Phylogenetic signal in characters from Aristotle’s History of Animals

The influential Greek philosopher Aristotle (384-322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix from Aristotle’s Historia animalium and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia Linnaeus, 1758). This study suggests that even though taxonomy was obviously not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

Two new species of Ageniella Banks, 1912 (Hymenoptera: Pompilidae) from Brazil and updated keys

Ageniella Banks, 1912 is a paraphyletic group exclusive to the Nearctic and Neotropical regions. The genus has a remarkable morphological diversity among species and strong sexual dimorphism, hampering taxonomic studies of it. Herein, we add two new species to the Neotropical fauna of Ageniella: A. caerulea sp. nov. belonging to the subgenus Ameragenia and A. ruschi sp. nov. belonging to the subgenus Priophanes; both species are described and illustrated. A brief discussion of subgeneric characters and an updated taxonomic key to the species of Ageniella known from Brazil are provided.

Classifications of Iris L. genus at the biological and molecular levels as a basis for modern phylogenetic studies

Aim. To analyze and summarize literature data on the state of classification and taxonomy of Iris genus plants of Iridaceae family.Results and discussion. The genus Iris L. is one of the largest species of Iridaceae Juss family, which includes 1,800 species of 80 genera. Despite the fact that plants are very common as ornamental plants, there is currently no single classification for both horticultural and wild species of Iris genus. Various classifications and systems of irises have been proposed, the main difference between them is related to the understanding of the genus scope. The taxonomy of Iris genus underwent dramatic changes in the last century, especially in recent decades after the introduction of molecular methods. This paper deals with the analysis of current literature data on the existing classifications of Iris genus plants, the correspondence between taxonomic studies and the results of recent molecular studies. The data presented summarize the traditional classifications according to Rodionenko and Matthew, and also describe modern achievements in phylogenetic studies of this genus using functional genomic studies, involving molecular markers in irises. Conclusions. The data analyzed and summarized in the article can be useful for solving issues of taxonomy, phylogeny, genetics and practical problems of selection of plants of Iris genus; in addition, they will contribute to a more appropriate use of the Iris raw material in practical pharmacy.

Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov.

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.

Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations

Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based methods, offering great complementarity with microscopy. Metabarcoding approaches have been more commonly used over the last years, with a continuous increase in the amount of data generated. Depending on the researchers and the way they assigned barcodes to species (bioinformatic pipelines and molecular reference databases), the taxonomic assignment obtained for HTS DNA reads might vary. This is also true for traditional taxonomic studies by microscopy with regular adjustments of the classification and taxonomy. For those reasons (leading to non-homogeneous taxonomies), gap-analyses and comparisons between studies become even more challenging and the curation processes to find potential consensus names are time-consuming. Here, we present a web-based application (Phytool), developed with ShinyApp (Rstudio), that aims to make the harmonisation of taxonomy easier and in a more efficient way, using a complete and up-to-date taxonomy reference database for freshwater microalgae. Phytool allows users to homogenise and update freshwater phytoplankton taxonomical names from sequence files and data tables directly uploaded in the application. It also gathers barcodes from curated references in a user-friendly way in which it is possible to search for specific organisms. All the data provided are downloadable with the possibility to apply filters in order to select only the required taxa and fields (e.g. specific taxonomic ranks). The main goal is to make accessible to a broad range of users the connection between microscopy and molecular biology and taxonomy through different ready-to-use functions. This study estimates that only 25% of species of freshwater phytoplankton in Phytobs are associated with a barcode. We plead for an increased effort to enrich reference databases by coupling taxonomy and molecular methods. Phytool should make this crucial work more efficient. The application is available at https://caninuzzo.shinyapps.io/phytool_v1/

Taxonomic studies on the genus Isotrema (Aristolochiaceae) from China III: I. pseudohei, a new species from Yunnan, Southwest China

Isotrema pseudohei, a new species from Yunnan, Southwest China, is described and illustrated. It is morphologically similar to I. hei and I. moupinense, but differs from the former in the colour of flower and throat, the size of throat and the shape of gynostemium lobes, and from the latter in the shape of lamina and gynostemium lobes.

Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species

Historically, the diving duck, Baer’s Pochard (Aythya baeri) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of A. baeri has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between A. baeri and the other three Aythya mitochondrial genomes. Among 13 protein-coding genes of the four Aythya species, the fastest-evolving gene was ATP8 while the slowest-evolving gene was COII. Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows: Dendrocygna was an early diverging lineage that was fairly distant from the other ingroup taxa; Cygnus, Branta, and Anser were clustered into one branch that corresponded to the Anserinae subfamily; and Aythya, Asarcornis, Netta, Anas, Mareca, Mergus, Lophodytes, Bucephala, Tadorna, Cairina, and Aix were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other Aythya species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.

Padrões morfológicos na venação alar de espécies de Tetragona Lepeletier & Serville, 1828 do grupo clavipes (Hymenoptera: Apidae: Meliponini)

Tetragona Lepeletier & Serville, 1828 (Hymenoptera: Apidae) is a genus of stingless bees widely distributed in Brazil. It has 15 species distributed in the Neotropics, from Mexico to Uruguay, nine of which are found in Brazil. However, Tetragona elongata (Lepeletier & Serville, 1828), a species known only from the Southeast region and which had been synonymized with Tetragona clavipes (Fabricius, 1804), was revalidated without any justification. The aim of this study was to test whether the morphometrics analysis of the wings is efficient in the diagnosis of the species of this genus, in addition to testing the validity of the revalidation mentioned above. This technique was applied by accessing the right forewings of 660 workers of T. clavipes, T. elongata e T. quadrangula (Lepeletier, 1836), from five Brazilian collections. For the geometric morphometric analysis, 12 landmarks were selected. The software MorphoJ version 1.6 was used to do Discriminant Function analysis (1000 replications) and Canonical Variation Analysis (CVA). Between T. clavipes and T. elongata, there was a 100% variance between species (canonical variation analysis), suggesting that it may be an indication of speciation. Even though T. elongata has been revalidated, it still has overlapped with T. clavipes, which indicates to be the same species. Taxonomic studies are needed to synonymize them.

The tongue biofilm metatranscriptome identifies metabolic pathways associated with halitosis and its prevention

Halitosis is an oral condition caused by an increase in the concentration of volatile sulfur compounds (VSCs), such as methyl mercaptan and hydrogen sulfide, generated as a consequence of bacterial metabolism on the tongue biofilm. Microbial communities on the tongue of halitosis patients have been studied by bacterial culture, 16S rRNA taxonomic studies and metagenomics. However, there are currently no reports on the microbial gene-expression profiles. In this study, we performed RNAseq of tongue coating samples from control individuals and halitosis patients with different levels and composition of VSCs, as determined by gas chromatography. In this metatranscriptomic study, the activity of Streptococcus, Veillonella and Rothia species was associated with halitosis-free individuals while Prevotella, Fusobacterium and Leptotrichia species were associated with halitosis. Although methyl mercaptan is considered an indicator of halitosis, the metatranscriptome of patients in which only this VSC was present in elevated levels was similar to that of halitosis-free individuals. Veillonella dispar, Streptococcus parasanguinis and Rothia mucilaginosa were over-represented in halitosis-free communities in comparison to the rest of the groups, suggesting that these species could be used as a halitosis-free biomarkers. In contrast, the abundance of Prevotella shahi and Fusobacterium nucleatum were significantly higher when hydrogen sulfide concentration was over the established halitosis-threshold, making these species putative halitosis biomarkers. Finally, gene expression profiles showed a significant over-expression of genes involved in L-cysteine and L-homocysteine synthesis in halitosis-free individuals and an over-expression of genes responsible for cysteine degradation into hydrogen sulfide in halitosis patients. In addition, nitrate reduction into nitrite was also over-expressed in halitosis-free patients. In conclusion, halitosis was associated with communities that degrade amino acids and reduce sulfide, whereas tongue communities that produce L-cysteine from hydrogen sulfide and that reduce nitrate were associated with the absence of halitosis. The latter could provide new strategies to treat this condition.