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Jing W, Niu Z, Ma S, Yu H. New species and new record of Statherotmantis Diakonoff, 1973 from China (Lepidoptera: Tortricidae: Olethreutinae). Ecol Evol 2024; 14:e10906. [PMID: 38304272 PMCID: PMC10830350 DOI: 10.1002/ece3.10906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
In China, six species of Statherotmantis Diakonoff, 1973 were previously recorded. In the present study, four other species were recognized using morphology and DNA barcording analysis. Among these, three of which, S. miniscula sp. n., S. calva sp. n., and S. longiuscula sp. n., are described as new. In addition, one species, S. laetana Kuznetzov, 1988, is a new record for China. Adults and genitalia are illustrated, and keys to identify the Chinese species of Statherotmantis are provided.
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Affiliation(s)
- Wenqing Jing
- Shaanxi Key Laboratory for Animal ConservationNorthwest UniversityXi'anChina
| | - Zehua Niu
- Shaanxi Key Laboratory for Animal ConservationNorthwest UniversityXi'anChina
| | - Shuang Ma
- Shaanxi Key Laboratory for Animal ConservationNorthwest UniversityXi'anChina
| | - Haili Yu
- Shaanxi Key Laboratory for Animal ConservationNorthwest UniversityXi'anChina
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University)Ministry of EducationXi'anChina
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2
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Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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3
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Wei SF, Wang D, Zhang T, He ZQ. Revision of the genus Phyllotrella Gorochov, 1988 (Orthoptera: Gryllidae: Podoscirtinae: Podoscirtini). Zootaxa 2023; 5296:89-95. [PMID: 37518453 DOI: 10.11646/zootaxa.5296.1.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Indexed: 08/01/2023]
Abstract
The genus Phyllotrella Gorochov, 1988 presently comprises four described species, P. planidorsalis Gorochov, 1988, P. fumingi Sun & Liu, 2019, P. hainanensis Sun & Liu, 2019 and P. transversa Sun & Liu, 2019. In this study, the results of this genus are based on molecular and morphological features. The molecular result shows that the genetic distance among these individuals from different areas was 0.767%-1.386%. Thus, we consider them as same species. However, based on the similarities and differences of their male genitalia, we suggest treat these species as two subspecies P. planidorsalis planidorsalis (= P. hainanensis syn. nov. and P. transversa syn. nov.) and P. planidorsalis fumingi stat. nov.
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Affiliation(s)
- Shu-Fei Wei
- School of Life Sciences; East China Normal University; Shanghai 200241; China.
| | - Dan Wang
- School of Life Sciences; East China Normal University; Shanghai 200241; China.
| | - Tao Zhang
- School of Life Sciences; East China Normal University; Shanghai 200241; China.
| | - Zhu-Qing He
- Museum of Biology; School of Life Sciences; East China Normal University; Shanghai 200241; China.
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4
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Chimeno C, Rulik B, Manfrin A, Kalinkat G, Hölker F, Baranov V. Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach. PeerJ 2023; 11:e15336. [PMID: 37250705 PMCID: PMC10211366 DOI: 10.7717/peerj.15336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample's contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
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Affiliation(s)
- Caroline Chimeno
- Bavarian State Collection of Zoology (SNSB-ZSM), Munich, Germany
| | - Björn Rulik
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alessandro Manfrin
- Institute for Environmental Sciences, iES Landau, RPTU University of Kaiserslautern-Landau, Landau, Germany
| | - Gregor Kalinkat
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Viktor Baranov
- Estación Biológica de Doñana-CSIC/Doñana Biological Station-CSIC, Seville, Spain
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5
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Lees DC. The genome sequence of the red-line quaker, Agrochola lota (Clerck, 1759). Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.19285.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
We present a genome assembly from an individual male Agrochola lota (the Red-line Quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 636.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.
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6
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DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity. DIVERSITY 2023. [DOI: 10.3390/d15020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas.
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Yin Y, Yao LF, Hu Y, Shao ZK, Hong XY, Hebert PDN, Xue XF. DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea). Mol Ecol Resour 2022; 22:1986-1998. [PMID: 35178894 DOI: 10.1111/1755-0998.13599] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1,850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbor distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1,850 sequences were assigned to 531 Barcode Index Numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2,345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in BOLD, DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.
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Affiliation(s)
- Yue Yin
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Liang-Fei Yao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yue Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zi-Kai Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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8
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Totonchian N, Seiedy M, Katouzian AR, Husemann M. First DNA barcodes of Bembidion species (Coleoptera: Carabidae) from Iran. J NAT HIST 2022. [DOI: 10.1080/00222933.2021.2002454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Niloofar Totonchian
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Marjan Seiedy
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Ahmad-Reza Katouzian
- School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Martin Husemann
- Leibniz Institut zur Analyse des Biodiversitätswandels, Standort Hamburg, Hamburg, Germany
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9
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Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
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Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
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10
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D'Ercole J, Dincă V, Opler PA, Kondla N, Schmidt C, Phillips JD, Robbins R, Burns JM, Miller SE, Grishin N, Zakharov EV, DeWaard JR, Ratnasingham S, Hebert PDN. A DNA barcode library for the butterflies of North America. PeerJ 2021; 9:e11157. [PMID: 33976967 PMCID: PMC8061581 DOI: 10.7717/peerj.11157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
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Affiliation(s)
- Jacopo D'Ercole
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Paul A Opler
- Colorado State University, Fort Collins, CO, United States of America
| | | | - Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food, Guelph, Ontario, Canada
| | - Jarrett D Phillips
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert Robbins
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - John M Burns
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Scott E Miller
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States of America
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy R DeWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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11
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Yang W, Dong R, Song X, Yu H. The genus Syntozyga Lower (Lepidoptera, Tortricidae) in China, with descriptions of two new species. Zookeys 2021; 1028:95-111. [PMID: 33889047 PMCID: PMC8044070 DOI: 10.3897/zookeys.1028.60297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/03/2021] [Indexed: 11/27/2022] Open
Abstract
Species of the genus Syntozyga Lower, 1901 (Lepidoptera, Tortricidae, Olethreutinae) from China are studied. Syntozygaapicispinatasp. nov. and S.similispirographasp. nov. are described, S.pedias (Meyrick, 1920) is recorded for the first time from China, and S.spirographa (Diakonoff, 1968) is newly recorded from the Chinese mainland. Adults and genitalia are illustrated, and a distribution map of the Chinese species is given. Keys to identify the Chinese species of Syntozyga are provided. Species of the genus are well clustered in a neighbor-joining tree based on the sequence data of the COI gene. COI sequences corresponding to the new species and S.spirographa (Diakonoff, 1968) are submitted to BOLD.
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Affiliation(s)
- Wenxu Yang
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, Shaanxi Province, 710069, China Northwest University Xi'an China
| | - Ruiqin Dong
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, Shaanxi Province, 710069, China Northwest University Xi'an China
| | - Xueling Song
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, Shaanxi Province, 710069, China Northwest University Xi'an China
| | - Haili Yu
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, Shaanxi Province, 710069, China Northwest University Xi'an China.,Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, Shaanxi Province, 710069, China Northwest University Xi'an China
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12
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Li Q, Lin X, Li J, Liu B, Huang X. Differentiation in the eastern Asian Periphyllus koelreuteriae (Hemiptera: Aphididae) species complex driven by climate and host plant. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Divergent adaptation to different ecological conditions is regarded as important for speciation. For phytophagous insects, there is limited empirical evidence on species differentiation driven by climate and host plant. The recent application of molecular data and integrative taxonomic practice may improve our understanding of population divergence and speciation. Periphyllus koelreuteriae aphids feed exclusively on Koelreuteria (Sapindaceae) in temperate and subtropical regions of eastern Asia, and show morphological and phenological variations in different regions. In this study, phylogenetic and haplotype network analyses based on four genes revealed that P. koelreuteriae populations comprised three distinct genetic clades corresponding to climate and host plants, with the populations from subtropical highland regions and on Koelreuteria bipinnata host plants representing the most basal clade. These genetic lineages also showed distinct characteristics in terms of morphology and life cycle. The results indicate that P. koelreuteriae is a species complex with previously unrevealed lineages, whose differentiation may have been driven by climatic difference and host plant.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaolan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junjie Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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14
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Varga Z, Ronkay G, Nagy J, Ronkay L. Contribution to the taxonomy and phylogeny of the genus Polia Ochsenheimer, 1816 (Noctuidae, Noctuinae, Hadenini): species groups and pairs in the Holarctic subgenus Polia s. str. ACTA ZOOL ACAD SCI H 2020. [DOI: 10.17109/azh.66.1.35.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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Li Q, Deng J, Chen C, Zeng L, Lin X, Cheng Z, Qiao G, Huang X. DNA Barcoding Subtropical Aphids and Implications for Population Differentiation. INSECTS 2019; 11:E11. [PMID: 31877643 PMCID: PMC7022676 DOI: 10.3390/insects11010011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 11/16/2022]
Abstract
DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Jun Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Cui Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Linda Zeng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Xiaolan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Zhentao Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.L.); (J.D.); (C.C.); (L.Z.); (X.L.); (Z.C.)
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16
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Madden MJL, Young RG, Brown JW, Miller SE, Frewin AJ, Hanner RH. Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry. PLoS One 2019; 14:e0222291. [PMID: 31527883 PMCID: PMC6748562 DOI: 10.1371/journal.pone.0222291] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/26/2019] [Indexed: 11/19/2022] Open
Abstract
Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment of the immature stages of most arthropods is challenging; characters for identification are often dependent on adult morphology and reproductive structures. This study aims to strengthen the identification of such specimens through DNA barcoding, with a focus on microlepidoptera. A sample of 241 primarily immature microlepidoptera specimens intercepted at U.S. ports-of-entry from 2007 to 2011 were selected for analysis. From this sample, 201 COI-5P sequences were generated and analyzed for concordance between morphology-based and DNA-based identifications. The retrospective analysis of the data over 10 years (2009 to 2019) using the Barcode of Life Data (BOLD) system demonstrates the importance of establishing and growing DNA barcode reference libraries for use in specimen identification. Additionally, analysis of specimen identification using public data (43.3% specimens identified) vs. non-public data (78.6% specimens identified) highlights the need to encourage researchers to make data publicly accessible. DNA barcoding surpassed morphological identification with 42.3% (public) and 66.7% (non-public) of the sampled specimens achieving a species-level identification, compared to 38.3% species-level identification by morphology. Whilst DNA barcoding was not able to identify all specimens in our dataset, its incorporation into border security programs as an adjunct to morphological identification can provide secondary lines of evidence and lower taxonomic resolution in many cases. Furthermore, with increased globalization, database records need to be clearly annotated for suspected specimen origin versus interception location.
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Affiliation(s)
- Mary J. L. Madden
- Department of Integrated Biology, University of Guelph, Guelph, Ontario, Canada
| | - Robert G. Young
- Department of Integrated Biology, University of Guelph, Guelph, Ontario, Canada
| | - John W. Brown
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Scott E. Miller
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Andrew J. Frewin
- Department of Integrated Biology, University of Guelph, Guelph, Ontario, Canada
| | - Robert H. Hanner
- Department of Integrated Biology, University of Guelph, Guelph, Ontario, Canada
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17
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Huemer P, Wieser C, Stark W, Hebert PDN, Wiesmair B. DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) - a nearly perfect match of Linnean taxonomy. Biodivers Data J 2019; 7:e37734. [PMID: 31423084 PMCID: PMC6694074 DOI: 10.3897/bdj.7.e37734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023] Open
Abstract
The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Christian Wieser
- Landesmuseum Kärnten, Klagenfurt am Wörthersee, Austria Landesmuseum Kärnten Klagenfurt am Wörthersee Austria
| | | | - Paul D N Hebert
- Biodiversity Institute of Ontario, Guelph, Canada Biodiversity Institute of Ontario Guelph Canada
| | - Benjamin Wiesmair
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
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18
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Grenis K, Murphy SM. Direct and indirect effects of light pollution on the performance of an herbivorous insect. INSECT SCIENCE 2019; 26:770-776. [PMID: 29425403 DOI: 10.1111/1744-7917.12574] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 12/18/2017] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
Light pollution is a global disturbance with resounding impacts on a wide variety of organisms, but our understanding of these impacts is restricted to relatively few higher vertebrate species. We tested the direct effects of light pollution on herbivore performance as well as indirect effects mediated by host plant quality. We found that artificial light from streetlights alters plant toughness. Additionally, we found evidence of both direct and indirect effects of light pollution on the performance of an herbivorous insect, which indicates that streetlights can have cascading impacts on multiple trophic levels. Our novel findings suggest that light pollution can alter plant-insect interactions and thus may have important community-wide consequences.
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Affiliation(s)
- Kylee Grenis
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
| | - Shannon M Murphy
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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19
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Brito R, Specht A, Gonçalves GL, Moreira GRP, Carneiro E, Santos FL, Roque-Specht VF, Mielke OHH, Casagrande MM. Spodoptera marima: a New Synonym of Spodoptera ornithogalli (Lepidoptera: Noctuidae), with Notes on Adult Morphology, Host Plant Use and Genetic Variation Along Its Geographic Range. NEOTROPICAL ENTOMOLOGY 2019; 48:433-448. [PMID: 30515720 DOI: 10.1007/s13744-018-0654-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Spodoptera marima (Schaus, 1904) and Spodoptera ornithogalli (Guenée, 1852) are noctuid moths recognized for their economic importance in the New World. Historically, they have been considered cryptic species, being supposedly differentiated from each other by the absence of sexual dimorphism in S. marima, subtle differences in coloration on the hindwings and scale tufts of the ovipositor and the shape of male valva. The species are allopatric: North and Central America for S. ornithogalli and South America for S. marima. Previous phylogenetic studies using multilocus DNA sequences including a few specimens of S. marima suggested these species merge into a single clade. Here, we performed a comparative analysis to elucidate further their taxonomic status, using specimens of S. marima from various localities in Brazil. These species were recovered in the phylogenetic analysis as consistently mixed with each other in a major well-supported clade within Spodoptera. The existence of a spatial pattern for genetic structure was not clearly supported when two biogeographic regions (Neotropics and Neartic) were taken in separation; however, an individual-level isolation by distance was significant. The morphological characters traditionally used to differentiate the species were also not consistent. Therefore, we now consider S. marima a new junior synonym of S. ornithogalli. Results on host plant use demonstrated that it is a polyphagous species using more than 200 plants, which may mediate phenotypic variation along its geographical range.
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Affiliation(s)
- R Brito
- Depto de Zoologia, Univ Federal do Paraná, Curitiba, Paraná, Brasil
- Depto de Zoologia, Instituto de Biociências, Univ Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - A Specht
- Embrapa Cerrados, Planaltina, Distrito Federal, Brasil.
| | - G L Gonçalves
- Depto de Genética, Instituto de Biociências, Univ Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- Depto de Recursos Ambientales, Facultad de Ciencias Agronómicas, Univ de Tarapacá, Arica, Chile
| | - G R P Moreira
- Depto de Zoologia, Instituto de Biociências, Univ Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - E Carneiro
- Depto de Zoologia, Univ Federal do Paraná, Curitiba, Paraná, Brasil
| | - F L Santos
- Depto de Zoologia, Univ Federal do Paraná, Curitiba, Paraná, Brasil
- Univ do Estado de Mato Grosso, Campus de Alta Floresta, Alta Floresta, Mato Grosso, Brasil
| | - V F Roque-Specht
- Faculdade UnB Planaltina, Univ de Brasília, Planaltina, Distrito Federal, Brasil
| | - O H H Mielke
- Depto de Zoologia, Univ Federal do Paraná, Curitiba, Paraná, Brasil
| | - M M Casagrande
- Depto de Zoologia, Univ Federal do Paraná, Curitiba, Paraná, Brasil
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20
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Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, Butt A, Mansoor S, Hebert PDN. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One 2019; 14:e0217086. [PMID: 31116764 PMCID: PMC6530854 DOI: 10.1371/journal.pone.0217086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/04/2019] [Indexed: 01/16/2023] Open
Abstract
Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Abida Butt
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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21
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Kelnarova I, Jendek E, Grebennikov VV, Bocak L. First molecular phylogeny of Agrilus (Coleoptera: Buprestidae), the largest genus on Earth, with DNA barcode database for forestry pest diagnostics. BULLETIN OF ENTOMOLOGICAL RESEARCH 2019; 109:200-211. [PMID: 29784069 DOI: 10.1017/s0007485318000330] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL. All 329 Agrilus records available in the Barcode of Life Database format, including specimen images and geo data, are released through a public dataset 'Agrilus1 329' available at: dx.doi.org/10.5883/DS-AGRILUS1. All Agrilus species were identified using adult morphology and by using molecular phylogenetic trees, as well as distance- and tree-based algorithms. Most DNA-based species limits agree well with the morphology-based identification. Our results include cases of high intraspecific variability and multiple species para- and polyphyly. DNA barcoding is a powerful species identification tool in Agrilus, although it frequently fails to recover morphologically-delimited Agrilus species-group. Even though the current three-gene database covers only ~3% of the known Agrilus diversity, it contains representatives of all principal lineages from the Northern Hemisphere and represents the most extensive dataset built for DNA-delimited species identification within this genus so far. Molecular data analyses can rapidly and cost-effectively identify an unknown sample, including immature stages and/or non-native taxa, or species not yet formally named.
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Affiliation(s)
- I Kelnarova
- Department of Zoology,Faculty of Science UP,Olomouc,Czech Republic
| | - E Jendek
- Department of Forest Protection and Entomology,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences,Kamýcká 1176, CZ-165 21, Prague 6-Suchdol,Czech Republic
| | - V V Grebennikov
- Canadian Food Inspection Agency,960 Carling Avenue, Ottawa, ON K1A 0Y9,Canada
| | - L Bocak
- Department of Zoology,Faculty of Science UP,Olomouc,Czech Republic
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22
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Li Q, Yao J, Zeng L, Lin X, Huang X. Molecular and morphological evidence for the identity of two nominal species of Astegopteryx (Hemiptera, Aphididae, Hormaphidinae). Zookeys 2019; 833:59-74. [PMID: 31015776 PMCID: PMC6443623 DOI: 10.3897/zookeys.833.30592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/25/2019] [Indexed: 11/12/2022] Open
Abstract
The morphology of many insect species is usually influenced by environmental factors and therefore high phenotypic variation exists even within a species. This causes difficulty and uncertainty in species taxonomy, which can be remedied by using molecular data and integrative taxonomy. Astegopteryxbambusae and A.bambucifoliae are currently regarded as two closely related aphid species with similar bamboo hosts and overlapping distributions in the oriental region. However, in practice it is hard to distinguish between them. By incorporating molecular data from four mitochondrial and nuclear genes as well as morphological information from an extensive collection of live specimens, the present study indicates that A.bambucifoliae is a junior synonym of A.bambusae. The data also indicate that large-scale geographic patterns of population differentiation may exist within this species.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China Fujian Agriculture and Forestry University Fuzhou China
| | - Jiamin Yao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China Fujian Agriculture and Forestry University Fuzhou China
| | - Lingda Zeng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China Fujian Agriculture and Forestry University Fuzhou China
| | - Xiaolan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China Fujian Agriculture and Forestry University Fuzhou China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China Fujian Agriculture and Forestry University Fuzhou China
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23
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Kumar V, Kundu S, Chakraborty R, Sanyal A, Raha A, Sanyal O, Ranjan R, Pakrashi A, Tyagi K, Chandra K. DNA barcoding of Geometridae moths (Insecta: Lepidoptera): a preliminary effort from Namdapha National Park, Eastern Himalaya. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Abesh Sanyal
- Zoological Survey of India, Lepidoptera Division, Kolkata, India
| | - Angshuman Raha
- Zoological Survey of India, Lepidoptera Division, Kolkata, India
| | - Oyndrila Sanyal
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Rahul Ranjan
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- Zoological Survey of India, Lepidoptera Division, Kolkata, India
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24
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Varga Z, Ronkay G, Ronkay L. Taxonomic survey of the Polia (Polia) nebulosa species complex (Noctuidae, Noctuinae, Hadenini), with the description of two new subspecies. ACTA ZOOL ACAD SCI H 2019. [DOI: 10.17109/azh.65.2.107.2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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25
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Chen K, Zhang D, Li H. Systematics of the new genus Spinosuncus Chen, Zhang & Li with descriptions of four new species (Lepidoptera, Crambidae, Pyraustinae). Zookeys 2018:115-151. [PMID: 30532620 PMCID: PMC6281707 DOI: 10.3897/zookeys.799.23925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 10/01/2018] [Indexed: 11/12/2022] Open
Abstract
The new genus Spinosuncusgen. n. is proposed for three known species, S.contractalis (Warren, 1896), comb. n., S.praepandalis (Snellen, 1890), comb. n., and S.aureolalis (Lederer, 1863), comb. n. and four new species, S.rectacutussp. n., S.brevacutussp. n., S.curvisetaceussp. n., and S.quadracutussp. n. from the Oriental Region. An identification key is provided for all species. The habiti and genitalia of all species are figured. The monophyly of the genus is well supported by a phylogenetic analysis based on sequence data of the COI, 16S rRNA, and EF-1α genes. The potential sister groups of the new genus, the interspecific relationships and some intraspecific variations within the genus are discussed.
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26
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Huemer P, Hebert PDN, Mutanen M, Wieser C, Wiesmair B, Hausmann A, Yakovlev R, Möst M, Gottsberger B, Strutzenberger P, Fiedler K. Large geographic distance versus small DNA barcode divergence: Insights from a comparison of European to South Siberian Lepidoptera. PLoS One 2018; 13:e0206668. [PMID: 30388147 PMCID: PMC6214556 DOI: 10.1371/journal.pone.0206668] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/17/2018] [Indexed: 12/16/2022] Open
Abstract
Spanning nearly 13,000 km, the Palearctic region provides an opportunity to examine the level of geographic coverage required for a DNA barcode reference library to be effective in identifying species with broad ranges. This study examines barcode divergences between populations of 102 species of Lepidoptera from Europe and South Siberia, sites roughly 6,000 km apart. While three-quarters of these species showed divergence between their Asian and European populations, these divergence values ranged between 0-1%, distinctly less than the distance to the Nearest-Neighbor species in all but a few cases. Our results suggest that further taxonomic studies may be required for 16 species that showed either extremely low interspecific or high intraspecific variation. For example, seven species pairs showed low or no barcode divergence, but four of these cases are likely to reflect taxonomic over-splitting while the others involve species pairs that are either young or show evidence for introgression. Conversely, some of the nine species with deep intraspecific divergence at varied spatial levels may include overlooked species. Although these 16 cases require further investigation, our overall results indicate that barcode reference libraries based on records from one locality can be very effective in identifying specimens across an extensive geographic area.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Benjamin Wiesmair
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Axel Hausmann
- Section Lepidoptera, Bavarian State Collection of Zoology, Munich, Germany
| | - Roman Yakovlev
- Ecology Department, Altai State University, Barnaul, Russia
- Tomsk State University, Tomsk, Russia
| | - Markus Möst
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Brigitte Gottsberger
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Konrad Fiedler
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
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27
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deWaard JR, Levesque-Beaudin V, deWaard SL, Ivanova NV, McKeown JTA, Miskie R, Naik S, Perez KHJ, Ratnasingham S, Sobel CN, Sones JE, Steinke C, Telfer AC, Young AD, Young MR, Zakharov EV, Hebert PDN. Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding 1. Genome 2018; 62:85-95. [PMID: 30257096 DOI: 10.1139/gen-2018-0093] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
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Affiliation(s)
- Jeremy R deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Valerie Levesque-Beaudin
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Sujeevan Ratnasingham
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Crystal N Sobel
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Claudia Steinke
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Andrew D Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.,b Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Monica R Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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28
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Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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29
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Ivanov V, Lee KM, Mutanen M. Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression. Mol Ecol 2018; 27:1681-1695. [PMID: 29575366 DOI: 10.1111/mec.14564] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 02/23/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022]
Abstract
Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.
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Affiliation(s)
- Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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30
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Ullah M, Dong Y, Qiao P, Zhang Y, Yang Z. Delineating closely related species of Tylostega Meyrick (Lepidoptera: Crambidae: Spilomelinae) from mainland China using DNA barcodes. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1121-1127. [PMID: 29280404 DOI: 10.1080/24701394.2017.1419213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Integrative taxonomic study of three species of the genus Tylostega revealed that the genetic distances of the COI gene among the tested species was relatively large (3.27-7.60%). The Automatic Barcode Gap Discovery (ABGD) system performed better than the Barcode Index Number (BIN) in discriminating closely related species. This work provides a molecular baseline for future integrative taxonomic study of Crambidae.
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Affiliation(s)
- Misbah Ullah
- a Key Laboratory of Plant Protection Resources and Pest Management , Ministry of Education; Entomological Museum, College of Plant Protection, Northwest A&F University , Yangling , China
| | - Yanling Dong
- a Key Laboratory of Plant Protection Resources and Pest Management , Ministry of Education; Entomological Museum, College of Plant Protection, Northwest A&F University , Yangling , China
| | - Pingping Qiao
- a Key Laboratory of Plant Protection Resources and Pest Management , Ministry of Education; Entomological Museum, College of Plant Protection, Northwest A&F University , Yangling , China
| | - Yalin Zhang
- a Key Laboratory of Plant Protection Resources and Pest Management , Ministry of Education; Entomological Museum, College of Plant Protection, Northwest A&F University , Yangling , China
| | - Zhaofu Yang
- a Key Laboratory of Plant Protection Resources and Pest Management , Ministry of Education; Entomological Museum, College of Plant Protection, Northwest A&F University , Yangling , China
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31
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Hebert PDN, Ratnasingham S, Zakharov EV, Telfer AC, Levesque-Beaudin V, Milton MA, Pedersen S, Jannetta P, deWaard JR. Counting animal species with DNA barcodes: Canadian insects. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0333. [PMID: 27481785 PMCID: PMC4971185 DOI: 10.1098/rstb.2015.0333] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2016] [Indexed: 01/07/2023] Open
Abstract
Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Angela C Telfer
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Valerie Levesque-Beaudin
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Megan A Milton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Stephanie Pedersen
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Paul Jannetta
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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32
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Ortiz AS, Rubio RM, Guerrero JJ, Garre MJ, Serrano J, Hebert PD, Hausmann A. Close congruence between Barcode Index Numbers (bins) and species boundaries in the Erebidae (Lepidoptera: Noctuoidea) of the Iberian Peninsula. Biodivers Data J 2017; 5:e19840. [PMID: 28852323 PMCID: PMC5558050 DOI: 10.3897/bdj.5.e19840] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
The DNA barcode reference library for Lepidoptera holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for conservation assessment programs. We gathered sequences for the barcode region of the mitochondrial cytochrome c oxidase subunit I gene from 160 of the 176 nominal species of Erebidae moths (Insecta: Lepidoptera) known from the Iberian Peninsula. These results arise from a research project which constructing a DNA barcode library for the insect species of Spain. New records for 271 specimens (122 species) are coupled with preexisting data for 38 species from the Iberian fauna. Mean interspecific distance was 12.1%, while the mean nearest neighbour divergence was 6.4%. All 160 species possessed diagnostic barcode sequences, but one pair of congeneric taxa (Eublemma rosea and Eublemma rietzi) were assigned to the same BIN. As well, intraspecific sequence divergences higher than 1.5% were detected in four species which likely represent species complexes. This study reinforces the effectiveness of DNA barcoding as a tool for monitoring biodiversity in particular geographical areas and the strong correspondence between sequence clusters delineated by BINs and species recognized through detailed taxonomic analysis.
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Affiliation(s)
| | | | | | | | | | | | - Axel Hausmann
- Bavarian State Collection of Zoology, München, Germany
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Goldstein PZ, Nelson MW. Two psammophilic noctuids newly associated with beach plum, Prunus maritima (Rosaceae): The Dune Noctuid ( Sympistis riparia) and Coastal Heathland Cutworm ( Abagrotis benjamini) in Northeastern North America (Lepidoptera, Noctuidae). Zookeys 2017:61-89. [PMID: 28769603 PMCID: PMC5539367 DOI: 10.3897/zookeys.661.10867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/15/2017] [Indexed: 11/21/2022] Open
Abstract
Beach plum, Prunusmaritima Marshall, 1785 not Wangenh., 1787 (Rosaceae), currently under development as a potential crop, represents an under-acknowledged host plant for several Lepidoptera that have undergone declines in the northeastern USA. The Coastal Heathland Cutworm, Abagrotisnefascia (Smith, 1908), and the Dune Noctuid, Sympistisriparia (Morrison, 1875), are unrelated species of psammophilic noctuines (Lepidoptera: Noctuidae) regularly encountered on a localized basis in coastal southern New England and New York, and whose precise life history requirements are undocumented. We inferred and, based on field observation and rearing, corroborated beach plum as a larval host for these species in Massachusetts; the plant’s role in sustaining other moths with limited or contracting regional distributions is discussed. Sympistisriparia, belonging to a widely distributed complex of closely related species, has been associated specifically with both maritime and freshwater dunes. The eastern populations of Abagrotisnefascia represent a conspicuous range disjunction, separated from the nearest western populations by more than 2000 miles, and originally described by Franclemont as racebenjamini of Abagrotiscrumbi, both later synonymized with Abagrotisnefascia. Following examination of types and other material, an evaluation of putatively diagnostic features from both the original description and our own observations, genitalic characters, and the results of provisional barcode analyses, Abagrotisbenjamini Franclemont, stat. rev., is elevated to the rank of a valid species rather than representing eastern populations of Abagrotisnefascia (=crumbi) to which it originally referred.
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Affiliation(s)
- Paul Z Goldstein
- Research Entomologist, Systematic Entomology Laboratory, USDA, National Museum of Natural History, E-502, P.O. Box 37012, MRC 168, Washington, DC 20013-7012
| | - Michael W Nelson
- Invertebrate Zoologist, Natural Heritage & Endangered Species Program, Massachusetts Division of Fisheries & Wildlife, 1 Rabbit Hill Road, Westborough, MA 01581
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Zahiri R, Lafontaine JD, Schmidt BC, deWaard JR, Zakharov EV, Hebert PDN. Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America. PLoS One 2017; 12:e0178548. [PMID: 28570635 PMCID: PMC5453547 DOI: 10.1371/journal.pone.0178548] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/15/2017] [Indexed: 11/18/2022] Open
Abstract
This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.
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Affiliation(s)
- Reza Zahiri
- Canadian Food Inspection Agency, Ottawa Plant Laboratory, Entomology Unit, Ottawa, Ontario, Canada
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - J. Donald Lafontaine
- Agriculture and Agri-Food Canada, Biodiversity Program, Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa, Ontario, Canada
| | - B. Christian Schmidt
- Agriculture and Agri-Food Canada, Biodiversity Program, Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa, Ontario, Canada
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Lee Y, Lee W, Kanturski M, Foottit RG, Akimoto SI, Lee S. Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding. PLoS One 2017; 12:e0176582. [PMID: 28448639 PMCID: PMC5407777 DOI: 10.1371/journal.pone.0176582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022] Open
Abstract
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.
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Affiliation(s)
- Yerim Lee
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Wonhoon Lee
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Korea
| | - Mariusz Kanturski
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa, Katowice, Poland
| | - Robert G. Foottit
- Invertebrate Biodiversity, National Environmental Health Program, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Shin-Ichi Akimoto
- Laboratory of Systematic Entomology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Seunghwan Lee
- Laboratory of Insect Biosystematics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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36
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Ashfaq M, Akhtar S, Rafi MA, Mansoor S, Hebert PDN. Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan. PLoS One 2017; 12:e0174749. [PMID: 28339501 PMCID: PMC5365146 DOI: 10.1371/journal.pone.0174749] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/14/2017] [Indexed: 11/20/2022] Open
Abstract
Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Saleem Akhtar
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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37
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Yang Z, Landry JF, Hebert PDN. A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae). PLoS One 2016; 11:e0161449. [PMID: 27736878 PMCID: PMC5063472 DOI: 10.1371/journal.pone.0161449] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/24/2022] Open
Abstract
Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
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Affiliation(s)
- Zhaofu Yang
- Key laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, Shaanxi, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
| | - Jean-François Landry
- Agriculture and Agri-Food Canada, Ottawa Research & Development Centre, Ottawa, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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38
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Ashfaq M, Hebert PDN. DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests. Genome 2016; 59:933-945. [PMID: 27753511 DOI: 10.1139/gen-2016-0024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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Chambers EA, Hebert PDN. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016; 11:e0154363. [PMID: 27116180 PMCID: PMC4846166 DOI: 10.1371/journal.pone.0154363] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.
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Affiliation(s)
- E. Anne Chambers
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding. PLoS One 2016; 11:e0148602. [PMID: 26848744 PMCID: PMC4744053 DOI: 10.1371/journal.pone.0148602] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/21/2016] [Indexed: 12/17/2022] Open
Abstract
The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI) sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4%) was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5%) were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%–3.67%) suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU) identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having an extensively large habitat.
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Iftikhar R, Ashfaq M, Rasool A, Hebert PDN. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes. PLoS One 2016; 11:e0146014. [PMID: 26741134 PMCID: PMC4704811 DOI: 10.1371/journal.pone.0146014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/12/2015] [Indexed: 12/02/2022] Open
Abstract
Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5ʹ (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.
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Affiliation(s)
- Romana Iftikhar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Ashfaq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Akhtar Rasool
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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42
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Schmidt BC. Revision of the Lacinipolia vicina (Grote) complex (Noctuidae, Noctuinae, Eriopygini). Zookeys 2015:103-26. [PMID: 26692789 PMCID: PMC4668889 DOI: 10.3897/zookeys.527.9686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/09/2015] [Indexed: 11/25/2022] Open
Abstract
The Lacinipoliavicina (Grote) species complex, previously consisting of Lacinipoliavicina, Lacinipoliateligera (Morrison), Lacinipoliapensilis (Grote), and Lacinipoliasubalba Mustelin is revised to six species: Lacinipoliavicina (eastern USA), Lacinipoliateligera (southern Great Plains), Lacinipoliapensilis (Pacific Northwest and northern Rocky Mountains), Lacinipoliaacutipennis (Grote), stat. rev. (= Lacinipoliasubalbasyn. n.) (western North America), Lacinipoliasareta (Smith), stat. rev. (Canada and western USA) and Lacinipoliadimocki, sp. n. (California and Pacific Northwest). Lectotypes are designated for Lacinipoliavicina, Lacinipoliateligera and Lacinipoliapensilis.
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Affiliation(s)
- B Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Bldg., 960 Carling Ave., Ottawa, ON, Canada K1A 0C6
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Mustelin T, Crabo LG. Revision of the genus Aseptis McDunnough (Lepidoptera, Noctuidae, Noctuinae, Xylenini) with a description of two new genera, Paraseptis and Viridiseptis. Zookeys 2015:57-102. [PMID: 26692788 PMCID: PMC4668888 DOI: 10.3897/zookeys.527.9575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/12/2015] [Indexed: 11/12/2022] Open
Abstract
The genus Aseptis McDunnough (Lepidoptera, Noctuidae, Noctuinae, Xylenini, Xylenina) is revised to include 15 species based on morphological and molecular data. Several new synonymies are introduced. In addition, two genera are described because of significant morphological differences from Aseptis: Paraseptis gen. n., and Viridiseptis gen. n., resulting in the new combinations Paraseptis adnixa (Grote), comb. n., and Viridiseptis marina (Grote), comb. n. Although this work is primarily based on morphological data, DNA sequence data for the 658-base pair "barcode" segment of the mitochondrial gene for subunit 1 of cytochrome c oxidase was used as a secondary support for taxonomic changes within Aseptis and for the two new genera. Our work should provide clarity and stability in a previously difficult genus.
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Affiliation(s)
- Tomas Mustelin
- San Diego Natural History Museum, San Diego, California; 11904 Tallwood Court, Maryland 20854, USA
| | - Lars G Crabo
- Washington State University Adjunct Faculty; 724 14th Street, Bellingham, Washington 98225
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Arneodo JD, Balbi EI, Flores FM, Sciocco-Cap A. Molecular Identification of Helicoverpa armigera (Lepidoptera: Noctuidae: Heliothinae) in Argentina and Development of a Novel PCR-RFLP Method for its Rapid Differentiation From H. zea and H. gelotopoeon. JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:2505-2510. [PMID: 26318007 DOI: 10.1093/jee/tov254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/06/2015] [Indexed: 06/04/2023]
Abstract
Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae: Heliothinae) is among the most voracious global pests of agriculture. Adults of this species were identified recently in northern Argentina by dissection of male genitalia. In this work, a rapid and simple molecular tool was designed to distinguish H. armigera from the morphologically similar indigenous bollworms Helicoverpa zea (Boddie) and Helicoverpa gelotopoeon (Dyar), regardless of the life stage. Amplification of partial COI gene with a new primer pair, and subsequent digestion with endonuclease HinfI, yielded different RFLP profiles for the three main Helicoverpa pests currently present in South America. The method was validated in Helicoverpa specimens collected across Argentina, whose identity was further corroborated by COI sequencing and phylogenetic analysis. The data reported here constitute the first molecular confirmation of this pest in the country. The survey revealed the occurrence of H. armigera in northern and central Argentina, including the main soybean- and maize-producing area.
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Affiliation(s)
- Joel D Arneodo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, (1033) Buenos Aires, Argentina. Instituto de Microbiología y Zoología Agrícola (IMyZA) - Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y de los Reseros, (1686) Hurlingham, Argentina.
| | - Emilia I Balbi
- EEA- INTA Marcos Juárez, Ruta 12 km 3, (2580) Marcos Juárez, Argentina
| | - Fernando M Flores
- EEA- INTA Marcos Juárez, Ruta 12 km 3, (2580) Marcos Juárez, Argentina
| | - Alicia Sciocco-Cap
- Instituto de Microbiología y Zoología Agrícola (IMyZA) - Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y de los Reseros, (1686) Hurlingham, Argentina
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Lin X, Stur E, Ekrem T. Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes. PLoS One 2015; 10:e0138993. [PMID: 26406595 PMCID: PMC4583400 DOI: 10.1371/journal.pone.0138993] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/07/2015] [Indexed: 01/08/2023] Open
Abstract
DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.
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Affiliation(s)
- Xiaolong Lin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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Blagoev GA, deWaard JR, Ratnasingham S, deWaard SL, Lu L, Robertson J, Telfer AC, Hebert PDN. Untangling taxonomy: a
DNA
barcode reference library for
C
anadian spiders. Mol Ecol Resour 2015; 16:325-41. [DOI: 10.1111/1755-0998.12444] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/30/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Gergin A. Blagoev
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
| | - Jeremy R. deWaard
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
| | | | | | - Liuqiong Lu
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
| | - James Robertson
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
| | - Angela C. Telfer
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario University of Guelph Guelph ON Canada
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47
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Li Y, Gunter N, Pang H, Bocak L. DNA-based species delimitation separates highly divergent populations within morphologically coherent clades of poorly dispersing beetles. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yun Li
- The Museum of Biology; Sun Yat-sen University; Guangzhou 510275 Guangdong China
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
| | - Nicole Gunter
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
| | - Hong Pang
- The Museum of Biology; Sun Yat-sen University; Guangzhou 510275 Guangdong China
| | - Ladislav Bocak
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
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Hrček J, Godfray HCJ. What do molecular methods bring to host–parasitoid food webs? Trends Parasitol 2015; 31:30-5. [DOI: 10.1016/j.pt.2014.10.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/22/2014] [Accepted: 10/29/2014] [Indexed: 01/20/2023]
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Huemer P, Mutanen M, Sefc KM, Hebert PDN. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts. PLoS One 2014; 9:e115774. [PMID: 25541991 PMCID: PMC4277373 DOI: 10.1371/journal.pone.0115774] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/20/2014] [Indexed: 11/18/2022] Open
Abstract
This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen-Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Innsbruck, Austria
- * E-mail:
| | - Marko Mutanen
- Biodiversity Unit, Department of Biology, University of Oulu, Oulu, Finland
| | | | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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50
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Pentinsaari M, Hebert PDN, Mutanen M. Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences. PLoS One 2014; 9:e108651. [PMID: 25255319 PMCID: PMC4177932 DOI: 10.1371/journal.pone.0108651] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/03/2014] [Indexed: 11/22/2022] Open
Abstract
With 400 K described species, beetles (Insecta: Coleoptera) represent the most diverse order in the animal kingdom. Although the study of their diversity currently represents a major challenge, DNA barcodes may provide a functional, standardized tool for their identification. To evaluate this possibility, we performed the first comprehensive test of the effectiveness of DNA barcodes as a tool for beetle identification by sequencing the COI barcode region from 1872 North European species. We examined intraspecific divergences, identification success and the effects of sample size on variation observed within and between species. A high proportion (98.3%) of these species possessed distinctive barcode sequence arrays. Moreover, the sequence divergences between nearest neighbor species were considerably higher than those reported for the only other insect order, Lepidoptera, which has seen intensive analysis (11.99% vs up to 5.80% mean NN divergence). Although maximum intraspecific divergence increased and average divergence between nearest neighbors decreased with increasing sampling effort, these trends rarely hampered identification by DNA barcodes due to deep sequence divergences between most species. The Barcode Index Number system in BOLD coincided strongly with known species boundaries with perfect matches between species and BINs in 92.1% of all cases. In addition, DNA barcode analysis revealed the likely occurrence of about 20 overlooked species. The current results indicate that DNA barcodes distinguish species of beetles remarkably well, establishing their potential to provide an effective identification tool for this order and to accelerate the discovery of new beetle species.
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Affiliation(s)
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Marko Mutanen
- Department of Biology, University of Oulu, Oulu, Finland
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