ARTICLE | doi:10.20944/preprints201904.0160.v1
Subject: Engineering, Industrial And Manufacturing Engineering Keywords: digital supply chains; Industry 4.0; taxonomy; taxonomy of approaches
Online: 15 April 2019 (11:00:54 CEST)
Engineering the supply chain requires a design that possesses the flexibility of a complex adaptive system, consisting of interlinking architecture, with external dimensions and system germane internal elements. The complexity of the subject, the multiple environments, dimensions, elements and concepts, require a research that does not set any limits to the conceptual, analytical or empirical nature of the existing approaches present in practice. This present the rational for applying a taxonomy approach to investigate the integration engineering of supply chain architecture, design and engineering, and building a framework for integrating the existing supply chain approaches. The objectives of this paper are to critically analyse the key supply chain concepts and approaches, to assess the fit between the research literature and the practical issues of supply chain architecture, design and engineering, and to develop a methodology that could be used by practitioners when integrating supply chain architecture and design with strategy engineering. Taxonomy approach is applied to consider criteria for strategy architecture, hierarchical strategy design, strategy engineering, and integration of supply chain architecture, design and engineering as a conceptual system. The results from this paper derived with the findings that the relationship between supply chain architecture, design and engineering is weak and challenges remain in the process of adapting and aligning operations. This paper also derived with a novel approach for addressing these obstacles, based on a new methodology. The novelty that derives from this paper is a methodology for integrating supply chain architecture, design and engineering, with criteria that enable decomposing and building a digital (new and non-existent) supply chain as a system. The paper revealed a number of tools and mechanism which enabled the development of a new methodology for integrating the architecture, design and engineering of a supply chain. The review derived with improvements to current and existing theories for analysing interdependencies within and between their individual contexts. This issue is addressed with a hierarchical method for network design, applied for building and combining the integration criteria.
ARTICLE | doi:10.20944/preprints201905.0194.v1
Online: 15 May 2019 (12:08:36 CEST)
This work provides critical commentary on and corrections of a recently published taxonomy of Montiaceae. Valid citation and publication dates of novel taxa per the International Code of Nomenclature for Plants, Algae, and Fungi are summarized.
ARTICLE | doi:10.20944/preprints202101.0442.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Clavariaceae; fungal taxonomy; morphology.
Online: 22 January 2021 (12:07:39 CET)
Seventy-two clavarioid specimens from Johannes Rick's collection at PACA and BPI were revised. Eleven taxa are presented. Illustrations of the microstructures are provided for nine taxa. The description of Scytinopogon robustus includes information from recently collected specimens and SEM photographs of the basidiospores. A new combination, Clavulina ridleyi, is proposed.
REVIEW | doi:10.20944/preprints202307.1250.v1
Subject: Biology And Life Sciences, Other Keywords: tardigrade; reproduction; taxonomy; distribution; microbiome
Online: 18 July 2023 (14:14:36 CEST)
Paramacrobiotus species has been described from almost every corner of the world. To date 45 species have been reported from this genus. The species’ presence in different climatic conditions and habitat provides evidence of their adaptation to various harsh environments. In this review, we provide a concise summary of changes observed due to various cryptobiotic conditions in many species of this genus, geographical distribution of all the species, feeding behaviour, life history, microbiome community, Wolbachia endosymbiont identification, reproduction, phylogeny and general taxonomy of the species from genus Paramacrobiotus. Furthermore, we provide a new diagnostic key to the genus Paramacrobiotus based on the morphological and morphometric characters of adults and eggs.
CONCEPT PAPER | doi:10.20944/preprints202203.0069.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: prokaryotic taxonomy; classification; identification; genomics
Online: 3 March 2022 (17:18:57 CET)
Genomics has put prokaryotic rank-based taxonomy on a solid phylogenetic foundation. However, most taxonomic ranks were set long before the advent of DNA sequencing and genomics. In this concept paper, we thus ask the simple yet profound question: Should prokaryotic classification schemes besides the current phylum-to-species ranks be explored, developed, and incorporated into scientific discourse? Could such alternative schemes provide better solutions to the basic need of science and society for which taxonomy was developed, namely, precise and meaningful identification? A neutral genome-similarity based framework is then described that could allow alternative classification schemes to be explored, compared, and translated into each other without having to choose only one as the gold standard. Classification schemes could thus continue to evolve and be selected according to their benefits and based on how well they fulfill the need for prokaryotic identification.
CONCEPT PAPER | doi:10.20944/preprints202107.0546.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Bacterial nomenclature; taxonomy; microbial genomics
Online: 23 July 2021 (14:22:59 CEST)
The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names, while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice, while minimising difficulties. Adoption of linguistic pragmatism, obeying the rules while treating recommendations as merely optional will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed, while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.
ARTICLE | doi:10.20944/preprints202008.0608.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Pectobacterium; collection; taxonomy; host plants
Online: 27 August 2020 (09:43:59 CEST)
Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. To solve this difficulty, we analyzed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from non-host environments. MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. Results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species to the exception of P. polonicum. Yet, 6 strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, the P. versatile species, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. Analysis of P. versatile strains revealed that this species is endemic all over the world on various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from fresh water environment. Our work also revealed new host plants for several Pectobacterium spp.
REVIEW | doi:10.20944/preprints201911.0118.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Cnidaria; Hexacorallia; systematics; taxonomy; evolution
Online: 10 November 2019 (16:39:41 CET)
The present review provides an in-depth look into the complex topic of delimiting species in sea anemones. For most part of history this has been based on a small number of variable anatomic traits, many of which are used indistinctly across multiple taxonomic ranks. Early attempts to classify this group succeeded to comprise much of the diversity known to date, yet numerous taxa were mostly characterized by the lack of features rather than synapomorphies. Of the total number of species names within Actiniaria, about 77% are currently considered valid and more than half of them have several synonyms. Besides the nominal problem caused by large intraspecific variations and ambiguously described characters, genetic studies show that morphological convergences are also widespread among molecular phylogenies. On the contrary, spatial distribution has been emerging as a more reliable parameter to explain cryptic relationships among sea anemones. Integrative approaches and genome-wide data have been especially helpful to unveil the mechanisms behind the speciation process, which is typically marked by large genetic differences among populations, even from neighbouring localities. This paper further discusses current gaps in our knowledge and offers some future directions on how to address the issue of species delimitation in the extremely polymorphic group of sea anemones.
SHORT NOTE | doi:10.20944/preprints201904.0112.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Calandrinia, Cistanthe, Montiaceae, taxonomy, nomenclature.
Online: 9 April 2019 (12:49:18 CEST)
Calandrinia speciosa Lehm. and Calandrinia spectabilis Otto & Dietr. are 1830s-vintage validly-published names of Chilean plant species evidently pertaining to taxa currently classified in Cistanthesect. Cistanthe (Montiaceae). The taxonomic status of both names is problematic, because they were not typified or illustrated, their precise Chilean provenance is unknown, and their diagnoses/descriptions might apply to more than one species. Both names have been and continue to be applied taxonomically haphazardly. The existence of two later conceptually heterotypic synonyms of C. speciosa Lehm, viz. C. speciosa Lindl. non Lehm. and C. speciosa Hook. non Lehm., has exacerbated the confusion. The present work summarizes the history of the application of these names in botanical taxonomy and horticulture. Both likely, but not unequivocally, refer to plants of the later-described, typified, and otherwise well-documented species Calandrinia laxiflora Phil. [≡ Cistanthe laxiflora (Phil.) Peralta & D.I. Ford]. But persistent ambiguities justify proposals to reject both C. speciosa and C. spectabilis.
ARTICLE | doi:10.20944/preprints201810.0749.v1
Subject: Business, Economics And Management, Finance Keywords: Hellwig method; taxonomy; venture capital
Online: 31 October 2018 (10:38:26 CET)
Determining the level of PE/VC market development and the way it operates is extremely difficult. Despite countless reports and analyses concerning the PE/VC market, there is a lack of study on that sector based on a synthetic index. The usage of taxonomic methods in the PE/VC market analysis may be extremely useful in its proper characterizing. An in-depth study allows the identification of weaknesses and strengths as well as opportunities and threats related to a specific stage of PE/VC market development in a given country, that gives the opportunity to determine public activities that could affect the acceleration of this market development in future. The main objective of the study was to conduct a taxonomic analysis of the level of PE/VC market development in Europe, in 2010–2015. It is worth mentioning that the term “level of development” does not refer only to the value of investment or its dynamics, but to a set of objectified features that create one synthetic indicator. The conducted analysis using the Hellwig method allowed to determine the ranking of European countries in terms of the level of PE/VC market development, which reveal some significant differences in the functioning of the this market within Europe. Further detailed analysis of the designated groups of countries made it possible to determine the characteristics of such clusters. The construction of the level of private equity/venture capital market development ranking over the years enabled defining the current status and indicating the direction of possible changes.
ARTICLE | doi:10.20944/preprints202305.1117.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Palynology; Taxonomy; Pollen morphology; Convolvulaceae; Carajás.
Online: 16 May 2023 (07:24:00 CEST)
Canga vegetation has high ecological importance in the Serra dos Carajás, southeastern Amazonia, but it coexists with the potential threat of large-scale iron ore mining. Considering Convolvulaceae, this canga environment has only 17 species, and 15 of these species had their pollen grains described in detail in this present work, aiming to contribute to the taxonomic knowledge of critically endangered plants, including Ipomoea cavalcantei. Pollen grains were examined by light and scanning electron microscopy, and the morphological parameters obtained were statistically analyzed using principal component analysis. Therefore, Aniseia cernua was described for the first time in the literature. In general, the echinae morphology were the main differentiating character among the Ipomoea species and was the basis for the proposed pollen key. The family Convolvulaceae in Carajás is eurypalynous, and the genus Ipomoea may be classified as stenopalynous. The set of morphological characters statically treated and correlated was effective for the separation of Ipomoea.
ARTICLE | doi:10.20944/preprints202112.0146.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Chironomids; taxonomy; morphometry; principal component analysis
Online: 9 December 2021 (08:39:58 CET)
The larvae of some species of the subgenus Orthocladius s. str. (Diptera, Chironomidae) are here described for the first time with corrections and additions to the descriptions of adult males and pupal exuviae. The identification of larvae is generally not possible without association with their pupal exuviae and/or adult males, so the descriptions here are based only on reared material or on pupae with the associated larval exuviae. Usually, Chironomidae larvae can be separated on the basis of morphometric characters, and the most discriminant characters ones are: 1- the ratio between the width of median tooth of mentum (Dm) and the width of the first lateral tooth (Dl) = mental ratio (DmDl), 2- the ratio between the length of the first antennal segment (A1) and the combined length of segments 2-5 (A(2-5)2-5) = antennal ratio (AR). The shape of mandible, maxilla, and other body parts are almost identical in all the species considered in this study. The larva of Orthocladius (Symposiocladius) lignicola is very characteristic and can be separated by the shape of mentum and the larvae of all the known species of Symposiocladius are characterized by the presence of large Lauterborn organs on antennae and of tufts of setae on abdominal segments. The larvae of Orthocladius (Orthocladius) oblidens and Orthocladius (Orthocladius) rhyacobius can be distinguished from other species basing on their large Dm and to each other by AR. A principal component analysis was carried out using 5 characters: 1- Dm, 2- Dl, 3- length of A1, 4- width of A1 (A1W), 5- combined length of segments 2-5 (A2-5). The most discriminant characters were Dm and A1, confirming that DmDl and AR can be used to separate species at larval stage, but the large superposition of morphometric characters in different species confirms that association with pupal exuviae is in any case needed to identify larvae. In future perspective, the development of reference DNA barcodes from specimens identified by specialists is recommended since possibly the best tool for larvae identification, but association of barcodes with morphotypes is in any case fundamental.
COMMUNICATION | doi:10.20944/preprints202105.0701.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Natural products; databases; dereplication; taxonomy; NMR
Online: 28 May 2021 (12:59:37 CEST)
The recent revival of the study of organic natural products as renewable sources of medicinal drugs, cosmetics, dyes, and materials motivated the creation of general-purpose structural databases. Dereplication, the efficient identification of already reported compounds, relies on the grouping of structural, taxonomic and spectroscopic databases that focus on a particular taxon (species, genus, family, order…). A set of freely available python scripts, CNMRPredict, is proposed for the quick supplementation of taxon-oriented search results from the LOTUS database (lotus.naturalproducts.net) with predicted carbon-13 NMR data from the ACD/Labs (acdlabs.com) CNMR predictor and DB software to provide easily searchable databases. The database construction process is illustrated using Brassica rapa as taxon example.
ARTICLE | doi:10.20944/preprints201709.0047.v2
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Cyprinidae; Luciobarbus barbulus; Luciobarbus, Iran; taxonomy
Online: 1 October 2017 (06:30:03 CEST)
Western Iran barb species are scientifically, environmentally, and economically important. Some of them are the largest riverine freshwater species, which will grow in size and weight to 170 cm, and 120 kg respectively. There is little information on taxonomy or environmental status of these species Luciobarbus barbulus is one of the important large species. During the resent year since 2013, in order to find the new record of large barb species, sampling program carried out in western Iran,. Luciobarbus barbulus briefly described by Heckel (1849) but during the time, have been synonymized with other related species or vice versa, other similar species miss-identically have been known as this species. Also the synonymy of Luciobarbus barbulus with L. pectoralis remains uncertain. The possible syntypes of L. barbulus in Vienna Museum (NMW 53957 and NMW 6596) are in too poor condition to be of any value, being mostly bones, and are dried, and. The fleshy lip of NMW 6596, (measures 119.3 mm standard length) fold of the original description could not be discerned, teeth are missing and the dorsal fin is broken off short. In 1997 this was the only syntype recognized. The catalog in Vienna lists only 1 fish, while Heckel's description refers to several fishes!. So designing of Lecotype and re-description of L. barbulus is essential. In this paper the details of description and differences between these species are given.
ARTICLE | doi:10.20944/preprints201709.0135.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Cyprinidae; Luciobarbus barbulus; Luciobarbus; taxonomy; Iran
Online: 27 September 2017 (04:19:31 CEST)
Western Iran barb species are scientifically, environmentally, and economically important. Some of them are the largest riverine freshwater species, which will grow in size and weight to 170 cm, and 120 kg respectively. Although these species are vulnerable, there is little information on taxonomy or environmental status of the species Luciobarbus barbulus is one of the important large species. In order to find the new record on the present status of large barb species sampling program carried out in western Iran, during the resent year since 2013 to now. This species overlaps in distinction with L. mystaceus, L scheich, and other similar species. In this study re-description of L.barbulus is given. This species differs from L. mystaceus in having thick and very wide fleshy lip, inferior mouth and slightly shorter head. In Luciobarbus barbulus head is more inferior. The details of differences between these species are given. This species is one of stable growing fish without dimorphism, retain its shape from a fingerling species to a giant fish.
ARTICLE | doi:10.20944/preprints202309.0796.v1
Subject: Biology And Life Sciences, Parasitology Keywords: chiggers; taxonomy; Southeast Asia; parasites of birds
Online: 13 September 2023 (05:27:33 CEST)
Chigger mites were collected from 65 bird species in different regions of Thailand and Malaysia. In total, 21 species were recorded. The previously unknown fauna of chiggers parasitizing shorebirds of Thailand included one new species, Neacariscus (Whartonacarus) ... n. sp. as well as Neacariscus (Neacariscus) pluvius (Wharton, 1945) previously recorded only in Oceania; Neacariscus (Whartonacarus) shiraii (Sasa, Kano & Obata, 1952) (known from Oceania and Japan); and Neacariscus (Whartonacarus) sulae (Oudemans, 1910) and Schoengastia archaea (Taufflieb, 1960), both described from West Africa. Toritrombicula kirhocephales Goff, 1982 described from Papua New Guinea was for the first time recorded in Asia (Thailand). Neoschoengastia gallinarum (Hatori, 1920) and Helenicula comata (Womersley, 1952) were for the first time recorded in Thailand. Ascoschoengastia lorius (Gunther, 1939) was for the first time recorded in Malaysia. Finally, Ericotrombidium cosmetopode (Vercammen-Grandjean & Langston, 1971) described from free larvae, was for the first time recorded on a host (bird Pellorneum ruficeps Swainson); and Leptotrombidium miculum (Traub & Audy, 1954) was for the first time recorded on a bird host. New host species were recorded for the large part of the collected chigger species.
REVIEW | doi:10.20944/preprints202306.1753.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Botryosphaeriaceae; DNA sequence; Forest; Pseudofusicoccumaceae; Fungal Taxonomy
Online: 26 June 2023 (07:20:15 CEST)
The Botryosphaeriales order are best known for the diseases they cause in woody plants, as primary pathogens or latent pathogens residing in the woody tissue of asymptomatic hosts. In the first instance, Botryosphaeriales species have been identified in Venezuela using morphological de-scriptions in the 80's and 90's, and later, the mid-2000s using molecular techniques. The mor-phological descriptions of the asexual morphs were initially used for the identification of Botry-osphaeriales genera and species. Lasiodiplodia spp., (as L. theobromae) was the most isolated fungus in Venezuela within the Botryosphaeriales and has been found in more than 50% of the hosts in native and non-native plants, followed by Diplodia, Dothiorella, Fusicoccum, Lasiodiplodia, Micro-diplodia, Macrophomina, Neofusicoccum, Sphaeropsis, and Botryosphaeria, considered all of them cosmopolitan group. With molecular studies, that included DNA sequence data from multiple genes, such as the internal transcribed spacer of rDNA (ITS), translation elongation factor-1α (tef1), and β-tubulin (btub) used on the fungi isolated from woody plants, mainly trees or forest species, resulted in the presence of two families within the Botryosphaeriales order for Venezuela. Botryosphaeriaceae family with the genera: Botryosphaeria, Cophinforma, Diplodia, Lasiodiplodia and Neofusicoccum, and the Pseudofusicoccumaceae family that includes the genus Pseudofusicoccum. In Botryosphaeriaceae family was again the Lasiodiplodia genus the most predominant in most hosts, and the specie L. theobromae the most isolated in native and non-native plants; Botryosphaeria dothidea, Cophinforma atrovirens, Diplodia scrobiculata (syn. Diplodia guayanensis), Lasiodiplodia brasi-liensis, L. crassispora, L. pseudotheobromae, Neofusicoccum arbuti (syn. N. andinum), N. parvum, and N. ribis are cosmopolitan species, and they were isolated from native and non-native plants; while Pseudofusicoccum stromaticum was found in plantations non-native of Acacia mangium, E. urophylla x E. grandis, Eucalyptus urophylla, and reported exclusively in South America; Lasiodiplodia venezue-lensis has only been reported in Venezuela, from native and non-native plants. The presence, distribution, diversity, and symptoms of these fungi, mainly of the new genus, new species, and reports found in Venezuela and other parts of the world, were also reviewed.
ARTICLE | doi:10.20944/preprints202103.0578.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: ampelography; geometry; grapevine; morphology; peduncle; shape; taxonomy
Online: 24 March 2021 (12:00:37 CET)
Ampelography, the botanical discipline dedicated to the identification and classification of grapevine cultivars, was grounded on the description of morphological characters and more recently is based on the application of DNA polymorphisms. New methods of image analysis may help to optimize morphological approaches in ampelography. The objective of this study was the classification of representative cultivars of Vitis vinifera conserved in the Spanish collection of IMIDRA according to seed shape. Thirty eight cultivars representing the diversity of this collection were analyzed. A consensus seed silhouette was defined for each cultivar representing the geometric figure that better adjusted to their seed shape. All the cultivars tested were classified in ten morphological groups, each corresponding to a new model. The models are geometric figures defined by equations and similarity to each model is evaluated by quantification of percent of the area shared by the two figures, the seed and the model (J index). The comparison of seed images with geometric models is a rapid and convenient method to classify cultivars. A large proportion of the collection may be classified according to the new models described and the method permits to find new models according to seed shape in other cultivars.
ARTICLE | doi:10.20944/preprints202010.0203.v2
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Herbarium curation; Melastomataceae; Neotropics; New World; Taxonomy
Online: 19 October 2020 (11:16:45 CEST)
The following guide is aimed at aiding in the curation of herbarium collections in Melastomataceae, with an emphasis on the New World species. It contains a summary of the taxonomic realignments at the tribal and generic level within Neotropical taxa of Melastomataceae, as well as some general comments for other groups. A table with a generic linear sequence is also provided, as well as tables with new and synonymized New World genera since 2005 and all currently accepted species. Lastly, a table with the synonyms of over 1000 accepted Neotropical species that have been impacted by these generic realignments is also provided.
COMMUNICATION | doi:10.20944/preprints201809.0299.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: barcoding; biodiversity; genetics; mollusc; phylogeny; snails; taxonomy
Online: 17 September 2018 (10:30:16 CEST)
We aimed to apply DNA barcoding tool for the molecular identification of horn snails T. telescopium using mitochondrial cytochrome oxidase I gene (mt-COI) and to investigate their evolutionary relationship along with location-specific bio-geographical variations. The molecular data sets of this study indicate that strong probability of T. telescopium species taxonomic confirmation using mt-COI sequences. Results of the phylogenetic analysis suggest that Telescopium sp. was monophyletic with disseminated nodes and the evolution of group II originated from group I. The substantial genetic distance among the mt-COI sequences (0.005 to 0.184) were noticed. Large divergence between the south-west coast of India and Australia region population indicates limited gene flow between the two continents. Our study suggests that the genera Telescopium is globally ubiquitous but genetically showing inter-region differentiation. We conclude that mt-COI gene can be used to identify gastropod T. telescopium species.
ARTICLE | doi:10.20944/preprints202308.1364.v1
Subject: Biology And Life Sciences, Insect Science Keywords: biodiversity; COI; DNA barcoding; insects; Lepidoptera; Polyommatus; taxonomy
Online: 18 August 2023 (10:32:50 CEST)
The need for multi-gene analysis in evolutionary and taxonomic studies is generally accepted. However, sequencing of multiple genes is not always possible. For various reasons, short mito-chondrial DNA barcodes are the only source of molecular information for some species in many genera, although multilocus data are available for other species of the same genera. In particular, such a situation exists in the species-rich butterfly subgenus Polyommatus (Agrodiaetus). Here, we analysed partitioning of this subgenus into species groups by using three data sets. The first data set was represented by short mitochondrial DNA barcodes for all analysed samples. The second and third data sets were represented by combination of short mitochondrial DNA barcodes for a part of the taxa with longer mitochondrial sequences COI+tRNA-Leu+COII (data set 2) and with longer mitochondrial COI+tRNA-Leu+COII and nuclear 5.8S rDNA+ITS2+28S rDNA sequences (data set 3) for the remaining species. We show that DNA barcoding approach (data set 1) failed to reveal the taxonomic structure resulting in numerous polytomies in the phylogenetic tree ob-tained. Combined analysis of the mitochondrial and nuclear sequences (data sets 2 and 3) re-vealed the species groups and position within these species groups even for the taxa for which only short DNA barcodes were available.
ARTICLE | doi:10.20944/preprints202202.0117.v1
Subject: Biology And Life Sciences, Virology Keywords: Bunyavirales; Nairoviridae; Peribunyaviridae; Phenuiviridae; taxonomy; nomenclature; species demarcation
Online: 8 February 2022 (14:38:01 CET)
In recent years, the taxonomy of the families of Phenuiviridae, Nairoviridae, and Peribunyavidae in Bunyavirales was updated frequently, because many novel viruses in these families have been identified and the species demarcation criteria of these families have been changed. As per these criteria and sequence analysis, we found that the taxonomy of 19 species in these families should be revised. We presented six proposals for optimizing virus species taxonomy using the examples from these families. First, the species demarcation criteria for the same family (e.g., Peribunyavidae) should be unified. Second, the methods and parameters for the taxonomic calculation in the same order (e.g., Bunyavirales) should be unified. Third, virus species taxonomy should be based on phylogenetic relationships, rather than a cutoff value of sequence identities that is a self-contradictory demarcation criterion, although sequence identities aid virus taxonomy greatly. Fourth, virus species taxonomy should be based on the phylogenetic relationship of a key viral gene (e.g., the RdRp gene of Bunyavirales), which is important for the taxonomy of virus recombinants or reassortants. Fifth, a virus can be demarcated without a species before its biomedical significance has been revealed. Sixth, names of all viruses and virus species should be constituted exclusively with common characters (English letters and Arab numbers), to minimize difficulty in spelling and communication. These proposals are rational, flexible, and can accommodate all known viruses. They can also bridge the taxonomy history and the future demands due to their flexibility.
REVIEW | doi:10.20944/preprints202201.0310.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: DNA barcoding; metabarcoding; BOLD; taxonomy; biodiversity; molecular marker.
Online: 20 January 2022 (15:15:36 CET)
Systematics plays the most crucial role in biodiversity conservation which is at stake due to anthropogenic activities and environmental degradations. The ever-increasing decline of classical taxonomic expertise drives the need to develop molecular marker-based tools for quick, efficient, and reliable detection of organisms, to assess their ecological impacts for deepening our understanding of systematic and evolutionary relationships between organisms which is central to biology. The pace of alpha taxonomy has quickened by its integration with an increasingly fashionable and novel concept called DNA barcoding which utilizes a short genetic marker or barcode to categorize species for enhanced biodiversity assessment. As a supplementary but not complete alternative of systematics research, DNA barcoding, however, not error-free, brings precision in identification by solving existing problems of classical taxonomy and phylogenetics, irrespective of the growth stage of organisms, particularly for known taxa rather than unknown ones. Mitochondrial gene Cytochrome C Oxidase 1 (COI) serves as a universal animal barcode but there is no such universal barcode for plants and developing a suitable one is more challenging. With the recent advancement of Next Generation Sequencing (NGS), DNA metabarcoding technology is advancing rapidly. Still, ambiguity and error prevail with the correct identification of species due to some problems. After extensive analysis of the existing DNA barcoding papers, this review discusses commonly used DNA barcodes in plants and animals, their roles, advantages, limitations to solve existing problems of conservation biology and add the author’s views and recommendations.
ARTICLE | doi:10.20944/preprints202110.0229.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Canary Islands; cryptic invasion; molecular phylogeny; Persicaria; taxonomy
Online: 15 October 2021 (14:34:13 CEST)
A cryptic invader of the genus Persicaria is recently increasing in the damper, northern parts of La Palma and Gran Canaria in the Canary Islands (Spain) and locally behaves as an invasive species. Examination of historical herbarium specimens showed this species to be present in Gran Canaria since the 1960’s and the same probably applies to La Palma. Up to now, this species had been assigned to the Old World weed P. maculosa. However, morphologically these plants clearly correspond with P. hydropiperoides, a common and widespread weed native to the New World, and morphologically similar indeed to P. maculosa. Diagnostic features for these two species, as well as for another similar species (P. decipiens, originally described from the Canary Islands), are compared, thoroughly discussed and copiously illustrated. The current distribution, ecology and naturalization status of P. hydropiperoides in the Canary Islands are also assessed. The variability of P. hydropiperoides is discussed, more precisely the taxonomic position of a southern ‘race’ of it that is sometimes referred to as a distinct species, P. persicarioides. In addition to our morphology-based study, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the plastid DNA region trnL-F.
CONCEPT PAPER | doi:10.20944/preprints202010.0160.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: nomenclature; Candidatus; metagenome-assembled genomes; genome-based taxonomy
Online: 7 October 2020 (15:08:01 CEST)
Latin binomials, popularised in the eighteenth century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent unmet need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: marine nematodes; mtCOI; DNA taxonomy; meiofauna; Mexican Caribbean
Online: 4 July 2019 (09:51:50 CEST)
Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first on the taxonomy of Mexican nematodes to integrate morphological and molecular data. We add seven new morphological records for the Mexican Caribbean: Anticomid sp1, Cylicolaimus sp1, Oncholaimus sp2, Platycoma sp1, Catanema sp1, Enopliodes spp., and Metachromadora spp. We recover 55 COI sequences that represent 20 species. Of the studied sites, Cozumel had 12 species and Cancún had two species (Rhips sp1 and Monoposthia mirabilis) represented by several individuals. All sequences are new for the genetic international databases GenBank and BOLD. Phylogenetic analyses and species delineation methods support the occurrence of the 20 entities and confirm the high resolution of COI sequences in delimiting species. ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. DNA taxonomy was demonstrated to be an efficient, fast, and low-cost method to address a taxonomical shortfall of meiofaunal organisms.
ARTICLE | doi:10.20944/preprints201904.0329.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Cistanthe; Chilean floristic region; species; specioids; taxonomy; nomenclature
Online: 6 May 2019 (09:37:06 CEST)
Cistanthe subspeciosa Hershk. (Cistanthe Spach sect. Cistanthe; Montiaceae) here is described as a herbaceous to suffruticose perennial from the vicinity of Copiapó, Chile. Its epithet is juxtaposed with its rank in order to highlight its subspecific aesthetic. In particular, the specioid is infrequent, locally restricted, and lacks unique diagnostic traits. Rather, it is diagnosed by a combination of traits characteristic of different Cistanthe species from the region, none of which can be identified as the referential species to which Cs. subspeciosa might be considered subspecific. The intersection between species nomenclature and species ontology thus is discussed. I hypothesize that Cs. subspeciosa is irrigated primarily by mountain runoff rather than localized precipitation, and that it might be both resistant to and dependent upon high substrate metal concentrations characteristic of the Copiapó region. The ornamental value of this and other Cistanthe species is discussed. Finally, additional historical details pertaining to Calandrinia spectabilis Otto & Dietr. and Cistanthe philhershkovitziana are provided.
ARTICLE | doi:10.20944/preprints202308.1208.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Mitochondrial genome; Calanoida; Arthropod phylogeny; Molecular taxonomy; Chennai coast
Online: 16 August 2023 (11:18:22 CEST)
Copepods are the most abundant metazoans on Earth, exhibit remarkable species diversity and global distribution. Accurate species identification of copepods presents a challenge due to their cryptic nature, necessitating meticulous examination and differentiation. To address this challenge, innovative approaches utilizing molecular markers have emerged, enabling more reliable and precise species identification. Mitochondrial genes, which are characterized by high variability, have proven invaluable in uncovering taxonomically significant variations among copepod species. In this study, we present the first complete mitochondrial genome analysis of the marine calanoid copepod Bestiolina similis (Sewell, 1914). Recent investigations employing whole mitochondrial genome-based phylogenetic analyses have generated considerable interest in exploring the deep branching patterns of arthropods. The complete mitochondrial genome of B. similis spans 23,704 base pairs and includes 13 protein-coding genes and 20 transfer RNA genes. The nucleotide composition of the mitochondrial genome is characterized by 43.42% adenine, 43.22% thymine, 6.48% guanine, and 6.88% cytosine. Maximum likelihood-based phylogenetic analysis of the mitochondrial genome were constructed of the available copepod species. Mitochondrial ge-nome-based phylogenies often reveal intriguing and distinctive topologies compared to traditional phylogenetic approaches. However, the sequencing of copepod mitochondrial genomes, particularly within the calanoid copepods remains limited. Therefore, this study aims to construct a phylogenetic tree based on the extracted mitochondrial genome, incorporating available data, to enhance our understanding of the evolutionary relationships among calanoid copepods.
ARTICLE | doi:10.20944/preprints202306.0212.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Cheiridiidae; False scorpions; Levant; Species List; Syarinidae; Taxonomy; Zoogeography
Online: 2 June 2023 (14:16:19 CEST)
The location of Israel at the junction of three continents leads to a unique faunal combination of Palearctic and Afrotropic zoogeographic origins. Following systematic revisions over the past sixty years and the discovery of new species, the only available key to the pseudoscorpions (Arachnida: Pseudoscorpiones) of Israel (Beier 1963) has become outdated. We provide here an up-to-date checklist of the pseudoscorpion species of Israel including distribution maps, and the first illustrated identification key of the Israeli fauna based on morphological characters. Prior to our study this fauna comprised twelve families, 26 genera and 52 morphospecies, including several “subspecies”. We increase this number and list 61 pseudoscorpion morphospecies that belong to 28 genera and fourteen families. Most species are Palearctic and Mediterranean, and only a few are Afrotropic. Two families new to Israel are reported here for the first time: Syarinidae and Cheiridiidae. Both families are cosmopolitan and have representatives in the Mediterranean region. The putative new species are presented here at a genus level and will be described separately elsewhere.
ARTICLE | doi:10.20944/preprints202201.0425.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transposon; order; triplet frequency; tRNA; clustering; taxonomy; symmetry; photosystem
Online: 27 January 2022 (17:40:07 CET)
A comprehensive presentation of a variety of biologically sounding properties of genomes is present; chloroplast genomes are used as a biological matter. Triplet frequency composition is the general issue standing behind the properties. Besides, the new alignment-free error-tolerant method of sequences comparison highly efficient for in/del mismatches is present, for transposons search. Triplet frequency dictionaries determined for a genome, or for a part of that latter were studied through various clustering techniques. The interplay between triplet composition and function reveals on tRNA genes unambiguously shows the prevalence of the function encoded in tRNA gene over the phylogeny: the genes gather into the clusters comprising the genes encoding the same amino acid; more exactly, few gene families exhibit fine cluster pattern corresponding the synonymous codons of amino acid. Previously reported symmetry in chloroplast genomes is shown for a set of gymnosperm: that is mirror symmetry, rotational symmetry, and the second Chargaff's parity rule asymmetry. A family of transposons was found in gymnosperm chloroplast genomes. This family is revealed through the novel comparison method based on convolution calculation, for a set of DNA sequences.
REVIEW | doi:10.20944/preprints202111.0463.v2
Subject: Environmental And Earth Sciences, Paleontology Keywords: taxonomy; biogeography; evolution; domestication; dispersal; pollen; archaeology; hemp; drugs
Online: 2 December 2021 (08:55:17 CET)
Cannabis is among the oldest human domesticates and has been subjected to intensive artificial (human-mediated) selection throughout history to create a wide array of varieties and biotypes for diverse uses, including fibre, food, biofuel, medicine and drugs. This paper briefly reviews the available literature on the taxonomy, evolutionary origin and domestication of this plant, as well as its worldwide dispersal, in both its wild and cultivated forms. Emphasis is placed on Europe and especially on the Iberian Peninsula. Today, it is accepted that Cannabis is a monospecific genus with two subspecies, C. sativa subsp. sativa and C. sativa subsp. indica, originating in Europe and Asia, respectively, by allopatric differentiation after geographic isolation fostered by Pleistocene glacial-interglacial cycles. Palynological and phylogeographic evidence situates the Cannabis ancestor on the NE Tibetan Plateau during the mid-Oligocene. The timing and place of domestication is still a matter of debate between contrasting views that defend single or multiple Neolithic domestication centres situated in different parts of the Eurasian supercontinent, notably central/southeastern China and the Caucasus region. Recent meta-analyses have suggested that wild Cannabis may have already been spread across Europe in the Pleistocene, and its domestication could have occurred during the European Copper/Bronze ages. According to the available reviews and meta-analyses, pre-anthropic dispersal of Cannabis into the Iberian Peninsula seems to have occurred only in postglacial times, and the earlier signs of cultivation date to the Early Medieval Ages. However, the palynological and archaeological evidence used to date is insufficient for a sound assessment, and the development of thorough Iberian databases to address further meta-analysis is essential for more robust conclusions. Some clues are provided for these achievements to be fulfilled.
ARTICLE | doi:10.20944/preprints202306.1515.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: 6 new taxa; ascomycetes; asexual morph; filamentous fungi; phylogeny; taxonomy
Online: 21 June 2023 (09:44:52 CEST)
Helicosporous hyphomycetes is a class of filamentous fungi that shows promising application prospects in metabolizing bioactive natural compounds. During a study of helicosporous fungi in China, six new helicosporous taxa were collected and isolated from decaying wood in Guangxi Zhuang Autonomous Region, China. Morphological comparisons with multi-gene phylogenetic analyses revealed that these six taxa belong to Helicosporium (Tubeufiaceae, Tubeufiales), and they can be recognized as three novel species, named Helicosporium liuzhouense, H. multidentatum and H. nanningense. Detailed descriptions and illustrations of the newly discovered taxa and comparisons with similar fungi are provided. In addition, a list and a key to accepted Helicosporium species are provided.
ARTICLE | doi:10.20944/preprints202305.0755.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Causality extraction; Organizational data; Stakeholder Taxonomy; Natural Language Processing; NLP
Online: 10 May 2023 (13:36:31 CEST)
This article presents a state-of-the-art system to extract and synthesize causal statements from company reports into a directed causal graph. The extracted information is organized by the relevance to different stakeholder groups’ benefits (customers, employees, investors, and the community/environment). The presented method of synthesizing extracted data into a knowledge graph comprises a framework that can be used for similar tasks in other domains, e.g. medical information. The current work addresses the problem of finding, organizing, and synthesizing a view of the cause-and-effect relationships based textual data, in order to inform and even prescribe the best actions that may affect target business outcomes related to different stakeholders’ benefits (customers, employees, investors, and the community/environment).
ARTICLE | doi:10.20944/preprints202211.0405.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: sustainability; solar energy; land-use; Taxonomy regulation; territorial planning; biodiversity
Online: 22 November 2022 (04:05:51 CET)
Solar energy (SE) is essential for decarbonization of our economy and for energetic transition. Solar energy can be a sustainable economic activity as long as a balance is struck between the benefits it brings to climate change mitigation and the damage it can cause to biodiversity and ecosystems. Here we study this balance in an area with high biodiversity under pressure for installation of numerous photovoltaic plants (PPs). Our results show that developers give priority to the cheapest land close to connection points, while other values (e.g., environmental, landscape) are secondary. The regulatory process carried out by the Administration does not ensure the preservation of natural values, as several PPs with a high impact on important conservation areas have been approved. Experts' allegations provide quality information to the Administration to evaluate and demand changes to the projects presented. Such demands show that companies are willing to relocate plants to land occupied by olive groves. In this way, greater efficiency is achieved in land occupation, as well as shorter evacuation lines, water savings and less environmental impact. Prior strategic territorial planning could have avoided the impact of PPs already built, made the deployment of new PPs compatible with biodiversity conservation, and contributed to improving the management of key resources, such as subway aquifers. The proposed regulatory changes to the environmental assessment procedure (exclusion of renewables and public participation from the procedure) are detrimental, as they will make SE unable to meet the requirements of the Taxonomy Regulation.
ARTICLE | doi:10.20944/preprints202111.0557.v1
Subject: Biology And Life Sciences, Virology Keywords: Bacterial nomenclature; archaeal nomenclature; genome taxonomy; shotgun metagenomics; Candidatus names
Online: 30 November 2021 (10:53:50 CET)
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.
ARTICLE | doi:10.20944/preprints202102.0623.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: history of biology; history of zoology; taxonomy; biological nomenclature; metazoans
Online: 26 February 2021 (15:32:17 CET)
The great 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 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). This study suggests that even though taxonomy was clearly 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.
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Rhodococcus equi; Rhodococcus hoagii; bacterial nomenclature; bacterial taxonomy; bacterial systematics
Online: 2 February 2020 (06:56:32 CET)
A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified to Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Being R. equi a well-known animal and zoonotic human pathogen, and the name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii, ATCC 7005T, does not correspond with the original description of C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii clearly designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii, does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mixup with a Corynebacterium (Rhodococcus) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi, according to Rules 56ab of the Code.
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: corticolous; Dong Nai; Nam Cat Tian National Park; Porinaceae; taxonomy
Online: 8 April 2019 (13:30:10 CEST)
An identification key to twenty-nine species of Porina known from the country is provided. In addition, new records of Porina interstes, P. nuculastrum, and P. rhaphidiophora are described from the protected rain forests in southern Vietnam. A detailed taxonomic account of each species is provided and supported by its ecology, distribution, and illustrations.
ARTICLE | doi:10.20944/preprints201808.0496.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Montiaceae, taxonomy, phylogeny, biogeography, evolution, Calandrinia, Cistanthe, Lewisiopsis, Philippiamra, Rumicastrum
Online: 8 October 2018 (14:02:59 CEST)
Montiaceae (Portulacineae) comprise a clade of at least 270 species primarily of western America and Australia. This work uses existing phylogenetic metadata to elaborate a new cladistic taxonomic synthesis, and clarifies morphological circumscriptions of several poorly known species. A total of 21 taxa are validated, seven new and 14 necessary nomenclatural recombinations). Hypotheses of Montiaceae historical biogeography and phenotypic evolution are evaluated in light of recent metadata.
ARTICLE | doi:10.20944/preprints202308.1674.v3
Subject: Biology And Life Sciences, Insect Science Keywords: China; Sycanus; taxonomy; DNA barcoding; species delimitation; phylogeny; new species; biology
Online: 5 September 2023 (02:40:40 CEST)
Due to the variation of the body coloration and the similarity of the related species, there are still some unresolved problems and debates in the taxonomic study of the genus Sycanus in China. We conducted the inter-specific phylogenetic analyses and the species delimitation for Sycanus in China based on DNA barcoding dataset of the mitochondrial cytochrome c oxidase subunit I gene of 81 samples and partial 28S rDNA sequences of 34 samples. The result showed that all the samples were divided into twelve species by integrating the results of DNA barcoding and morphological comparison. In the present paper, the genus Sycanus in China was reviewed systematically, all species were described or re-described, keyed, illustrated and photographed, among them, Sycanus taiwanensis Zhao & Cai sp. nov., Sycanus flavicorius Li & Cai sp. nov. and Sycanus hainanensis Wang & Cai sp. nov. were described as new to science. The biological informations of Sycanus falleni Stål, 1863 and Sycanus croceus Hsiao, 1979 were briefly recorded.
DATA DESCRIPTOR | doi:10.20944/preprints202106.0368.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Microbial Mash database, Mash distance, Genome containment, Type material, Microbial taxonomy
Online: 14 June 2021 (14:54:32 CEST)
The analysis of curated genomic, metagenomic, and proteomic data are of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw form in free international repositories, its access requires plenty of computing, storage, and processing capacities for the domestic user. The purpose of the study is to offer a comprehensive set of genomic and proteomic reference data, in an accessible and easy-to-use form to the scientific community. A representative type material set of genomes, proteomes and metagenomes were directly downloaded from the site: https://www.ncbi.nlm.nih.gov/assembly/ and from Genome Taxonomy Database, associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy raw reduced representations, by using Mash software. Our dataset contains near to 100 GB of space disk reduced to 585.78 MB and represents 87,476 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with computational resources. Potential uses of this dataset include but are not limited to, microbial species delimitation, estimation of genomic distances, genomic novelties, paired comparisons between proteomes, genomes, and metagenomes.
ARTICLE | doi:10.20944/preprints202305.1524.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ascomycota; asexual fungi; marine fungi; multi-locus phylogeny; new taxa; taxonomy; ultrastructure
Online: 22 May 2023 (12:25:58 CEST)
The genus Amphichorda has been recently re-erected as an independent linage from Beauveria, circumscribed within Cordycipitaceae. However, its phylogenetic relationships with other members of this family remain obscure. In our on-going efforts to expand the knowledge on the diversity of culturable ascomycetes from the Mediterranean Sea, we isolated several specimens of Amphichorda. Preliminary sequence analyses revealed great phylogenetic distance with accepted Amphichorda species and a close relation to Onychophora coprophila. Onychophora is a monotypic genus of enteroblastic conidiogenous cells, presumably related to Acremonium (Bionectriaceae); while Amphichorda exhibits holoblastic conidiogenesis. Here, we examine representative strains of Amphichorda species to resolve the taxonomy of the genus and the above-mentioned fungi combining morphological, ultrastructure and multi-locus phylogenetic analyses (ITS, LSU, tef1, BenA). The results revealed Amphichorda as a member of the Bionectriaceae, where its asexual morphs represent a transition between enteroblastic and holoblastic conidiogenesis for this group of fungi. We also describe and illustrate Amphichorda littoralis sp. nov., and propose the new combination Amphichorda coprophila. In addition, we stablish key phenotypic features to distinguish Amphichorda species and demonstrate the higher salt tolerance degree of A. littoralis, consistent with its marine origin. This work provides a comprehensive framework for future studies in the genus.
Subject: Biology And Life Sciences, Plant Sciences Keywords: Calandrinia compressa; Calandrinia pilosiuscula; Montiaceae; Chilean Floristic Region; taxonomy; nomenclature; natural history
Online: 25 June 2020 (15:45:13 CEST)
Calandrinia compressa Schrad. ex DC (Prodr. 3: 359. 1828) is the name currently widely applied to a polymorphic annual species of Calandrinia sect. Calandrinia endemic to the Chilean Floristic Region. A total of ten validly published heterotypic names plus six horticultural designations (and orthographic variants thereof) have been considered at some point as taxonomically the same as C. compressa. Two additional heterotypic taxa and their synonyms and two other designations possibly refer to this species. Two other taxa sometimes referred to this species are excluded. I treat here a total of 77 distinct nomenclaturally valid names and invalid designations and variants thereof. The type of one of the valid and legitimate names, Calandrinia pilosiuscula DC (Rev. Portulac. 9. 1827), is judged here to be taxonomically the same as the type of C. compressa. Because of its chronological priority, Calandrinia pilosiuscula DC must be accepted as the correct name for Calandrinia compressa Schrad. ex DC when the two are considered taxonomic synonyms. Here, the taxonomic history of this taxon is articulated and, where possible, types are identified and/or designated. The natural and anthropogenic history of the species is summarized critically in a theoretical context.
ARTICLE | doi:10.20944/preprints202305.1744.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Frankenia; Frankeniaceae; nomenclature; ITS phylogeny; plant endemics; plant morphology; southern African flora; taxonomy
Online: 25 May 2023 (05:44:36 CEST)
The taxonomic identity and phylogenetic relationships of several southern African perennial taxa related to Frankenia repens are discussed. In particular, F. nodiflora Lam., a misunderstood species described from the Cape region and synonymised to F. pulverulenta, is restored for plants endemic to salt-pans and riverbeds in the coastal lowlands across the Cape plains (Western Cape Province, South Africa). Further, a revision of morphologically close plants, usually identified as F. pulverulenta or F. repens, also occurring in similar saline ecosystems of the inland western South Africa revealed the existence of two distinct new entities not matching any described taxa of the genus. Molecular analyses of nuclear ribosomal (ITS1-5.8S-ITS2 region) DNA sequence data together with morphological divergence allow recognition of those taxa at species rank, within an independent lineage close to F. repens. In consequence, two new species are described in the so-called “F. repens group”: F. nummularia from the Nama-Karoo Biome (Western Cape and Northern Cape Provinces), and F. namaquana from the Succulent Karoo Biome (Northern Cape Province). Full morphological description and type designation are reported for each accepted species, as well as data on ecology, habitat, distribution and taxonomic relationships to other close relatives are given. Further, an identification key is presented to facilitate recognition of the southern African taxa of Frankenia.
ARTICLE | doi:10.20944/preprints202011.0589.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Orchid, Longifoliae; Speciosae; Fuliginosae; Flaccidae; Coelogynae; Tomentosae; Verrucosae; phylogeny; morphology; taxonomy; Malaysia; classifications
Online: 23 November 2020 (14:23:47 CET)
The phylogenetic relationships among the Peninsular Malaysian orchid genus Coelogyne were studied by morphological characteristics and by sequencing the internal transcribed region (ITS) from the nuclear ribosomal DNA (nrDNA). Coelogyne is a large genus of about 200 species distributed in pantropical areas from the Himalayas, Sri Lanka, India, Southern China and throughout South East Asia to Papua New Guinea. The widely accepted previous classification system was exclusively based on floral morphology. There were very few molecular systematic studies of Coelogyne done in Peninsular Malaysia thus far. In this study, 59 Coelogyne taxa were collected from throughout Peninsular Malaysia and 57 of them were identified to the species level. To study the phylogeny of this genus, morphological characters were utilized together with molecular evidences to generate the systematic hypotheses. Cluster analysis was performed using both the vegetative and floral characters. The results showed that three sections of Peninsular Malaysian Coelogyne, namely Longifoliae, Speciosae and Fuliginosae were sister groups which were more closely related by forming one clade than they were with the other sections. Another clade consisted of four other sections, namely Flaccidae, Coelogynae, Tomentosae and Verrucosae. Molecular phylogenies obtained by using the Neighbour Joining method revealed the close relationship between the sections Tomentosae and Verrucosae, whereas usage of the Maximum Likelihood method demonstrated that three sections namely Longifoliae, Speciosae and Fuliginosae were sister groups since they formed a single clade.
ARTICLE | doi:10.20944/preprints201810.0378.v1
Subject: Business, Economics And Management, Business And Management Keywords: sustainable development; sustainability; business model; sustainable business model; modeling; review; survey; classification; taxonomy
Online: 17 October 2018 (08:34:46 CEST)
A sustainable business model describes the rationale of how an organization creates, delivers, and captures value, in economic, social, cultural or other contexts in a sustainable way. The process of sustainable business model construction forms an innovative part of business strategy. Different industries and business types have utilized sustainability business models to satisfy their economic, environmental and social goals simultaneously. This study is conducted to present the state of the art of sustainable business models in various application areas. The business models are classified and reviewed in different application groups. To do so, a review is conducted, and the findings reveal that the application of sustainability business models can be classified in 16 unique categories. The key contribution of this study is providing an insight about the state of the art of sustainable business models in various application areas and its research path.
REVIEW | doi:10.20944/preprints202309.0352.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ectoparasite; Taxon cycle; relict; Great speciator; Invasive species; Supertramp; Endangered species; Conservation; Taxonomy; Phylogeny
Online: 6 September 2023 (03:30:42 CEST)
This overview of extant Siphonaptera lists 19 families with major hosts and general distribution, estimated numbers of genera, species, and subspecies, with a brief taxonomic and phylogenetic review. With around 10 new species described annually, global flea fauna has an estimated extant 249 genera, 2215 species, and 714 subspecies, mostly mammal parasites but 5% of species are on birds. Host specificity varies from euryxenous (i.e. infesting two or more host orders)(e.g. cat fleas, Ctenocephalides felis felis) to monoxenous (e.g. rabbit fleas, Spilopsyllus cuniculi) . The largest family is the paraphyletic Hystrichopsyllidae, making up a third of all flea species. The largest monophyletic family, Ceratophyllidae (rodent and bird fleas), comprise another 20%, and has dispersed to every continent including Antarctica. Fleas descend from scorpionflies (Mecoptera), possibly snow scorpionflies (Boreidae) or Nannochoristidae, and even giant fossils found from the Mesozoic could be Siphonaptera. Flea diversification shows evidence of taxon cycles: "Relict" families such as helmet fleas (Stephanocircidae) have a disjunct distribution reflecting the breakup of Gondwanaland, 70 million years ago. "Niche specialists" include nest fleas (Anomiopsyllus), bat fleas (Ischnopsyllidae), and burrowing fleas, the chigoes (Tungidae). By contrast, Ceratophyllidae fleas could be considered "great speciators". Cat fleas and several other synanthropic flea species are invasive "supertramps". Although those species are intensively studied, many flea species and their hosts require urgent surveys and conservation.
ARTICLE | doi:10.20944/preprints202012.0297.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Rhizobium; species complex; bacterial taxonomy; core genes; housekeeping genes; average nucleotide identity; speciation; genospecies
Online: 12 December 2020 (11:51:22 CET)
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at around 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterise isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterising the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
ARTICLE | doi:10.20944/preprints202305.1701.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: ITS phylogeny; plant endemics; plant morphology; South African flora; Spergularia; Sperguleae; taxonomy; trnL-trnF phylogeny.
Online: 24 May 2023 (05:20:49 CEST)
The name “Spergularia hanoverensis Simon” has been misapplied for an endemic taxon confined to inland semi-desert ecosystems in central-western South Africa. It is commonly accepted to be a small annual species occurring in saline habitats in a wide elevation range, but its real identity still remains obscure. In the context of a taxonomic and phylogenetic research on the African species of Spergularia, we found that the name apparently was never validly published still. After revision of herbarium material housed in the South African herbaria, a voucher collected from Hanover was found at PRE bearing some labels handwritten by E. Simon that suggest it might be an intended type for the name. Additional herbarium material and wild populations from Karoo region were identified that matched the samples in that voucher, and taxonomic research was conducted to clarify their identity. Those Karoo plants show a woody dense compact habit, woody perennial at base; stems prostrate to ascendent; leaves entirely glabrous, somewhat glaucous; with large white-hyaline conspicuous stipules; inflorescence glanduliferous, many-flowered subdichasial cyme, with minute bracts; flowers small, with white petals about equalling sepals, stamens 78, and styles free from base; capsule small, with seeds dimorphic, unwinged to broadly winged, with testa always densely tuberculate, among other characters. Molecular analyses of plastid (trnL-trnF region) and nuclear ribosomal (5.8S-ITS2 region) DNA sequence data support morphological differentiation of the Karoo plants, for which the name S. hanoverensis is here effectively published. A full morphological description, as well as data on ecology, habitat, distribution, and taxonomic and phylogenetic relationships of S. hanoverensis are compared to other members of the “South African group”, namely S. glandulosa. S. namaquensis, and S. quartzicola, from which the new species considerably differs. Adaptative significance of dimorphic seeds of S. hanoverensis is briefly commented in context to habitat preference of the species. An identification key is presented for the South African related taxa.
ARTICLE | doi:10.20944/preprints202308.1358.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: artificial intelligence; classification models; educational data mining; educational machine learning; feature selection; student performance prediction; taxonomy
Online: 18 August 2023 (09:52:57 CEST)
. Identifying students who might have difficulty in their course of studies ahead of time is crucial. There can be many reasons for performance issues, such as personality, family, social, and/or economic. We advocate that educational systems should use machine learning to predict students’ performance based on performance factors. This would allow educational professionals and institutions to put in place a preventive plan to help students towards achievements of their educational goals and success. In this chapter, we propose a student performance prediction method and evaluate its performance. We provide a taxonomy of performance factors that help to gauge students performance from different perspectives and give insights on the categories and features that have more significant impact on students’ performance. The results of this work can be used by education institutions to put in place a student-centric approach to tackle performance issues before they create long-term effects on student’s life. In addition, it will help education policymakers to introduce a tailored approach for the population in specific areas.
ARTICLE | doi:10.20944/preprints202208.0197.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: Deep neural networks; Adversarial Attacks; Poisoning; Backdoors; Trojans; Taxonomy; Ontology; Knowledge Base; Explainable AI; Green AI
Online: 10 August 2022 (09:39:07 CEST)
Deep neural networks (DNN) have successfully delivered a cutting-edge performance in several fields. With the broader deployment of DNN models on critical applications, the security of DNNs becomes an active and yet nascent area. Attacks against DNNs can have catastrophic results, according to recent studies. Poisoning attacks, including backdoor and Trojan attacks, are one of the growing threats against DNNs. Having a wide-angle view of these evolving threats is essential to better understand the security issues. In this regard, creating a semantic model and a knowledge graph for poisoning attacks can reveal the relationships between attacks across intricate data to enhance the security knowledge landscape. In this paper, we propose a DNN Poisoning Attacks Ontology (DNNPAO) that would enhance knowledge sharing and enable further advancements in the field. To do so, we have performed a systematic review of the relevant literature to identify the current state. We collected 28,469 papers from IEEE, ScienceDirect, Web of Science, and Scopus databases, and from these papers, 712 research papers were screened in a rigorous process, and 55 poisoning attacks in DNNs were identified and classified. We extracted a taxonomy of the poisoning attacks as a scheme to develop DNNPAO. Subsequently, we used DNNPAO as a framework to create a knowledge base. Our findings open new lines of research within the field of AI security.
REVIEW | doi:10.20944/preprints202202.0284.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Recreational fisheries fishery management; introgressive hybridization; stocking; non-native species; allochthonous species; trout fishing; trout taxonomy
Online: 23 February 2022 (03:09:39 CET)
During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the Southwestern Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.
ARTICLE | doi:10.20944/preprints202107.0335.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Pseudomonadaceae; long-read sequencing; hybrid assembly; Taxonomy; Phylogeny; Non-Ribosomal Peptide Synthetases (NRPS); Cyclic Lipopeptides (CLPs).
Online: 14 July 2021 (13:11:32 CEST)
The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution. In this study, whole genome se-quencing enabled us to define 43 new Pseudomonas species and to provide an update of the Pseu-domonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including 316 and 313 type strains of Pseudomonas, respectively, re-vealed sixteen groups of Pseudomonas and justified the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incor-rectly assigned at the species level and among those, 19 strains were shown to represent an addi-tional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle and metabolic potential of Pseudomonas spp.
ARTICLE | doi:10.20944/preprints201803.0252.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Curculionidae; Cossoninae; Rhyncolini; Rhyncolina; taxonomy; new species; mature larva; morphology; host plant; Cape Verde; biogeography; microclimate; species competition
Online: 29 March 2018 (14:53:47 CEST)
The genus Aphanommata in the Old World is reviewed. Aphanommata kuscheli sp. nov. from São Nicolau and A. strakai sp. nov. from Fogo (both Cape Verde islands) are described. Aphanommata euphorbiarum (Wollaston, 1867) from Santo Antão in the Cape Verde islands is redescribed and its lectotype is designated. All three Aphanommata species from the Cape Verde islands as well as A. filum (Mulsant & Rey, 1859) from Old World are diagnosed, illustrated, and keyed. Mature larva of A. kuscheli sp. nov. is described, larval morphology is discussed and the current state of knowledge about immature stages of Cossoninae is summarized. Vertical and inter-insular distributional pattern of Cape Verde Aphanommata and Pselactus is reviewed and discussed.
ARTICLE | doi:10.20944/preprints202112.0480.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: cp-rbcL; nr-ITS region; biodiversity; distribution; Mediterranean-Atlantic Europe; mosses; nomenclature; taxonomy; Trichostomum herzogii nom. nov.; Trichostomum meridionale sp. nov.
Online: 30 December 2021 (08:58:49 CET)
The morphologically variable moss Trichostomum brachydontium is very common in south and west Europe, particularly under Mediterranean and Atlantic climates. A morphological study was conducted alongside a molecular phylogenetic study based on nr ITS and cp rbcL regions in order to assess if T. brachydontium is an exceptionally polymorphic species as evidenced by the number of described infraspecific taxa from the last century or, alternatively, if it includes more than one species, and if so, to find the valid name for them. Phylogenetic analyses of both nuclear and chloroplast datasets show that there are four well-supported clades. While the ITS based tree is in good agreement with the morphological data, there are a few inconsistencies with reference to the rbcL tree; this may be explained by incomplete lineage sorting or by hybridization. The morphological survey revealed well-defined discriminate differences between the four phylogenetic lineages. The taxonomic conclusions include the recognition of four species: T. brachydontium s.s., T. herzogii (a new name proposed for var. cuspidatum), T. littorale and T. meridionale (a new name proposed for var. densum). Lectotypes are designated for T. brachydontium and T. littorale. Our results underline the ongoing need of integrative studies to examine further the underestimated diversity of the T. brachydontium complex in other regions.
REVIEW | doi:10.20944/preprints202009.0182.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Ralstonia solanacearum species complex; taxonomy; phylogenomic; plant bacteria; tomato wilt; bacterial wilt; brown rot of potato; Granville Wilt of tobacco; moko disease of banana; Bugtok disease; spewy eye
Online: 8 September 2020 (10:19:34 CEST)
The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separation of Ralstonia solanacearum into three genomic species. Frequent name changes occurred as methodology transitioned from phenotypic, biochemical, and molecular studies, to genomics and functional genomics. The diversity, wide host range and geographical distribution of R. solanacearum has resulted in its inclusion in a “species complex” as genomic analyses of elucidated phylogenetic relationships among strains. Current advances in phylogenetics and functional genomics now open new avenues for research into the epidemiology and control of the devastating bacterial wilt disease.