this strain were optimized in a laboratory bioreactor. Notably, a bacterial liquid culture water solution comprising 1.5% strain NB4 facilitated complete germination of wheat (Triticum aestivum L.), seeds and produced high-quality sprouts. The 16S rRNA gene sequence of strain NB4 was submitted to the GenBank database under accession number MT670424.1, identifying it as Agrobacterium Pusense RP 1. Conclusion: This research aimed to develop an effective biofertilizer to tackle the pressing issue of food security. The project’s cornerstone was Agrobacterium pusense RP 1, nitrogen-fixing strain isolated and identified through rigorous research. Keywords: Isolation and identification of nitrogen-fixing bacteria, cultivation in bioreactor, germination of wheat seeds, Agrobacterium pusense.

Biology, morphometric and integrative taxonomy of litchi fruit borer, Conopomorpha sinensis Bradley, 1986: A major pest of litchi (Litchi chinensis Sonn.)

Abstract Conopomorpha sinensis (Lepidoptera: Gracillariidae), commonly known as the litchi fruit borer, is a devastating pest of litchi, leading to substantial economic losses in fruit production. The present study was incepted to supplement updated information on biology, morphometrics, integrative taxonomy, and phylogenetic analysis of C. sinensis. The duration of developmental stages such as egg, larval, pre-pupal, pupal, male and female adult lasts for 3.45 ± 1.13, 11.10 ± 2.52, 2.05 ± 0.51, 5.85 ± 0.88, 5.55 ± 1.00, and 9.00 ± 1.12 days, respectively. The average fecundity was 33.10 ± 6.84 eggs/female. The head capsule width for five larval instars was 0.11 ± 0.01, 0.18 ± 0.02, 0.34 ± 0.01, 0.58 ± 0.04, and 0.64 ± 0.06 mm, respectively. Phylogenetic analysis revealed distinct species-groups formed by C. sinensis with other fruit borer species considered (C. cramerella, C. litchiella Bradley, and Thaumatotibia batrachopa (Meyrick)). Understanding the life cycle of C. sinensis and its correct identification is crucial for targeted pest control strategies. Traditional and molecular taxonomy assist in rapid and accurate species identification and understanding of the evolutionary relationships among Conopomorpha species.

Prognostic nomograms for young breast cancer: A retrospective study based on the SEER and METABRIC databases.

Young breast cancer (YBC) is a subset of breast cancer that is often more aggressive, but less is known about its prognosis. In this study, we aimed to generate nomograms to predict the overall survival (OS) and breast cancer-specific survival (BCSS) of YBC patients. Data of women diagnosed with YBC between 2010 and 2020 were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. The patients were randomly allocated into a training cohort (n = 15,227) and internal validation cohort (n = 6,526) at a 7:3 ratio. With the Cox regression models, significant prognostic factors were identified and used to construct 3-, 5-, and 10-year nomograms of OS and BCSS. Data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database were used as an external validation cohort (n = 90). We constructed nomograms incorporating 10 prognostic factors for OS and BCSS. These nomograms demonstrated strong predictive accuracy for OS and BCSS in the training cohort, with C-indexes of 0.806 and 0.813, respectively. The calibration curves verified that the nomograms have good prediction accuracy. Decision curve analysis demonstrated their practical clinical value for predicting YBC patient survival rates. Additionally, we provided dynamic nomograms to improve the operability of the results. The risk stratification ability assessment also showed that the OS and BCSS rates of the low-risk group were significantly better than those of the high-risk group. Here, we generated and validated more comprehensive and accurate OS and BCSS nomograms than models previously developed for YBC. These nomograms can help clinicians evaluate patient prognosis and make clinical decisions.

Genome sequencing in the management of myelodysplastic syndromes and related disorders.

Myeloid neoplasms originate from the clonal proliferation of hematopoietic stem cells, which is driven by the acquisition of somatic genetic mutations. Within these disorders, myelodysplastic syndromes (MDS) are specifically characterized by morphologic abnormalities (dysplasia) and impaired maturation of myeloid precursors (ineffective hematopoiesis), resulting in peripheral blood cytopenia. Several studies have advanced the field of MDS, with a few landmark papers leading to a paradigm shift, opening new avenues of research and enabling a molecular revolution. These seminal papers include the first description of the 5q- syndrome, the identification of somatic mutations of TET2 in myeloid neoplasms, the detection of common pathway mutations in the splicing machinery, and the discovery of clonal hematopoiesis. The somatic genomic landscape of MDS is now well-defined. Genes that are recurrently mutated include epigenetic regulators, as well as genes of RNA splicing machinery, transcription regulation, DNA repair control, cohesin complex, and signal transduction. Furthermore, several disorders with a germline genetic predisposition to MDS have been identified, collectively accounting for up to 15% of all MDS cases. Genomic profiling can significantly improve the diagnostic approach to MDS, allowing the identification of distinct nosologic entities such as SF3B1-mutant or TP53-mutant MDS. The Molecular International Prognostic Scoring System for MDS (IPSS-M) has already proven to be a valuable tool for individualized risk assessment and treatment decisions. In addition, the recently developed molecular taxonomy of MDS will likely facilitate the implementation of precision medicine approaches for these disorders. This will necessitate the establishment of specialized infrastructures within public health systems, involving close collaboration between healthcare institutions, academia, and the life sciences industry.

Whole-genome-based taxonomy as the most accurate approach to identify Flavobacterium species.

The genus Flavobacterium comprises a diversity of species, including fish pathogens. Multiple techniques have been used to identify isolates of this genus, such as phenotyping, PCR genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using Average Nucleotide Identity (ANI) and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and F. psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.

Molecular phylogeny reveals a new genus and species of freshwater mussel (Bivalvia, Unionidae, Gonideinae) from Jiangxi, China

Freshwater mussels of the tribe Gonideini (Bivalvia: Unionidae: Gonideinae) constitute one of the most taxonomically diverse groups and serve as keystone species in riverine and lacustrine ecosystems across East Asia. A new genus and species of Gonideini (Bivalvia: Unionidae) is described from Jiangxi, China, as Pseudopostolata angulagen. et sp. nov. based on an integrative analysis of shell morphology and molecular data. The validity of the new genus and species is supported by distinct conchological features: a short, rounded anterior; a long, wide posterior; a slightly downward-curved dorsal margin; and a distinctly obtuse angle at the center of the posterior margin. The multi-locus (COI + 16S rRNA + 28S rRNA) phylogeny showed that the species formed a monophyletic group in the tribe Gonideini of the subfamily Gonideinae. Pseudopostolata angulagen. et sp. nov. is identified as the sister group to a clade comprising the genera Postolata, Cosmopseudodon, Obovalis, Ptychorhynchus, Parvasolenaia, and Koreosolenaia. We emphasize the significant morphological convergence in freshwater mussels, particularly within Gonideini, highlighting the necessity of an integrated taxonomic approach for accurate generic classification of this group.

Pollen morphology and fruit anatomy of the enigmatic monotypic genus Dicranocarpus (Coreopsideae, Asteraceae)

Dicranocarpus is a monotypic genus endemic to the Chihuahuan Desert with atypical attributes among species of tribe Coreopsideae. Phylogenetic position of Dicranocarpus parviflorus has been controversial. A molecular phylogeny showed that the taxon was closely related to Dahlia; however, further analyses with a wider sampling of Dahlia, also including Hidalgoa, identified the genus in a more distant clade. The objective of this study is to gather anatomical attributes from the cypselae as well as palynological characters along with macromorphology to determine whether Dicranocarpus shares characters with these genera in Coreopsideae. Our results show that although the pollen of D. parviflorus does not possess attributes that distinguish it from the rest of the tribe Coreopsideae, they were useful to confirm its membership in the tribe. The cypselae anatomy identified that D. parviflorus has characters of taxonomic value that differentiate this species from the rest of the Coreopsideae. The three most significant novel characters in Dicranocarpus were in the outer mesocarp, consisting of tracheoidal-like cells forming irregular rows up to 250 μm in length, an aerenchyma in the middle mesocarp, and the lack of phytomelanin and calcium oxalate crystals. Furthermore, the results of the phytomelanin patterns in the studied taxa highlight the need for further anatomical studies of the cypselae to fully understand the evolution of phytomelanin deposition in the tribe Coreopsideae and even in the Heliantheae Alliance. Macromorphological, palynological and anatomical attributes of the cypsela in Dicranocarpus were not shared with Dahlia. Moreover, the sexual condition of the disc and ray florets shared with Hidalgoa has evolved independently in lineages of Asteraceae.

Do morphometric data improve phylogenetic reconstruction? A systematic review and assessment

BackgroundIsolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses.ResultsPhylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets.ConclusionsAn exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

Hidden in the plains: Two new extra‐andean species of Euathlus (Mygalomorphae, Theraphosidae) from Argentina with comments on their sexual behaviour

AbstractTwo new species of Euathlus (Verhandlungen der Kaiserlich‐Königlichen Zoologisch‐Botanischen Gesellschaft in Wien, 1875, 25, 125) from Argentina are described. Euathlus ameghinoi sp. n. and Euathlus ventus sp. n. are the first records for the Patagonian Steppe. Here we used mitochondrial DNA (cox1) to perform the first molecular phylogeny of some representatives of the genus. In addition, we present the first description of the sexual behaviour of the genus. Both molecular and cladistic morphological analysis showed the genus Euathlus as monophyletic, and new species were recovered as sister groups. New species show new morphological variations of typical characters for the genus (e.g. tibial apophyses and palpal organs).

Molecular phylogeny and cryptic morphology: A combined approach to taxonomic novelties in Polycarpaea (Caryophyllaceae) from Vietnam.

Three new species of Polycarpaea from Vietnam, Polycarpaea vanphongensis V.T. Tran, H.T. Truong & N.V. Binh, Polycarpaea chungana V.T. Tran, H.T. Truong & N.V. Binh, Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh are described and illustrated based on evidence of molecular sequence data from two markers (ITS1-5.8S-ITS2 and rps16) and combined morphological characteristics. Polycarpaea vanphongensis is closely related to Polycarpaea gaudichaudi Gagnep., Polycarpaea arenaria (Lour.) Gagnep., Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh but differs by its stem glabrous, leaf ovate to elliptic, glabrous, ovary oblong ovoid, base obtuse, apex attenuate, capsule oblong void, 3.8 mm long. Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh differs from the three species mentioned above by its stem being densely villous, leaf spathulate, ciliate, ovary ovoid, base acute, apex obtuse, capsule ovoid, 1.2 mm long. Polycarpaea chungana V.T. Tran, H.T. Truong & N.V. Binh is most similar to Polycarpaea lignosa Gagnep., but differs in having leaf oblong or linear, sparse ciliate, sepal and petal apex deeply concaved or slightly bifid, ovary ovoid, ovoid, 0.8-1.0 mm long. Furthermore, the achievements of analysis using molecular data on the systematic positions of 7 other species are results that have not been in previous molecular analyses.

Half of the Diversity Undescribed: Integrative Taxonomy Reveals 32 New Species and a High Cryptic Diversity in the Scopariinae and Crambinae of the Philippines (Lepidoptera: Crambidae)

The Crambinae and Scopariinae (Lepidoptera: Crambidae) of the Philippines are revised here using DNA barcoding and morphology. In the Scopariinae, 20 species are reported from the Philippines, of which 14 are described as new: Scoparia abo sp. n., S. aenea sp. n., S. bicornuta sp. n., S. fulvida sp. n., S. ifugaoensis sp. n., S. luzonensis sp. n., S. masiita sp. n., S. negrosensis sp. n., S. tenuispina sp. n., Eudonia penicula sp. n., Micraglossa kianganensis sp. n., and Micraglossa polisensis sp. n. In the Crambinae, 42 species are found in the Philippines, with half of them described here as new: Calamotropha anacantha sp. n., Calamotropha philippinensis sp. n., Catoptria philippinensis sp. n., Culladia pseudoscoparia sp. n., Gargela aculea sp. n., Gargela acutibrachium sp. n., Gargela bidentella sp. n. , Glaucocharis altissima sp. n., Glaucocharis hamulus sp. n., Glaucocharis kayumanggi sp. n., Glaucocharis kabundukanis sp. n., Glaucocharis negrosensis sp. n., Glaucocharis uncusellus sp. n., Glaucocharis sungay sp. n., Metaeuchromius makintabus sp. n., Metaeuchromius rizali sp. n., Microchilo bundoki sp. n., Microchilo cebuano sp. n., Microchilo imminutela sp. n., and Microchilo spinosus sp. n. Scoparia philippinensis (Hampson, 1917) and Metaeuchromius micralis (Hampson, 1919) comb. nov. as well as female genitalia of Calamotropha obliterans (Walker, 1863) are redescribed, and first descriptions of male genitalia of Glaucocharis clytia (Błeszyński, 1966) and Calamotropha unicolorellus (Zeller, 1863) are provided. Euchromius brunnealis (Hampson, 1919) syn.nov. is synonymized with Metaeuchromius micralis comb. nov. Culladia tonkinella (Walker, 1865), Eudonia barbipennis (Hampson, 1897), Gargela minuta Song, Chen & Wu, 2009, Gargela polyacantha Li, 2019, Gargela xanthocasis (Meyrick, 1897), Glaucocharis lathonia (Błeszyński, 1966) and Glaucocharis clytia (Bleszynski, 1966) are reported here for the first time from the Philippines. DNA barcodes of 359 specimens indicate a perfect match with the Molecular Operational Taxonomy Unit (“MOTU”) in 45 of the 66 morphospecies (68%), while nineteen of the morphospecies included one or more MOTUs, and three MOTUs were shared among more than one morphospecies. Forty MOTUs represented by females only suggest further unrecognized species in these groups. An apparent endemism rate of 95% is observed in mountain-dwelling Scopariinae, while the Crambinae show a lower endemism rate of roughly 50% presumably due to the occurrence of many lowland species. Further expeditions to undersampled islands and mountains will surely reveal additional species.

Lamyropsis macracantha (Asteraceae, Cardueae) is a Cirsium based on morphology and nuclear ITS/ETS sequence data

We apply both morphology and molecular systematics approaches to resolve the dispute over the generic affiliation of Lamyropsis macracantha. Based on observations of herbarium specimens (including type material) and living plants, as well as phylogenetic analyses based on ITS/ETS sequences, we demonstrate that Lamyropsis macracantha is a member of Cirsium.

Is it all Phacelia pinnatifida? Molecular delimitations and taxonomic revision of Phacelia sect. Glandulosae in South America based on ddRADseq

AbstractPhacelia sect. Glandulosae, with ca. 62 taxa, is the most diverse of the 11 sections of the genus Phacelia (Hydrophyllaceae). The family is largely restricted to North and Central America, but the genus Phacelia has an amphitropical distribution with nine species reported from western South America, five of which have been assigned to P. sect. Glandulosae. These species are found in arid to semi‐arid Andean habitats between 1000 and 5000 m a.s.l. Species delimitation has long been confounded for this plant group in South America by some degree of taxonomic chaos – lack of typifications, dozens of synonyms, different names used for the same taxon between different countries – and poor representation in molecular phylogenies. Here, we try to improve our understanding by employing a ddRADseq strategy to investigate phylogenetic relationships of all South American representatives of P. sect. Glandulosae based on a total of 33 sampled specimens. Both maximum likelihood and species tree inference analyses of the ddRADseq data resulted in a well‐resolved topology. All five species currently recognized in P. sect. Glandulosae in South America form a highly supported monophylum including P. nana, previously considered as belonging to P. sect. Euglypta. However, the currently recognized morphospecies form a clade with very short branch lengths indicating coalescence processes at the level of population, except for P. artemisioides, which is clearly sister to the rest. Additionally, different morphospecies and ecotypes are largely retrieved as poly‐ and/or paraphyletic. Based on these results and on re‐evaluation of the morphological characters traditionally used to delineate species within P. sect. Glandulosae, we argue that these characters are of limited diagnostic value. We recommend recognizing only two South American species within this section: polymorphic P. pinnatifida and its closely related sister species P. artemisioides. A revised formal taxonomy is provided.

Genomics and evolutionary analysis of Chlorella variabilis-infecting viruses demarcate criteria for defining species of giant viruses.

Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of Chlorella variabilis, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date (>400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2-3 strain of C. variabilis (OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of Nucleocytoviricota revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.IMPORTANCEChloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of Chlorella-like green algae. They are host-specific, and some isolates can only replicate within a single strain of Chlorella variabilis. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.

Classes and phyla of the kingdom Fungi

AbstractFungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Two in one: DNA taxonomy of Acronicta major complex (Lepidoptera: Noctuidae) reveals previous misidentifications and faunal connection in East Asia

The Korean populations of Acronicta major (Bremer, 1864) were reexamined with genital morphology and DNA barcodes. They were turned out to be a mixture of the true A. major and another species, Acronicta gigasa Chang, 1991. The alleged aberration of A. major, ab. anaedinella Strand, 1916, is associated with A. gigasa. The distributional range of A. gigasa is expanded to include Korea and southern China. A possible faunistic belt crossing Korea, southern China and Taiwan is discussed with exemplar lepidopterans. The divergence patterns of A. major and A. gigasa in East Asia are hinted by our estimation of their COI genetic distances. Our finding raises an issue of reconsideration in the hitherto-known information on the distribution, host-range and pest status of A. major in Korea.

Using active learning methodologies to teach sequence analysis and molecular phylogeny.

The great development of high-throughput molecular biology techniques and the consequent generation of massive data have made Bioinformatics essential for undergraduate Bioscience students. The importance of this scientific discipline is evidenced by the huge number of specialized publications, tools, and databases available. Training in Bioinformatics equips undergraduates with transferable skills that can be applied in all fields of Biology, such as programming abilities, data analysis, database management, biological knowledge, statistics, problem solving, and interdisciplinary collaboration. Over the past decade, there has been a notable increase in the number of higher education institutions worldwide that have adopted a competency-based curricula. This approach places a significant emphasis on the actions and skills that students are expected to develop, rather than merely focusing on the information, they are required to memorize. In this educational context, the use of active learning strategies has been demonstrated to enhance student comprehension and competency development. This paper describes the implementation of an active learning approach in a hands-on lesson performed by undergraduate students of Biology at the University of Malaga (Spain). Its main objective is to introduce students to molecular databases and information search systems on genes, proteins, and phylogeny. This is achieved within the framework of a smart campus, which integrates technological and sustainable resources to promote a positive and productive learning environment for the university community. This work presents the content and procedure of this practical activity, as well as the evaluation method and the results of a student survey to assess their opinions.

Integrative taxonomy of Tethya: description of four new species based on morphology, phylogeny and microbiome diversity

The genus Tethya, one of the most iconic groups in the phylum Porifera. includes nearly 100 valid species. Tethya shows a nearly cosmopolitan distribution, and thus this clade could help elucidate global mechanisms of speciation in sponges. Contrasting with many other marine organisms, Tethya peaks in diversity in the temperate region, with only ∼30% of diversity occurring in the tropics. This pattern may however be related to a lack of studies in the tropics, masked by dubious taxonomic identifications. To address this question, we studied new collections from the Western Atlantic (Caribbean and Brazil) and the Northeastern Atlantic, as well as museum material from the Indian Ocean. Combining morphological investigation with molecular phylogenetics and the study of the sponge’s microbial communities, we conclude that four constitute new species that we describe here: Tethya martini Riesgo, Giribet, & Santodomingo, sp. nov.; Tethya simoni Santodomingo, Zea, & Riesgo, sp. nov.; Tethya erici Díez-Vives, Santodomingo, Moles, & Riesgo, sp. nov.; Tethya orioni Kenny, Santodomingo & Riesgo, sp. nov. Some species thought to be widespread (e.g., T. aurantium and T. seychellensis), each represent multiple species with unique geographic distributions. A phylogenetic analysis of Tethya (based on COI and 28S rRNA sequence data) recovered five main clades, which were also characterized by distinct prokaryotic communities. This suggests that microbiomes could be used as a guide for taxonomic identification in Tethya. We finally explored the existence of a phylosymbiotic pattern in sponges at different levels of prokaryotic taxonomic resolution (i.e., at phylum, class, and genus-level analysis of prokaryotes). Remarkably, our analysis revealed high levels of coevolution of Tethya and their associated microbial communities, even when microbiomes were analysed at the genus level. Our findings support the use of an integrative approach to better understand the evolutionary history of sponges. http://zoobank.org/urn:lsid:zoobank.org:pub:54F80E5E-99A4-43CE-BA3A-BCD01E715595

Three new species of the genus ‘Carteria’ (Chlamydomonadales, Chlorophyceae) with the proposal of correct generic names

ABSTRACT ‘Carteria’ is a genus of quadriflagellate chlamydomonadalean green algae, however this genus is not thought to be a monophyletic group. In this study, we investigated nine strains of ‘Carteria’ newly isolated from China by morphological comparisons and molecular phylogeny of 18S rDNA and rbcL genes. Five strains could be identified as existing ‘Carteria’ species. Four strains with clearly different morphology and independent phylogenetic positions compared with the described ‘Carteria’ species were identified as three new species. Since the original type species, Carteria cordiformis, has been recognized as a prasinophyte alga, the generic name Carteria cannot be applied to other species previously assigned to ‘Carteria’. Six ‘Carteria’ species (including three new species) and one Pseudocarteria species of Carteria-Clade I were transferred to the genus Corbierea, and the description of this genus was emended. A new genus, Staurocarteria gen. nov. was proposed for Carteria-Clade II.