Data-specific substitution models improve protein-based phylogenetics.

Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses.

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees.

tvBOT is a user-friendly and efficient web application for visualizing, modifying, and annotating phylogenetic trees. It is highly efficient in data preparation without requiring redundant style and syntax data. Tree annotations are powered by a data-driven engine that only requires practical data organized in uniform formats and saved as one table file. A layer manager is developed to manage annotation dataset layers, allowing the addition of a specific layer by selecting the columns of a corresponding annotation data file. Furthermore, tvBOT renders style adjustments in real-time and diversified ways. All style adjustments can be made on a highly interactive user interface and are available for mobile devices. The display engine allows the changes to be updated and rendered in real-time. In addition, tvBOT supports the combination display of 26 annotation dataset types to achieve multiple formats for tree annotations with reusable phylogenetic data. Besides several publication-ready graphics formats, JSON format can be exported to save the final drawing state and all related data, which can be shared with other users, uploaded to restore the final drawing state for re-editing or used as a style template for quickly retouching a new tree file. tvBOT is freely available at: https://www.chiplot.online/tvbot.html.

Using pose estimation to identify regions and points on natural history specimens.

A key challenge in mobilising growing numbers of digitised biological specimens for scientific research is finding high-throughput methods to extract phenotypic measurements on these datasets. In this paper, we test a pose estimation approach based on Deep Learning capable of accurately placing point labels to identify key locations on specimen images. We then apply the approach to two distinct challenges that each requires identification of key features in a 2D image: (i) identifying body region-specific plumage colouration on avian specimens and (ii) measuring morphometric shape variation in Littorina snail shells. For the avian dataset, 95% of images are correctly labelled and colour measurements derived from these predicted points are highly correlated with human-based measurements. For the Littorina dataset, more than 95% of landmarks were accurately placed relative to expert-labelled landmarks and predicted landmarks reliably captured shape variation between two distinct shell ecotypes ('crab' vs 'wave'). Overall, our study shows that pose estimation based on Deep Learning can generate high-quality and high-throughput point-based measurements for digitised image-based biodiversity datasets and could mark a step change in the mobilisation of such data. We also provide general guidelines for using pose estimation methods on large-scale biological datasets.

DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity.

The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and 'species groups' within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include 'species-complexes' previously considered as a single taxon. Our results revealed the presence of three species groups, 'C. amplexus', 'C. conspicillatus' and 'C. haematopterus' and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.

A refreshed approach to homology-Prioritizing epistemology over metaphysics.

Unease with the inclusion of "sameness" in Owen's definition of homology characterizes a substantial part of the literature on this subject, where this term has acquired an increasingly strict metaphysical flavor. Taken for granted the existence of body features that are "the same," their existence has been explained by appealing to universal laws of form, as the product of common ancestry, or in terms of proximal causes responsible for the emergence of conserved developmental modules. However, a fundamentally different approach is possible, if we shift attention from metaphysics to epistemology. We may reword Owen's statement as follows: organs of different animals, in so far as they can be described as the same despite any difference in form and function, are called homologues. The proposed framework provides an umbrella for both the traditional, all-or-nothing concept of homology, and the less fashionable alternatives of factorial or partial homology, as well as for an extension of homology from form to function. No less attractive is the prospect to handle also ghost homologues, the body parts or organs of which there is non-objective evidence in a given clade, but can nevertheless be represented, in a description that encapsulates some of the traits observable in their extant homologue in the sister clade. Stripped of its different and constraining metaphysical explanations, homology survives as an anchor concept to which different nomadic disciplines and research agendas can be associated.

Creencias implícitas sobre la noción de personas responsables e irresponsables: un estudio mediante el análisis factorial de la taxonomía de términos de personalidad en español / Implicit beliefs about the notion of responsible and irresponsible people: a study through factor analysis of the taxonomy of personality terms in Spanish

Antecedentes: se investiga mediante análisis factorial la estructura dimensional subyacente a las creencias implícitas acerca de dos prototipos: persona responsable e irresponsable. Método: 520 estudiantes universitarios evaluaron el grado de adecuación a estos prototipos de los 50 adjetivos de personalidad de la Taxonomía de términos de personalidad en español (TAX 50) de Iraegui Torralbo y Quevedo-Aguado (2002). Los resultados se analizaron mediante análisis factoriales con rotaciones oblicuas y ortogonales, y método de extracción Análisis de Componentes Principales. Resultados: los análisis factoriales con rotación ortogonal mostraron cuatro componentes independientes que explicaban la estructura subyacente a las creencias sobre los prototipos. El componente que más varianza explicaba era combinación de dos factores de la taxonomía TAX 50: Responsabilidad e Integridad. Conclusiones: desde una aproximación léxica, el método utilizado permite conocer la estructura factorial subyacente a las creencias acerca de prototipos de personas responsables e irresponsables. La metodología utilizada ayuda a investigar la contribución de cada uno de los Cinco Grandes factores de personalidad a la descripción lega de prototipos de personas (AU)

Do we have infraspecific taxa of Salvia macrosiphon Boiss. (Lamiaceae) in Iran?

BACKGROUND: Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. METHODS AND RESULTS: We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno-Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes. CONCLUSIONS: The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.

Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling.

Deep neural networks (DNNs) have been recently proposed for quartet tree phylogeny estimation. Here, we present a study evaluating recently trained DNNs in comparison to a collection of standard phylogeny estimation methods on a heterogeneous collection of datasets simulated under the same models that were used to train the DNNs, and also under similar conditions but with higher rates of evolution. Our study shows that using DNNs with quartet amalgamation is less accurate than several standard phylogeny estimation methods we explore (e.g., maximum likelihood and maximum parsimony). We further find that simple standard phylogeny estimation methods match or improve on DNNs for quartet accuracy, especially, but not exclusively, when used in a global manner (i.e., the tree on the full dataset is computed and then the induced quartet trees are extracted from the full tree). Thus, our study provides evidence that a major challenge impacting the utility of current DNNs for phylogeny estimation is their restriction to estimating quartet trees that must subsequently be combined into a tree on the full dataset. In contrast, global methods (i.e., those that estimate trees from the full set of sequences) are able to benefit from taxon sampling, and hence have higher accuracy on large datasets.

Research on Music Style Classification Based on Deep Learning.

Music style is one of the important labels for music classification, and the current music style classification methods extract features such as rhythm and timbre of music and use classifiers to achieve classification. The classification accuracy is not only affected by the classifier but also limited by the effect of music feature extraction, which leads to poor classification accuracy and stability. In response to the abovementioned defects, a deep-learning-based music style classification method will be studied. The music signal is framed using filters and Hamming windows, and the MFCC coefficient features of music are extracted by discrete Fourier transform. A convolutional recurrent neural network structure combining CNN and RNN is designed and trained to determine the parameters to achieve music style classification. Analysis of the simulation experimental data shows that the classification accuracy of the studied classification method is at least 93.3%, and the classification time overhead is significantly reduced, the classification results are stable, and the results are reliable.

Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies.

BACKGROUND: Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation. OBJECTIVES: This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning. METHODS: We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples. RESULTS: We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects. DISCUSSION: Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.

Use of the proteomic tool MALDI-TOF MS in termite identification.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) has proved effective for the identification of many arthropods. A total of 432 termite specimens were collected in Mali, Cote d'Ivoire, Togo, Senegal, Switzerland and France. Morphologically, 22 species were identified, including Ancistrotermes cavithorax, Amitermes evuncifer, Cryptotermes brevis, Cubitermes orthognathus, Kalotermes flavicollis, Macrotermes bellicosus, Macrotermes herus, Macrotermes ivorensis, Macrotermes subhyalinus, Microcerotermes parvus, Microtermes sp., Odontotermes latericius, Procubitermes sjostedti, Promirotermes holmgreni, Reticulitermes grassei, Reticulitermes lucifugus, Reticulitermes santonensis, Trinervitermes geminatus, Trinervitermes occidentalis, Trinervitermes togoensis, Trinervitermes sp., Trinervitermes trinervoides and Trinervitermes trinervius. Analysis of MALDI-TOF MS spectra profiles from termites revealed that all were of high quality, with intra-species reproducibility and inter-species specificity. Blind testing of the spectra of 389 termites against our updated database with the spectra of 43 specimens of different termite species revealed that all were correctly identified with log score values (LSVs) ranging from 1.65 to 2.851, mean 2.290 ± 0.225, median 2.299, and 98.4% (383) had LSVs > 1.8. This study is the first on the use of MALDI-TOF for termite identification and shows its importance as a tool for arthropod taxonomy and reinforces the idea that MALDI-TOF MS is a promising tool in the field of entomology.

Digital Single-operator Cholangioscopy (DSOC) Improves Interobserver Agreement (IOA) and Accuracy for Evaluation of Indeterminate Biliary Strictures: The Monaco Classification.

BACKGROUND: Visual characteristics seen during digital single-operator cholangioscopy (DSOC) have not been validated. The aim of this 2-phase study was to define terminology by consensus for the visual diagnosis of biliary lesions to develop a model for optimization of the diagnostic performance of DSOC. MATERIALS AND METHODS: In phase 1 (criteria identification), video-cholangioscopy clips were reviewed by 12 expert biliary endoscopists, who were blinded to the final diagnosis. Visual criteria were consolidated into the following categories: (1) stricture, (2) lesion, (3) mucosal features, (4) papillary projections, (5) ulceration, (6) abnormal vessels, (7) scarring, (8) pronounced pit pattern.During the second phase (validation), 14 expert endoscopists reviewed DSOC (SpyGlass DS, Boston Scientific) clips using the 8 criteria to assess interobserver agreement (IOA) rate. RESULTS: In phase 1, consensus for visual findings were categorized into 8 criteria titled the "Monaco Classification." The frequency of criteria were: (1) presence of stricture-75%, (2) presence of lesion type-55%, (3) mucosal features-55%, (4) papillary projections-45%, (5) ulceration-42.5%, (6) abnormal vessels-10%, (7) scarring-40%, and (8) pronounced pit pattern-10%. The accuracy on final diagnosis based on visual impression alone was 70%.In phase 2, the IOA rate using Monaco Classification criteria ranged from slight to fair. The presumptive diagnosis IOA was fair (κ=0.31, SE=0.02), and overall diagnostic accuracy was 70%. CONCLUSIONS: The Monaco classification identifies 8 visual criteria for biliary lesions on single-operator digital cholangioscopy. Using the criteria, the IOA and diagnostic accuracy rate of DSOC is improved compared with prior studies.

Taxonomic, morphometric and limnological assessment of the commercially important ichthyofauna of Sakhakot Stream, Malakand, Pakistan / Avaliação taxonômica, morfométrica e limnológica da ictiofauna comercialmente importante do Riacho Sakhakot, Malakand, Paquistão

The present study was conducted for the taxonomic, morphometric and limnological assessment of the commercially important ichthyofauna of Sakhakot Stream, Malakand, Pakistan. The study area was divided into three sites along the water course namely Dargai Stream, Sakhakot Stream and Shergarh Stream. Fish samples were collected randomly during January to August 2017 with the help of fish gears. A taxonomic key was designed for the collected fish specimens. Ten fish species were identified belonging to 3 orders and 4 families. Family Cyprinidae was the dominant family with seven representative species while families Siluridae, Nemacheilidae and Mastacembelidae were represented by one species each. Lower mean total length and standard length was recorded in Puntius conchonius (Hamilton, 1822) as 9.2 ± 0.6 cm and 7.3 ± 0.6 cm respectively, while highest mean total length and standard length was recorded in Mastacembelus armatus (Lacepede, 1800) as 28.1 ± 1.7 cm and 15.9 ± 2.4 cm respectively. Mean pH of the water ranged from 6.1 at Shergarh Stream in August to 8.7 at Sakhakot Stream in January. Average temperature range was recorded from 10.9 °C in January at Dargai Stream to 18.7 °C in August at Shergarh Stream. No statistically significant difference was found for temperature (p = 0.96) and pH (p = 0.14) in the three water streams. The present study will provide a baseline for the rearing and enhancement of wild stock of the commercially important ichthyofauna in the field of aquaculture and fisheries.

O presente estudo foi realizado para a avaliação taxonômica, morfométrica e limnológica da ictiofauna comercialmente importante do Riacho Sakhakot, Malakand, Paquistão. A área de estudo foi dividida em três locais ao longo do curso de água, nomeadamente Riacho Dargai, Riacho Sakhakot e Riacho Shergarh. As amostras de peixes foram coletadas aleatoriamente durante janeiro e agosto de 2017, com a ajuda de artes de peixes. Uma chave taxonômica foi projetada para os espécimes de peixes coletados. Foram identificadas dez espécies de peixes pertencentes a 3 ordens e 4 famílias. A família Cyprinidae foi a família dominante, com sete espécies representativas, enquanto as famílias Siluridae, Nemacheilidae e Mastacembelidae foram representadas por uma espécie cada. O comprimento total médio mais baixo e o comprimento padrão foram registrados em Puntius conchonius (Hamilton, 1822) como 9.2 ± 0.6 cm e 7.3 ± 0.6 cm, respectivamente, enquanto o comprimento total médio e o comprimento padrão mais altos foram registrados em Mastacembelus armatus (Lacepede, 1800) como 28.1 ± 1.7 cm e 15.9 ± 2.4 cm, respectivamente. O pH médio da água variou de 6.1 no Riacho Shergarh em agosto a 8.7 no Riacho Sakhakot em janeiro. A faixa de temperatura média foi registrada de 10.9 °C em janeiro no Riacho Dargai a 18.7 °C em agosto no Riacho Shergarh. Não foi encontrada diferença estatisticamente significativa para temperatura (p = 0,96) e pH (p = 0,14) nos três cursos de água. O presente estudo fornecerá uma linha de base para a criação e aprimoramento do estoque selvagem da ictiofauna comercialmente importante no campo da aquicultura e pesca.

Taxonomic and geographic bias in 50 years of research on the behaviour and ecology of galagids.

Identifying knowledge gaps and taxonomic and geographic bias in the literature is invaluable for guiding research towards a more representative understanding of animal groups. Galagids are nocturnal African primates and, for many species, detailed information on their behaviour and ecology is unavailable. To identify gaps and bias in the literature we reviewed published peer-reviewed research articles on galagid behaviour and ecology over a 50-year period from January 1971 to December 2020. Using the Web of Science and Google Scholar databases, we identified 758 articles, assessed 339 full texts for eligibility and included 211 in the review. Species of Otolemur have been extensively researched in comparison to other genera (78.2% of studies; Euoticus: 13.3% of studies; Galago: 66.4% of studies; Galagoides: 20.9% of studies; Paragalago: 22.3% of studies; Sciurocheirus: 15.2% of studies). The most common category of research was physiology (55.0% of studies), followed by behavioural ecology (47.4% of studies), and fewer studies were on genetics and taxonomy (16.1% of studies) and habitat and distribution (14.2% of studies). Text mining revealed that the word 'behaviour' was the most common word used in abstracts and keywords, and few words were related to ecology. Negative binomial regression revealed that mean body mass and geographic range size were significant positive predictors of the total number of scientific outputs on each species. Research on wild populations was carried out in only 24 (60%) of the 40 countries galagids are thought to inhabit. Studies were undertaken in locations with lower mean annual temperatures and higher human population densities over warmer and less populated areas. We encourage a more equal sampling effort both taxonomically and geographically that in particular addresses the paucity of research on smaller species and those with restricted ranges. Research on in situ populations, especially in warmer and remote areas, is urgently needed, particularly in West, Central and some Southern African countries.

The hump-shaped effect of plant functional diversity on the biological control of a multi-species pest community.

Plant taxonomic and functional diversity promotes interactions at higher trophic levels, but the contribution of functional diversity effects to multitrophic interactions and ecosystem functioning remains unclear. We investigated this relationship in a factorial field experiment comparing the effect of contrasting plant communities on parasitism rates in five herbivore species. We used a mechanistic trait-matching approach between plant and parasitoids to determine the amount of nectar available and accessible to parasitoids. This trait-matching approach best explained the rates of parasitism of each herbivorous species, confirming the predominant role of mass-ratio effects. We found evidence for an effect of functional diversity only in analyses considering the ability of plant communities to support the parasitism of all herbivores simultaneously. Multi-species parasitism was maximal at intermediate levels of functional diversity. Plant specific richness had a negligible influence relative to functional metrics. Plant communities providing large amounts of accessible nectar and with intermediate levels of functional diversity were found to be the most likely to enhance the conservation biological control of diverse crop herbivores.

South Africa's contribution of insect records on the BOLD system.

South Africa is the third most biodiverse country in the world and insects represent a large part of its faunal diversity, as is seen globally. With more than 65,000 described animal species in South Africa, insects represent 44,088 species. While there are still a lot of species yet to be identified, progress may be hindered by the few insect taxonomists available in South Africa and subsequently, the time-consuming nature and costs of the methods used during species identification. DNA barcoding, on the other hand, has become a valuable tool for documenting biodiversity with the use of a small DNA fragment such as cytochrome oxidase subunit 1 (COI). This paper aims to assess South Africa's contribution to the Barcode of Life Database (BOLD) as well as highlight the regions that are under-represented on BOLD. From the 4,984,215 Insecta records on BOLD, South Africa contributed 56,392 insect records, with only 16.85% of that total identified to species level. The Gauteng Province had the most represented insect samples submitted to BOLD with 63.57% followed by Kwazulu-Natal (15.74%), and Mpumalanga (5.73%). However, the Free State, Limpopo, and the Northern Cape provinces are all under-represented on BOLD. This is evident as both the Northern Cape and Limpopo provinces contain one or more biodiversity hotspots which in turn displays the high levels of biodiversity that could still be recorded on BOLD. Improving our understanding with regards to DNA barcoding data linked to geographical regions, as well as specific insect groups, can highlight the areas in need of more research.