1
|
Wei R, Ge Y, Qi L, Han M, Zeng H, Hu Y, Zou L, Cheng X, Wu X, Na Q. Revealing Brownish Mycena Diversity in China: New Discoveries and Taxonomic Insights. J Fungi (Basel) 2024; 10:439. [PMID: 38921425 PMCID: PMC11204746 DOI: 10.3390/jof10060439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Within the genus Mycena, species exhibiting brownish basidiomata present considerable challenges in identification due to similar coloration. This study underscores the significance of pileipellis types and cheilocystidia characteristics as critical in delimiting brownish Mycena species. To clarify the principal taxonomic characters and their utility in distinguishing between brownish Mycena species, a morphological taxonomy and phylogenetic analysis were performed. Five new species from China were introduced and characterized through a comprehensive morphological anatomy and phylogenetic substantiation: M. campanulatihemisphaerica sp. nov., M. digitifurcata sp. nov., M. kunyuensis sp. nov., M. limitis sp. nov., and M. oryzifluens sp. nov. Discussions of these taxa are supplemented with morphological illustrations. The phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods based on sequences from the internal transcribed spacer and the large subunit regions of nuclear ribosomal RNA. With the addition of these five new species, the worldwide count of brownish Mycena increases to 94, and a key to the 29 known species of brownish Mycena from China is presented.
Collapse
Affiliation(s)
- Renxiu Wei
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, China; (R.W.); (Y.G.); (M.H.); (X.C.)
| | - Yupeng Ge
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, China; (R.W.); (Y.G.); (M.H.); (X.C.)
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China;
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, China
| | - Liangliang Qi
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Menghui Han
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, China; (R.W.); (Y.G.); (M.H.); (X.C.)
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China;
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, China
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, China;
| | - Li Zou
- College of Forestry, Northeast Forestry University, Harbin 150040, China;
| | - Xianhao Cheng
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, China; (R.W.); (Y.G.); (M.H.); (X.C.)
| | - Xiaoming Wu
- Kunyushan National Nature Reserve, Yantai 264112, China;
| | - Qin Na
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, China; (R.W.); (Y.G.); (M.H.); (X.C.)
| |
Collapse
|
2
|
Landers E, Claridge B, Kuhn W, Seymour V, Peek H, Fluet S, Ramgren J, Phelps J, Paulk B, Cordner L, Blaschke J. Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park. ENVIRONMENTAL ENTOMOLOGY 2024:nvae058. [PMID: 38853372 DOI: 10.1093/ee/nvae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.
Collapse
Affiliation(s)
- Emerie Landers
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brandon Claridge
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA
| | - Will Kuhn
- Discover Life in America, 1316 Cherokee Orchard Road, Gatlinburg, TN, 37738, USA
| | - Victoria Seymour
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Hettie Peek
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Scout Fluet
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Ramgren
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Phelps
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brayden Paulk
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Lydia Cordner
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jeremy Blaschke
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| |
Collapse
|
3
|
Na Q, Zeng H, Hu Y, Ding H, Ke B, Zeng Z, Liu C, Cheng X, Ge Y. Morphological and phylogenetic analyses reveal five new species of Porotheleaceae (Agaricales, Basidiomycota) from China. MycoKeys 2024; 105:49-95. [PMID: 38708027 PMCID: PMC11066505 DOI: 10.3897/mycokeys.105.118826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The first occurrence of Marasmiellomycena and Pulverulina in the Chinese mycobiota are reported, M.tomentosa and P.flavoalba, two new species and M.albodescendens, a new combination, revealed by phylogenetic analyses and morphological study. These newly-recorded genera, Marasmiellomycena, which can be distinguished by their agaricoid basidiomata, dark-coloured stipe, sarcodimitic tramal structure, stipitipellis with yellow to yellowish-brown pigments and yellow-pigmented thick-walled caulocystidia and Pulverulina, which differs from other genera of Porotheleaceae by its pruinose stipe, decurrent lamellae, inamyloid basidiospores and absence of hymenial cystidia. We also formally describe three other new species of Porotheleaceae collected from Chinese temperate to subtropical zones of Fujian and Zhejiang Provinces: Clitocybulafuscostriata, Gerronemabrunneosquamulosum and Leucoinocybesubglobispora. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae, based on a multi-locus (ITS, nrLSU and rpb2) dataset. According to this analysis, Chrysomycena, Clitocybula, Delicatula, Hydropodia, Hydropus, Leucoinocybe, Marasmiellomycena, Megacollybia, Pulverulina, Trogia and Vizzinia are monophyletic. However, Gerronema is identified as polyphyletic and, additionally, Porotheleum does not form a monophyletic group either because Porotheleumparvulum and Porotheleumalbidum are "unassigned" in phylogenetic analysis. The results of our phylogenetic analyses, coupled with morphological observations, confirm recognition of these new taxa. Morphological descriptions, photographs, line drawings and comparisons with closely-related taxa are presented for the new species. A key to the 22 species belonging to nine genera of Porotheleaceae in China is also provided.
Collapse
Affiliation(s)
- Qin Na
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, ChinaNanjing Institute of Environmental SciencesNanjingChina
| | - Hui Ding
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, ChinaNanjing Institute of Environmental SciencesNanjingChina
| | - Binrong Ke
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Zhiheng Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Changjing Liu
- College of Criminal Science and Technology, Nanjing Police University, Nanjing 210042, ChinaNanjing Police UniversityNanjingChina
| | - Xianhao Cheng
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yupeng Ge
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| |
Collapse
|
4
|
McMullin RT, Simon ADF, Brodo IM, Wickham SB, Bell-Doyon P, Kuzmina M, Starzomski BM. DNA barcoding aids in generating a preliminary checklist of the lichens and allied fungi of Calvert Island, British Columbia: Results from the 2018 Hakai Terrestrial BioBlitz. Biodivers Data J 2024; 12:e120292. [PMID: 38469225 PMCID: PMC10925859 DOI: 10.3897/bdj.12.e120292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/24/2024] [Indexed: 03/13/2024] Open
Abstract
Background Bioblitzes are a tool for the rapid appraisal of biodiversity and are particularly useful in remote and understudied regions and for understudied taxa. Lichens are an example of an often overlooked group, despite being widespread in virtually all terrestrial ecosystems and having many important ecological functions. New information We report the lichens and allied fungi collected during the 2018 terrestrial bioblitz conducted on Calvert Island on the Central Coast of British Columbia, Canada. We identified 449 specimens belonging to 189 species in 85 genera, increasing the total number of species known from Calvert Island to 194, and generated Internal Transcribed Spacer (ITS) sequences for 215 specimens from 121 species. Bryoriafurcellata, Chaenothecopsislecanactidis and C.nigripunctata were collected for the first time in British Columbia. We also found Pseudocyphellariarainierensis, which is listed as Special Concern on the federal Species at Risk Act, and other rarely reported species in British Columbia including Opegraphasphaerophoricola, Protomicarealimosa, Raesaeneniahuuskonenii and Sareadifformis. We demonstrate that DNA barcoding improves the scope and accuracy of expert-led bioblitzes by facilitating the detection of cryptic species and allowing for consistent identification of chemically and morphologically overlapping taxa. Despite the spatial and temporal limitations of our study, the results highlight the value of intact forest ecosystems on the Central Coast of British Columbia for lichen biodiversity, education and conservation.
Collapse
Affiliation(s)
- Richard Troy McMullin
- Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, K1P 6P4, CanadaCanadian Museum of Nature, PO Box 3443, Station DOttawa, Ontario, K1P 6P4Canada
| | - Andrew D. F. Simon
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, V8P 5C2, CanadaSchool of Environmental Studies, University of VictoriaVictoria, British Columbia, V8P 5C2Canada
| | - Irwin M. Brodo
- Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, K1P 6P4, CanadaCanadian Museum of Nature, PO Box 3443, Station DOttawa, Ontario, K1P 6P4Canada
| | - Sara B. Wickham
- Hakai Institute, PO Box 309, Heriot Bay, British Columbia, VOP 1H0, CanadaHakai Institute, PO Box 309Heriot Bay, British Columbia, VOP 1H0Canada
| | - Philip Bell-Doyon
- Department of Biology, Université Laval, Québec, Québec, G1V 0A6, CanadaDepartment of Biology, Université LavalQuébec, Québec, G1V 0A6Canada
| | - Maria Kuzmina
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, CanadaCentre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of GuelphGuelph, Ontario, N1G 2W1Canada
| | - Brian M. Starzomski
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, V8P 5C2, CanadaSchool of Environmental Studies, University of VictoriaVictoria, British Columbia, V8P 5C2Canada
| |
Collapse
|
5
|
Niego AGT, Thongklang N, Hyde KD, Raspé O. Introduction of two novel species of Hymenopellis (Agaricales, Physalacriaceae) from Thailand. MycoKeys 2023; 98:253-271. [PMID: 37534304 PMCID: PMC10390987 DOI: 10.3897/mycokeys.98.104517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/29/2023] [Indexed: 08/04/2023] Open
Abstract
Hymenopellis is the most diverse genus in the group of oudemansielloid/xeruloid taxa (Physalacriaceae). This genus has a worldwide distribution with records mostly from Europe and America. Asian taxa are least represented. In this paper on Hymenopellis from Thailand, two novel species are introduced, and a Hymenopellis collection affine to H.orientalis is described. Macro and micromorphological characters are described. Maximum likelihood and Bayesian phylogenetic analyses were performed on combined ITS and nrLSU regions to confirm taxonomical placement and infer the phylogenetic affinities of the studied species. Hymenopellisstraminea sp. nov. is straw-yellow, with medium-sized basidiomata, abundant and diverse in form cheilocystidia, few, narrowly lageniform to fusiform pleurocystidia, and clamp connections at the lower part of the stipe. Hymenopellisutriformis sp. nov. has mostly utriform pleurocystidia and 2-spored basidia. In the inferred phylogenies, the new species from this study formed distinct clades well supported by bootstrap proportions and posterior probabilities. The studied specimen affine to H.orientalis produced 2-spored basidia whereas published descriptions of other specimens mention 4-spored basidia. Moreover, the genetic distance between ITS sequences of this specimen and that of a Hymenopellisorientalis specimen from GenBank was 1.30-2.57%. Therefore, the conspecificity of our specimen with H.orientalis is uncertain, and additional specimens are needed to fully confirm its identity.
Collapse
Affiliation(s)
- Allen Grace T. Niego
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | | | - Kevin D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Iloilo Science and Technology University, La Paz, Iloilo 5000, Philippines
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Olivier Raspé
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| |
Collapse
|
6
|
Srivathsan A, Ang Y, Heraty JM, Hwang WS, Jusoh WFA, Kutty SN, Puniamoorthy J, Yeo D, Roslin T, Meier R. Convergence of dominance and neglect in flying insect diversity. Nat Ecol Evol 2023; 7:1012-1021. [PMID: 37202502 PMCID: PMC10333119 DOI: 10.1038/s41559-023-02066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/06/2023] [Indexed: 05/20/2023]
Abstract
Most of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA barcodes. Here this approach is applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries and numerous habitats (>225,000 specimens belonging to >25,000 species in 458 families). We find that 20 insect families (10 belonging to Diptera) account for >50% of local species diversity regardless of clade age, continent, climatic region and habitat type. Consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate insect diversity are 'dark taxa' in that they suffer from extreme taxonomic neglect, with little signs of increasing activities in recent years. Taxonomic neglect tends to increase with diversity and decrease with body size. Identifying and tackling the diversity of 'dark taxa' with scalable techniques emerge as urgent priorities in biodiversity science.
Collapse
Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Yuchen Ang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - John M Heraty
- Department of Entomology, University of California, Riverside, CA, USA
| | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Wan F A Jusoh
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jayanthi Puniamoorthy
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
7
|
Song F, Deng YF, Yan HF, Lin ZL, Delgado A, Trinidad H, Gonzales-Arce P, Riva S, Cano-Echevarría A, Ramos E, Aroni YP, Rivera S, Arakaki M, Ge XJ. Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru. Sci Data 2023; 10:294. [PMID: 37208352 DOI: 10.1038/s41597-023-02206-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Lomas formations or "fog oases" are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world's deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora's composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.
Collapse
Affiliation(s)
- Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yun-Fei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhe-Li Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Amalia Delgado
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Huber Trinidad
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Paúl Gonzales-Arce
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Sebastián Riva
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Asunción Cano-Echevarría
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Elmer Ramos
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Yaquelin Pamela Aroni
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Soledad Rivera
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Mónica Arakaki
- División Botánica, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima, 11, Perú
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| |
Collapse
|
8
|
Meeus S, Silva-Rocha I, Adriaens T, Brown PMJ, Chartosia N, Claramunt-López B, Martinou AF, Pocock MJO, Preda C, Roy HE, Tricarico E, Groom QJ. More than a Bit of Fun: The Multiple Outcomes of a Bioblitz. Bioscience 2023; 73:168-181. [PMID: 36936381 PMCID: PMC10020829 DOI: 10.1093/biosci/biac100 10.3897/biss.5.74361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Bioblitzes are a popular approach to engage people and collect biodiversity data. Despite this, few studies have actually evaluated the multiple outcomes of bioblitz activities. We used a systematic review, an analysis of data from more than 1000 bioblitzes, and a detailed analysis of one specific bioblitz to inform our inquiry. We evaluated five possible bioblitz outcomes, which were creating a species inventory, engaging people in biological recording, enhancing learning about nature, discovering a species new to an area, and promoting an organization. We conclude that bioblitzes are diverse but overall effective at their aims and have advantages over unstructured biodiversity recording. We demonstrate for the first time that bioblitzes increase the recording activity of the participants for several months after the event. In addition, we provide evidence that bioblitzes are effective at bringing people and organizations together to build communities of professionals and amateurs, critical for conserving and protecting biodiversity.
Collapse
Affiliation(s)
| | | | - Tim Adriaens
- Research Institute for Nature and Forest, Brussels, Belgium
| | - Peter M J Brown
- Zoology in the School of Life Sciences at Anglia Ruskin University, Cambridge, England, United Kingdom
| | - Niki Chartosia
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | | | - Michael J O Pocock
- UK Centre for Ecology and Hydrology in Wallingford, England, United Kingdom
| | | | - Helen E Roy
- UK Centre for Ecology and Hydrology in Wallingford, England, United Kingdom
| | - Elena Tricarico
- Department of Biology at the University of Florence, Sesto Fiorentino, Italy
| | | |
Collapse
|
9
|
Meeus S, Silva-Rocha I, Adriaens T, Brown PMJ, Chartosia N, Claramunt-López B, Martinou AF, Pocock MJO, Preda C, Roy HE, Tricarico E, Groom QJ. More than a Bit of Fun: The Multiple Outcomes of a Bioblitz. Bioscience 2023; 73:168-181. [PMID: 36936381 PMCID: PMC10020829 DOI: 10.1093/biosci/biac100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Bioblitzes are a popular approach to engage people and collect biodiversity data. Despite this, few studies have actually evaluated the multiple outcomes of bioblitz activities. We used a systematic review, an analysis of data from more than 1000 bioblitzes, and a detailed analysis of one specific bioblitz to inform our inquiry. We evaluated five possible bioblitz outcomes, which were creating a species inventory, engaging people in biological recording, enhancing learning about nature, discovering a species new to an area, and promoting an organization. We conclude that bioblitzes are diverse but overall effective at their aims and have advantages over unstructured biodiversity recording. We demonstrate for the first time that bioblitzes increase the recording activity of the participants for several months after the event. In addition, we provide evidence that bioblitzes are effective at bringing people and organizations together to build communities of professionals and amateurs, critical for conserving and protecting biodiversity.
Collapse
Affiliation(s)
| | | | - Tim Adriaens
- Research Institute for Nature and Forest, Brussels, Belgium
| | - Peter M J Brown
- Zoology in the School of Life Sciences at Anglia Ruskin University, Cambridge, England, United Kingdom
| | - Niki Chartosia
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | | | - Michael J O Pocock
- UK Centre for Ecology and Hydrology in Wallingford, England, United Kingdom
| | | | - Helen E Roy
- UK Centre for Ecology and Hydrology in Wallingford, England, United Kingdom
| | - Elena Tricarico
- Department of Biology at the University of Florence, Sesto Fiorentino, Italy
| | | |
Collapse
|
10
|
Liu C, Ashfaq M, Yin Y, Zhu Y, Wang Z, Cheng H, Hebert P. Using DNA metabarcoding to assess insect diversity in citrus orchards. PeerJ 2023; 11:e15338. [PMID: 37168534 PMCID: PMC10166080 DOI: 10.7717/peerj.15338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Background DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples. Methods The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE). Results These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H') showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67-0.68; BC = 0.19-0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
Collapse
Affiliation(s)
- Chenxi Liu
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Yanfang Yin
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanjuan Zhu
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Cheng
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Paul Hebert
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
11
|
Thiyagaraja V, Ertz D, Lücking R, Wanasinghe DN, Aptroot A, Cáceres MEDS, Hyde KD, Tapingkae W, Cheewangkoon R. Taxonomic and Phylogenetic Reassessment of Pyrgidium (Mycocaliciales) and Investigation of Ascospore Morphology. J Fungi (Basel) 2022; 8:jof8090966. [PMID: 36135691 PMCID: PMC9500946 DOI: 10.3390/jof8090966] [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: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence of molecular data. In order to investigate the systematic position of Pyrgidium, two specimens collected in Brazil and Thailand, respectively, were used to generate mtSSU, SSU, LSU and ITS sequences. However, given that most other representatives of this order only have LSU and ITS sequences available, the phylogenetic reconstruction was limited to these two markers. The phylogenetic analyses confirmed placement of the genus within Mycocaliciales, the genus possessing a sister group relationship with the lichenicolous genus Sphinctrina. Detailed morphological descriptions and illustrations are provided, including those for type specimens of the various synonyms subsumed under the hitherto only accepted species, Pyrgidium montellicum (Beltr.) Tibell. The ascospore morphology was investigated using compound and scanning electronic microscopy (SEM). Principal component analysis (PCA) was performed for the ascospore size using PC-ORD 7. The molecular data and re-examination of the type specimens support the monospecific nature of this genus.
Collapse
Affiliation(s)
- Vinodhini Thiyagaraja
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - Damien Ertz
- Research Department, Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium
- Fédération Wallonie-Bruxelles, Service Général de l’Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavallée 1, BE-1080 Bruxelles, Belgium
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, Germany
| | - Dhanushka N. Wanasinghe
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - André Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, s/n Bairro Universitário, Campo Grande CEP 79070-900, Brazil
| | | | - Kevin D. Hyde
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - Wanaporn Tapingkae
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
| |
Collapse
|
12
|
Na Q, Hu Y, Zeng H, Song Z, Ding H, Cheng X, Ge Y. Updated taxonomy on Gerronema (Porotheleaceae, Agaricales) with three new taxa and one new record from China. MycoKeys 2022; 89:87-120. [PMID: 36760827 PMCID: PMC9849079 DOI: 10.3897/mycokeys.89.79864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/16/2022] [Indexed: 11/12/2022] Open
Abstract
Only three Gerronema (Porotheleaceae) species have been previously recorded in China. Here, we report collections of a fourth species in China: G.nemorale Har. Takah., which is widely distributed in Chinese temperate to subtropical zones. We also formally describe three new species, collected from Anhui, Fujian, and Zhejiang provinces: G.baishanzuense sp. nov., G.microcarpum sp. nov., and G.zhujian sp. nov. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae based on a multi-locus (ITS + nLSU) dataset. The results, which indicate that Gerronema is polyphyletic, support the taxonomic recognition of the three new species. Morphological descriptions, photographs, line drawings, and comparisons with closely related taxa are presented for the new and newly recorded species. A key to the seven species of Gerronema in China is also provided.
Collapse
Affiliation(s)
- Qin Na
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, 8 Jiangwangmiao street, Nanjing 210042, ChinaNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible FungiFuzhouChina
| | - Zhizhong Song
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Hui Ding
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, 8 Jiangwangmiao street, Nanjing 210042, ChinaNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Xianhao Cheng
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yupeng Ge
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| |
Collapse
|
13
|
Domènech M, Wangensteen OS, Enguídanos A, Malumbres‐Olarte J, Arnedo MA. For all audiences: Incorporating immature stages into standardised spider inventories has a major impact on the assessment of biodiversity patterns. Mol Ecol Resour 2022; 22:2319-2332. [DOI: 10.1111/1755-0998.13625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/19/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Marc Domènech
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science University of Tromsø The Arctic University of Norway Norway
| | - Alba Enguídanos
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
| | - Jagoba Malumbres‐Olarte
- Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Faculty of Agrarian and Environmental Sciences Rua Capitão João d’Ávila 9700‐042 Terceira Açores Portugal
- Finnish Museum of Natural History University of Helsinki P.O.Box 17 Pohjoinen Rautatiekatu 13) 00014 Helsinki Finland
| | - Miquel A. Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio) Universitat de Barcelona Av. Diagonal 643 E‐08028 Barcelona Spain
| |
Collapse
|
14
|
Young MR, Hebert PDN. Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 2022; 10:e12845. [PMID: 35178296 PMCID: PMC8815377 DOI: 10.7717/peerj.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
Collapse
Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
15
|
Kjærandsen J. Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library. INSECTS 2022; 13:insects13020147. [PMID: 35206721 PMCID: PMC8879535 DOI: 10.3390/insects13020147] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary DNA barcoding is a method by which a specific region of the mitochondrial genome is used to quantify genetic distances within and between animal species. Most DNA barcodes of the world are assembled on the Barcode of Life online database BoldSystems (BOLD). There, machine-generated barcode index numbers (BINs) are automatically assigned to clusters of specimens thought to represent species. I review the current state of DNA barcoding of the superfamily Sciaroidea, a diverse insect group consisting of close to 16,000 described fly species in eight families. To date, over 1.2 million specimens of Sciaroidea have been barcoded and the 56,648 assigned BINs on BOLD already represent 3.5 times the number of described species. Still, 95% of the BINs have currently no associated scientific name and very little effort has been put into building a quality-checked reference library where named species are linked to the BINs on BOLD. In the Nordic region, however, substantial progress is made towards building a complete reference library. While DNA barcoding has tremendous potential for advancing the knowledge for many diverse groups of insects, its potential will never be fully reached absent more engagement of trained taxonomists to build voucher collections, curate the reference libraries, and describe new species. Abstract DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.
Collapse
Affiliation(s)
- Jostein Kjærandsen
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, P.O. Box 6050 Langnes, NO-9037 Tromsø, Norway
| |
Collapse
|
16
|
Boucher S, Savage J. DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana. Zookeys 2022; 1083:147-168. [PMID: 35115876 PMCID: PMC8807582 DOI: 10.3897/zookeys.1083.76651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.
Collapse
Affiliation(s)
- Stéphanie Boucher
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-de-Bellevue, H9X 3V9, Quebec, CanadaMcGill UniversityQuebecCanada
| | - Jade Savage
- Bishop’s University, Sherbrooke, J1M 1Z7, Quebec, CanadaBishop’s UniversitySherbrookeCanada
| |
Collapse
|
17
|
Yamashita Y, Ogura‐Tsujita Y, Nagata N, Kurosawa T, Yukawa T. Molecular identification of seed‐feeding flies dissected from herbarium specimens clarifies the 100‐year history of parasitism by
Japanagromyza tokunagai
in Japan. Ecol Res 2021. [DOI: 10.1111/1440-1703.12283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yumi Yamashita
- Graduate School of Symbiotic Systems Science and Technology Fukushima University 1 Kanayagawa, Fukushima Fukushima Japan
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Yuki Ogura‐Tsujita
- Faculty of Agriculture Saga University, 1 Honjyo Saga Japan
- United Graduate School of Agricultural Sciences Kagoshima University Kagoshima Japan
| | - Nobuaki Nagata
- Department of Anthropology National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Takahide Kurosawa
- Faculty of Symbiotic Systems Science Fukushima University Fukushima Fukushima Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
| |
Collapse
|
18
|
Steinke D, Braukmann TWA, Manerus L, Woodhouse A, Elbrecht V. Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.59201] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Malaise trap is a popular device for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors influence its collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distances (3 m increments from 3 to 30 m). The second experiment involved a total of 10 traps set up in a row at 3 m distance intervals for three consecutive weeks.
Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs drops considerably at about 18 m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitats which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.
Collapse
|
19
|
Magoga G, Fontaneto D, Montagna M. Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Mol Ecol Resour 2021; 21:1475-1489. [PMID: 33565247 DOI: 10.1111/1755-0998.13352] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
Collapse
Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca Sulle Acque (IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy.,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici, Italy
| |
Collapse
|
20
|
Nitta JH, Ebihara A, Smith AR. A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica. PLoS One 2020; 15:e0241231. [PMID: 33206674 PMCID: PMC7673574 DOI: 10.1371/journal.pone.0241231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/11/2020] [Indexed: 11/18/2022] Open
Abstract
Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.
Collapse
Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Alan R. Smith
- The University Herbarium, University of California at Berkeley, Berkeley, California, United States of America
| |
Collapse
|
21
|
Layton KKS, Dempson B, Snelgrove PVR, Duffy SJ, Messmer AM, Paterson IG, Jeffery NW, Kess T, Horne JB, Salisbury SJ, Ruzzante DE, Bentzen P, Côté D, Nugent CM, Ferguson MM, Leong JS, Koop BF, Bradbury IR. Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol Appl 2020; 13:1055-1068. [PMID: 32431752 PMCID: PMC7232759 DOI: 10.1111/eva.12922] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.
Collapse
Affiliation(s)
- Kara K. S. Layton
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brian Dempson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul V. R. Snelgrove
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven J. Duffy
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Amber M. Messmer
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - John B. Horne
- National Oceanic and Atmospheric AdministrationSouthwest Fisheries Science CenterLa JollaCAUSA
| | | | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - David Côté
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | | | - Jong S. Leong
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
| | - Ben F. Koop
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
- Centre for Biomedical ResearchUniversity of VictoriaVictoriaBCCanada
| | - Ian R. Bradbury
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| |
Collapse
|
22
|
Nicolai A, Guernion M, Guillocheau S, Hoeffner K, Le Gouar P, Ménard N, Piscart C, Vallet D, Hervé MET, Benezeth E, Chedanne H, Blémus J, Vernon P, Cylly D, Hotte H, Loïs G, Mai B, Perez G, Ouisse T, Monard C, Wiegand C, Caudal JP, Butet A, Dahirel M, Barbe L, Balbi M, Briand V, Bormans M, Charrier M, Bouger G, Jung V, Le Lann C, Pannard A, Petillon J, Rantier Y, Marguerie D, Tougeron K, Devogel P, Dugravot S, Dubos T, Garrin M, Carnet M, Gouraud C, Chambet A, Esnault J, Poupelin M, Welk E, Bütof A, Dubois GF, Humbert G, Marie-Réau O, Norvez O, Richard G, Froger B, Rochais C, Potthoff M, Ayati K, Bellido A, Rissel A, Santonja M, Farcy JO, Collias E, Sene L, Cluzeau D, Supper R. Transdisciplinary Bioblitz: Rapid biotic and abiotic inventory allows studying environmental changes over 60 years at the Biological Field Station of Paimpont (Brittany, France) and opens new interdisciplinary research opportunities. Biodivers Data J 2020; 8:e50451. [PMID: 32269479 PMCID: PMC7125239 DOI: 10.3897/bdj.8.e50451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/29/2020] [Indexed: 11/22/2022] Open
Abstract
Background The Biological Field Station of Paimpont (Station Biologique de Paimpont, SBP), owned by the University of Rennes and located in the Brocéliande Forest of Brittany (France), has been hosting student scientific research and field trips during the last 60 years. The study area of the SBP is a landscape mosaic of 17 ha composed of gorse moors, forests, prairies, ponds and creeks. Land use has evolved over time. Historical surveys by students and researchers focused on insects and birds. With this study, we aimed to increase the range of taxa observations, document changes in species composition and landscape and provide a basis for interdisciplinary research perspectives. We gathered historical data, implemented an all-taxon biodiversity inventory (ATBI) in different habitats of the SBP study area, measured abiotic factors in the air, water and soil and performed a photographical landscape observation during the BioBlitz held in July 2017. New information During the 24 h BioBlitz, organised by the SBP and the EcoBio lab from the University of Rennes and the French National Center of Scientific Research (CNRS), different habitats were individually sampled. Seventy-seven experts, accompanied by 120 citizens and 12 young people participating in the European Volunteer Service, observed, identified and databased 660 species covering 5 kingdoms, 8 phyla, 21 classes, 90 orders and 247 families. In total, there were 1819 occurrences including records identified to higher taxon ranks, thereby adding one more kingdom and four more phyla. Historical data collection resulted in 1176 species and 4270 occurrences databased. We also recorded 13 climatic parameters, 10 soil parameters and 18 water parameters during the BioBlitz. Current habitats were mapped and socio-ecological landscape changes were assessed with a diachronic approach using 32 historical photographs and historical maps. The coupling of historical biodiversity data with new biotic and abiotic data and a photographic comparison of landscape changes allows an integrative understanding of how the SBP changed from agriculturally-used land to a managed natural area within the last 60 years. Hence, this BioBlitz represents an important holistic sampling of biodiversity for studies on trophic webs or on trophic interactions or on very diverse, but connected, habitats. The integration of social, biotic and abiotic data opens innovative research opportunities on the evolution of socio-ecosystems and landscapes.
Collapse
Affiliation(s)
- Annegret Nicolai
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Muriel Guernion
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Sarah Guillocheau
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Kevin Hoeffner
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Pascaline Le Gouar
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Nelly Ménard
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Christophe Piscart
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Dominique Vallet
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Morgane E T Hervé
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Elora Benezeth
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Hughes Chedanne
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Jérémie Blémus
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Philippe Vernon
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Daniel Cylly
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Hoël Hotte
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Grégoire Loïs
- MNHN, UMR 7204 CESCO, Paris, France MNHN, UMR 7204 CESCO Paris France
| | - Barbara Mai
- unaffiliated, Rennes, France unaffiliated Rennes France
| | - Grégoire Perez
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Tiphaine Ouisse
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Cécile Monard
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Claudia Wiegand
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Jean-Pierre Caudal
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Alain Butet
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Maxime Dahirel
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Lou Barbe
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Manon Balbi
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Valérie Briand
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Myriam Bormans
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Maryvonne Charrier
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Guillaume Bouger
- Université Rennes 1, Observatoire des Sciences de l'Univers de Rennes (OSUR), UMS 3343, Rennes, France Université Rennes 1, Observatoire des Sciences de l'Univers de Rennes (OSUR), UMS 3343 Rennes France
| | - Vincent Jung
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Cécile Le Lann
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Alexandrine Pannard
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Julien Petillon
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Yann Rantier
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Dominique Marguerie
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Kevin Tougeron
- Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR, Rennes, France Université Rennes 1, UMR-CNRS 6553 EcoBio/OSUR Rennes France
| | - Pierre Devogel
- Université Rennes 1, EA 7462 G-TUBE, Rennes, France Université Rennes 1, EA 7462 G-TUBE Rennes France
| | - Sébastien Dugravot
- Université Rennes 1, EA 7462 G-TUBE, Rennes, France Université Rennes 1, EA 7462 G-TUBE Rennes France
| | - Thomas Dubos
- Groupe Mammalogique de Bretagne, Redon, France Groupe Mammalogique de Bretagne Redon France
| | | | | | | | - Audrey Chambet
- Université Rennes 1, Collections de botanique et herbiers, Rennes, France Université Rennes 1, Collections de botanique et herbiers Rennes France
| | - Joël Esnault
- Conservatoire Botanique National de Brest, Brest, France Conservatoire Botanique National de Brest Brest France
| | - Maxime Poupelin
- CPN les p'tites natures de Brocéliande, Paimpont, France CPN les p'tites natures de Brocéliande Paimpont France
| | - Erik Welk
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany Martin-Luther-Universität Halle-Wittenberg Halle Germany
| | - Astrid Bütof
- unaffiliated, Halle, Germany unaffiliated Halle Germany
| | | | - Guillaume Humbert
- Université Pierre et Marie Curie, Paris, France Université Pierre et Marie Curie Paris France
| | | | - Olivier Norvez
- Agence Française de la Biodiversité, Cesson-Sévigné, France Agence Française de la Biodiversité Cesson-Sévigné France
| | - Gaëlle Richard
- Université Rennes 1, Collection Zoologie, Rennes, France Université Rennes 1, Collection Zoologie Rennes France
| | - Benoît Froger
- Bretagne Vivante, Brest, France Bretagne Vivante Brest France
| | - Céline Rochais
- Université Rennes 1, Station Biologique de Paimpont, UMR 6552 EthoS, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR 6552 EthoS Paimpont France
| | - Martin Potthoff
- Universität Göttingen, CBL, Göttingen, Germany Universität Göttingen, CBL Göttingen Germany
| | - Khaoula Ayati
- Faculty of Science of Bizerte, Zarzuna, Tunisia Faculty of Science of Bizerte Zarzuna Tunisia
| | - Alain Bellido
- Encyclopédie de Brocéliande, Paimpont, France Encyclopédie de Brocéliande Paimpont France
| | - Alain Rissel
- Encyclopédie de Brocéliande, Paimpont, France Encyclopédie de Brocéliande Paimpont France
| | - Mathieu Santonja
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | - Eric Collias
- unaffiliated, Rennes, France unaffiliated Rennes France
| | - Lina Sene
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Daniel Cluzeau
- Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR, Paimpont, France Université Rennes 1, Station Biologique de Paimpont, UMR-CNRS 6553 EcoBio/OSUR Paimpont France
| | - Régis Supper
- Université Rennes 1, Station Biologique de Paimpont, Paimpont, France Université Rennes 1, Station Biologique de Paimpont Paimpont France
| |
Collapse
|
23
|
Khomenko A, Utevsky S, Utevsky A, Trontelj P. Unrecognized diversity of Trochetaspecies (Hirudinea: Erpobdellidae): resolving a century-old taxonomic problem in Crimean leeches. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1739776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Andrii Khomenko
- Department of Zoology and Animal Ecology, V. N. Karazin Kharkiv National University, Maidan Svobody 4, Kharkiv, 61022, Ukraine
| | - Serge Utevsky
- Department of Zoology and Animal Ecology, V. N. Karazin Kharkiv National University, Maidan Svobody 4, Kharkiv, 61022, Ukraine
| | - Andriy Utevsky
- Department of Zoology and Animal Ecology, V. N. Karazin Kharkiv National University, Maidan Svobody 4, Kharkiv, 61022, Ukraine
| | - Peter Trontelj
- Department of Biology, University of Ljubljana, PO Box 2995, Ljubljana, SI-1001, Slovenia
| |
Collapse
|
24
|
Imada Y. A novel leaf-rolling chironomid, Eukiefferiella endobryonia sp. nov. (Diptera, Chironomidae, Orthocladiinae), highlights the diversity of underwater chironomid tube structures. Zookeys 2020; 906:73-111. [PMID: 32021557 PMCID: PMC6989570 DOI: 10.3897/zookeys.906.47834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/17/2019] [Indexed: 11/15/2022] Open
Abstract
The non-biting midges, Chironomidae (Diptera), are dominant components of most freshwater ecosystems. Many chironomids construct tubes or cases as larvae out of various materials bound together with silk. The structures of tubes show a wide range of variation, and some are morphologically comparable to those of caddisflies. Herein a new species is described, Eukiefferiella endobryonia sp. nov., which exhibits a very unusual behavior in which it constructs tubes from aquatic mosses. This species' fourth-instar larvae construct their cases exclusively from the leaves of Fontinalis mosses (Hypnales: Fontinalaceae) and exhibit a stereotyped behavior in which they remain attached to the apical shoot of the moss stem. The larvae then pupate within the case. The case of E. endobryonia sp. nov. represents one of only a few examples of chironomid tubes made exclusively out of plants. Based on the species delimitation analyses using the partial COI sequences, together with some morphological and behavioral characteristics, this species is hypothesized to be a member of devonica group, and especially may have a close affinity to E. dittmari (Lehman). A provisional typology for the diversity of chironomid tube structures is provided, with a summary of different tube structures, which can be used for future research.
Collapse
Affiliation(s)
- Yume Imada
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, JapanEhime UniversityEhimeJapan
| |
Collapse
|
25
|
Fajana HO, Gainer A, Jegede OO, Awuah KF, Princz JI, Owojori OJ, Siciliano SD. Oppia nitens C.L. Koch, 1836 (Acari: Oribatida): Current Status of Its Bionomics and Relevance as a Model Invertebrate in Soil Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:2593-2613. [PMID: 31433516 DOI: 10.1002/etc.4574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
The oribatid soil mite Oppia nitens C.L. Koch, 1836, is a model microarthropod in soil ecotoxicity testing. This species has a significant role in supporting soil functions and as a suitable indicator of soil contamination. Despite its significance to the environment and to ecotoxicology, however, very little is known of its biology, ecology, and suborganismal responses to contaminants in the soil. In the present review, we present detailed and critical insights into the biology and ecology of O. nitens in relation to traits that are crucial to its adaptive responses to contaminants in soil. We used a species sensitivity distribution model to rank the species sensitivity to heavy metals (cadmium and zinc) and neonicotinoids (imidacloprid and thiacloprid) compared with other standardized soil invertebrates. Although the International Organization for Standardization and Environment and Climate Change Canada are currently standardizing a protocol for the use of O. nitens in soil toxicity testing, we believe that O. nitens is limited as a model soil invertebrate until the molecular pathways associated with its response to contaminants are better understood. These pathways can only be elucidated with information from the mites' genome or transcriptome, which is currently lacking. Despite this limitation, we propose a possible molecular pathway to metal tolerance and a putative adverse outcome pathway to heavy metal toxicity in O. nitens. Environ Toxicol Chem 2019;38:2593-2613. © 2019 SETAC.
Collapse
Affiliation(s)
- Hamzat O Fajana
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Amy Gainer
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Olukayode O Jegede
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Kobby F Awuah
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Juliska I Princz
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | - Steven D Siciliano
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
26
|
Vilela DS, Koroiva R, Cordero-Rivera A, Guillermo-Ferreira R. A further study on Franciscobasis Machado & Bedê, 2016 (Odonata: Coenagrionidae), a newly described genus from Minas Gerais, Brazil. PLoS One 2019; 14:e0223241. [PMID: 31593578 PMCID: PMC6782088 DOI: 10.1371/journal.pone.0223241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 11/21/2022] Open
Abstract
The genus Franciscobasis Machado & Bedê, 2016 is endemic to the Serra da Canastra National Park in Minas Gerais state, Brazil. Two species of Franciscobasis were described simultaneously with the genus description: F. franciscoi and F. sonia, the latter described only from females. Through morphological and molecular analysis, we investigated if F. sonia may represent the young female of F. franciscoi. Resulting data did not present adequate differences between females to characterize them as different species. Therefore, we suggest that F. sonia is a junior synonym of F. franciscoi, and the female of F. franciscoi goes through a complex ontogenetic color change.
Collapse
Affiliation(s)
- Diogo Silva Vilela
- Graduate Program in Entomology, Department of Biology, University of São Paulo (USP), Ribeirão Preto, Brazil
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
| | - Ricardo Koroiva
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Adolfo Cordero-Rivera
- ECOEVO Lab, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
| | - Rhainer Guillermo-Ferreira
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
| |
Collapse
|
27
|
Taxonomic update of Clitocybula sensu lato with a new generic classification. Fungal Biol 2019; 123:431-447. [DOI: 10.1016/j.funbio.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/14/2019] [Accepted: 03/19/2019] [Indexed: 11/23/2022]
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Linking morphological and molecular taxonomy for the identification of poultry house, soil, and nest dwelling mites in the Western Palearctic. Sci Rep 2019; 9:5784. [PMID: 30962473 PMCID: PMC6453913 DOI: 10.1038/s41598-019-41958-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/20/2019] [Indexed: 01/03/2023] Open
Abstract
Because of its ability to expedite specimen identification and species delineation, the barcode index number (BIN) system presents a powerful tool to characterize hyperdiverse invertebrate groups such as the Acari (mites). However, the congruence between BINs and morphologically recognized species has seen limited testing in this taxon. We therefore apply this method towards the development of a barcode reference library for soil, poultry litter, and nest dwelling mites in the Western Palearctic. Through analysis of over 600 specimens, we provide DNA barcode coverage for 35 described species and 70 molecular taxonomic units (BINs). Nearly 80% of the species were accurately identified through this method, but just 60% perfectly matched (1:1) with BINs. High intraspecific divergences were found in 34% of the species examined and likely reflect cryptic diversity, highlighting the need for revision in these taxa. These findings provide a valuable resource for integrative pest management, but also highlight the importance of integrating morphological and molecular methods for fine-scale taxonomic resolution in poorly-known invertebrate lineages.
Collapse
|
30
|
Trophic interactions among dead-wood-dependent forest arthropods in the southern Appalachian Mountains, USA. FOOD WEBS 2019. [DOI: 10.1016/j.fooweb.2018.e00112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
31
|
Abstract
The state of knowledge of diversity of Collembola in Canada was assessed by examination of literature and DNA barcode data. There are 474 described extant Collembola species known from Canada, a significant change compared to the 520 species estimated to occur in Canada in 1979 (Richards 1979) and the 341 reported in the most recent national checklist (Skidmore 1993). Given the number of indeterminate or cryptic species records, the dearth of sampling in many regions, and the growing use of genetic biodiversity assessment methods such as Barcode Index Numbers, we estimate the total diversity of Collembola in Canada to be approximately 675 species. Advances in Collembola systematics and Canadian research are discussed.
Collapse
Affiliation(s)
| | - Sophya Stebaeva
- The Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, RussiaThe Severtsov Institute of Ecology and EvolutionMoscowCanada
| |
Collapse
|
32
|
Moose RA, Schigel D, Kirby LJ, Shumskaya M. Dead wood fungi in North America: an insight into research and conservation potential. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.32.30875] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Saproxylic fungi act as keystone species in forest ecosystems because they colonise and decompose dead wood, facilitating colonisation by later species. Here, we review the importance of intact forest ecosystems to dead wood fungi, as well as trends in their diversity research and challenges in conservation. Saproxylic communities are sensitive to transition from virgin forests to managed ecosystems, since the latter often results in reduced tree diversity and the removal of their natural habitat dead wood. The impact of dead wood management can be quite significant since many saproxylic fungi are host-specific. The significance of citizen science and educational programmes for saproxylic mycology is discussed with the emphasis on the North American region. We intend to raise the awareness of the role that dead wood fungi play in forest health in order to support development of corresponding conservational programmes.
Collapse
|
33
|
Li S, Qian X, Zheng Z, Shi M, Chang X, Li X, Liu J, Tu T, Zhang D. DNA barcoding the flowering plants from the tropical coral islands of Xisha (China). Ecol Evol 2018; 8:10587-10593. [PMID: 30464830 PMCID: PMC6238132 DOI: 10.1002/ece3.4545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/19/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
AIM DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future. LOCATION Xisha Islands, China. METHODS This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic-based method to assess the barcoding resolution. RESULTS All the three DNA barcodes showed high levels of PCR success (96%-99%) and sequencing success (98%-100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%-90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes. MAIN CONCLUSIONS This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
Collapse
Affiliation(s)
- Shengchun Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zexin Zheng
- South China Agricultural UniversityGuangzhouChina
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaoyu Chang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaojuan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Dörler D, Kropf M, Laaha G, Zaller JG. Occurrence of the invasive Spanish slug in gardens: can a citizen science approach help deciphering underlying factors? BMC Ecol 2018; 18:23. [PMID: 30068321 PMCID: PMC6071400 DOI: 10.1186/s12898-018-0179-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 07/22/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The Spanish slug (Arion vulgaris, also known as A. lusitanicus) is considered one of the most invasive species in agriculture, horticulture and private gardens all over Europe. Although this slug has been problematic for decades, there is still not much known about its occurrence across private gardens and the underlying meteorological and ecological factors. One reason for this knowledge gap is the limited access of researchers to private gardens. Here we used a citizen science approach to overcome this obstacle and examined whether the occurrence of Arionidae in Austrian gardens was associated with meteorological (air temperature, precipitation, global solar radiation, relative humidity) or ecological factors (plant diversity, earthworm activity). Occurrence of the invasive A. vulgaris versus the similar-looking native A. rufus was compared using a DNA-barcoding approach. RESULTS Slugs were collected from 1061 gardens from the dry Pannonian lowland to the wet alpine climate (altitudinal range 742 m). Slug abundance in gardens was best explained and negatively associated with the parameters "sum of the mean air temperature in spring", "number of frost days in the previous winter" and "mean daily global solar radiation on the day of data collection". Precipitation, plant diversity and earthworm activity were also related to slug abundance, but positively. Out of our genetic sampling of collected slugs, 92% belonged to A. vulgaris. CONCLUSIONS Our study showed that citizen science (i) is a feasible approach to record species occurrence in restricted areas across a wide geographical range and (ii) could be more widely employed in order to identify underlying environmental factors of species occurrence.
Collapse
Affiliation(s)
- Daniel Dörler
- Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Matthias Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Gregor Laaha
- Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Johann G. Zaller
- Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| |
Collapse
|
36
|
Insect diversity in the Saharo-Arabian region: Revealing a little-studied fauna by DNA barcoding. PLoS One 2018; 13:e0199965. [PMID: 29985924 PMCID: PMC6037371 DOI: 10.1371/journal.pone.0199965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/18/2018] [Indexed: 11/19/2022] Open
Abstract
Although insects dominate the terrestrial fauna, sampling constraints and the poor taxonomic knowledge of many groups have limited assessments of their diversity. Passive sampling techniques and DNA-based species assignments now make it possible to overcome these barriers. For example, Malaise traps collect specimens with minimal intervention while the Barcode Index Number (BIN) system automates taxonomic assignments. The present study employs Malaise traps and DNA barcoding to extend understanding of insect diversity in one of the least known zoogeographic regions, the Saharo-Arabian. Insects were collected at four sites in three countries (Egypt, Pakistan, Saudi Arabia) by deploying Malaise traps. The collected specimens were analyzed by sequencing 658 bp of cytochrome oxidase I (DNA barcode) and assigning BINs on the Barcode of Life Data Systems. The year-long deployment of a Malaise trap in Pakistan and briefer placements at two Egyptian sites and at one in Saudi Arabia collected 53,092 specimens. They belonged to 17 insect orders with Diptera and Hymenoptera dominating the catch. Barcode sequences were recovered from 44,432 (84%) of the specimens, revealing the occurrence of 3,682 BINs belonging to 254 families. Many of these taxa were uncommon as 25% of the families and 50% of the BINs from Pakistan were only present in one sample. Family and BIN counts varied significantly through the year, but diversity indices did not. Although more than 10,000 specimens were analyzed from each nation, just 2% of BINs were shared by Pakistan and Saudi Arabia, 4% by Egypt and Pakistan, and 7% by Egypt and Saudi Arabia. The present study demonstrates how the BIN system can circumvent the barriers imposed by limited access to taxonomic specialists and by the fact that many insect species in the Saharo-Arabian region are undescribed.
Collapse
|
37
|
Fagan-Jeffries EP, Cooper SJB, Bertozzi T, Bradford TM, Austin AD. DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Mol Ecol Resour 2018; 18:1132-1143. [PMID: 29791787 DOI: 10.1111/1755-0998.12904] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/07/2018] [Indexed: 01/10/2023]
Abstract
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 99 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this. In this study, museum ethanol samples and recent field collections were mined for hundreds of specimens of microgastrine wasps, which were then barcoded for the COI region, ITS2 ribosomal spacer and the wingless nuclear genes, using a pooled sequencing approach on an Illumina Miseq system. Full COI sequences were obtained for 525 individuals which, when combined with 162 publicly available sequences, represented 417 haplotypes, and a total of 236 species were delimited using a consensus approach. By more than doubling the number of known microgastrine wasp species in Australia, our study highlights the value of DNA barcoding in the context of employing high-throughput sequencing methods of bulk ethanol museum collections for biodiversity assessment.
Collapse
Affiliation(s)
- Erinn P Fagan-Jeffries
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Steven J B Cooper
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Terry Bertozzi
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Tessa M Bradford
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Andrew D Austin
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
38
|
Kuzmina ML, Braukmann TWA, Zakharov EV. Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01155. [PMID: 30131897 PMCID: PMC5991581 DOI: 10.1002/aps3.1155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The detection of environmental DNA (eDNA) using high-throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring. METHODS A protocol was developed to detect pondweeds in water samples using atpB-rbcL and ITS2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario (RARE). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank. RESULTS We detected two species earlier documented at the experimental site during ecological surveys (Potamogeton crispus and Stuckenia pectinata) and three species new to the RARE checklist (P. foliosus, S. filiformis, and Zannichellia palustris). DISCUSSION Our targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats.
Collapse
Affiliation(s)
- Maria L. Kuzmina
- Centre for Biodiversity GenomicsUniversity of Guelph50 Stone Road EastGuelphOntarioN1G2W1Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity GenomicsUniversity of Guelph50 Stone Road EastGuelphOntarioN1G2W1Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity GenomicsUniversity of Guelph50 Stone Road EastGuelphOntarioN1G2W1Canada
| |
Collapse
|
39
|
Hebert PDN, Braukmann TWA, Prosser SWJ, Ratnasingham S, deWaard JR, Ivanova NV, Janzen DH, Hallwachs W, Naik S, Sones JE, Zakharov EV. A Sequel to Sanger: amplicon sequencing that scales. BMC Genomics 2018; 19:219. [PMID: 29580219 PMCID: PMC5870082 DOI: 10.1186/s12864-018-4611-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/20/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. RESULTS By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion). CONCLUSIONS SMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.
Collapse
Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Thomas W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6018, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6018, USA
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
40
|
Ellwood ER, Kimberly P, Guralnick R, Flemons P, Love K, Ellis S, Allen JM, Best JH, Carter R, Chagnoux S, Costello R, Denslow MW, Dunckel BA, Ferriter MM, Gilbert EE, Goforth C, Groom Q, Krimmel ER, LaFrance R, Martinec JL, Miller AN, Minnaert-Grote J, Nash T, Oboyski P, Paul DL, Pearson KD, Pentcheff ND, Roberts MA, Seltzer CE, Soltis PS, Stephens R, Sweeney PW, von Konrat M, Wall A, Wetzer R, Zimmerman C, Mast AR. Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar. Bioscience 2018; 68:112-124. [PMID: 29599548 PMCID: PMC5862351 DOI: 10.1093/biosci/bix143] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions—content now foundational to the growing WeDigBio event.
Collapse
Affiliation(s)
- Elizabeth R Ellwood
- La Brea Tar Pits & Museum, in Los Angeles, California, and was with the Department of Biological Science at Florida State University, in Tallahassee
| | - Paul Kimberly
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Robert Guralnick
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Kevin Love
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Shari Ellis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Julie M Allen
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Jason H Best
- Botanical Research Institute of Texas, in Fort Worth
| | - Richard Carter
- Biology Department at Valdosta State University, in Georgia
| | | | - Robert Costello
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Michael W Denslow
- Florida Museum of Natural History at the University of Florida, in Gainesville, and the Department of Biology at Appalachian State University, in Boone, North Carolina
| | - Betty A Dunckel
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Meghan M Ferriter
- Smithsonian Institution Transcription Center at the Smithsonian Institution Office of the Chief Information Officer, in Washington, DC
| | | | | | | | - Erica R Krimmel
- Department of Biology at The Chicago Academy of Sciences and the Peggy Notebaert Nature Museum, in Chicago, Illinois
| | - Raphael LaFrance
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Joann Lacey Martinec
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Andrew N Miller
- Illinois Natural History Survey at the University of Illinois Urbana-Champaign
| | | | | | - Peter Oboyski
- Essig Museum of Entomology at the University of California, in Berkeley
| | - Deborah L Paul
- Institute for Digital Information and Scientific Communication at Florida State University, in Tallahassee
| | - Katelin D Pearson
- Department of Biological Science at Florida State University, in Tallahassee
| | - N Dean Pentcheff
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Mari A Roberts
- William and Lynda Steere Herbarium at the New York Botanical Garden
| | | | - Pamela S Soltis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Patrick W Sweeney
- Yale Peabody Museum of Natural History at Yale University, in New Haven, Connecticut
| | - Matt von Konrat
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Adam Wall
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Regina Wetzer
- Research and Collections at the Natural History Museum of Los Angeles County
| | | | - Austin R Mast
- Department of Biological Science at Florida State University, in Tallahassee
| |
Collapse
|
41
|
Ballesteros JA, Hormiga G. Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae). Mol Phylogenet Evol 2018; 121:183-197. [PMID: 29337274 DOI: 10.1016/j.ympev.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.
Collapse
Affiliation(s)
- Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States; Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, United States.
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States
| |
Collapse
|
42
|
Liu S, Yang C, Zhou C, Zhou X. Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world. Gigascience 2017; 6:1-8. [PMID: 29077841 PMCID: PMC5726475 DOI: 10.1093/gigascience/gix104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/26/2017] [Accepted: 10/23/2017] [Indexed: 01/17/2023] Open
Abstract
Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.
Collapse
Affiliation(s)
- Shanlin Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- BGI-Shenzhen, Shenzhen, 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen, Denmark
| | | | - Chengran Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China
- National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing 100193, People's Republic of China
| |
Collapse
|
43
|
Schmidt O, Hausmann A, Cancian de Araujo B, Sutrisno H, Peggie D, Schmidt S. A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys). Biodivers Data J 2017; 5:e20006. [PMID: 29134041 PMCID: PMC5676197 DOI: 10.3897/bdj.5.e20006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).
Collapse
Affiliation(s)
- Olga Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Axel Hausmann
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | | | - Hari Sutrisno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djunijanti Peggie
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Stefan Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| |
Collapse
|
44
|
|
45
|
|
46
|
Steinke D, deWaard JR, Gomon MF, Johnson JW, Larson HK, Lucanus O, Moore GI, Reader S, Ward RD. DNA barcoding the fishes of Lizard Island (Great Barrier Reef). Biodivers Data J 2017:e12409. [PMID: 28765727 PMCID: PMC5515069 DOI: 10.3897/bdj.5.e12409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/12/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada.,Department of Integrative Biology - University of Guelph, Guelph, Canada
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada
| | | | - Jeffrey W Johnson
- Queensland Museum, PO Box 3300, South Brisbane QLD 4101, Australia, Brisbane, Australia
| | - Helen K Larson
- Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | | | | | | | - Robert D Ward
- CSIRO Marine and Atmospheric Research, Hobart, Australia
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Phylogeography of the Asian rice gall midge Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) in Thailand. Genetica 2017; 145:37-49. [PMID: 28070758 DOI: 10.1007/s10709-016-9944-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified. Overall, the haplotype diversity for COI and 12S genes of the Thai population was high, but the nucleotide diversity was quite low. Altogether, the phylogenetic tree and pairwise F st values indicated that Thai RGM populations recently expanded and were homogeneously distributed throughout the country, except for some populations in the north, which most likely became recently isolated from the main population. Two non-coding repeat motifs, that were recently observed in the mitogenome of RGM in India, were absent in Thai populations and replaced by an 89 bp non-coding sequence. Tandem nucleotide repeats of the sequence TA were also observed. The repeat copy number varied from 2 to 11 and was not correlated with geographical repartition of the midge. Finally, COI barcoding divergence between Indian and Thai populations was high (6.3% in average), giving insights into the potential existence of an RGM species complex in Asia.
Collapse
|
49
|
Geiger MF, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert PDN, Rulik B. Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany? Biodivers Data J 2016:e10671. [PMID: 27932930 PMCID: PMC5136679 DOI: 10.3897/bdj.4.e10671] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: “Nationalpark Bayerischer Wald” in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. New information In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.
Collapse
Affiliation(s)
| | | | | | | | - Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|