Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability

Studies in Mycology, Год журнала: 2022, Номер 102(1), С. 53 - 93

Опубликована: Июнь 30, 2022

Язык: Английский

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Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins

Database, Год журнала: 2022, Номер 2022

Опубликована: Янв. 1, 2022

DNA metabarcoding is a widespread approach for the molecular identification of organisms. While associated wet-lab and data processing procedures are well established highly efficient, reference databases taxonomic assignment can be implemented to improve accuracy identifications. Insects among organisms which DNA-based most commonly used; yet, DNA-metabarcoding database specifically curated their species using software requiring local lacking. Here, we present COins, 5' region cytochrome c oxidase subunit I sequences (COI-5P) insects that includes over 532 000 representative >106 formatted QIIME2 platform. Through combination automated manually steps, developed this starting from all COI available in Barcode Life Data System insects, focusing on comply with several standards, including species-level identification. COins was validated previously published (bulk samples Malaise traps) its efficiency compared other publicly (not specific insects). allow an increase up 30% identifications thus represent valuable resource insects' data, especially when needed https://doi.org/10.6084/m9.figshare.19130465.v1.

Язык: Английский

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Shedding light on dark taxa in sky‐island Appalachian leaf litter: Assessing patterns of endemicity using large‐scale, voucher‐based barcoding

Insect Conservation and Diversity, Год журнала: 2023, Номер 17(1), С. 16 - 30

Опубликована: Ноя. 2, 2023

Abstract Developing systematic conservation plans depends on a wealth of information region's biodiversity. For ‘dark taxa' such as arthropods, data are usually very incomplete and in most cases left out from assessments. Sky islands important often fragile biodiversity hotspots. Southern Appalachian high‐elevation spruce–fir forests represent particularly threatened sky‐island ecosystem, hosting numerous endemic species, but their arthropods remain understudied. Here we use voucher‐based megabarcoding to explore genetic differentiation among leaf‐litter arthropod communities these highlands, examine the extent which they dispersed more or less coherent manageable distributed unit. We assembled dataset comprising than 6000 COI sequences representing diverse groups assess species richness sharing across peaks ranges. Comparisons were standardised taxa using automated delimitation, measuring endemism levels by putative species. Species was high, with sites 86 199 litter (not including mites myriapods). Community profiles suggest that around one fourth unique single sky third all limited particular range. Across major taxa, endemicity lowest Araneae, highest neglected like Isopoda, Pseudoscorpionida, Protura Diplura. habitat host significantly distinct communities, high local endemicity. This is first work provide clear picture peak range uniqueness for taxonomically broad sample. Ensuring protection sizeable fraction will therefore require attention at relatively fine spatial scale.

Язык: Английский

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SPdel: A pipeline to compare and visualize species delimitation methods for single‐locus datasets

Molecular Ecology Resources, Год журнала: 2023, Номер 23(8), С. 1959 - 1965

Опубликована: Сен. 13, 2023

An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with methods would help to a rapid and biodiversity assessment. The cluster data sets orthologous sequences in operational taxonomic units (MOTU). particular, based on single gene are easily integrated widely used DNA barcoding approach. We developed SPdel user-friendly pipeline integrate different single-gene methods. designed calculate compare MOTUs obtained by approaches. also outputs diverse ready-to-publish quality figures, that facilitate interpretation results. aims researchers improve

Язык: Английский

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Integrative taxonomy reveals new, widely distributed tardigrade species of the genus Paramacrobiotus (Eutardigrada: Macrobiotidae)

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Фев. 7, 2023

Abstract In a moss sample collected in Ribeiro Frio, Madeira, Paramacrobiotus gadabouti sp. nov. was found and described using the integrative taxonomy approach. The new species is based on morphological morphometric data from both phase-contrast light microscopy (PCM), as well scanning electron (SEM). Moreover, four DNA markers, three nuclear (18S rRNA, 28S ITS-2) one mitochondrial (COI) were used to elucidate phylogenetic position of within family Macrobiotidae. has microplacoid that placed it Parmacrobiotus richtersi group exhibit richtersi- type eggs having processes terminated with cap-like structures. most similar Pam. alekseevi , filipi garynahi but differs them mainly details egg morphology morphometrics. Unlike other this group, which confirmed bisexual showed limited distribution, yet another parthenogenetic wide demonstrating at least some tardigrades confirm hypothesis 'everything everywhere'.

Язык: Английский

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Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Ecology and Evolution, Год журнала: 2022, Номер 12(5)

Опубликована: Май 1, 2022

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude species, which well defined complex shape male genitalia. Here, we how COI barcode data reflect morphological species entities thus their usability for accelerated inventorization. We conducted dedicated field surveys Sri Lanka collect species-rich highly endemic Sericini (Coleoptera: Scarabaeidae). Congruence among results series protocols de novo delimitation with morphology-based identifications was investigated. Different methods, such as Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species Partitioning (ASAP), Index Number (BIN) assignments, resulted different numbers molecular operational taxonomic units (MOTUs). All methods showed both over-splitting lumping morphologically identified species. Only 18 observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence between expressed match ratio low, ranging 0.57 0.67. TCS multirate PTP (mPTP) highest ratio, while assignment lowest splitting events. mPTP lumped more than any other method. Principal coordinate analysis (PCoA) on ratio-based distance matrix revealed incongruent outcomes multiple although applied same data. Our confirm that alone unlikely correctly delimit particular, when using only single approach. encourage integration various approaches data, particularly morphology, validate boundaries.

Язык: Английский

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Hidden island endemic species and their implications for cryptic speciation within soil arthropods

Journal of Biogeography, Год журнала: 2022, Номер 49(7), С. 1367 - 1380

Опубликована: Май 25, 2022

Abstract Aim Specialisation to the soil environment is expected constrain spatial scale of diversification within animal lineages. In this context, flightless arthropod lineages, adapted environments, but with broad geographical ranges, represent something an anomaly. Here we investigate process one such ‘anomalous’ specialist, eyeless and beetle species strongly endogean distributed across several oceanic islands. Location Canary Islands. Taxon Geomitopsis franzi Coiffait, 1978 (Coleoptera, Staphylinidae). Methods We performed integrative study, including molecular phylogenetics, population genomics morphometry. Four DNA regions (two mitochondrial two nuclear) were amplified sequenced for 159 specimens from 58 localities sampled five islands phylogenetic analyses, a dated tree was obtained using mitogenome dataset. ddRAD‐seq data generated evaluate mtDNA lineages in sympatry against biological concept. Results found high levels genetic differentiation (>8% COI gene divergence) among populations different geographically coherent single Lineages Tenerife presented significant patterns isolation by distance, providing evidence that species. Morphometric analyses revealed limited variation. Main conclusions comprised at least seven merit consideration as species, best considered complex cryptic The morphological variation these consistent adaptation placing strong constraints on change. evolution should be favoured when are coupled dispersal ability, trait broadly characterises mesofauna.

Язык: Английский

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Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda)

Genes, Год журнала: 2022, Номер 13(12), С. 2273 - 2273

Опубликована: Дек. 2, 2022

In the context of diminishing global biodiversity, validity and practicality species delimitation methods for identification many neglected undescribed biodiverse have been paid increasing attention. DNA sequence-based are mainly classified into two categories, namely, distance-based tree-based methods, widely adopted in studies. present study, we performed three (ad hoc threshold, ABGD, ASAP) four (sGMYC, mGMYC, PTP, mPTP) analyses based on Trochoidea COI data analyzed discordance between them. Moreover, also observed performance these at different taxonomic ranks (the genus, subfamily, family ranks). The results suggested that approach is generally superior to approach, with ASAP method being most efficient. terms phylogenetic single threshold version better than multiple GMYC, PTP showed higher efficiency mPTP delimiting species. Additionally, GMYC was found be significantly influenced by rank, showing poorer datasets genus level levels. Finally, our highlighted cryptic diversity within (Mollusca: Vetigastropoda) might underestimated, which provides quantitative evidence excavating lineages

Язык: Английский

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A description of Aliichlorella ignota gen. et sp. nov. and a comparison of the efficiency of species delimitation methods in the Chlorella‐clade (Trebouxiophyceae, Chlorophyta)

Phycological Research, Год журнала: 2024, Номер 72(3), С. 180 - 190

Опубликована: Апрель 15, 2024

Abstract The present study reports a new representative of Chlorella ‐clade that was newly isolated from the Lake Vos'merka (Samara region, Russian Federation). 18S–ITS1–5.8S–ITS2 sequence analyses indicated studied strain ACSSI 368 and related chlorelloides , pulchelloides formed an separate cluster in ‐clade, unrelated to holotype genus – vulgaris. independent place also confirmed by genetic distances. individual species status 368, compared with sister C. morphological differences (cell number per colony, type chloroplast, autospores), distances interspecific level fragment, alone internal transcribed spacer 1 (ITS1) 2 (ITS2) sequences, one complementary base change ITS1, results delimitation using five methods. A description provided as authentic Aliichlorella ignota . Currently, includes comb. nov. In general, six different algorithms were used study. ASAP (i.e. assemble automatic partitioning) LocMin ‘local minimum’ function) showed synchronous results, but their accuracy respect closely somewhat lower. mlPTP algorithm simultaneously aimed combine at same time divide slightly distinguishing strains within into several molecular operational taxonomic units. bPTP separated excessively representatives species. generalized mixed Yule coalescent (GMYC) consistent most modern understanding taxonomy. However, method is time‐consuming because, for its implementation, it necessary carry out long preparatory work. KoT less accurate than GMYC although this because does not require preliminary construction ultrametric trees.

Язык: Английский

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A race against extinction: The challenge to overcome the Linnean amphibian shortfall in tropical biodiversity hotspots

Diversity and Distributions, Год журнала: 2024, Номер 30(12)

Опубликована: Авг. 22, 2024

Abstract Aim There is an urgent need to explore, characterize, describe and preserve as many species possible prevent their decline. Tropical biodiversity hotspots harbour most of the known land diversity vast amounts undiscovered undescribed species. Here, we quantify taxonomically unassessed amphibian richness in Madagascar, one best‐studied explored tropical worldwide, identify knowledge gaps conservation implications. Location Madagascar. Time Period Present. Major Taxa Studied Amphibians. Methods We used Madagascar fauna a model unveil neglected by analysing 10,873 mitochondrial sequences using delimitation algorithms incorporating all previously published bioacoustics, distributional, morphological nuclear data with integrative approach. Results Besides currently described 413 species, identified 408 divergent lineages. Among this, 310 fit category candidate pending taxonomic assessment, while 98 are considered deep conspecific These figures suggest that could be twice high represented current taxonomy. Geographically, these occur well‐studied areas within island. Main Conclusions Despite being countries worldwide for amphibians, found awaiting assessment Paradoxically, this concentrates on highly regions, emphasizing importance exploring inventorying new areas. Our results highlight magnitude Linnean Wallacean shortfalls, affecting both estimates distribution ranges biogeographic setting fauna. Current efforts should consider novel unexplored they will likely yet discovered. expect similar patterns across less studied realms encourage researchers perform such studies different clades before becomes irremediably lost.

Язык: Английский

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