Taxonomic Framework Research Articles

A Methodological Approach for Assessing the Interaction Between Rural Landscapes and Built Structures: A Case Study of Winery Architecture in Tuscany, Italy

This research aims to investigate the dynamics of interaction and interdependence between winery architecture and the rural landscape, with a particular focus on the Tuscany region in Italy. The primary objective is to analyze a selection of wineries deemed iconic and exemplary for the topic, assessing their relationship with the surrounding territory and landscape. To this end, specifically designed analytical frameworks are employed, grounded in experimental methodologies and criteria well-established in the relevant scientific literature. This methodology integrates a wide range of qualitative and quantitative indicators from scientific literature, organizing them within various taxonomic frameworks. Through tailored analytical forms, the research examines how design choices impact the agrarian context, highlighting the pivotal role of winery architecture in strengthening territorial identity and fostering a model of sustainable tourism. This paper introduces an adaptable interpretive method applicable across contexts, suitable for professionals and decision-makers. The findings present a framework for evaluating landscape systems, demonstrating how passive and advanced strategies enhance eco-efficiency and landscape perception, and adding ethical, aesthetic, and functional value. Moreover, the research contributes to rural landscape discourse, highlighting winery architecture’s role in balancing sustainability, driving economic development, and preserving rural environments.

VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.

The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to PASC (Pairwise Sequence Comparison), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.

Best practices for the naming of species

Abstract The process of describing a species has evolved considerably since the modern age of taxonomy was initiated with the publication of the 10th edition of Linnaeus’ Systema Naturæ in 1758. Nevertheless, the basic unit of the taxonomic framework remains the species group (species and subspecies). As a result, it is incumbent upon individuals undertaking species-group descriptions to strive for the highest standards, just as it is for reviewers and editors to hold authors to those same standards. The clear and mounting biodiversity crisis, the increasing proliferation of journals, the multiplication of journals publishing only in electronic format, the decline in the number of trained taxonomists, and the complex and at times misinterpreted wording of the rules governing taxonomy have resulted in a growing number of species names that are unavailable because one or more aspects required of a species-level taxonomic description are lacking. Here, we present best practices for the required elements of a taxonomic description and identify some of the common pitfalls leading to an inadequate description resulting in an unavailable name. We also suggest best practices that would enhance taxonomic descriptions and make them more informative.

Insights into brachyuran crab phylogeny: exploring the mitochondrial genome of Arcotheres sinensis (Brachyura, Pinnotheridae)

Abstract The phylogeny of species of Brachyura, particularly within the family Pinnotheridae, remains incompletely understood. To enhance the taxonomy and systematics of the Pinnotheridae, we conducted a comprehensive study aimed at elucidating the phylogenetic position of Arcotheres sinensis. Consequently, we sequenced and annotated the complete mitochondrial genome of A. sinensis, The results revealed that the circular mitogenome of A. sinensis spans 16 520 bp in length. Distinct from typical mitogenomes, A. sinensis contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes and 23 transfer RNA genes. The A + T content of the A. sinensis mitogenome is 71.63%, with both AT-skew and GC-skew being negative. The lengths of the 23 tRNA genes range from 62 to 72 bp. All tRNA genes exhibit typical cloverleaf structures, except for the trnS1 gene, which lacks the dihydrouridine (DHU) arm. Selection pressure analysis revealed that all PCGs are under evolutionary selection, with cox1 experiencing strongest purifying selection and atp8 undergoing weakest purifying selection. Compared to ancestral Brachyura, the gene order of A. sinensis has been rearranged from R-N--E to -E-N-R and the sequence I-Q-M has transitioned to Q-I-M. Phylogenetic analysis unequivocally positions A. sinensis within the taxonomic framework of the family Pinnotheridae, highlighting its intimate phylogenetic relationship with congeners within the same familial clade, notably Arcotheres purpureus and Pinnotheres excussus. These findings contribute to a better understanding of the status and evolutionary history of Pinnotheridae species.

Identification of a novel mycovirus belonging to the "flexivirus"-related family with icosahedral virion.

The order Tymovirales currently comprises five viral families with positive-sense RNA [(+)RNA] genomes that infect plants, fungi, and insects. Virion morphologies within the order Tymovirales differ between families, with icosahedral virions in the Tymoviridae and filamentous virions in the other "flexi"viridae families. Despite their different morphologies, these viruses are placed in the same order based on phylogenetic analyses of replicase-associated polyproteins. However, one of the families in the Tymovirales, Deltaflexiviridae, is considered to be capsidless because there have been no published reports of virion isolation. Here, we report that a new "flexivirus"-related (+)RNA virus, prospectively named Fusarium oxysporum icosahedral virus 1 (FoIV1), is icosahedral and that most deltaflexiviruses may have icosahedral virions. Phylogenetic analyses based on replicase-associated polyproteins indicated that FoIV1 forms a distinct group in the Tymovirales with some viruses originally assigned to the Deltaflexiviridae. Electron microscopy, protein analysis, and protein structure predictions indicate that FoIV1 open reading frame 4 encodes a single jelly-roll (SJR)-like coat protein (CP) that constitutes the icosahedral virions. Results of clustering analyses based on amino acid sequences and predicted CP structures suggested that most of the deltaflexiviruses have icosahedral virions composed of SJR-like CPs as in FoIV1, rather than having filamentous virions or capsidless. These results challenge the conventional understanding of viruses in the order Tymovirales, with important implications for revising its taxonomic framework and providing insights into the evolutionary relationships within this diverse and broad host range group of (+)RNA viruses.

LINgroups as a Robust Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies.

As a central organizing principle of biology, bacteria and archaea are classified into a hierarchical structure across taxonomic ranks from kingdom to subspecies. Traditionally, this organization was based on observable characteristics of form and chemistry but recently, bacterial taxonomy has been robustly quantified using comparisons of sequenced genomes, as exemplified in the Genome Taxonomy Database (GTDB). Such genome-based taxonomies resolve genomes down to genera and species and are useful in many contexts yet lack the flexibility and resolution of a fine-grained approach. The Life Identification Number (LIN) approach is a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. Utilizing LINgroup as an organizational concept helps resolve some of the confusion and unforeseen negative effects resulting from nomenclature changes of microorganisms that are closely related by overall genomic similarity (often due to genome-based reclassification). Our experimental results demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework. They also reveal the robustness of LIN assignment to hyper-parameter changes when considering within-species taxonomic groups.

Taxonomy in crisis: Addressing the shortage of taxonomists in a biodiversity hotspot era

In the era of biodiversity crises, where the extinction rates are accelerating at an unprecedented pace, taxonomy—the science of classification, description, and identification of organisms—stands as a critical tool for understanding and preserving the natural world. Yet, paradoxically, this field is in crisis. The shortage of trained taxonomists has become a significant bottleneck in biodiversity research and conservation efforts, especially in regions designated as biodiversity hotspots, which are home to the most unique and endangered species on the planet. This editorial explores the implications of this crisis, the challenges facing taxonomy today, and the steps needed to ensure the discipline can continue to play a pivotal role in safeguarding Earth’s biodiversity. Taxonomy provides the foundational knowledge necessary for a variety of scientific disciplines and conservation efforts. Accurate species identification is the first step toward understanding ecosystem dynamics, species interactions, and evolutionary relationships. Without a robust taxonomic framework, it becomes impossible to prioritize conservation efforts effectively. Conservation strategies depend heavily on identifying species at risk of extinction, protecting endangered habitats, and managing invasive species—all tasks that rely on precise taxonomic data.

Molecular phylogenetic studies on Trigonella section Ellipticae (Trifolieae, Fabaceae) from India utilising nrDNA (ITS) and cpDNA (trnL–trnF & petL–psbE)

This study highlights the critical importance of species delimitation in biodiversity conservation, focusing on the poorly understood Indian Trigonella species, with focus on T. sect. Ellipticae. Despite their ecological and socio-economic significance, these species, primarily found in the northwest Himalayas, have been inadequately catalogued and preserved. Adapted to harsh, dry environments, T. sect. Ellipticae exhibits morphological traits that complicate traditional species delimitation due to significant overlap among species boundaries. To address these challenges, we integrated molecular sequence data (nrDNA ITS and cpDNA (trnL–trnF & petL–psbE)) with morphological analysis, confirming the monophyly of Trigonella and revealing distinct evolutionary lineages within T. sect. Ellipticae. While nrDNA ITS sequences alone proved insufficient for resolving species relationships, phylogenetic investigations utilizing plastid data identified three distinct clades, enhancing taxonomic clarity. The study also suggests that observed morphological variations in T. cachemiriana may be due to phenotypic plasticity rather than distinct evolutionary lineages. We propose a new combination, T. emodi var. gracilis, to better represent the diversity within this group. Overall, this research underscores the necessity of combining molecular and morphological approaches for effective species delimitation, contributing to broader biodiversity conservation efforts in India, where many species remain inadequately catalogued. As the urgency for conservation increases, refining taxonomic frameworks is essential for ensuring that conservation strategies are based on accurate biological data.

Phylogenomics reveal species limits and inter-relationships in the narrow-range endemic lycian salamanders

Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.

Phylogenomic analyses of the Listeriaceae family support species reclassification and proposal of a new family and new genera.

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.

Annotated checklist of Rubus L. (Rosaceae) from South America.

The diversity of Rubus in South America is much understudied and a taxonomic framework needs to be established as a basis for future revisionary and phylogenetic work. Our review identified 110 names based on South American specimens which were published since 1767. Each name was then classified according to its botanical description and type material. Additionally, where necessary, we suggest appropriate lecto-, neo-, or epitypes. A comprehensive list of synonyms is provided and representative herbarium specimens for each country are cited to tentatively document geographical range. In total, we accept 46 species of Rubus recorded across South America, propose 19 new synonyms, restore R.organensis, previously a synonym of R.brasiliensis, provide a replacement name for the latter, and include new country records of R.azuayensis, R.laegaardii and R.rusbyi. This checklist serves as an essential starting point for future monographic and evolutionary studies on Rubus in South America.

Biomimetic Origami: A Biological Influence in Design.

Origami, the art of paper folding, has long fascinated researchers and designers in its potential to replicate and tap the complexity of nature. In this paper, we pursue the crossing of origami engineering structures and biology, the realm of biologically-inspired origami structures categorized by the two biggest taxonomy kingdoms and DNA origami. Given the diversity of life forms that Earth comprises, we pursue an analysis of biomimetic designs that resemble intricate patterns and functionalities occurring in nature. Our research begins by setting out a taxonomic framework for the classification of origami structures based on biologically important kingdoms. From each of these, we explore the engineering structures inspired by morphological features, behaviors, and ecological adaptations of organisms. We also discuss implications in realms such as sustainability, biomaterials development, and bioinspired robotics. Thus, by parlaying the principles found in nature's design playbook through the art of folding, biologically inspired origami becomes fertile ground for interdisciplinary collaboration and creativity. Through this approach, we aim to inspire readers, researchers, and designers to embark on a journey of discovery in which the boundaries between art, science, and nature are blurred, providing a foundation for innovation to thrive.

An annotated catalogue of the Procridinae of the World (Lepidoptera: Zygaenidae)

Almost 90 years have passed after the last publication of a catalogue of the family Zygaenidae of the world (Bryk, 1936). At that time there was no correct understanding of the taxonomic, genetic and ecological framework of the subfamily Procridinae. Many species of this subfamily were included into the Chalcosiinae and Zygaeninae. A new contemporary annotated catalogue consisting of five tribes, 94 genera and 570 species of Procridinae is provided. This is the first ever published complete worldwide catalogue of the subfamily. All together, 1111 taxa (including synonyms) are discussed. Three new tribes (Thyrassiini, tribus nov., Pollanisini tribus nov. and Cleleini tribus nov.), two new genera (Afromalamblia gen. nov. and Psudohedina gen. nov.) as well as four new subgenera (Longiterna subgen. nov., Afroterna subgen. nov., Obscuriterna subgen. nov., and Eurasiterna subgen. nov.) aredescribed. 36 comb. nov., 14 stat. nov. and 3 syn. nov. are established.

Assessment of nine markers for phylogeny, species and haplotype identification of Kappaphycus species and Eucheuma denticulatum (Solieriaceae, Rhodophyta)

ABSTRACT Molecular studies have contributed to the taxonomy of carrageenan-producing Kappaphycus spp. and Eucheuma denticulatum. However, unresolved species complexes and the lack of standardization in the use of genetic markers impede the identification of specimens and the delineation of a robust taxonomic framework. Here, nine molecular markers (cox1, cox2–3 spacer, cox2, cox3, COB, ITS, psbA, UPA and rbcL) were used to generate a multilocus phylogeny for 113 fresh eucheumatoid samples and four herbarium specimens. Analyses of species delineation and genetic distances confirmed the monophyly of currently accepted taxa. These analyses suggest that clades previously reported as K. striatus KS1 and KS2 are conspecific, and that E. denticulatum EDA ‘spinosum’ and EDB ‘endong/cacing’ are also conspecific. The results also unveiled possible new taxa from Hawaii and Indonesia. Each molecular marker and combinations thereof were assessed with regard to species identification, ease of amplification and sequencing, and haplotype characterization. All genetic markers recorded at least 94% success in the amplification and sequencing of fresh specimens, with cox1 being the most phylogenetically informative. Automatic partitioning, phylogenetic and tree-based assessments showed cox1, cox2–3 spacer, cox2 and rbcL were able to correctly identify species while cox1+ rbcL, COB+rbcL, cox2+ rbcL or cox1+ COB+rbcL trees best represented the phylogeny with consistently high nodal support. Among individual markers, cox1 identified the greatest number of haplotypes, while UPA, partial rbcL (750 bp), ITS, cox3 and cox2–3 spacer were able to retrieve information from herbarium specimens of 12–16 years of age. These molecular results provide a basis for a database essential for the taxonomic framework, cultivar development and germplasm conservation of eucheumatoids.

Bio-inspired classification and evolution of multirotor Micro Aerial Vehicles (MAVs): A comprehensive review

Multirotor Micro Aerial Vehicles (MAVs) have become essential in many applications like surveillance, disaster management, and aerial inspection. The diverse demands of these applications have led to numerous design innovations, growing the MAV landscape substantially. However, such growth has made it challenging to understand the evolution and classification of MAV designs based on their functions and features. We address this challenge by introducing a novel, bio-inspired taxonomic classification framework for MAVs. Our framework spans six hierarchical ranks, each containing a diverse set of categories that classify MAVs from distinct design perspectives. It enables a proper comparison of the MAV designs in the literature, revealing their key similarities and differences. It also helps to trace the evolution of MAVs over time, identifying research trends and potential gaps. Lastly, it offers insights into future MAV design trajectories, providing a complete and clear understanding of the MAV design landscape.

Phylogenomics analysis of Scutellaria (Lamiaceae) of the world

BackgroundScutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family’s largest genera, encompassing approximately 500 species found in both temperate and tropical montane regions. Recognized for its significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer, anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and horticulture. Comprehending Scutellaria’s taxonomy is pivotal for its effective utilization and conservation. However, the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a stable and reliable classification system.ResultsThis study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subgeneric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive sequences, and ten highly variable regions, including trnK–rps16, trnC–petN, petN–psbM, accD–psaI, petA–psbJ, rpl32–trnL, ccsA–ndhD, rps15–ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species identification, phylogeny, and population genetics.ConclusionsThe phylogeny of Scutellaria, based on the most comprehensive sample collection to date and complete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The extensive examination of chloroplast genome characteristics establishes a solid foundation for the future development and utilization of Scutellaria, an important medicinal plant globally.

New ammonoid records and the definition of the base of the German Hemberg-Stufe (Famennian III, Upper Devonian)

In the revised ammonoid biostratigraphy of Becker (1993), the base of the German Hemberg-Stufe (Hembergian, middle Famennian, Upper Devonian III) was defined by the entry of Pernoceras dorsatum (Wedekind, 1918). However, this taxon is an invalid junior homonym of Tornoceras simplex var. dorsata Gürich, 1900 and Wedekind`s form was poorly defined and originally not illustrated. Based on a review of Wedekind material and unpublished collections from two trenches at the Enkeberg type section, the defining taxon of the Hembergian is re-assigned to Protornoceras genulobatum (Sobolew, 1914b). The species is discussed in the context of previous records of Tornoceras dorsatum and in the taxonomic framework of the Aulatornoceratinae, especially of the genera Protornoceras and Pernoceras. In the revised regional and international zonation scheme, UD III-A becomes a regional Prot. genulobatum Zone and international Protornoceras Genozone. Some other Protornoceras, questionable Falcitornoceras, and Pernoceras are described. These include Prot. rhenicum n. sp., Prot. umbilicatoides (Sobolew, 1914a), Prot. aff. delepinei (Petter, 1975), and Prot. aff. crebriseptum (Raymond, 1909) from the Enkeberg, Prot. aff. genulobatum from Beringhauser Tunnel, the Rhenish Perno. kochi (Wedekind, 1908), and the Russian Pernoceras kirsaense n. sp.

A comprehensive taxonomy for forest fire risk assessment: bridging methodological gaps and proposing future directions.

Forest fire risk assessment plays a crucial role in the environmental management of natural hazards, serving as a key tool in the prevention of forest fires and the protection of various species. As these risks continue to evolve with environmental changes, the pertinence of contemporary research in this field remains undiminished. This review constructs a comprehensive taxonomic framework for classifying the existing body of literature on forest fire risk assessment within forestry studies. The developed taxonomy categorizes existing studies into 8 primary categories and 23 subcategories, offering a structured perspective on the methodologies and focus areas prevalent in the domain. We categorize a sample of 170 articles to present recent trends and identify research gaps in forest fire risk assessment literature. The classification facilitates a critical evaluation of the current research landscape, identifying areas in need of further exploration. Particularly, our review identifies underrepresented methodologies such as optimization modeling and some advanced machine learning techniques, which present routes for future inquiry. Moreover, the review underscores the necessity for model development that is tailored to specific regional data sets but also adaptable to global data resources, striking a balance between local specificity and broad applicability. Emphasizing the dynamic nature of forest fire behavior, we advocate for models that integrate the burgeoning field of machine learning and multi-criteria decision analysis to refine predictive accuracy and operational effectiveness in fire risk assessment. This study highlights the great potential for new ideas in modeling techniques and emphasizes the need for increased collaboration among research communities to improve the effectiveness of assessing forest fire risks.

Conservation implications of a genomic‐based taxonomy for threatened allopatric Agriades butterflies

Abstract A good knowledge of the evolutionary history of organisms and an accurate taxonomic framework are keys for efficient biodiversity conservation measures. This is particularly relevant for European butterflies, which are often used as bioindicator organisms and umbrella species for conservation. The Holarctic butterfly genus Agriades includes seven European arctic‐alpine species of which several have a debated taxonomic status. They are localized and allopatric, and at least two of them are of high conservation concern, namely A. aquilo (in Europe, restricted to northern Scandinavia) and A. zullichi (endemic to southern Spain). Despite high conservation value and taxonomic uncertainty, molecular studies on these taxa are limited to DNA barcodes. We investigated the evolutionary history and species delimitation of West Palearctic Agriades using double‐digest RAD sequencing (ddRADseq). Various analyses using genomic data suggested the presence of one species in the glandon species group and one or two in the pyrenaicus species group. The differentiation within the former group (i.e., glandon, aquilo, zullichi) appears to be relatively recent, although the main allopatric populations represent evolutionary significant units (ESUs). Notable geographic structure was found within the pyrenaicus species group, with four allopatric ESUs detected. Wolbachia screening highlighted the presence of several allele combinations, some associated with particular Agriades populations. Genomic data revealed the evolutionary trajectory of European Agriades and a tendency for taxonomic oversplitting within this genus. These findings aid conservation by providing genetic background for region or population prioritization (including ESUs), and for the management of potential population reinforcement or reintroductions.

Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities

BackgroundHigh-throughput sequencing of the full-length 16S rRNA gene has improved the taxonomic classification of prokaryotes found in natural environments. However, sequencing of shorter regions from the same gene, like the V4-V5 region, can provide more cost-effective high throughput. It is unclear which approach best describes prokaryotic communities from underexplored environments. In this study, we hypothesize that high-throughput full-length 16S rRNA gene sequencing combined with adequate taxonomic databases improves the taxonomic description of prokaryotic communities from underexplored environments in comparison with high-throughput sequencing of a short region of the 16S rRNA gene.ResultsTo test our hypothesis, we compared taxonomic profiles of seawater samples from the Arctic Ocean using: full-length and V4-V5 16S rRNA gene sequencing in combination with either the Genome Taxonomy Database (GTDB) or the Silva taxonomy database. Our results show that all combinations of sequencing strategies and taxonomic databases present similar results at higher taxonomic levels. However, at lower taxonomic levels, namely family, genus, and most notably species level, the full-length approach led to higher proportions of Amplicon Sequence Variants (ASVs) assigned to formally valid taxa. Hence, the best taxonomic description was obtained by the full-length and GTDB combination, which in some cases allowed for the identification of intraspecific diversity of ASVs.ConclusionsWe conclude that coupling high-throughput full-length 16S rRNA gene sequencing with GTDB improves the description of microbiome profiling at lower taxonomic ranks. The improvements reported here provide more context for scientists to discuss microbial community dynamics within a solid taxonomic framework in environments like the Arctic Ocean with still underrepresented microbiome sequences in public databases.