The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D791 - D797

Опубликована: Ноя. 11, 2023

Abstract UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region offers nearly 10 million such sequences reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned unique digital object identifier (DOI) to promote unambiguous referencing across studies. users have contributed over 600 000 third-party annotations, which shared with range databases other community resources. Recent improvements facilitate detection cross-kingdom biological associations integration undescribed groups organisms everyday pursuits. Serving as twin eukaryotic biodiversity communities worldwide, latest release improved avenues discovery, precise taxonomic communication knowledge platforms.

Язык: Английский

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How to describe a new species in zoology and avoid mistakes

Zoological Journal of the Linnean Society, Год журнала: 2024, Номер unknown

Опубликована: Март 27, 2024

Abstract Taxonomy is the science of discovering, naming, describing, diagnosing, identifying, and classifying different kinds taxa, from species to families. It lays foundation for all biological sciences. The rapid increase in both taxonomic descriptions malpractice recent decades indicates a need consistency procedure quality research publications dealing with recognition new name changes, nomenclatural acts. Indeed, there are numerous examples literature works that fall short basic procedures minimum standards required naming according mandatory provisions recommendations International Code Zoological Nomenclature, accepted best practice, journal editorial policy. Here, we provide practical guidelines key elements name, describe, publish animal or revise status species. We then discuss some common pitfalls should be avoided. Mistakes commonly made include failure read Code, review primary literature, examine type material, construct taxon correctly, explicitly establish taxon, adequate typification, clearly differentiate register publication ZooBank, manner compliant Code. these mistakes, mainly butterflies (Insecta: Lepidoptera: Papilionoidea) and, extent, reptiles because groups seem have an unusually high level poor practice.

Язык: Английский

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How taxonomic change influences forecasts of the Linnean shortfall (and what we can do about it)?

Journal of Biogeography, Год журнала: 2024, Номер 51(8), С. 1365 - 1373

Опубликована: Март 8, 2024

Abstract The gap between the number of described species and that actually exist is known as Linnean shortfall fundamental importance for biogeography conservation. Unsurprisingly, there have been many attempts to quantify its extent different taxa regions. In this Perspective , we argue such forecasts remain highly problematic because does depend not only on rates exploration (sampling undescribed taxa) which estimates commonly based but also taxonomic change (lumping splitting). These changes concepts adopted information methods used delimit species. Commonly estimating unknown (e.g. discovery curves, taxon ratios) can underestimate or overestimate if they do effectively account trends change. A further complication history well documented most typically available in biodiversity databases. Moreover, wide geographic variation adoption delimitation mean comparison even same regions may be unreliable. Given high likelihood future major taxa, propose two main strategies consider influence species: (i) a conservative approach shortfall, restricting analysis groups where taxonomies are relatively stable (ii) explicitly incorporating metrics into models estimates. short, relevant will achieved by accounting dynamic nature process itself.

Язык: Английский

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Species Diagnosis and DNA Taxonomy

Methods in molecular biology, Год журнала: 2024, Номер unknown, С. 33 - 52

Опубликована: Янв. 1, 2024

Язык: Английский

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The 5 ‘D’s of Taxonomy: A User’s Guide

The Quarterly Review of Biology, Год журнала: 2024, Номер 99(3), С. 131 - 156

Опубликована: Авг. 16, 2024

Язык: Английский

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How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)

Zoological Journal of the Linnean Society, Год журнала: 2024, Номер 201(4)

Опубликована: Авг. 1, 2024

Abstract A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with description a new species green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies evidence used and errors in nomenclature. We here use case this problematic publication to: (i) highlight common issues affecting delimitations, especially an over-reliance on mitochondrial DNA data, reiterate best practices; (ii) reanalyse data available for establish true current state knowledge lines further research; (iii) analyse nomenclatural history status genus. While our analysis reveals significant morphological variation both yellow anacondas, denser sampling informative nuclear markers are required meaningful delimitation Eunectes. Tracing name-bearing types establishes Trinidad as type locality Boa murina Linnaeus, 1758 allows identification extant lectotype species. Finally, we emphasize responsibility journals authors ensure that published taxonomic work meets burden substantiate descriptions named compliance rules zoological

Язык: Английский

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Antholoba fabiani sp. nov. (Actiniaria, Metridioidea, Antholobidae fam. nov.), a new species and family of sea anemone of the southwestern Atlantic, Brazil

Marine Biodiversity, Год журнала: 2024, Номер 54(3)

Опубликована: Апрель 5, 2024

Язык: Английский

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Molecular phylogeny of the operculated land snail family Pupinidae (Caenogastropoda, Cyclophoroidea) in mainland Southeast Asia

Zoologica Scripta, Год журнала: 2025, Номер unknown

Опубликована: Апрель 7, 2025

Abstract The operculated land snail family Pupinidae from mainland Southeast Asia has been systematically revised based on shell morphology. Despite previous morphological studies, the evolutionary relationships within this remained unclear. This study represents first comprehensive molecular phylogeny of group, utilising two mitochondrial (COI and 16S rRNA) nuclear (5.8S rRNA + ITS2 28S genetic markers. Additionally, we conducted phylogenetic analyses Pupina species 1106 loci generated through double‐digest restriction site‐associated DNA sequencing (ddRADseq). It turned out that Asian Pollicaria emerged as a sister clade to Central American Aperostoma Megalomastomatidae, leading resurrection Pollicariidae. Among remaining pupinid genera, Tortulosa was nested Coptocheilus clade, while Pupinella were not monophyletic. previously recognised arula group found be monophyletic reclassified into Tylotoechus (formerly subgenus), distinctive conchological characters such an extending parietal tooth callus wide, outward‐curving posterior canal. However, some retrieved monophyletic, suggesting presence multiple ‘cryptic species’. Divergence time estimation indicated split could date back Late Triassic Early Cretaceous, with diversification genera occurring during Middle Jurassic Cretaceous. successful reconstruction robust using ddRADseq demonstrates significant potential RADseq techniques in elucidating deeply divergent taxa. Further studies incorporating type destructus keraudrenii are necessary justify usage these genera.

Язык: Английский

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Phylogenetic Analysis and Its Influence on Classification

Опубликована: Янв. 1, 2025

Язык: Английский

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An integrative taxonomic treatment of the Mycetophilidae (Diptera: Bibionomorpha) from Singapore reveals 115 new species on 730km²

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 5, 2023

Abstract “Open ended” or “dark taxa” are species-rich clades that so abundant and diverse conventional taxonomic methods tend to struggle with the onslaught of specimens species. New approaches based on presorting putative species affordable barcodes may make tackling these taxa manageable. However, this will still require limiting geographic scope revisions, given most countries biogeographic regions have too many for comprehensive coverage. We demonstrate power approach by carrying out a revision fungus gnats (Diptera: Mycetophilidae) Singapore. The material revised here was obtained from 496 Malaise trap samples caught 71 traps placed at 107 collecting sites in different habitats: mangroves, swamp forests, freshwater swamps, primary rainforests, types secondary forests (old, maturing, young, urban). Based molecular morphological data more than 1,456 specimens, we delimit 120 data. Of these, only 4 5 previously described. remaining 115 new science described here. name 99 species, since 14 currently known females cannot prepare fully satisfying diagnosis ( Manota spp. A–G Neoempheria A–G), two lack Epicypta sp. A H). match ratio between morphology standard MOTUs (3% clusters) overall high (95%) even higher ratios (99%) observed 5% Objective Clustering ABGD (P=0.060). Overall, undescribed is an astonishing 23:1. Only revising Singapore fauna increases number Oriental Mycetophilidae over 25%. This highlights size impediment gnats. Most diversity belongs three 22 genera— Osten-Sacken (31 species), Winnertz (29 species) Williston (14 but also describe genus, Integricypta , gen. n. It Mycetophilinae Mycetophilini sistergroup Aspidionia Colless. sequenced, illustrated, named are: Leptomorphus rafflesi ; Monoclona simhapura Azana demeijeri leekongchiani Sciophilinae ); Tetragoneura crawfurdi chola dayuan farquhari Ectrepesthoneura johor Tetragoneurinae Mohelia zubirsaidi Allactoneura tumasik limbosengi banzu tantocksengi bukittimah chiamassie danmaxi mahuan temenggong Clastobasis sritribuana bugis oranglaut Leiinae Parempheriella mait longyamen peranakan sachmatich merlio sabana sangabo shicheng ujong subaraji kokoiyeeae mandai malacca sinkapho singapura xinjiapo puluochung merdeka neesoon pulau cinkappur temasek polunini fajar riatanae Mycomyinae Allodia glorialimae Brachycampta murphyi limtzepengi teopohlengi Exechia tanswiehiani alinewongae Mycetophila chngseoktinae georgettechenae aishae Platyprosthiogyne phanwaithongae gohsookhimae rahimahae lynetteseahae neilaae snehalethaae Platurocypta adeleneweeae tanhoweliangi constancesingamae jennylauae limchiumeiae janetyeeae kohkhenglianae daintoni holltumi sp.n. alii ridleyi chezaharaae tanjiakkimi gehminae jackieyingae khatijunae purchoni foomaoshengi ganengsengi nanyangu nus peterngi maggielimae yupeigaoae annwee wallacei lamtoongjini catherinelimae grootaerti joaquimae cheesweeleeae janetjesudasonae fatimahae fergusondavie teosoonkimae shirinae hoyuenhoeae ). Metanepsia malaysiana Kallweit, Eumanota racola Søli, defectiva (Edwards), dizonalis (Edwards) (all Sumatra and/or Malaysian peninsula). Two belong Chalastonepsia be one genus. gnoristine genus Vecella Wu & Yang proposed as synonym P. guadunana (Wu Yang), n . comb ., corresponding additional Palearctic Barcodes second set 1,567 suggest presence 24 MOTUs. thus estimate approximately 85% all routinely enter identified concludes discussion biogeography generic composition mycetophilid southern end Malay Peninsula.

Язык: Английский

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