Taxonomic Details Research Articles

ANAgdb: a multi-omics and taxonomy database for ANA-grade

BackgroundThe ANA-grade, encompassing early-diverging angiosperm lineages, Amborellales, Nymphaeales, and Austrobaileyales, represents a fundamental phase in the evolutionary history of flowering plants. Since the completion of key assembly of the Amborella genome, the continuous influx of omics data from the lineage underscores the need for a specialized database.ResultsHere, we introduce the ANA-grade Genome Database (ANAgdb, https://anagenome.cn/), which integrates multi-omics data including 11 genomes, 167 transcriptomes, and 10 miRNAomes, as well as extensive taxonomic details specific to the ANA-grade. Designed with an array of user-friendly tools, ANAgdb not only facilitates the effective storage, querying, and analysis of data but also enables the integration and dissemination of crucial genomic and taxonomic information.ConclusionBy integrating the comprehensive resources and tools, ANAgdb aims to significantly advance research in phylogenomics and taxonomic studies, providing a robust platform for researchers to explore the genetic and morphological diversities of these ancient plant lineages.

Christella parasitica (l.) Lev.: a potent pharmacological and pesticidal pteridophyte

Pteridophytes are the foremost vascular cryptogam on earth, and hold a unique position in plant evolution. Ferns are one of the prominent representatives of pteridophytes. This group of vascular cryptogams are distributed into 35 families with 568 genera having 13,000 species. The family Thelypteridaceae encompasses around 37 genera and has a diversity comprising 1190 species. Among these Christella parasitica (L.) Lev. (Thelypteridaceae) is one of the fern, which is an invasive vascular cryptogam with potent secondary metabolites, distinct anatomical features, pharmacological attributes along with significant pesticidal characters and anti-microbial properties. Its various applied aspects will be helpful for the researchers to focus on the thrust areas yet to be explored. Comprehensive taxonomic details of the plant have been coming out of various flora books, journals & suggestions from eminent scientists. The plant is highly active against autoimmune & gynecological disorders, food poisoning and sluggishness. However it also contributes for anti-microbial & bio-pesticidal activities. Thus, Christella parasitica holds immense potential as both a pharmacological agent and a natural pesticide. Its dual functionality highlights the importance of deeper investigation into its bioactive compounds, which may lead to innovative developments in both medicinal therapies and sustainable agricultural practices.

Assessing Recent Technologies for Addressing Microplastic Pollution and Pushing the Case of Bioremediation as an Attractive Approach.

Microplastics are emerging sources of environmental pollutants that are increasingly of concern because of their harmful impacts on aquatic life and thereby humans. Their accumulation in the environment is in direct proportion to global plastic production; their being nondegradable, recalcitrant and of a persistent nature creates an urgent need to address this issue on a global scale. Recent reports have demonstrated the presence of microplastics in marine life, and directly becoming a part of the food chain when seafood is ingested by humans. The repercussions of these studies point to an even larger scale presence of microplastics across varied habitats, which are yet to be sampled. Bioremediation, using various microorganisms such as bacteria, algae and fungi, alone or as consortia or in biofilm form can be used as an effective remediation tool. Genetically modified microorganisms for focused removal of microplastics and metagenomics studies, providing taxonomic details of uncultured organisms, are also expected to provide an additional catalogue of technologies in this field. This review offers a comprehensive overview of microplastic sources, existing technologies for treating microplastics and an in-depth analysis of bioremediation mechanisms, its components, and the results from various studies which provide sufficient clues as to the directions to be chosen to address microplastics pollution and can facilitate and instruct researchers to further investigate the more practical approaches and create new and innovative strategies for advanced remediation of microplastic in the future.

Commented checklist of the Odonata from Colombia

Colombian odonatological history was scarce until two decades ago. Here, we present an updated, thoroughly vetted, and refined checklist of taxonomic and geographical records of Colombian odonates, built upon the previous publication in 2011. To achieve this, we conducted an extensive literature review, and curated the most representative biological collections of odonates in the country. Our goal was to integrate new records and recently described species, while excluding misidentifications or doubtful identifications due to a lack of support from taxonomic revisions and specimens in collections. We report a total of 536 species, reflecting a 38% increase in odonate richness since the last published checklist in 2011. This number positions Colombia among the top ten countries with the highest number of odonates worldwide. We include important taxonomic details for each species in the checklist, the availability of female and/or larva description(s), and the IUCN species assessment. We also highlight rare or puzzling species, which records for the country are controversial. It is noteworthy that the majority of these contributions stem from local Colombian research efforts that have enriched our national reference collections, including ANDES-E, CEUA, and UARC. Geographically, the department with the highest diversity is Meta with 205 species followed by Antioquia with 170 species. The latter holds the highest number of endemics across the country. We anticipate that this effort will be the basis and inspiration to future research on Colombian odonatofauna, especially in underexplored areas, and will encourage conservation initiatives for freshwater ecosystems across the country.

A user-friendly method to get automated pollen analysis from environmental samples.

Automated pollen analysis is not yet efficient on environmental samples containing many pollen taxa and debris, which are typical in most pollen-based studies. Contrary to classification, detection remains overlooked although it is the first step from which errors can propagate. Here, we investigated a simple but efficient method to automate pollen detection for environmental samples, optimizing workload and performance. We applied the YOLOv5 algorithm on samples containing debris and c. 40 Mediterranean plant taxa, designed and tested several strategies for annotation, and analyzed variation in detection errors. About 5% of pollen grains were left undetected, while 5% of debris were falsely detected as pollen. Undetected pollen was mainly in poor-quality images, or of rare and irregular morphology. Pollen detection remained effective when applied to samples never seen by the algorithm, and was not improved by spending time to provide taxonomic details. Pollen detection of a single model taxon reduced annotation workload, but was only efficient for morphologically differentiated taxa. We offer guidelines to plant scientists to analyze automatically any pollen sample, providing sound criteria to apply for detection while using common and user-friendly tools. Our method contributes to enhance the efficiency and replicability of pollen-based studies.

The genus Athyrium (Woodsiaceae) in Arunachal Pradesh state, India

This paper deals with the diversity and distribution of Athyrium in Arunachal Pradesh, N.E. India. 28 species are reported here from the state. The first authentic report of Athyrium flabellulatum from Arunachal Pradesh is also made here. Taxonomic details of the species are given. The distribution pattern of species by districts is also studied using exploratory data analysis.

New Distributional Records of Three Rare Ferns from Odisha, India

Niyamgiri and Kotgah Wildlife Sanctuary are part of the Eastern Ghats located at Odisha. The altitude range of these mountain ranges between 400–1516 m shows the diversity of vegetation due to their undulating mountain peaks, deep gorges, valleys and numerous springs. Three species viz., Amblovenatum opulentum (Kaulf.) J. P. Roux, Pronephrium articulatum (Houlston & T. Moore) Holttum and Sphaerostephanos hirtisorus (C. Chr.) Holttum (Family: Thelypteridaceae) collected from Niyamgiri hill and Kotgarh Wildlife Sanctuary are recorded for the first time from Odisha state. The same are documented here with taxonomic details and photographs of herbaria

Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum.

An endophytic actinobacterium, designated strain PLAI 1-29T, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29T was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus Streptomyces. Strain PLAI 1-29T produced a spiral spore chain on aerial mycelium and grew at 15-40 °C, pH 6-10 on International Streptomyces Project 2 agar. The maximum NaCl concentration for growth was 9 % (w/v). Cells of strain PLAI 1-29T presented ll-diaminopimelic acid, arabinose, galactose and ribose. The detected phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The genome-based taxonomic details revealed the assignment of strain PLAI 1-29T to the genus Streptomyces and exhibited low threshold values for the delineation of a novel species by average nucleotide identity-blast (84.0%), average amino acid identity (80.0%) and digital DNA-DNA hybridization (27.6%) with its closest type strain, Streptomyces xinghaiensis S187T. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29T and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29T (=TBRC 7645T=NBRC 113170T) is considered to represent a new Streptomyces species, for which we propose the name Streptomyces zingiberis sp. nov.

Variable Region Sequences Influence 16S rRNA Performance.

16S rRNA gene sequences are commonly analyzed for taxonomic and phylogenetic studies because they contain variable regions that can help distinguish different genera. However, intra-genus distinction using variable region homology is often impossible due to the high overall sequence identities among closely related species, even though some residues may be conserved within respective species. Using a computational method that included the allelic diversity within individual genomes, we discovered that certain Escherichia and Shigella species can be distinguished by a multi-allelic 16S rRNA variable region single nucleotide polymorphism (SNP). To evaluate the performance of 16S rRNAs with altered variable regions, we developed an in vivo system that measures the acceptance and distribution of variant 16S rRNAs into a large pool of natural versions supporting normal translation and growth. We found that 16S rRNAs containing evolutionarily disparate variable regions were underpopulated both in ribosomes and in active translation pools, even for an SNP. Overall, this study revealed that variable region sequences can substantially influence the performance of 16S rRNAs and that this biological constraint can be leveraged to justify refining taxonomic assignments of variable region sequence data. IMPORTANCE This study reevaluates the notion that 16S rRNA gene variable region sequences are uninformative for intra-genus classification and that single nucleotide variations within them have no consequence to strains that bear them. We demonstrated that the performance of 16S rRNAs in Escherichia coli can be negatively impacted by sequence changes in variable regions, even for single nucleotide changes that are native to closely related Escherichia and Shigella species; thus, biological performance is likely constraining the evolution of variable regions in bacteria. Further, the native nucleotide variations we tested occur in all strains of their respective species and across their multiple 16S rRNA gene copies, suggesting that these species evolved beyond what would be discerned from a consensus sequence comparison. Therefore, this work also reveals that the multiple 16S rRNA gene alleles found in most bacteria can provide more informative phylogenetic and taxonomic detail than a single reference allele.

Phytochemicals: A Promising Alternative for the Prevention of Alzheimer's Disease.

Alzheimer's disease (AD) is a neurological condition that worsens with ageing and affects memory and cognitive function. Presently more than 55 million individuals are affected by AD all over the world, and it is a leading cause of death in old age. The main purpose of this paper is to review the phytochemical constituents of different plants that are used for the treatment of AD. A thorough and organized review of the existing literature was conducted, and the data under the different sections were found using a computerized bibliographic search through the use of databases such as PubMed, Web of Science, Google Scholar, Scopus, CAB Abstracts, MEDLINE, EMBASE, INMEDPLAN, NATTS, and numerous other websites. Around 360 papers were screened, and, out of that, 258 papers were selected on the basis of keywords and relevant information that needed to be included in this review. A total of 55 plants belonging to different families have been reported to possess different bioactive compounds (galantamine, curcumin, silymarin, and many more) that play a significant role in the treatment of AD. These plants possess anti-inflammatory, antioxidant, anticholinesterase, and anti-amyloid properties and are safe for consumption. This paper focuses on the taxonomic details of the plants, the mode of action of their phytochemicals, their safety, future prospects, limitations, and sustainability criteria for the effective treatment of AD.

AN OUTBREAK OF Yponomeuta padella (LINNAEUS, 1758) ON Prunus cornuta (HIMALAYAN BIRD CHERRY) IN KULLU DISTRICT, HIMACHAL PRADESH, INDIA

Invasive insect pests are one of the greatest and fastest-growing threats to natural resources like agricultural biodiversity, animal sector and social progresses are profusely hampered through insect infestation. Through this present study, it was first recorded that Yponomeuta padella attack Prunus cornuta (Himalayan Bird Cherry) leaves in high altitudinal transition zone forests of North Western Himalaya in India. The first damage was observed duringthe month of July, 2022 and randomly collected egg masses form the infested leaves of Prunus cornuta. This species identified through its morphological and genital characteristics. A complete biology of ermine moth, morphology and genital characteristics were studied to update the taxonomic details of the species. More than 90% infestation in leaves was recorded in some trees in the study area. As an alternative, an integrated pest management system needs to be developed for better insect's sustainable management.

Digitizing the coral reef: Machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats

Abstract Coral reefs are the most biodiverse marine ecosystems, and host a wide range of taxonomic diversity in a complex spatial community structure. Existing coral reef survey methods struggle to accurately capture the taxonomic detail within the complex spatial structure of benthic communities. We propose a workflow to leverage underwater hyperspectral image transects and two machine learning algorithms to produce dense habitat maps of 1150 m2 of reefs across the Curaçao coastline. Our multi‐method workflow labelled all 500+ million pixels with one of 43 classes at taxonomic family, genus or species level for corals, algae, sponges, or to substrate labels such as sediment, turf algae and cyanobacterial mats. With low annotation effort (only 2% of pixels) and no external data, our workflow enables accurate (Fbeta of 87%) survey‐scale mapping, with unprecedented thematic detail and with fine spatial resolution (2.5 cm/pixel). Our assessments of the composition and configuration of the benthic communities of 23 image transects showed high consistency. Digitizing the reef habitat and community structure enables validation and novel analysis of pattern and scale in coral reef ecology. Our dense habitat maps reveal the inadequacies of point sampling methods to accurately describe reef benthic communities.

BRYOCRUMIA VIVICOLOR, A RHEOPHYTIC, HYPNACEOUS MOSS, NEW TO THE WESTERN HIMALAYAS, INDIA

The Indian Himalayan sector is well known to support the diversified bryophyte species and communities due to varied phytoclimatical conditions met within different dissected topographical zones. Many potential wilderness areas are still waiting to be explored in terms of their exuberant bryodiversity. During a bryoexploratory survey of an unexplored high-altitude area in the Garhwal Himalayan region, we came across an interesting rheophytic moss Bryocrumia L. E. Anderson. The genus Bryocrumia is represented in India by two species, viz. B. vivicolor (Broth. et Dixon) W. R. Buck and B. malabarica Manju, Prajitha, Prakashkumar et W. Z. Ma. Both of these pleurocarpous species are known to be confined in the southern part of the country. From the Indian Himalayan sector, this moss genus has never been documented earlier. Recently, B. vivicolor has been reported for the first time from the Tungnath area (2,100–3,000 m above sea level) in the Garhwal region of Uttarakhand state as a new addition to the Western Himalayan moss flora, indicating its new distributional range. This hypnaceous moss was found colonising the slopy, wet, submerged rock surfaces along small streams and seepages in mixed oak forests on way to Tungnath. The key characteristics include its rheophilic habit, stem lacking central strand, variable leaf forms, indistinct double costa and round to obtuse leaf apex with prorate tip cells. The present paper provides taxonomic details of this rare moss, representing its wide geographical distribution in India.

DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands.

Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.

An Algorithmic Approach to Reducing Taxonomic Detail from Actual Datasets to their Metadata Representation to Increase Findabilty

An Algorithmic Approach to Reducing Taxonomic Detail from Actual Datasets to their Metadata Representation to Increase Findabilty

Pollen Morphology of Rosa sericea Complex and Their Taxonomic Contribution

In this research, the pollen morphology of the Rosa sericea complex has been studied by Scanning Electron Microscope (SEM). The present study aimed to provide baseline information for the taxonomic identification of the R. sericea complex taxa. The pollen sculpture, outline, and aperture show variability in the studied taxa. The R. sericea complex includes taxonomically challenging species with undistinguishable boundaries. Identifying taxon boundaries in closely related species is fundamental to investigating evolution and biodiversity. Taxa circumscription of R. sericea complex is insufficient, unresolved, and is a prerequisite for comprehensive systematic revisions. To resolve these issues, we have attempted to identify some important diagnostic characters for the species of R. sericea complex. This research studied different qualitative and quantitative characteristics of R. sericea complex pollen. The qualitative characteristics included polar and equatorial view, sculpture, pollen outline, apertures, exine, size category, and polarity of pollen. In contrast, the quantitative features include polar and equatorial diameter, P/E, colpi length and width, and distance between colpi. Pollen of this complex is mono and tricolporate. The morphological characters studied here provide very few taxonomic details with which to separate the species of the complex into distinct taxa. Some of the studied characters offer important information for species delimitation including sculpture, pollen outline, and apertures.

Evaluation of visual encounter surveys as a method for the rapid assessment of fish presence and relative density in high mountain lakes

Abstract Introduced fish are a widespread ecological threat in originally fishless high mountain lakes. However, basic distribution data are largely missing for most high mountain regions. Using time‐consuming standard methods (e.g. Nordic standard fishing nets) to assess fish distribution and relative densities at a relevant spatial scale can be impracticable, because of the large number of high mountain lakes. To overcome this problem, alternative rapid monitoring methods would be helpful. Visual encounter survey (VES) is a candidate method that enables observing fish from the shoreline. It takes only minutes to implement and is already widely used for amphibian monitoring in high mountain lakes and ponds. VES was evaluated as a method for monitoring introduced salmonids and cyprinids (the most widespread fish families) in 52 high mountain lakes. The probability of detecting both families by VES rapidly approaches 100% as the relative densities of fish increase, and false absences are restricted to populations living at low relative densities. VES also provides simple indications about fish relative densities, distinguishing between high‐density and low‐density populations. As VES usually does not enable fish species identifications, we propose VES as a useful method to describe large fish distribution inventories, not needing high taxonomic detail, but necessary for planning large‐scale conservation measures.

Why eDNA fractions need consideration in biomonitoring.

The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four‐scenario concept that aims at enhancing spatial and temporal resolution of eDNA‐based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA‐based biodiversity data. Finally, future avenues of research towards eDNA fraction‐specific analyses are outlined to unravel the full potential of eDNA‐based studies targeting micro‐ and macro‐organisms.

A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing.

Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.

PTITAN2: Permutation of treatment labels and Threshold Indicator Taxa ANalysis

Background: Taxa Indicator Threshold ANalysis (TITAN) was developed to identify thresholds along environmental gradients where rapid changes in taxa frequency and relative abundance are observed. TITAN determines separate change-points for increasing and decreasing taxa in aggregate, as well as change-points for individual taxa, with associated confidence intervals generated using bootstrapping. However, if TITAN is applied to different classes of observations, additional analyses besides using non-overlapping confidence intervals are needed to establish whether change-points differ between treatments or groups because non-overlapping confidence intervals can indicate significant differences but overlapping confidence intervals do not necessarily mean the null hypothesis cannot be rejected. Methods: To address this, we present a new R package, pTITAN2, which is an extension to the existing TITAN2 package. The pTITAN2 package was developed to enable comparisons of TITAN output between treatments by permutating the observed data between treatments and rerunning TITAN on the permuted data. Results: The pTITAN2 package includes two functions, occurrences and permute. The occurrences function selects the taxonomic codes to be used in a TITAN run while maintaining the most taxonomic details. The permute function is then used to create a list of permuted sets of taxa and environmental gradients. TITAN is then run again on the permuted data and p-value test can be calculated using the observed and permuted TITAN output to test for statistical differences between treatment effects. Conclusions: The package pTITAN2 is an extension of the existing TITAN2 package and enables users to perform the appropriate statistical tests and determine statistical differences without using overlapping confidence intervals.