Taxonomic System Research Articles

Self-help for taxonomists: three things we must do for taxonomy to survive

Knapp & Boxshall (2010) concluded that “at the very time when the importance of biodiversity has been realised, our capability of describing and documenting it has been eroded to a crisis point.” It seems to me that little has changed since then but other contributions are focusing on the overall problem so I want to use this article to highlight three practical challenges for taxonomy going forwards. 1. Maintaining and enhancing the system of Reciprocal Illumination. 2. Building and maintaining taxonomic information systems. 3. Addressing issues of societal relevance.

Taxonomic study of Endogonaceae in the Japanese islands: New species of Endogone, Jimgerdemannia, and Vinositunica, gen. nov.

ABSTRACTSpecies of Endogonaceae (Endogonales, Mucoromycotina) are characterized by the formation of relatively large sporocarps and zygosporangia. Numerous species in this family remain undescribed or have unclear phylogenetic positions. In Asia specifically, the species diversity of this family is almost completely unknown. However, many mycobionts of bryophytes belonging to several novel clades in Endogonaceae have recently been identified phylogenetically. Therefore, establishing a robust taxonomic system for this family is essential. We obtained numerous sporocarps of undescribed Endogonaceae-like species from the Japanese islands. Morphological observation and multilocus phylogenetic analysis of nuc 18S rDNA (18S), nuc 28S rDNA (28S), and portions of two nuclear protein-coding regions—translation elongation factor 1-alpha (tef1) and RNA polymerase II large subunit (rpb1)—from these species resulted in the description of one new species each of Endogone and Jimgerdemannia and two new species of Vinositunica, gen. nov. Because Vinositunica is characterized by purplish sporocarps and red-wine-colored chlamydospores up to 700 μm in diameter, we emended the definition of Endogonaceae.

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.

Kombucha, a fermented tea generated from the co‐culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.

Effect of Tillage and Water Management on Aggregate Stability of a Gleyic Cambisols

The objective of this study was to determine the effect of tillage and water management on the physical stability of irrigated lowland rice field, in Kwalkwalawa, Sokoto State. The experiment was carried out in a farmer`s field, near the Usmanu Danfodiyo University Teaching and Research Farm, Kwalkwalawa, Sokoto State. The coordinates of the area were taken using global positioning system (GPS) model Garmin etrex 20.0, which shows that the area is located on (N13°05.963”E005°12.650” and at 252 m asl). The soils of the study area were classified as Aeric Endoaquepts at subgroup level in the USDA Soil Taxonomy System which correlated with Gleyic Cambisols in the World Reference Base. The treatments consisted of factorial combination of two tillage systems (conventional tillage (CT) and reduced tillage (RT), three irrigation water managements (Alternate one, two and three days irrigation intervals, which were carried out from one week after transplanting to hard dough stage) and three rice varieties (FARO 44, 60 and 61) all laid in a split-plot design and replicated three times. After harvest, disturbed soil samples were collected with the aid of soil auger, prepared and passed through 5 mm sieve for aggregate stability determination. Result reveals that a consistent trend in aggregate size fraction was observed between the two tillage systems in both years, were a significant decrease in values of aggregate fractions of both the CT and RT in 2019 compared to in 2018. Aggregate size fraction of 5-2 mm had a significantly high value of RT compared to CT, 2-0.25 mm fractions were at par (0.41) while a greater value of aggregate fractions for CT in both 0.25-0.005 mm and ˂0.005 mm were observed compared to RT. Alternate days to irrigation and sampling depths increase with a corresponding in all the aggregate size classes in the two years of this study. A significant difference in mean weight diameter (MWD) and geometric mean diameter (GMD) between the two tillage, water management and depth was noticed in both years of the trial where RT and alternate one day had high value while MWD and GMD increase with increasing depth.

An annotated checklist of bryophytes of Europe, Macaronesia and Cyprus

ABSTRACT Introduction. Following on from work on the European bryophyte Red List, the taxonomically and nomenclaturally updated spreadsheets used for that project have been expanded into a new checklist for the bryophytes of Europe. Methods. A steering group of ten European bryologists was convened, and over the course of a year, the spreadsheets were compared with previous European checklists, and all changes noted. Recent literature was searched extensively. A taxonomic system was agreed, and the advice and expertise of many European bryologists sought. Key results. A new European checklist of bryophytes, comprising hornworts, liverworts and mosses, is presented. Fifteen new combinations are proposed. Conclusions. This checklist provides a snapshot of the current European bryophyte flora in 2019. It will already be out-of-date on publication, and further research, particularly molecular work, can be expected to result in many more changes over the next few years.

The complete mitochondrial genome of brown algae: Sargassum fusiforme (Harvey) Setchell

We describe the complete mitochondrial genome sequence of Sargassum fusiforme. This mitogenome is a circular molecule of 34,695 bp in length and had an overall GC content of 37.54%%. Gene annotation showed that 35 protein-coding genes, 2 open reading frames, 25 transfer RNA genes, and 3 ribosomal RNA genes. The phylogenetic tree based on Bayesian shows that S. fusiforme belongs to genus Sargassum, support current taxonomic systems.

A Holistic Sustainable Finance Model for the Sustainable Capital Market

This paper, has systematized the literature review, and with its critical view towards international and especially European sustainable finance policy and methodologies, has marked three important problems that affect up until today the design and implementation of environmental, social and sustainable policies in the sustainable financial performance of capital market. Environmental, social and sustainable performance measures, as well as the taxonomy system, the evaluation and notification of information that are related to the consequences of sustainable policies, represent a modern challenge for creating a completer methodology in the field of sustainable finance. In a practical level the challenge still remains: 1) if the policies, methodologies and researches in this category, allow researchers and financial stakeholders, as well as firms managers to follow and to evaluate sustainable finance in a reliable manner, 2) if the sustainable policies of firms are successful and recognized by the capital market. As every new scientific field, so “Sustainable Finance” must be framed with theories that should define the efficient operation of “Sustainable Market Capital” and get new holistic “Sustainable Finance model” created. The purpose of this paper is to define the theory of Sustainable Capital Market and the Holistic Sustainable Finance Models.

Identification of Ethiopian Yam (<i>Dioscorea</i> spp.) Collections and Their Phenotypic Diversity Study

Yam plant has a major role in Ethiopia particularly in densely populated areas of south, southwestern, and western parts of the country. It grows in a wide range of soils with an altitude range of 1140 to 2200 masl. This study was done to identify yam species collected from major producing areas of the country. The total of sixty yam accessions from ten different geographic origins of South and Oromiya region of Ethiopia were used. The collected samples were planted in complete randomized block design at two research sites of South Agricultural Research Institute. Forty-five qualitative morphological characterizations were used to characterize and identify Dioscorea species. Among these qualitative characters observed in the study presence and absence of spines on stems and roots, number of male and female inflorescence, stem length, twining direction, and flesh color were the major traits considered for species identification. The organoleptic properties evaluation was carried out using fifteen selected local farmers. Statistical analysis was done using Numerical Taxonomy and Multivariate Analysis System Version 2.02 NTSYpc software program and the data reduction function of SPSS for windows. Based on this study, sixty yam germplams of ten major growing areas of the country were identified into six Dioscorea species. These identified Dioscorea species were again subjected to qualitative morphological characterization and 33 morphological traits revealed variability. This implies presence of high diversity in yam (Dioscorea species) of Ethiopia. Most of the morphological variations among the yam genotypes were contributed by young petiole color, tendency of tuber to branch, and tuber flesh color. Hence, these morphological traits could be taken as useful traits for identification of yam cultivars.

'Author Contribution Details' and not 'Authorship Sequence' as a merit to determine credit: A need to relook at the current Indian practice.

The Medical Council of India (MCI) has made research publications in indexed medical journals an obligatory requirement for promotion of medical teachers. In 2015, MCI guidelines said the first and the second author would receive credit for a research paper. In 2017, the amended guidelines provided credit to the first and the corresponding authors instead. We reviewed the common types of authorship order in medical publications from across the world and noted that before the 1990s, corresponding authors were rarely acknowledged and were not considered more important than any of the co-authors. By 2016, the corresponding author was usually the first or the last author. With an increase in collaborative research globally, more and more papers are published with multiple first, last or corresponding authors. Some journals have revised their Instructions to Authors to acknowledge co-first authors equally. Since 2017, PubMed also displays equal contributors in the author byline while still allowing searches for 'First author' and 'Last author' supporting the 'first and last author emphasis'. However, most guidelines mention that the authorship order is a collective decision of the authors. Any association between authorship sequence and credit for an article is debatable. Some journals allow or even insist on authorship statements to explain each contributor's role. Standardized vocabularies and taxonomies such as the Contributor Roles Taxonomy (CRediT) system can highlight contributions of individual authors. Some suggest doing away with the authorship order altogether. Readers and assessors should look at the 'author contribution details' rather than the 'authorship order' before drawing any conclusions about contributions of each author.

Nursing diagnoses and NIC interventions in adult males undergoing radical prostatectomy.

To determine NANDA-I nursing diagnoses and NIC nursing interventions in patients who underwent radical prostatectomy. A cross-sectional and descriptive study was conducted in a research and teaching hospital in western Turkey between June 2016 and June 2017. The sample included adult patients diagnosed with prostate cancer in the immediate postoperative period of radical prostatectomy. Data collection was performed using Gordon's Functional Health Patterns, NANDA-International and Nursing Interventions Classification Taxonomy Systems. Participants were 54 adult patients. The main nursing diagnoses were in the classes of "physical injury", "self-care", "hydration" and "physical comfort". Some nursing diagnoses were identified in all patients, namely: "risk for deficient fluid volume", "risk for imbalanced fluid volume", "impaired urinary elimination". The most selected NIC interventions were in the classes of "risk management", "elimination management", "coping assistance", "tissue perfusion management" and "self-care facilitation". future studies with larger populations are needed to explore the nursing diagnoses and effects of nursing interventions on patients who underwent radical prostatectomy.

Integrated taxonomic approaches to seven species of capillariid nematodes (Nematoda: Trichocephalida: Trichinelloidea) in poultry from Japan and Indonesia, with special reference to their 18S rDNA phylogenetic relationships.

Morphological and genetic analyses were performed on seven species of the family Capillariidae (Nematoda: Trichocephalida: Trichinelloidea), viz. Eucoleus perforans, Eucoleus contortus, Aonchotheca bursata, Baruscapillaria obsignata, Capillaria anatis, Capillaria phasianina, and Capillaria spinulosa, detected in poultry from Japan and Indonesia. Two Eucoleus spp., perforating the esophageal mucosa of the Japanese green pheasant farmed in Japan (E. perforans) and domestic goose in Indonesia (E. contortus), were morphologically characterized. Furthermore, we observed substantial nucleotide differences between their 18S ribosomal RNA gene (rDNA), revealing maximum identity (97.27%) over the 1797-bp length. Similarly, B. obsignata in the small intestine of Japanese green pheasants in Japan, a chicken, geese, domestic pigeons, and a turkey in Indonesia, and C. anatis in the ceca of chickens in Indonesia were morphologically and molecular-genetically compared with previously reported isolates of these species in Japan. Aonchotheca bursata collected from the small intestine of the Japanese green pheasant was also molecular-genetically characterized for the first time; however, sequencing of the 18S rDNA of C. phasianina from the cecum of the same bird was unsuccessful. Capillaria worms in the ceca of a domestic duck and geese in Indonesia were identified as C. spinulosa, which had only previously been recorded in wild birds of the Anseriformes in the Palaearctic region. Morphologically, this species was closest to Capillaria pudendotecta recorded from the ceca of wild and captive swans, except for the lack of vaginal appendages in female worms and shorter esophagi relative to the body length in both male and female worms. Phylogenetically, these two species were closely related, although substantial nucleotide changes were noted. The 18S rDNA nucleotide sequences of the species isolated here were consistent with the recent taxonomic system established for Capillariidae based primarily on the morphology of male caudal ends.

Soil detachment capacity of shallow overland flow in Earth-Rocky Mountain Area of Southwest China

In process-based erosion models, soil detachment capacity (Dc) is a pivotal parameter that is typically estimated by hydraulic parameters. Purple soil in Earth-Rocky Mountain Area of Southwest China is a unique soil resource with characteristics including fast physical weathering, soft texture, and rich nutrient reserves. However, the prediction accuracy of Dc and its relationship with certain hydraulic parameters remains poorly understood for purple soil, which is defined as an Entisol in the US Soil Taxonomy system. The objective of this study was to investigate the relationship between Dc of shallow overland flow and hydraulic parameters to establish an accurate model for purple soil. A series of 825 flume experiments were conducted in a 12 m × 0.3 m hydraulic flume. Flow discharge was 8.33 × 10−3 to 41.67 × 10−3 m2 s−1, slope gradient was 8.7% to 39.1%, and rill length was 0.5 m to 10 m. Results showed that flow discharge and slope, stream power, and effective stream power were effective predictors of Dc. However, flow depth, flow velocity, shear stress and unit stream power were relatively poor predictors. Stream power was the optimal parameter for predicting the Dc of shallow overland flow. Flow discharge, slope and effective stream power were also useful parameters for predicting Dc. Linear equation between Dc and stream power was the optimal model for predicting Dc, which was recommended when flow depth and flow velocity data were available; however, power equation among Dc, flow discharge and slope also showed good performance in predicting Dc, which was recommended when only flow discharge and slope data were available. The results of this study provide theoretical guidance for predicting sediment yield in Earth-Rocky Mountain Area of Southwest China as well as a decision-making basis for controlling soil and water loss in Earth-Rocky Mountain Area of Southwest China.

Inventory study of plants collection in the Medicinal Thematic Garden, Cibodas Botanic Gardens

CBG’s plant collection managed and displayed in the garden based on the taxonomic classification system and thematic system. Plant collection that managed as a thematic system displayed and managed as a thematic garden. The aim of this study is to conduct an inventory study of CBG medicinal thematic garden collections and to do a literature study about the potential medicinal use of plant collection in CBG medicinal thematic gardens. Data collected through surveyed, checked and validated in the information system of CBG plants data collection from CBG Registration Unit. Recorded medicinal use of surveyed plant collection was identified by the literature study. Data were analyzed descriptively. The result of the study showed that there were 26 species from 23 genera and 22 families of medicinal plant species in CBG medicinal thematic garden. Based on ICD-10-WHO, CBG medicinal plant collections can treat 14 ICD-10-WHO diseases. From these 14 diseases, eight diseases can be treated by five CBG medicinal plant collections. These species were utilized as a medicinal plant by using part of the plant (root, leaves, bark, flowers, fruit, seeds, sap) or the whole plant through pounded or boiled processing, and mixed it with other ingredients.

The DSM's Reconnection to Psychoanalytic Theory through the Alternative Model for Personality Disorders.

Often believed to have Kraepelinian origins, the Diagnostic and Statistical Manual of Mental Disorders-5th Edition (DSM-5) defines personality disorders using a categorical, hierarchical taxonomic system. This system possesses many long-standing problems for clinical practice, including a large assortment of symptom combinations that contribute to problematic heterogeneity and likely impair diagnostic validity. The DSM diagnostic system was at one time heavily influenced by psychoanalytic theory (Shorter 2005). A desire for greater theoretical neutrality then encouraged a shift away from psychoanalytic theory, resulting in the problematic atheoretical model of personality pathology introduced in DSM-III (1980) and still used today. The Alternative Model for Personality Disorders (AMPD), introduced in DSM-5 (2013), is an attempt to reconcile many of the categorical model's issues and directly parallels primary themes that characterize psychoanalytic models of personality. After a review of the historical development of DSM, three current systems for diagnosing personality pathology-the DSM-5's categorical model (2013), its AMPD (2013), and the Psychodynamic Diagnostic Manual (2nd ed.; Alliance of Psychoanalytic Organizations 2017) are compared. The comparison illustrates how the AMPD brings psychoanalytic theory back into the DSM system and acknowledges the implications of a more psychoanalytic DSM.

Genome constitution and differentiation of subgenomes in Siberian and Far Eastern endemic species of the genus Elymus (Poaceae) according to the sequencing of the nuclear gene waxy

Fifty-three species of perennial grasses in the genus Elymus L. (Poaceae), which are widespread in Russia, are generally assumed to have three haplome combinations: StH, StY and StHY. The StH-genome species, endemic to Russia, remain the least studied. R. Mason-Gamer and co-authors have previously shown in a series of studies that a molecular phylogenetic analysis of the low-copy gene waxy (GBSS1) sequences significantly complements cytogenetic data on the genomic constitution and evolutionary relationships among both North American and Asian species of the genus Elymus. To determine the species’ genomic constitution and to evaluate the level of phylogenetic differentiation, we examined the GBSS1 gene in 18 species of Elymus from Siberia and the Russian Far East, including the fol- lowing 14 endemics: E. charkeviczii, E. jacutensis, E. kamczadalorum, E. komarovii, E. kronokensis, E. lenensis, E. macrourus, E. margaritae, E. subfibrosus, E. sajanensis, E. transbaicalensis, E. peschkovae, E. uralensis, and E. viridiglumis.PCR amplification products of GBSS1 gene fragments (including exons 9–14) were cloned and 6–8 clones per accession were sequenced. It appears that all the species studied have St and H subgenomic gene variations. The most significant differences between the subgenomic variants St and H were found in intron 13. The H subgenome contains a 21-bp-long deletion in intron 13 in all Elymus genotypes, probably derived from a common ancestor of the H and P genomes. Instead of this deletion, all St subgenomes have a relatively conservative sequence similar to that of the genus Pseudoroegneria, whose ancestor is considered to be the donor of the modern St subgenome for all Elymus species. Cluster phylogenetic analysis revealed differentiation in St and H subgenome sequences into two evolutionary variants: St1 vs. St2 and H1 vs. H2, respectively. Variants of the St and H subgenomes were found homologous to various modern species of the ancestral genera Pseudoroegneria and Hordeum: St1 to P. strigosa, St2 to P. spicata, H1 to H. jubatum, and H2 to H. californicum. The details of the relationships between Russian and North American species of the genus, as well as a number of microevolutionary interconnections in the group of boreal endemic species of Siberia and the Russian Far East were revealed. The new results obtained here are essential for the development of a phylogenetically oriented taxonomic system for the genus Elymus.

In silico design and in vitro validation of a novel PCR-RFLP assay for determination of phylogenetic clusters of streptokinase gene alleles in streptococci groups

Streptokinase (SK), a heterogeneous plasminogen (Pg) activator protein secreted by groups A, C and G streptococci (GAS/GCS/GGS) is a virulence factor composed of three structural domains; SKα/SKβ/SKγ. Phylogenetic analysis of the major variable region of SKβ (sk-V1; nucleotides 448–791; 343bp) which classifies the SK alleles into SK1/SK2 clusters and SK2a/SK2b sub-clusters, is an approved assay to categorize clinical/natural streptococcal-isolates into co-related functional/pathogenesis groups. Herein, we describe a novel PCR-RFLP assay that in combination with Numerical Taxonomy and multivariate analysis System (NTSYS) resulted to dendrograms with complete adaption to that of the phylogenetic analysis of sk-V1-based clustering. In silico analyses by 30 restriction enzymes on GenBank-acquired sk-V1 sequences of known streptococcal clusters, resulted to the selection of “BsrI, MseI and Tsp45I″ enzymes that produced proper patterns to construct the expected dendrograms. In vitro analysis of the selected enzymes on clinical isolates of GAS/GCS/GGS validated the production of the same in silico-observed digestion patterns. Comparison of the constructed dendrogram and phylogenetic trees of selected GenBank and clinical isolates of streptococci indicated complete adaptation. Assessment of Pg-activation activity in selected clinical isolates indicated the expected co-related functionalities of the classified SK-clusters by the invented PCR-RFLP/NTSYS method. The simplicity of the assay relieves the need of sequencing/phylogenetic analyses for SK-clustering.

The problem of naming commercial seaweeds

Although there are different naming systems for economic seaweeds, including local vernacular, legal, and institutional names, there is a general understanding that naming systems are underpinned by correct scientific taxonomy and nomenclature. The molecular revolution in taxonomy, causing huge changes in delimitation of taxa, together with a perceived inability of scientific taxonomy and nomenclature to keep up with these changes is a major problem. For example, it is suggested that the majority of marine natural products from seaweeds are described in the scientific literature linked to taxonomically incorrect names. The different naming systems are here described and compared, with examples showing mismatches between up-to-date scientific taxonomy, nomenclature, and current commercial and legal naming practices. It is considered feasible that a consensus will soon be reached on taxonomic systems for commercially important groups, and scientific names of taxa updated to incorporate this new information. It is essential that names from other nomenclatural systems be increasingly underpinned by scientific, evolutionarily-based taxonomy. The critical communication role played by the website Algaebase.org as a highly reliable and up-to-date source of nomenclatural information is highlighted, as is the need for naming of material with commercial potential to be backed up by DNA barcoding in the future, once the taxonomy of economically important groups has been thoroughly investigated.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of theirphylogeny and evolution.

GOTIT: A laboratory application software for optimizing multi‐criteria species‐based research

Abstract Storing, managing and sharing the ever‐increasing amount of species occurrence data and biological vouchers is a cornerstone of biodiversity science. The convergence of morphology‐ and DNA‐based methods for species delimitation has accentuated the need for optimizing laboratory workflow by generating new analytical processes, diversifying taxonomic reference systems and identification protocols and multiplying vouchers. Yet, laboratory information management systems dedicated to multi‐criteria species‐based research are rare or they have not been made openly available to biodiversity professionals. We developed GOTIT (Gene Occurrence and Taxa in Integrative Taxonomy), a database structure and web application for optimizing productivity at various steps of a laboratory's workflow including research project design, sampling gap analysis, sampling planning, species identification, DNA sequencing, information sharing and contributing data to global biodiversity facilities. GOTIT manages the different steps of a species‐occurrence data production process from sampling to sequencing, the storage of specimen lots, slides and DNA extracts and their assignment to morphology‐based and DNA‐based species hypotheses. The application also accommodates species occurrence data and DNA sequence metadata from external sources and the bibliographic referencing of information. GOTIT is designed to optimize research activities on the diversity and evolution of species which have a strong geographic component, such as biogeography and phylogeography. A key feature of GOTIT is the ability to assign multiple species hypotheses based on morphology and molecular delimitation methods to the same set of specimens. This integrative taxonomic approach allows to explore how different aspects of speciation, such as morphological distinguishability and genetic isolation, vary in strength relative to each other across taxa and geographic regions. Another key feature is traceability which promotes repeatability and minimizes duplicate work among multiple users. Any species data refer to a set of localities, sampling methods, biological vouchers, analytical protocols and delimitation methods that can be traced. The application is free and open‐source with extensive documentation and demo version. Developers can reuse the source code or develop new add‐ons to fulfill a laboratory's specific requirements although the application can be used as such to manage species occurrence data for a wide range of taxa.

Machine Learning and Deep Learning Methods for Intrusion Detection Systems: A Survey

Networks play important roles in modern life, and cyber security has become a vital research area. An intrusion detection system (IDS) which is an important cyber security technique, monitors the state of software and hardware running in the network. Despite decades of development, existing IDSs still face challenges in improving the detection accuracy, reducing the false alarm rate and detecting unknown attacks. To solve the above problems, many researchers have focused on developing IDSs that capitalize on machine learning methods. Machine learning methods can automatically discover the essential differences between normal data and abnormal data with high accuracy. In addition, machine learning methods have strong generalizability, so they are also able to detect unknown attacks. Deep learning is a branch of machine learning, whose performance is remarkable and has become a research hotspot. This survey proposes a taxonomy of IDS that takes data objects as the main dimension to classify and summarize machine learning-based and deep learning-based IDS literature. We believe that this type of taxonomy framework is fit for cyber security researchers. The survey first clarifies the concept and taxonomy of IDSs. Then, the machine learning algorithms frequently used in IDSs, metrics, and benchmark datasets are introduced. Next, combined with the representative literature, we take the proposed taxonomic system as a baseline and explain how to solve key IDS issues with machine learning and deep learning techniques. Finally, challenges and future developments are discussed by reviewing recent representative studies.