Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)

European Journal of Taxonomy, Journal Year: 2020, Volume and Issue: 719(1)

Published: Oct. 2, 2020

Species are often presumed to be apparent in nature, but practice they may difficult recognise, especially when viewed across continents rather than within a single site. Coalescent-based Poisson-tree-process (PTP) models applied fast-evolving genes promise one quantitative criterion for recognising species, complete with the estimates of uncertainty that required scientific method. Such methods face challenges discerning between widespread polytypic species and complexes closely related, restricted-range species. In particular, ‘over-sampling’ many related individuals could risk causing groups less closely-related other appearing relatively more distinct consequently them being interpreted falsely as separate Some most persistent taxonomic problems among bumblebees (genus Bombus Latreille, 1802) subgenus Melanobombus von Dalla Torre, 1880. For global revision we use COI barcodes seek reduce from localised over-sampling by filtering data include only unique haplotypes. Unique haplotypes give conservative results unfiltered data, still increase number comparison recent morphological treatments. After integrative assessment coalescents groups, accepted shows non-linear sample size plateaus an 47% (to 25 species) compared previous estimate (of 17) based on morphology alone. variable species-complexes, our revised improve match patterns expected both genetic divergence-with-distance sympatry, leading three main inferences. (1) The particularly sichelii Radoszkowski, 1859, is (2) We detect two candidates broad concepts each former B. lapidarius (Linnaeus, 1758), miniatus Bingham, 1897, rufofasciatus Smith, 1852. Within s. lat. find insufficient evidence corroborate candidate no coalescent or support claim bisiculus Lecocq, Biella, Martinet & Rasmont, 2019 described southern Italy, weak uncorroborated different much broader group samples southeastern Europe excluding Turkey. stronger subtle corroborates str. eurythorax Wang, 1892 stat. rev. well prshewalskyi Morawitz, 1880 (3) Our ‘split’ clearly what has long been keriensis 1887, lat., supporting novel species: alagesianus Reinig, 1930 rev., incertoides Vogt, 1911 str., qilianensis sp. nov., separandus 1909 tibeticus nov. A lectotype designated name neotype alagesianus. phylogeny including slower-evolving provide deeper relationships, time calibration this phylogeny, ancestral distributions, all Bayesian framework. first keys identifying Melanobombus.

Language: Английский

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Opportunities and challenges of macrogenetic studies

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(12), P. 791 - 807

Published: Aug. 18, 2021

Language: Английский

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Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

Ecology and Evolution, Journal Year: 2019, Volume and Issue: 9(5), P. 2996 - 3010

Published: Feb. 16, 2019

Abstract DNA barcoding has greatly accelerated the pace of specimen identification to species level, as well delineation. Whereas application matching unknown specimens known is straightforward, its use for delimitation more controversial, discovery hinges critically on present levels haplotype diversity, patterning standing genetic variation that exists within and between species. Typical sample sizes molecular biodiversity assessment using barcodes range from 5 10 individuals per However, required are necessary fully gauge at level presumed be strongly taxon‐specific. Importantly, little attention been paid determining appropriate reveal majority intraspecific any one In this paper, we a brief outline current literature methods size estimation COI barcode sampling completeness. The importance adequate studies stressed, with variety metazoan taxa, through reviewing foundational statistical population models, specific ray‐finned fishes (Chordata: Actinopterygii). Finally, promising avenues further research in area highlighted.

Language: Английский

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Review of the Swedish species of Ophion (Hymenoptera: Ichneumonidae: Ophioninae), with the description of 18 new species and an illustrated key to Swedish species

European Journal of Taxonomy, Journal Year: 2019, Volume and Issue: 550

Published: Sept. 12, 2019

The Swedish species of Ophion Fabricius, 1798 are revised. More than 4800 specimens and relevant type material were studied; 234 sampled produced COI sequences. study recognises 41 species, 18 which described as new to science, mainly from Fennoscandian material: angularis Johansson & Cederberg sp. nov., arenarius autumnalis borealis broadi brocki confusus ellenae inclinans kallanderi matti norei paraparvulus paukkuneni splendens sylvestris tenuicornis nov. vardali Barcoding analysis also indicated the possible presence at least three additional, partly cryptic but these cannot be separated morphologically with certainty this point. costatus Ratzeburg, 1848 artemisiae Boie, 1855 interpreted defined. slaviceki Kriechbaumer, 1892 is excluded synonymy luteus Linnaeus, 1758 stat. rev. polyguttator (Thunberg, 1824) variegatus Rudow, 1883 O. obscuratus 1798. redescribed a neotype designated. albistylus Szépligeti, 1905 (syn. nov.) synonymized pteridis 1879 frontalis Strobl, 1904 areolaris Brauns, 1889 syn. Eleven reported Sweden for first time: artemisiae, crassicornis Brock, 1982, costatus, dispar 1895, forticornis Morley, 1915, kevoensis Jussila, 1965, ocellaris Ulbricht, 1926, perkinsi subarcticus Hellén, wuestneii 1892. shows that number previously have been treated highly variable taxa, actually consist several valid separable using morphological characters. An illustrated key determination provided.

Language: Английский

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High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: March 9, 2021

The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate captured 62% total haplotype diversity show most species possess a few common haplotypes many rare ones. Specimens in dataset have an average 95.3% probability being correctly identified. Mitochondrial displayed elevated richness southern refugia, establishing generality this key biogeographic pattern entire taxonomic group. Fifteen percent involved sharing, two thirds these cases may reflect need further research. This unique resource conservation studying evolutionary processes, cryptic species, phylogeography, ecology.

Language: Английский

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Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(6), P. 1904 - 1921

Published: April 9, 2021

Abstract Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust the diversity of taxonomic compartments targeted as well each barcode gene specificities. We built and tested pipeline based on read correction with DADA2 allowing analysing data from prokaryotic (16S) eukaryotic (18S, COI) life compartments. implemented option cluster amplicon sequence variants (ASVs) into operational units (OTUs) swarm, network‐based clustering algorithm, curate ASVs/OTUs using LULU. Finally, assignment was via Ribosomal Database Project Bayesian classifier (RDP) BLAST. validated this ribosomal mitochondrial markers metazoan mock communities 42 deep‐sea sediment samples. The results show that ASVs OTUs describe different levels biotic diversity, choice which depends research questions. They underline advantages complementarity LULU‐curation producing biodiversity inventories at level approaching one obtained morphological criteria. While removes intraspecific variation, LULU effectively spurious clusters, originating errors or intragenomic variability. Swarm affected alpha beta differently depending genetic marker. Specifically, d‐ values > 1 appeared be less appropriate 18S metazoans. Similarly, increasing LULU’s minimum ratio proved essential avoid losing species in sample‐poor sets. Comparing BLAST RDP underlined accurate assignments can RDP, but highlighted concerted effort build comprehensive, ecosystem‐specific databases.

Language: Английский

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Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths

Frontiers in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 9

Published: Feb. 18, 2021

Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named recognized, many of which difficult to identify using morphology only. Here we explore use DNA barcodes as a tool for identification and discovery in European gracillariids. We present barcode library including 6,791 COI sequences representing 242 (92%) resident species. Our results indicate high congruence between 91.3% (221/242) forming monophyletic clades that can be identified accurately alone. The remaining 8.7% represent cases non-monophyly making their uncertain barcodes. Species discrimination based on Barcode Index Number system (BIN) was successful 93% 7% sharing BINs. discovered 21 undescribed candidate species, six were confirmed from an integrative approach; other 15 require additional material study confirm preliminary evidence. Most these new found mountainous regions Mediterranean countries, South-Eastern Alps Balkans, nine only islands. addition, 13 classified deep conspecific lineages, comprising total 27 BINs no intraspecific morphological differences found, known ecological differentiation. Double-digest restriction-site associated sequencing (ddRAD) analysis showed strong mitonuclear discrepancy four out five studied. This discordance not explained by Wolbachia -mediated genetic sweeps. Finally, 26 “unassessed splits” containing 71 some involving geographical isolation or specialization will further test whether they cryptic

Language: Английский

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Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(9), P. e0222291 - e0222291

Published: Sept. 17, 2019

Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment the immature stages most arthropods challenging; characters identification are often dependent on adult morphology reproductive structures. This study aims to strengthen such specimens through DNA barcoding, with a focus microlepidoptera. A sample 241 primarily microlepidoptera intercepted U.S. from 2007 2011 were selected analysis. From this sample, 201 COI-5P sequences generated analyzed concordance between morphology-based DNA-based identifications. The retrospective analysis data over 10 years (2009 2019) using Barcode Life Data (BOLD) system demonstrates importance establishing growing barcode reference libraries use in specimen identification. Additionally, public (43.3% identified) vs. non-public (78.6% highlights need encourage researchers make publicly accessible. barcoding surpassed morphological 42.3% (public) 66.7% (non-public) sampled achieving species-level identification, compared 38.3% by morphology. Whilst was not able identify all our dataset, its incorporation into border security programs as an adjunct can provide secondary lines evidence lower resolution many cases. Furthermore, increased globalization, database records be clearly annotated suspected origin versus interception location.

Language: Английский

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Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(5), P. 1475 - 1489

Published: Feb. 10, 2021

Abstract In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating discovery through DNA taxonomy and inventory metabarcoding. this study, effect some intrinsic factors on efficiency various single‐marker methods (fixed variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested more than 90 empirical data sets, derived from a set 7,237 COI sequences attributed to 542 leaf beetles (Coleoptera: Chrysomelidae). The considered were: (i) number haplotypes per (as proxy genetic diversity), (ii) geographic among conspecific collection localities sampling width), (iii) difficulty related morphological identification species, (iv) taxonomic rank. Distance‐based methods, with average 70% match identification, outperformed those relying phylogenetic trees, less 59%. A high found have negative efficiency, whereas large distances within had positive effect. All delimitations (except GMYC) were significantly affected by presence that are difficult identified, decreasing their efficiency. Finally, only method influenced rank showing lower in sets at genus higher levels. observed biases we highlighted affecting could accounted when developing input analyses obtain reliable representation biological diversity.

Language: Английский

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DNA Barcoding Medicinal Plant Species from Indonesia

Plants, Journal Year: 2022, Volume and Issue: 11(10), P. 1375 - 1375

Published: May 21, 2022

Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or taxonomical tool. very important in medicinal use, not only for purposes but also authentication of products. Here, total 61 Indonesian from 30 families pair ITS2, matK, rbcL, trnL primers were study consisting molecular sequence analyses. This aimed analyze how four identified regions (ITS2, trnL) aid conservation investigate their effectiveness studied species. resulted 212 sequences new ones Though there no ideal perfect region target species, we recommend matK main identification, ITS2 rbcL alternative complementary regions. These findings will be useful forensic studies that support plants national global use.

Language: Английский

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