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

Studies in Mycology, Journal Year: 2022, Volume and Issue: 102(1), P. 53 - 93

Published: June 30, 2022

Language: Английский

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

Database, Journal Year: 2022, Volume and Issue: 2022

Published: Jan. 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.

Language: 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, Journal Year: 2023, Volume and Issue: 17(1), P. 16 - 30

Published: Nov. 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.

Language: Английский

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

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(8), P. 1959 - 1965

Published: Sept. 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

Language: Английский

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

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Feb. 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'.

Language: 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, Journal Year: 2022, Volume and Issue: 12(5)

Published: May 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.

Language: Английский

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

Journal of Biogeography, Journal Year: 2022, Volume and Issue: 49(7), P. 1367 - 1380

Published: May 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.

Language: Английский

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

Genes, Journal Year: 2022, Volume and Issue: 13(12), P. 2273 - 2273

Published: Dec. 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

Language: Английский

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Integrative Taxonomy of Ourapteryx Leach (Geometridae, Lepidoptera) Based on Molecular and Morphological Evidences

Journal of Zoological Systematics & Evolutionary Research, Journal Year: 2025, Volume and Issue: 2025(1)

Published: Jan. 1, 2025

Ourapteryx is widely distributed in the Palearctic and Oriental regions, with highest species diversity found China. As of 2024, 95 described have been recorded globally; however, no comprehensive revision this genus has published. Identifying based solely on wing patterns challenging due to their extreme similarity, often leading frequent misidentifications oversight cryptic species. In study, we utilized 68 morphological species, along 1050 COI sequences, develop an integrative taxonomy for . This integrates morphological, molecular, distributional, ecological evidences. Our findings identified nine candidate (labeled as sp1–sp7, O. horishana brachycerca ), increasing total number recognized from 77. Using updated checklist, compared four molecular delimitation methods against outcomes taxonomy. The analysis indicated that a 2% threshold produced efficiency. Additionally, explored reasons behind morpho‐molecular discordance presence hidden study underscores importance reliability taxonomy, which relies multiple lines evidence accurate identification classification.

Language: Английский

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Challenges in the recognition of trematode species: Consideration of hypotheses in an inexact science

Journal of Helminthology, Journal Year: 2025, Volume and Issue: 99

Published: Jan. 1, 2025

Abstract The description and delineation of trematode species is a major ongoing task. Across the field there has been, currently still is, great variation in standard this work sophistication proposal taxonomic hypotheses. Although most are relatively unambiguously distinct from their congeners, many either morphologically very similar, including rapidly growing component cryptic species, or highly variable despite little to no molecular for DNA markers. Here we review challenges context provided us by historical literature, use morphological, geographical, host, data. We observe that potential associated with all these information sources. As result, encourage careful hypotheses consideration underlying concepts frank acknowledgement weaknesses conflict It seems clear single source data provides wholly reliable answer our but nuanced multiple sources (the ‘integrated approach’) best possibility developing will stand test time.

Language: Английский

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