Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(6), P. 1772 - 1787

Published: Jan. 27, 2021

Abstract Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation PCR and sequencing artefacts co‐amplification nuclear pseudogenes (NUMTs). The application read abundance thresholds denoising methods is efficient in reducing noise accompanying authentic amplicon sequence variants (ASVs). However, these procedures do not fully account for complex nature concomitant sequences highly variable DNA contribution specimens a metabarcoding sample. We propose, as complement to denoising, Multidimensional Abundance Threshold Evaluation ( metaMATE ) framework, novel approach that allows comprehensive examination multiple dimensions filtering evaluation prevalence unwanted denoised datasets. requires set ASVs input, designates subset being either (mitochondrial haplotypes) or nonauthentic (NUMTs erroneous sequences) comparison external reference data analysing nucleotide substitution patterns. (i) facilitates strategies, which are structured with regard library phylogeny applied range increasing threshold values, (ii) evaluates their performance quantifying collateral effects on removal ASVs. output from decision‐making about required stringency can used improve reliability intraspecific genetic information derived metabarcode data. framework implemented software (available at https://github.com/tjcreedy/metamate ).

Language: Английский

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Consistent community assembly but contingent species pool effects drive β‐diversity patterns of multiple microbial groups in desert biocrust systems

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(13)

Published: May 15, 2024

Abstract One of the key goals ecology is to understand how communities are assembled. The species co‐existence theory suggests that community β‐diversity influenced by pool and assembly processes, such as environmental filtering, dispersal events, ecological drift biotic interactions. However, it remains unclear whether there similar patterns among different soil microbial groups all these mechanisms play significant roles in mediating patterns. By conducting a broad survey across Chinese deserts, we aimed address questions investing biological crusts (biocrusts). Through amplicon‐sequencing, acquired data for multiple groups, is, total bacteria, diazotrophs, phoD ‐harbouring taxa, fungi. Our results have shown varying distance decay rates with bacteria showing weaker distance‐decay relationship than other groups. impact on varied diazotrophs being significantly influenced. While contributions specific processes effects local were consistently observed Homogenous selection limitation emerged crucial Precipitation C:P factors This study has substantially advanced our understanding structured desert biocrust systems.

Language: Английский

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Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(3), P. 847 - 861

Published: Sept. 8, 2021

Metabarcoding of DNA extracted from community samples whole organisms (whole organism DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities provide rapid, accurate high resolution data for novel molecular ecology research. The growth this field has been accompanied by considerable development that builds on microbial metabarcoding methods develop appropriate efficient sampling laboratory protocols communities. However, considerably less attention focused ensuring bioinformatic are adapted comprehensively in wocDNA metabarcoding. In study we examined over 600 papers identified 111 studies performed COI wocDNA. We then systematically reviewed the employed these identify state-of-the-art. Our results show increasing use diversity characterised a clear absence harmonisation, temporal trends little change situation. literature showed (i) heterogeneity across pipelines, tasks tools used, (ii) limited or no adaptation procedures nature fragment, (iii) worrying underreporting tasks, software parameters. Based upon findings propose set recommendations think should consider ensure appropriate, comprehensive comparable. believe adhering will improve long-term integrative potential biodiversity science.

Language: Английский

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Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(5), P. 1120 - 1135

Published: Jan. 15, 2021

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers potential much deeper understanding global biodiversity through integration massive quantities molecular inventory data generated independently at local, regional scales. The universality, reliability efficiency HTS can potentially facilitate seamless linking among species assemblages from different sites, hierarchical levels diversity, any taxonomic group regardless prior knowledge. However, collective international efforts are required to optimally exploit site-based synthesis, that present limited microbial domain. To contribute development an analogous strategy nonmicrobial terrestrial domain, symposium entitled "Next Generation Biodiversity Monitoring" was held November 2019 Nicosia (Cyprus). brought together evolutionary geneticists, ecologists scientists involved diverse initiatives using as core tool assessment. In this review, we summarize consensus emerged 3-day symposium. We converged on opinion effective Genomic Observatories network synthesis should be spatially led strategically united under umbrella metabarcoding approach. Subsequently, outline HTS-based collectively build integrative framework generation.

Language: Английский

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Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond global change. However, large-scale syntheses may be compromised if workflows differ from each other. There are ongoing efforts improve standardization the reporting inventory harmonization at stage metabarcode has yet addressed. A modular framework harmonized generation a pathway navigate complex structure terrestrial metazoan biodiversity. Here, through our collective expertise practitioners, method developers, researchers leading initiatives we seek initiate generation, arthropod module. We develop initial set submodules covering 5 main steps generation: (i) sample acquisition; (ii) processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, sequencing; (v) sequence metadata deposition, providing backbone To achieve this, identified key points harmonization, reviewed current state art, distilled existing knowledge within submodules, thus promoting best practice by guidelines recommendations reduce universe methodological options. advocate adoption further development encourage modules other fractions step toward synthesis harmonization.

Language: Английский

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High consistency of trophic niches in generalist arthropod species (Oribatida, Acari) across soil depth and forest type

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(12)

Published: Dec. 1, 2022

Many traits including trophic niche parameters are attributed to species. However, generalist species may vary in niches with environments, making species-based knowledge hard extrapolate beyond local food webs. Here we tested consistency oribatid mite (Acari), one of the most abundant arthropods that occupy all levels soil We used stable isotope analysis compare 40 Oribatida co-occur litter (O

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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Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera)

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 24, 2022

Abstract The soil fauna of the tropics remains one least known components biosphere. Long-term monitoring this is hampered by lack taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate approach, we studied ants, springtails termites 100 paired samples from Barro Colorado Island, Panama. was extracted Berlese-Tullgren funnels then either sorted traditional taxonomy known, individual barcodes (“traditional samples”) or processed metabarcoding (“metabarcoding samples”). We detected 49 ant, 37 springtail 34 termite species 3.46 million reads COI gene, at a mean sequence length 233 bp. Traditional identification yielded 80, 111 15 termites, respectively; 98%, 37% 100% these had Barcode Index Number (BIN) allowing for direct comparison Ants were best surveyed through methods, better metabarcoding, equally well both techniques. Species richness underestimated, faunal composition different in samples, mostly because ant not detected. prevalence increased their abundance seasonal shifts similar between samples. Probable false positive negative records reasonably low (13–18% common species). conclude that appear suitable long-term tropical rainforests. For schemes should complemented additional alates Malaise light traps.

Language: Английский

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Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods

Metabarcoding and Metagenomics, Journal Year: 2023, Volume and Issue: 7

Published: Nov. 23, 2023

Biodiversity is declining at alarming rates worldwide and large-scale monitoring urgently needed to understand changes their drivers. While classical taxonomic identification of species time labour intensive, the combination with DNA-based methods could upscale activities achieve larger spatial coverage increased sampling effort. However, challenges remain for when number individuals per and/or biomass estimates are required. Several methodological advancements exist improve potential DNA metabarcoding abundance analysis, which however need further evaluation. Here, we discuss laboratory, as well some bioinformatic adjustments workflows regarding estimation from arthropod community samples. Our review includes pre-laboratory processing such specimen photography, laboratory use spike-in an internal standard like correction factors. We conclude that photography coupled currently promises greatest estimates, but approaches spike-ins factors promising pursue further.

Language: Английский

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