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Brower AVZ, DeSalle R. DNA Barcodes in Taxonomic Descriptions. Methods Mol Biol 2024; 2744:105-115. [PMID: 38683313 DOI: 10.1007/978-1-0716-3581-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).
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Affiliation(s)
- Andrew V Z Brower
- USDA APHIS PPQ Pest Exclusion and Import Programs, Riverdale, MD, USA
| | - Robert DeSalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
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Fernandez-Triana JL, Shimbori EM, Whitfield JB, Penteado-Dias AM, Shaw SR, Boudreault C, Sones J, Perez K, Brown A, Manjunath R, Burns JM, Hebert PDN, Smith MA, Hallwachs W, Janzen DH. A revision of the parasitoid wasp genus Alphomelon Mason with the description of 30 new species (Hymenoptera, Braconidae). Zookeys 2023; 1175:5-162. [PMID: 37636532 PMCID: PMC10448698 DOI: 10.3897/zookeys.1175.105068] [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: 04/17/2023] [Accepted: 06/02/2023] [Indexed: 08/29/2023] Open
Abstract
The parasitoid wasp genus Alphomelon Mason, 1981 is revised, based on a combination of basic morphology (dichotomous key and brief diagnostic descriptions), DNA barcoding, biology (host data and wasp cocoons), and distribution data. A total of 49 species is considered; the genus is almost entirely Neotropical (48 species recorded from that region), but three species reach the Nearctic, with one of them extending as far north as 45° N in Canada. Alphomelon parasitizes exclusively Hesperiinae caterpillars (Lepidoptera: Hesperiidae), mostly feeding on monocots in the families Arecaceae, Bromeliaceae, Cannaceae, Commelinaceae, Heliconiaceae, and Poaceae. Most wasp species parasitize either on one or very few (2-4) host species, usually within one or two hesperiine genera; but some species can parasitize several hosts from up to nine different hesperiine genera. Among species with available data for their cocoons, roughly half weave solitary cocoons (16) and half are gregarious (17); cocoons tend to be surrounded by a rather distinctive, coarse silk (especially in solitary species, but also distinguishable in some gregarious species). Neither morphology nor DNA barcoding alone was sufficient on its own to delimit all species properly; by integrating all available evidence (even if incomplete, as available data for every species is different) a foundation is provided for future studies incorporating more specimens, especially from South America. The following 30 new species are described: cruzi, itatiaiensis, and palomae, authored by Shimbori & Fernandez-Triana; and adrianguadamuzi, amazonas, andydeansi, calixtomoragai, carolinacanoae, christerhanssoni, diniamartinezae, duvalierbricenoi, eldaarayae, eliethcantillanoae, gloriasihezarae, guillermopereirai, hazelcambroneroae, josecortesi, keineraragoni, luciarosae, manuelriosi, mikesharkeyi, osvaldoespinozai, paramelanoscelis, paranigriceps, petronariosae, ricardocaleroi, rigoi, rostermoragai, sergioriosi, and yanayacu, authored by Fernandez-Triana & Shimbori.
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Affiliation(s)
- Jose L. Fernandez-Triana
- Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Ave., Ottawa, K1A0C6, Canada
| | - Eduardo M. Shimbori
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito, S/N, Ciudad Universitaria, Coyoacán, C.P. 04510, Ciudad de México, Mexico
| | | | | | - Scott R. Shaw
- College of Agriculture and Natural Resources, University of Wyoming, Laramie, USA
| | - Caroline Boudreault
- Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Ave., Ottawa, K1A0C6, Canada
| | - Jayme Sones
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
| | - Kate Perez
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
| | - Allison Brown
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
| | - Ramya Manjunath
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
| | - John M. Burns
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA
| | - P. D. N. Hebert
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
| | - M. Alex Smith
- Canadian Centre for DNA Barcoding, University of Guelph, Guelph, Canada
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Ramamonjisoa MM, Rasoamanana N, Fisher BL. Description of the male of Erromyrma Bolton & Fisher, 2016 (Hymenoptera, Formicidae). Zookeys 2023; 1163:61-77. [PMID: 37250365 PMCID: PMC10220497 DOI: 10.3897/zookeys.1163.95696] [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: 09/27/2022] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
The male of the myrmicine genus Erromyrma is described for the first time on the basis of two specimens of Erromyrmalatinodis (Mayr, 1872) collected in northern Madagascar. We used COI barcoding to confirm the identification of the male specimens as conspecific with Erromyrmalatinodis. We provide an illustrated male-based key to the four Myrmicinae tribes (Attini, Crematogastrini, Solenopsidini, Stenammini) and to the Solenopsidini genera (Adelomyrmex, Erromyrma, Solenopsis, Syllophopsis and Monomorium) for the Malagasy region.
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Affiliation(s)
- Manoa M. Ramamonjisoa
- Madagascar Biodiversity Center, BP 6257, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, MadagascarMadagascar Biodiversity CenterAntananarivoMadagascar
| | - Nicole Rasoamanana
- Madagascar Biodiversity Center, BP 6257, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, MadagascarMadagascar Biodiversity CenterAntananarivoMadagascar
| | - Brian L. Fisher
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USACalifornia Academy of SciencesSan FranciscoUnited States of America
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Lin TH, Chan KW, Hsu FC, Lin CC, Tseng HY. Putative source and niche shift pattern of a new alien ant species ( Odontomachus troglodytes) in Taiwan. PeerJ 2023; 11:e14718. [PMID: 36778144 PMCID: PMC9910184 DOI: 10.7717/peerj.14718] [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: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 02/09/2023] Open
Abstract
Alien species may pose substantial impacts on biodiversity around the globe through international trade and travel. A niche shift hypothesis was proposed to explain the adaptive change of alien or invasive species in new habitats. However, whether niche shifts occur in alien species likely depends on both characteristics inherent to the species itself and its original distribution. Here we identified a newly exotic trap-jaw ant (Odontomachus troglodytes) in Taiwan by morphological and phylogenetic analyses. The possible distribution range and the niche shift pattern were evaluated using ecological niche modelling. The results indicated that exotic O. troglodytes in the newly distributed area displayed a significant niche shift with low niche overlap and high niche expansion. This study reveals a long-distance invasive event from central Africa to Southeast Asia (more than 10,000 km) and predicts the potential distribution range of this new alien species in Taiwan.
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Affiliation(s)
- Tzong-Han Lin
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Kai-Wei Chan
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Feng-Chuan Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Chung-Chi Lin
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Hui-Yun Tseng
- Department of Entomology, National Taiwan University, Taipei, Taiwan
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Wurz A, Tscharntke T, Martin DA, Osen K, Rakotomalala AANA, Raveloaritiana E, Andrianisaina F, Dröge S, Fulgence TR, Soazafy MR, Andriafanomezantsoa R, Andrianarimisa A, Babarezoto FS, Barkmann J, Hänke H, Hölscher D, Kreft H, Rakouth B, Guerrero-Ramírez NR, Ranarijaona HLT, Randriamanantena R, Ratsoavina FM, Raveloson Ravaomanarivo LH, Grass I. Win-win opportunities combining high yields with high multi-taxa biodiversity in tropical agroforestry. Nat Commun 2022; 13:4127. [PMID: 35882849 PMCID: PMC9325886 DOI: 10.1038/s41467-022-30866-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/23/2022] [Indexed: 11/09/2022] Open
Abstract
Resolving ecological-economic trade-offs between biodiversity and yields is a key challenge when addressing the biodiversity crisis in tropical agricultural landscapes. Here, we focused on the relation between seven different taxa (trees, herbaceous plants, birds, amphibians, reptiles, butterflies, and ants) and yields in vanilla agroforests in Madagascar. Agroforests established in forests supported overall 23% fewer species and 47% fewer endemic species than old-growth forests, and 14% fewer endemic species than forest fragments. In contrast, agroforests established on fallows had overall 12% more species and 38% more endemic species than fallows. While yields increased with vanilla vine density and length, non-yield related variables largely determined biodiversity. Nonetheless, trade-offs existed between yields and butterflies as well as reptiles. Vanilla yields were generally unrelated to richness of trees, herbaceous plants, birds, amphibians, reptiles, and ants, opening up possibilities for conservation outside of protected areas and restoring degraded land to benefit farmers and biodiversity alike. Resolving ecological-economic trade-offs is a challenge in agriculture. Here, Wurz et al. find that in Malagasy vanilla agroforests, vanilla yield is generally not related to tree, herbaceous plant, bird, amphibian, reptile and ant biodiversity, creating opportunities for conservation outside protected areas.
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Affiliation(s)
- Annemarie Wurz
- Agroecology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany. .,Conservation Ecology, Department of Biology, Philipps-University Marburg, Marburg, Germany.
| | - Teja Tscharntke
- Agroecology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany.,Centre for Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Dominic Andreas Martin
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Kristina Osen
- Tropical Silviculture and Forest Ecology, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Anjaharinony A N A Rakotomalala
- Agroecology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany.,Entomology Department Faculty of Science, University of Antananarivo, PO Box 906, Antananarivo, 101, Madagascar
| | - Estelle Raveloaritiana
- Agroecology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany.,Plant Biology and Ecology Department, University of Antananarivo, University of Antananarivo, Antananarivo, Madagascar
| | - Fanilo Andrianisaina
- Department of Tropical Agriculture and Sustainable Development, Higher School of Agronomic Science,University of Antananarivo, Antananarivo, Madagascar
| | - Saskia Dröge
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Division of Forest, Nature and Landscape, KU Leuven, Leuven, Belgium
| | - Thio Rosin Fulgence
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar.,Natural and Environmental Sciences, Regional University Centre of the SAVA Region (CURSA), Antalaha, Madagascar
| | - Marie Rolande Soazafy
- Natural and Environmental Sciences, Regional University Centre of the SAVA Region (CURSA), Antalaha, Madagascar.,Doctoral School of Natural Ecosystems (EDEN), University of Mahajanga, Mahajanga, Madagascar
| | - Rouvah Andriafanomezantsoa
- Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | - Aristide Andrianarimisa
- Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | - Jan Barkmann
- Department of Agricultural Economics and Rural Development, Research Unit Environmental- and Resource Economics, University of Göttingen, Göttingen, Germany
| | - Hendrik Hänke
- Department of Agricultural Economics and Rural Development, Research Unit Environmental- and Resource Economics, University of Göttingen, Göttingen, Germany
| | - Dirk Hölscher
- Centre for Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Tropical Silviculture and Forest Ecology, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Holger Kreft
- Centre for Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Bakolimalala Rakouth
- Plant Biology and Ecology Department, University of Antananarivo, University of Antananarivo, Antananarivo, Madagascar
| | - Nathaly R Guerrero-Ramírez
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | | | - Romual Randriamanantena
- Natural and Environmental Sciences, Regional University Centre of the SAVA Region (CURSA), Antalaha, Madagascar
| | | | | | - Ingo Grass
- Ecology of Tropical Agricultural Systems, University of Hohenheim, Garbenstrasse 13, 70599, Stuttgart, Germany
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Liao H, Terayama M, Eguchi K. Revision of Taiwanese and Ryukyuan species of Pristepyris Kieffer, 1905, with description of a new species (Hymenoptera, Bethylidae). Zookeys 2022; 1102:1-42. [PMID: 36761152 PMCID: PMC9848667 DOI: 10.3897/zookeys.1102.84953] [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: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 11/12/2022] Open
Abstract
The pristocerine genus Pristepyris comprises 38 valid species recorded worldwide, except in the Australian Region. Of them, three species, namely P.mieae (Terayama, 1995), P.tainanensis (Terayama, 1995) and P.takasago (Terayama, 1996), have been recorded from Taiwan and three species, i.e. P.ishigakiensis (Yasumatsu, 1955), P.minutus (Yasumatsu, 1955) and P.ryukyuensis (Terayama, 1999), from the Ryukyus in Japan. In the present study, the species-level classification of both Taiwanese and Ryukyuan species of Pristepyris was revised using newly-collected specimens by the external and male genital morphological as well as molecular phylogenetic analysis. Overall, six species of Pristepyris were recorded from Taiwan and the Ryukyus. Among these, five were previously recorded for the region and were revised here: P.ishigakiensis, P.mieae, P.ryukyuensis, P.tainanensis and P.zhejiangensis. Additionally, a new species, P.seqalu sp. nov., is herein described and illustrated. Furthermore, the species P.minutus is transferred to Eleganesia and P.takasago is synonymized under P.minutus. Due to the new combination of Pristepyrisminutus, a key to Taiwanese and Ryukyuan species of the genus Eleganesia, based on male morphology, is provided in Appendix 1. We confirmed for the first time the correspondence between the male and female species of P.zhejiangensis by molecular data. High compatibility in species delimitation patterns, suggested by the morphological and molecular phylogenetic approaches, highlighted the significance of the former approach for accurately classifying aged voucher specimens of Pristocerinae in public collections.
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Affiliation(s)
- Hauchuan Liao
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, JapanTokyo Metropolitan UniversityTokyoJapan
| | - Mamoru Terayama
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, JapanTokyo Metropolitan UniversityTokyoJapan
| | - Katsuyuki Eguchi
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, JapanTokyo Metropolitan UniversityTokyoJapan,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, Nagasaki 852-8523, JapanNagasaki UniversitySakamotoJapan
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Salata S, Fisher BL. Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region. PeerJ 2022; 10:e13263. [PMID: 35497190 PMCID: PMC9053301 DOI: 10.7717/peerj.13263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Background The Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species. Methods The diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses. Results We recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatron Fischer & Fisher, 2013 and P. spinosa Forel, 1891 stat. nov. Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabrior Forel, 1891 syn. nov., P. picata Forel, 1891 syn. nov., P. picata gietleni Forel, 1905 syn. nov., P. picata bernhardae Emery, 1915 syn. nov., and P. decepticon Fischer & Fisher, 2013 syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst invasive species worldwide, occurs in both natural and disturbed sites in the Malagasy region. The two remaining members of the megacephala group, most likely endemic to this region, are also present in anthropogenic habitats and often co-occur with P. megacephala. It appears that the Malagasy members of the group are generalists and dominant in anthropogenic habitats. Additionally, we documented the presence of supermajors in colonies of P. spinosa-a phenomenon previously not known for this group.
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Affiliation(s)
- Sebastian Salata
- California Academy of Sciences, San Francisco, CA, USA,Myrmecological Laboratory, Department of Biodiversity and Evolutionary Taxonomy, University of Wroclaw, Wroclaw, Lower Silesia, Poland
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Juszkiewicz DJ, White NE, Stolarski J, Benzoni F, Arrigoni R, Baird AH, Hoeksema BW, Wilson NG, Bunce M, Richards ZT. Full Title: Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach. Mol Phylogenet Evol 2022; 172:107469. [DOI: 10.1016/j.ympev.2022.107469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
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Liao H, Terayama M, Eguchi K. Revision of Taiwanese and Ryukyuan species of Eleganesia Alencar & Azevedo, 2018 (Hymenoptera, Bethylidae). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Csősz S, Loss AC, Fisher BL. Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae). PeerJ 2021; 9:e10900. [PMID: 33717685 PMCID: PMC7934650 DOI: 10.7717/peerj.10900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; of these, three are new to science: Aphaenogaster bresslerisp. n., A. gonacantha (Emery, 1899), A. makaysp. n., A. sahafinasp. n., and A. swammerdamiForel, 1886. In addition, three new synonymies were found for A. swammerdami Forel, 1886 (A. swammerdami clara Santschi, 1915 syn. n., A. swammerdami curta Forel, 1891 syn. n. and A. swammerdami spinipes Santschi, 1911 syn. n.). Descriptions and redefinitions for each taxon and an identification key for their worker castes using qualitative traits and morphometric data are given. Geographic maps depicting species distributions and biological information regarding nesting habits for the species are also provided.
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Affiliation(s)
- Sandor Csősz
- Evolutionary Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Ana C Loss
- National Institute of the Atlantic Forest, Santa Teresa, Brazil
| | - Brian L Fisher
- Entomology, California Academy of Sciences, San Francisco, CA, USA
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Boer P, Loss AC, Bakker F, Beentjes K, Fisher BL. Monomorium sahlbergi Emery, 1898 (Formicidae, Hymenoptera): a cryptic globally introduced species. Zookeys 2020; 979:87-97. [PMID: 33192132 PMCID: PMC7609494 DOI: 10.3897/zookeys.979.55342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
The discovery in the Netherlands in a shipping container of the ant Monomoriumsahlbergi Emery, 1898, a species similar to the invasive pharaoh ant M.pharaonis (Linnaeus, 1758), led to a quest to better define the distribution of this species, which was initially obscure due to uncertain specimen identifications. Here it is shown that M.sahlbergi, like M.pharaonis, is found worldwide, almost certainly as a result of introductions. Including quarantine interceptions, this species is recorded from seven global biogeographic regions, but its established outdoor distribution is currently limited to the tropics and subtropics. Monomoriumdichroum Forel, 1902 is here presented as a junior synonym of M.sahlbergisyn. nov. based on morphometric and CO1 analyses.
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Affiliation(s)
- Peter Boer
- Department of Terrestrial Zoology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands Naturalis Biodiversity Center Leiden Netherlands
| | - Ana Carolina Loss
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA California Academy of Sciences San Francisco United States of America.,National Institute of the Atlantic Forest (INMA), Santa Teresa, ES, Brazil National Institute of the Atlantic Forest Santa Teresa Brazil
| | - Frederique Bakker
- Department of Terrestrial Zoology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands Naturalis Biodiversity Center Leiden Netherlands
| | - Kevin Beentjes
- Department of Terrestrial Zoology, Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands Naturalis Biodiversity Center Leiden Netherlands
| | - Brian L Fisher
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA California Academy of Sciences San Francisco United States of America
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Sharaf MR, Gotzek D, Guénard B, Fisher BL, Aldawood AS, Al Dhafer HM, Mohamed AA. Molecular phylogenetic analysis and morphological reassessments of thief ants identify a new potential case of biological invasions. Sci Rep 2020; 10:12040. [PMID: 32694527 PMCID: PMC7374620 DOI: 10.1038/s41598-020-69029-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/01/2020] [Indexed: 11/13/2022] Open
Abstract
Species delimitation offered by DNA-based approaches can provide important insights into the natural history and diversity of species, but the cogency of such processes is limited without multigene phylogenies. Recent attempts to barcode various Solenopsidini ant taxa (Hymenoptera: Formicidae: Myrmicinae), including the thief ant Solenopsis saudiensis Sharaf & Aldawood, 2011 described from the Kingdom of Saudi Arabia (KSA), were precipitated by the unexpected existence of a closely related species, the Nearctic S. abdita Thompson, 1989 within the S. molesta species complex native to Florida. This finding left the species status of the former uncertain. Here, we investigated the taxonomy and phylogeny of these two species to determine whether or not S. abdita represents a new global tramp species. We inferred a phylogeny of the two species using DNA sequence data from four nuclear genes (Abd-A, EF1α-F1, EF1α-F2, and Wingless) and one mitochondrial gene (COI) sampled from populations in Florida, Guatemala, Hawaii, and Saudi Arabia. Both species clustered into one distinct and robust clade. The taxonomy of S. saudiensis was re‐examined using morphometrics. A reassessment of the morphological characters used to diagnose the worker and queen castes were consistent with molecular evidence. Based on combined morphological and molecular evidences S. saudiensis is declared as a junior synonym of S. abdita (syn. nov.). In addition, our findings indicate that S. abdita is a novel global tramp species which has a far wider distribution than previously thought and has established itself in many new habitats and different geographic realms.
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Affiliation(s)
- Mostafa R Sharaf
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia.
| | - Dietrich Gotzek
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Brian L Fisher
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Abdulrahman S Aldawood
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Hathal M Al Dhafer
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Amr A Mohamed
- Department of Entomology, Faculty of Science, Cairo University, PO Box 12613, Giza, Egypt
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13
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Hanchipura Mallesh MS, Asokan R, Gadad H, Duleep Kumar S, Kumar R, Prakash T. DNA barcoding and phylogenetic analysis of leafhoppers associated with Aster Yellow disease on China aster, Marigold and Chrysanthemum. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:64-72. [PMID: 32148145 DOI: 10.1080/24701394.2020.1735378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Cicadellidae (Auchenorrhyncha: Hemiptera) are important agricultural, horticultural and ornamental pests. But it is very difficult to define nymphs and female adults using morphological characteristics. This research was aimed at understanding the variety of leafhoppers species and defining the prospective cause of the aster-yellow disease in China Aster, Marigold and Chrysanthemum. Two surveys were conducted in and around Pune, Maharashtra and Bengaluru, Karnataka between November 2016 and February 2017. The mitochondrial cytochrome oxidase subunit I (mtCOI) region marker was used in the species diagnosis and genetic diversity research. Through the use of mtCOI molecular marker eight different leafhoppers species were identified as Sogatella furcifera, Homalodisca insolita, Amrasca biguttula, Balclutha incise and Balclutha abdominalis and Japanagallia trifurcate. Whereas at genus level identified as Toya, Empoasca, Perkinsiella, Hishimonus, Tambocerus, Phaconeura, Curena, Psammotettix and Graphocophala species. These results are strongly corroborated with morphological identification. On the basis of multiple sequence alignment of the mtCOI gene, a species phylogenetic tree with the highest likelihood was drawn. All the leafhopper species clustered together in accordance with the species data collected from the database of the different geographic regions from the NCBI GenBank and Barcode of Life (BOLD). Such results suggest that it is important to use both molecular and morphological methods to ensure accurate identification of organisms. To conclude, this research contributes valuable knowledge to molecular biology and recognizes leafhopper species that serve as major phytoplasma vectors.
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Affiliation(s)
| | - Ramasamy Asokan
- Bio-Pesticide Laboratory, Division of Biotechnology, ICAR Indian Institute of Horticultural Research (IIHR), Bangalore, India
| | - Hanamant Gadad
- Bio-Pesticide Laboratory, Division of Biotechnology, ICAR Indian Institute of Horticultural Research (IIHR), Bangalore, India
| | - Samuel Duleep Kumar
- Division of Plant Pathology, ICAR Indian Institute of Horticultural Research (IIHR), Bangalore, India
| | - Rajiv Kumar
- Division of Floriculture and Medicinal Plants, ICAR Indian Institute of Horticultural Research (IIHR), Bangalore, India
| | - Tejaswini Prakash
- Division of Floriculture and Medicinal Plants, ICAR Indian Institute of Horticultural Research (IIHR), Bangalore, India
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14
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Rasool KG, Husain M, Salman S, Tufail M, Sukirno S, Aldawood AS. DNA barcoding of the fire ant genus Solenopsis Westwood (Hymenoptera: Formicidae) from the Riyadh region, the Kingdom of Saudi Arabia. Saudi J Biol Sci 2019; 27:184-188. [PMID: 31889834 PMCID: PMC6933196 DOI: 10.1016/j.sjbs.2019.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/18/2019] [Accepted: 06/30/2019] [Indexed: 11/29/2022] Open
Abstract
The ant genus Solenopsis Westwood, 1840 is the largest in Myrmicinae subfamily having almost 200 described species worldwide. They are commonly distributed in the tropics and temperate areas of the world. Some invasive Solenopsis species are very dreadful. We have already reported a fire ant species, Solenopsis saudiensis Sharaf & Aldawood, 2011, identified using traditional morphometric approaches of species identification. Present study was carried out to develop DNA Barcoding to identify Solenopsis saudiensis and to elucidate genetic structure of the various S. saudiensis populations across their distribution range in Riyadh, Saudi Arabia. The comparison of DNA barcodes showed no genetic diversity among six populations and a queen from S. saudiensis analyzed from the Riyadh region. This genetic resemblance probably reflects their adaptation toward a specific habitat, thus constituting a single and strong gene pool. Our comprehensive field survey did not provide any evidence of Solenopsis species except S. saudiensis in the Riyadh region. Solenopsis saudiensis populations were only found around date palm trees indicating their strong association with date palm groves. Moreover, S. saudiensis has 83–86% sequence identity to other Solenopsis spp. from other parts of the world. Interestingly, the highest sequence identity of (86%) was with that of Solenopsis molesta Say, 1836, the thief ant, from the USA. This study provides a working laboratory procedure and a reference library for the identification of Solenopsis saudiensis.
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Affiliation(s)
- Khawaja Ghulam Rasool
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mureed Husain
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shehzad Salman
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Tufail
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
| | | | - Abdulrahman S Aldawood
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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15
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Matos-Maraví P, Matzke NJ, Larabee FJ, Clouse RM, Wheeler WC, Sorger DM, Suarez AV, Janda M. Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus). Mol Ecol 2018; 27:4090-4107. [PMID: 30106242 DOI: 10.1111/mec.14835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 01/05/2023]
Abstract
Nonequilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential nonequilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera that E.O. Wilson used when first proposing the hypothesis. We used model-based inference and a newly developed trait-dependent dispersal model to jointly estimate ancestral biogeography, ecology (habitat preferences for forest interiors, vs. "marginal" habitats, such as savannahs, shorelines, disturbed areas) and the linkage between ecology and dispersal rates. We found strong evidence that habitat shifts from forest interior to open and disturbed habitats increased macroevolutionary dispersal rate. In addition, lineages occupying open and disturbed habitats can give rise to both island endemics re-occupying only forest interiors and taxa that re-expand geographical ranges. The phylogenetic predictions outlined in this study can be used in future work to evaluate the relative weights of neutral (e.g., geographical distance and area) and non-neutral (e.g., trait-dependent dispersal) processes in historical biogeography and community ecology.
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Affiliation(s)
- Pável Matos-Maraví
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.,Department of Zoology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Fredrick J Larabee
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia.,Department of Entomology and Department of Animal Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Ronald M Clouse
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York
| | - Daniela Magdalena Sorger
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina.,Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Andrew V Suarez
- Department of Entomology and Department of Animal Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Milan Janda
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.,Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Morelia, Mexico
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16
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Chen Y, Zhou S. Phylogenetic Relationships Based on DNA Barcoding Among 16 Species of the Ant Genus Formica (Hymenoptera: Formicidae) from China. JOURNAL OF INSECT SCIENCE 2017; 17:117. [PMCID: PMC5710517 DOI: 10.1093/jisesa/iex092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Indexed: 06/16/2023]
Abstract
In this study, we sequenced fragments of cytochrome oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), and internal transcribed spacer 2 (ITS2) genes from 150 specimens belonging to 16 species of the ant genus Formica from China. Odontoponera transversa from Ponerinae and Polyergus samurai from Formicinae were added as distant relative and close relative outgroups, respectively. Neighbor-joining, maximum parsimony, and Bayesian interference methods were used to analyze their phylogenetic relationships based on CO1 gene sequence as well as combined sequence data of CO1 + ITS1, CO1 + ITS2, and CO1 + ITS1 + ITS2. The results showed that nine Formica species (i.e., Formica sinensis, Formica manchu, Formica uralensis, Formica sanguinea, Formica gagatoides, Formica candida, Formica fusca, Formica glauca, and Formica sp.) formed monophyletic clades, which in agreement with the results based on morphological taxonomy. By comparing the results of DNA barcoding and morphological taxonomy, we propose that Formica aquilonia maybe a junior synonym of F. polyctena and that cryptic species could likely existed in Formica sinae. Further studies on morphology, biology, and geography are needed to confirm this notion.
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Affiliation(s)
- Yuan Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, No.15 Yucai Road, Qixing District, Guilin, Guangxi, China
| | - Shanyi Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, No.15 Yucai Road, Qixing District, Guilin, Guangxi, China
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17
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Fusu L. An integrative taxonomic study of European Eupelmus (Macroneura) (Hymenoptera: Chalcidoidea: Eupelmidae), with a molecular and cytogenetic analysis of Eupelmus (Macroneura) vesicularis: several species hiding under one name for 240 years. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Oliveira AA, Campos AEC, Harakava R. Genetic Diversity of Urban Camponotus Mayr (Hymenoptera: Formicidae) Ants Revealed by Capture of Alates and DNA Sequencing. NEOTROPICAL ENTOMOLOGY 2017; 46:499-506. [PMID: 28185208 DOI: 10.1007/s13744-017-0489-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
The Camponotus Mayr genus of carpenter ants is one of the largest in species number and widely represented in the Neotropical Region. Most species are generalists and capable of exploiting diverse habitats including urban environments. Urban green areas can act as a repository of regional biodiversity, thus we investigated whether this is valid for the largest city in South America. We compared the richness of Camponotus spp. in two green areas in regions with distinct urbanization profiles and also with previous surveys made in smaller cities and in natural areas of the original Atlantic Forest. Besides the usual capture of worker specimens, we included capture of alates to improve the species richness sampling. Morphological identification of Camponotus spp. is challenging, even more when alates are included. To assist in specimen identification, we performed DNA sequencing of mitochondrial and nuclear markers. The richness observed in the less stressed urban area was higher than in the more stressed one. Camponotus spp. reported in natural areas are largely represented in the urban area. DNA sequencing for specimen identification is hampered by the lack of corresponding sequences in the GenBank, but it helped to associate workers and alates of the same species and indicated the existence of cryptic species in the genus. Capture of alates allowed detection of several species for which workers were not sampled; therefore, it is a valuable tool for surveying diversity of Camponotus or other ant taxa with arboreal or hypogeic habits.
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Affiliation(s)
- A A Oliveira
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, São Paulo, SP, CEP 04014-002, Brazil
| | - A E C Campos
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, São Paulo, SP, CEP 04014-002, Brazil
| | - R Harakava
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, São Paulo, SP, CEP 04014-002, Brazil.
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19
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Koroiva R, Pepinelli M, Rodrigues ME, Roque FDO, Lorenz-Lemke AP, Kvist S. DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation. PLoS One 2017; 12:e0182283. [PMID: 28763495 PMCID: PMC5538745 DOI: 10.1371/journal.pone.0182283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.
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Affiliation(s)
- Ricardo Koroiva
- Ecology and Conservation Graduate Program, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mateus Pepinelli
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Marciel Elio Rodrigues
- Laboratório de Organismos Aquáticos, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Fabio de Oliveira Roque
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Aline Pedroso Lorenz-Lemke
- Laboratório de Evolução e Biodiversidade, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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20
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Egloff W, Agosti D, Kishor P, Patterson D, Miller J. Copyright and the Use of Images as Biodiversity Data. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e12502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document the attributes (characters) of organisms, with emphasis on those can be used to distinguish species from each other. Character information is compiled in the scientific literature as text, tables, and images. The information is presented according to conventions that vary among taxonomic domains; such conventions facilitate comparison among similar species, even when descriptions are published by different authors.
There is considerable uncertainty within the taxonomic community as to how to re-use images that were included in taxonomic publications, especially in regard to whether copyright applies. This article deals with the principles and application of copyright law, database protection, and protection against unfair competition, as applied to images. We conclude that copyright does not apply to most images in taxonomic literature because they are presented in a standardized way and lack the individuality that is required to qualify as ‘copyrightable works’. There are exceptions, such as wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes (such as visual art). Further exceptions may apply to collections of images that qualify as a database in the sense of European database protection law. In a few European countries, there is legal protection for photographs that do not qualify as works in the usual sense of copyright. It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration. In observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.
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21
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Rakotonirina JC, Csősz S, Fisher BL. Revision of the Malagasy Camponotus edmondi species group (Hymenoptera, Formicidae, Formicinae): integrating qualitative morphology and multivariate morphometric analysis. Zookeys 2017:81-154. [PMID: 28050160 PMCID: PMC4843987 DOI: 10.3897/zookeys.572.7177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/20/2016] [Indexed: 11/16/2022] Open
Abstract
The Malagasy Camponotusedmondi species group is revised based on both qualitative morphological traits and multivariate analysis of continuous morphometric data. To minimize the effect of the scaling properties of diverse traits due to worker caste polymorphism, and to achieve the desired near-linearity of data, morphometric analyses were done only on minor workers. The majority of traits exhibit broken scaling on head size, dividing Camponotus workers into two discrete subcastes, minors and majors. This broken scaling prevents the application of algorithms that uses linear combination of data to the entire dataset, hence only minor workers were analyzed statistically. The elimination of major workers resulted in linearity and the data meet required assumptions. However, morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. Prior species hypotheses and the goodness of clusters were tested on raw data by confirmatory linear discriminant analysis. Due to the small sample size available for some species, a factor known to reduce statistical reliability, hypotheses generated by exploratory analyses were tested with extreme care and species delimitations were inferred via the combined evidence of both qualitative (morphology and biology) and quantitative data. Altogether, fifteen species are recognized, of which 11 are new to science: Camponotusalamainasp. n., Camponotusandroysp. n., Camponotusbevohitrasp. n., Camponotusgalokosp. n., Camponotusmatsilosp. n., Camponotusmifakasp. n., Camponotusorombesp. n., Camponotustafosp. n., Camponotustratrasp. n., Camponotusvaratrasp. n., and Camponotuszavosp. n. Four species are redescribed: Camponotusechinoploides Forel, Camponotusedmondi André, Camponotusethicus Forel, and Camponotusrobustus Roger. Camponotusedmondiernesti Forel, syn. n. is synonymized under Camponotusedmondi. This revision also includes an identification key to species for both minor and major castes, information on geographic distribution and biology, taxonomic discussions, and descriptions of intraspecific variation. Traditional taxonomy and multivariate morphometric analysis are independent sources of information which, in combination, allow more precise species delimitation. Moreover, quantitative characters included in identification keys improve accuracy of determination in difficult cases.
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Affiliation(s)
- Jean Claude Rakotonirina
- Madagascar Biodiversity Center, BP 6257, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - Sándor Csősz
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, U.S.A
| | - Brian L Fisher
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, U.S.A
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22
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Che Y, Gui S, Lo N, Ritchie A, Wang Z. Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China. PLoS One 2017; 12:e0169006. [PMID: 28046038 PMCID: PMC5207705 DOI: 10.1371/journal.pone.0169006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/10/2016] [Indexed: 11/23/2022] Open
Abstract
We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37-65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125-110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.
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Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shunhua Gui
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Andrew Ritchie
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
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23
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Devi KM, Shantibala T, Debaraj H. The first complete mitochondrial genome of a Belostomatidae species, Lethocerus indicus, the giant water bug: An important edible insect. Gene 2016; 591:108-118. [PMID: 27390089 DOI: 10.1016/j.gene.2016.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 11/30/2022]
Abstract
Lethocerus indicus of the family Belostomatidae is one of the most preferred and delicious edible insects in different parts of South-East Asia including North-East, India. The mitogenome of L. indicus represents the first complete mitogenome sequence of a Belostomatidae species in Heteroptera order. The mitogenome of L. indicus is 16,251bp and contains 37 genes including 13 protein coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a large non-coding region. The genome has a typical gene order which is identical to other Heteroptera species. All tRNAs exhibit the classic cloverleaf secondary structure except tRNASer (AGN). All the PCGs employ a complete translation termination codon either TAA or TAG except COII. The nucleotide composition showed heavy biased toward AT accounting to 70.9% of total mitogenome. The overall A+T content of L. indicus mitogenome was comparatively lower than some other Heteropteran bugs mitogenomes. The control region is divided into seven different parts which includes the putative stem loop, repeats, tandem repeats, GC and AT rich regions. The phylogenetic relationship based on maximum-likelihood method using all protein coding genes was congruent with the traditional morphological classification that Belostomatidae is closely related to Nepidae. The complete mitogenome sequence of L. indicus provides fundamental data useful in conservation genetics and aquaculture diversification.
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Affiliation(s)
- Kshetrimayum Miranda Devi
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal- 795001, Manipur, India
| | - Tourangbam Shantibala
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal- 795001, Manipur, India.
| | - Hajarimayum Debaraj
- Animal Bioresources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal- 795001, Manipur, India
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Monckton SK. A revision of Chilicola (Heteroediscelis), a subgenus of xeromelissine bees (Hymenoptera, Colletidae) endemic to Chile: taxonomy, phylogeny, and biogeography, with descriptions of eight new species. Zookeys 2016; 591:1-144. [PMID: 27408541 PMCID: PMC4926649 DOI: 10.3897/zookeys.591.7731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/04/2016] [Indexed: 11/23/2022] Open
Abstract
The bee subgenus Chilicola (Heteroediscelis) Toro & Moldenke, 1979 (Hymenoptera, Colletidae, Xeromelissinae) is revised. The subgenus is considered endemic to Chile and occurs across a broad range of habitats. Eight new species are described: Chilicola (Heteroediscelis) charizard Monckton, sp. n., Chilicola (Heteroediscelis) curvapeligrosa Monckton, sp. n., Chilicola (Heteroediscelis) guanicoe Monckton, sp. n., Chilicola (Heteroediscelis) katherinae Monckton, sp. n., Chilicola (Heteroediscelis) lickana Monckton, sp. n., Chilicola (Heteroediscelis) mayu Monckton, sp. n., Chilicola (Heteroediscelis) packeri Monckton, sp. n., and Chilicola (Heteroediscelis) randolphi Monckton, sp. n. One of the existing species, Chilicola (Heteroediscelis) valparaiso Toro & Moldenke, 1979, syn. n., is treated as a junior synonym of Chilicola (Heteroediscelis) mantagua Toro & Moldenke, 1979, and the nine remaining valid species are redescribed. Thoroughly illustrated keys to species for males and females are provided, along with habitus images, images of male terminalia, distribution maps for each species, and a map of relevant Chilean biogeographic regions. Results of phylogenetic analyses are presented, based upon 74 morphological characters and on CO1 barcode sequences, analyzed both separately and as a combined dataset. Monophyly of the subgenus is supported, and groupings within the subgenus are discussed in light of a biogeographic analysis of their species distributions (spatial analysis of vicariance), whereby divergence between taxa is found to occur primarily via north-south disjunctions.
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Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae). PLoS One 2016; 11:e0146170. [PMID: 26800442 PMCID: PMC4723042 DOI: 10.1371/journal.pone.0146170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/14/2015] [Indexed: 12/30/2022] Open
Abstract
The bulk of models used to understand the species diversification on Madagascar have been constructed using vertebrate taxa. It is not clear how these models affect less vagile species that may interact at a variety of spatial scales. Several studies on vertebrates have divided Madagascar into east-west bioclimatic regions, suggesting there is a fundamental division between eastern wet-adapted and western dry-adapted taxa. An alternative model of ecogeographic constraints shows a north-south division. We test whether the diversification in a small arthropod with variable degrees of dispersal conform to either model of ecogeographic constraints proposed for vertebrate taxa. We employ a molecular taxonomic dataset using ~2 kilobases nuDNA (Wg, LW Rh, Abd-A, 28s) and 790 basepairs mtDNA (CO1), along with geographic and habitat data, to examine the diversification patterns of the ant genus Mystrium Roger, 1862, (Subfamily Amblyoponinae) from Madagascar. The nuclear and mitochondrial phylogenies were both congruent with morphospecies as indicated in a recent revision of the genus. Species of Mystrium practice different colony reproductive strategies (winged queens vs non-winged queens). Alternate reproductive strategies led to inequalities in female dispersal ability among species, providing an additional layer for examination of the impacts of vagility on divergence, especially when measured using a maternally inherited locus. Mystrium species distribution patterns support these models of ecogeographic constraints. Reproductive strategy effected how Mystrium mtDNA lineages were associated with large-scale habitat distinctions and various topographical features. Furthermore, in some cases we find microgeographic population structure which appears to have been impacted by localized habitat differences (tsingy limestone formations, littoral forest) on a scale much smaller than that found in vertebrates. The current system offers a finer scale look at species diversification on the island, and helps achieve a more universal understanding of the generation of biodiversity on Madagascar.
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Jowers MJ, Taheri A, Reyes-López J. The antAnochetus ghilianii(Hymenoptera, Formicidae), not a Tertiary relict, but an Iberian introduction from North Africa: Evidence from mtDNA analyses. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1061065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Paknia O, Bergmann T, Hadrys H. Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy. Mol Ecol Resour 2015; 15:1262-74. [DOI: 10.1111/1755-0998.12395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Omid Paknia
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Tjard Bergmann
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Heike Hadrys
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
- EEB; Yale University; New Haven Connecticut 06511 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York New York 10024 USA
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Lecocq T, Dellicour S, Michez D, Dehon M, Dewulf A, De Meulemeester T, Brasero N, Valterová I, Rasplus JY, Rasmont P. Methods for species delimitation in bumblebees (Hymenoptera, Apidae,Bombus): towards an integrative approach. ZOOL SCR 2015. [DOI: 10.1111/zsc.12107] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Lecocq
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
| | - Simon Dellicour
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; av. FD Roosevelt 50 1050 Brussels Belgium
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS UK
| | - Denis Michez
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
| | - Manuel Dehon
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
| | - Alexandre Dewulf
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
| | | | - Nicolas Brasero
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
| | - Irena Valterová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flamingovo nám 2 CZ-166 10 Prague Czech Republic
| | - Jean-Yves Rasplus
- Institut National de la Recherche Agronomique; UMR 1062 Centre de Biologie pour la Gestion des Populations; CS 30 016 F-34988 Montferrier/Lez Cedex France
| | - Pierre Rasmont
- Laboratory of Zoology; Research institute of Biosciences; University of Mons; Place du Parc 20 7000 Mons Belgium
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29
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Lecocq T, Brasero N, De Meulemeester T, Michez D, Dellicour S, Lhomme P, de Jonghe R, Valterová I, Urbanová K, Rasmont P. An integrative taxonomic approach to assess the status of Corsican bumblebees: implications for conservation. Anim Conserv 2014. [DOI: 10.1111/acv.12164] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Lecocq
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
| | - N. Brasero
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
| | | | - D. Michez
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
| | - S. Dellicour
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; Brussels Belgium
| | - P. Lhomme
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
| | - R. de Jonghe
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
| | - I. Valterová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
| | - K. Urbanová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
| | - P. Rasmont
- Research Institute of Biosciences; Laboratory of Zoology; University of Mons; Mons Belgium
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30
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Bertrand C, Janzen DH, Hallwachs W, Burns JM, Gibson JF, Shokralla S, Hajibabaei M. Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species. BMC Evol Biol 2014; 14:153. [PMID: 25005355 PMCID: PMC4112655 DOI: 10.1186/1471-2148-14-153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/17/2014] [Indexed: 11/22/2022] Open
Abstract
Background Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexes within them. Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica. Results Although no morphological traits appear to distinguish among the three, congruent nuclear and mitochondrial lineage patterns show that “Urbanus belli” in ACG is a complex of three sympatric species. A single strain of Wolbachia present in two of the three cryptic species indicates that Urbanus segnestami Burns (formerly Urbanus belliDHJ01), Urbanus bernikerni Burns (formerly Urbanus belliDHJ02), and Urbanus ehakernae Burns (formerly Urbanus belliDHJ03) may be biologically separated by Wolbachia, as well as by their genetics. Use of parallel sequencing through 454-pyrosequencing improved the utility of ITS2 as a phylogenetic marker and permitted examination of the intra- and interlineage relationships of ITS2 variants within the species complex. Interlineage, intralineage and intragenomic compensatory base pair changes were discovered in the secondary structure of ITS2. Conclusion These findings corroborate the existence of three cryptic species. Our confirmation of a novel cryptic species complex, initially suggested by DNA barcode lineages, argues for using a multi-marker approach coupled with next-generation sequencing for exploration of other suspected species complexes.
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Affiliation(s)
| | | | | | | | | | | | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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31
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Genetic Divergence, Implication of Diversity, and Conservation of Silkworm, Bombyx mori. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/564850] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genetic diversity is critical to success in any crop breeding and it provides information about the quantum of genetic divergence and serves a platform for specific breeding objectives. It is one of the three forms of biodiversity recognized by the World Conservation Union (IUCN) as deserving conservation.
Silkworm Bombyx mori, an economically important insect, reported to be domesticated over 5000 years ago by human to meet his requirements.
Genetic diversity is a particular concern because greater genetic uniformity in silkworm can increase vulnerability to pests and diseases.
Hence, maintenance of genetic diversity is a fundamental component in long-term management strategies for genetic improvement of silkworm which is cultivated by millions of people around the worlds for its lusture silk.
In this paper genetic diversity studies carried out in silkworm using divergent methods (quantitative traits and biochemical and molecular markers) and present level of diversity and factors responsible for loss of diversity are discussed.
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Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Tuama ÉÓ, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One 2014; 9:e89606. [PMID: 24595056 PMCID: PMC3940615 DOI: 10.1371/journal.pone.0089606] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 01/24/2014] [Indexed: 11/19/2022] Open
Abstract
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
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Affiliation(s)
- Ramona L. Walls
- The iPlant Collaborative, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - John Deck
- University of California, Berkeley, Berkeley, California, United States of America
| | - Robert Guralnick
- Department of Ecology and Evolutionary Biology and the CU Museum of Natural History, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Steve Baskauf
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Reed Beaman
- University of Florida, Florida Museum of Natural History, Gainesville, Florida, United States of America
| | - Stanley Blum
- Research Informatics, California Academy of Sciences, San Francisco, California, United States of America
| | - Shawn Bowers
- Gonzaga University, Computer Science, Spokane, Washington, United States of America
| | - Pier Luigi Buttigieg
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Neil Davies
- University of California, Berkeley, Gump South Pacific Research Station, Moorea, French Polynesia
| | - Dag Endresen
- GBIF Norway, Natural History Museum, University in Oslo, Oslo, Norway
| | - Maria Alejandra Gandolfo
- LH Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Robert Hanner
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Alyssa Janning
- School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America
| | - Leonard Krishtalka
- Biodiversity Institute and Ecology & Evolutionary Biology, The University of Kansas, Lawrence, Kansas, United States of America
| | - Andréa Matsunaga
- University of Florida, Gainesville, Florida, United States of America
| | - Peter Midford
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Norman Morrison
- The BioVeL Project, School of Computer Science, The University of Manchester, Manchester, United Kingdom
| | | | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, Santa Barbara, California, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America
| | - Brian J. Stucky
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Andrea Thomer
- Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, United States of America
| | - John Wieczorek
- 3101 VLSB, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jamie Whitacre
- Informatics Branch, Information Technology Office, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - John Wooley
- University of California San Diego, La Jolla, California, United States of America
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Fernández-Triana JL, Whitfield JB, Rodriguez JJ, Smith MA, Janzen DH, Hallwachs WD, Hajibabaei M, Burns JM, Solis MA, Brown J, Cardinal S, Goulet H, Hebert PDN. Review of Apanteles sensu stricto (Hymenoptera, Braconidae, Microgastrinae) from Area de Conservación Guanacaste, northwestern Costa Rica, with keys to all described species from Mesoamerica. Zookeys 2014; 383:1-565. [PMID: 24624021 PMCID: PMC3950464 DOI: 10.3897/zookeys.383.6418] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/15/2014] [Indexed: 01/20/2023] Open
Abstract
More than half a million specimens of wild-caught Lepidoptera caterpillars have been reared for their parasitoids, identified, and DNA barcoded over a period of 34 years (and ongoing) from Area de Conservación de Guanacaste (ACG), northwestern Costa Rica. This provides the world's best location-based dataset for studying the taxonomy and host relationships of caterpillar parasitoids. Among Hymenoptera, Microgastrinae (Braconidae) is the most diverse and commonly encountered parasitoid subfamily, with many hundreds of species delineated to date, almost all undescribed. Here, we reassess the limits of the genus Apanteles sensu stricto, describe 186 new species from 3,200+ parasitized caterpillars of hundreds of ACG Lepidoptera species, and provide keys to all 205 described Apanteles from Mesoamerica - including 19 previously described species in addition to the new species. The Mesoamerican Apanteles are assigned to 32 species-groups, all but two of which are newly defined. Taxonomic keys are presented in two formats: traditional dichotomous print versions and links to electronic interactive versions (software Lucid 3.5). Numerous illustrations, computer-generated descriptions, distributional information, wasp biology, and DNA barcodes (where available) are presented for every species. All morphological terms are detailed and linked to the Hymenoptera Anatomy Ontology website. DNA barcodes (a standard fragment of the cytochrome c oxidase I (COI) mitochondrial gene), information on wasp biology (host records, solitary/gregariousness of wasp larvae), ratios of morphological features, and wasp microecological distributions were used to help clarify boundaries between morphologically cryptic species within species-complexes. Because of the high accuracy of host identification for about 80% of the wasp species studied, it was possible to analyze host relationships at a regional level. The ACG species of Apanteles attack mainly species of Hesperiidae, Elachistidae and Crambidae (Lepidoptera). About 90% of the wasp species with known host records seem to be monophagous or oligophagous at some level, parasitizing just one host family and commonly, just one species of caterpillar. Only 15 species (9%) parasitize species in more than one family, and some of these cases are likely to be found to be species complexes. We have used several information sources and techniques (traditional taxonomy, molecular, software-based, biology, and geography) to accelerate the process of finding and describing these new species in a hyperdiverse group such as Apanteles. The following new taxonomic and nomenclatural acts are proposed. Four species previously considered to be Apanteles are transferred to other microgastrine genera: Dolichogenidea hedyleptae (Muesebeck, 1958), comb. n., Dolichogenidea politiventris (Muesebeck, 1958), comb. n., Rhygoplitis sanctivincenti (Ashmead, 1900), comb. n., and Illidops scutellaris (Muesebeck, 1921), comb. rev. One European species that is a secondary homonym to a Mesoamerican species is removed from Apanteles and transferred to another genus: Iconella albinervis (Tobias, 1964), stat. rev. The name Apanteles albinervican Shenefelt, 1972, is an invalid replacement name for Apanteles albinervis (Cameron, 1904), stat. rev., and thus the later name is reinstated as valid. The following 186 species, all in Apanteles and all authored by Fernández-Triana, are described as species nova: adelinamoralesae, adrianachavarriae, adrianaguilarae, adrianguadamuzi, aichagirardae, aidalopezae, albanjimenezi, alejandromasisi, alejandromorai, minorcarmonai, alvarougaldei, federicomatarritai, anabellecordobae, rostermoragai, anamarencoae, anamartinesae, anapiedrae, anariasae, andreacalvoae, angelsolisi, arielopezi, bernardoespinozai, bernyapui, bettymarchenae, bienvenidachavarriae, calixtomoragai, carloscastilloi, carlosguadamuzi, eliethcantillanoae, carlosrodriguezi, carlosviquezi, carloszunigai, carolinacanoae, christianzunigai, cinthiabarrantesae, ciriloumanai, cristianalemani, cynthiacorderoae, deifiliadavilae, dickyui, didiguadamuzi, diegoalpizari, diegotorresi, diniamartinezae, duniagarciae, duvalierbricenoi, edgarjimenezi, edithlopezae, eduardoramirezi, edwinapui, eldarayae, erickduartei, esthercentenoae, eugeniaphilipsae, eulogiosequeira, felipechavarriai, felixcarmonai, fernandochavarriai, flormoralesae, franciscopizarroi, franciscoramirezi, freddyquesadai, freddysalazari, gabrielagutierrezae, garygibsoni, gerardobandoi, gerardosandovali, gladysrojasae, glenriverai, gloriasihezarae, guadaluperodriguezae, guillermopereirai, juanmatai, harryramirezi, hectorsolisi, humbertolopezi, inesolisae, irenecarrilloae, isaacbermudezi, isidrochaconi, isidrovillegasi, ivonnetranae, jairomoyai, javiercontrerasi, javierobandoi, javiersihezari, jesusbrenesi, jesusugaldei, jimmychevezi, johanvargasi, jorgecortesi, jorgehernandezi, josecalvoi, josecortesi, josediazi, josejaramilloi, josemonteroi, joseperezi, joserasi, juanapui, juancarrilloi, juangazoi, juanhernandezi, juanlopezi, juanvictori, juliodiazi, juniorlopezi, keineraragoni, laurahuberae, laurenmoralesae, leninguadamuzi, leonelgarayi, lilliammenae, lisabearssae, luciariosae, luisbrizuelai, luiscanalesi, luiscantillanoi, luisgarciai, luisgaritai, luishernandezi, luislopezi, luisvargasi, manuelarayai, manuelpereirai, manuelriosi, manuelzumbadoi, marcobustosi, marcogonzalezi, marcovenicioi, mariachavarriae mariaguevarae, marialuisariasae, mariamendezae, marianopereirai, mariatorrentesae, sigifredomarini, marisolarroyoae, marisolnavarroae, marvinmendozai, mauriciogurdiani, milenagutierrezae, monicachavarriae, oscarchavesi, osvaldoespinozai, pablotranai, pabloumanai, pablovasquezi, paulaixcamparijae, luzmariaromeroae, petronariosae, randallgarciai, randallmartinezi, raulacevedoi, raulsolorsanoi, wadyobandoi, ricardocaleroi, robertmontanoi, robertoespinozai, robertovargasi, rodrigogamezi, rogerblancoi, rolandoramosi, rolandovegai, ronaldcastroi, ronaldgutierrezi, ronaldmurilloi, ronaldnavarroi, ronaldquirosi, ronaldzunigai, rosibelelizondoae, ruthfrancoae, sergiocascantei, sergioriosi, tiboshartae, vannesabrenesae, minornavarroi, victorbarrantesi, waldymedinai, wilbertharayai, williamcamposi, yeissonchavesi, yilbertalvaradoi, yolandarojasae, hazelcambroneroae, zeneidabolanosae.
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Affiliation(s)
- Jose L. Fernández-Triana
- Department of Integrative Biology and the Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1 Canada
- Canadian National Collection of Insects, 960 Carling Ave., Ottawa, ON K1A 0C6 Canada
| | | | | | - M. Alex Smith
- Department of Integrative Biology and the Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Daniel H. Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018 USA
| | - Winnie D. Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018 USA
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and the Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - John M. Burns
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, P.O.Box37012, MRC127, Washington, DC 20013-7012 USA
| | - M. Alma Solis
- Systematic Entomology Laboratory, USDA, c/o National Museum of Natural History, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - John Brown
- Systematic Entomology Laboratory, USDA, c/o National Museum of Natural History, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Sophie Cardinal
- Canadian National Collection of Insects, 960 Carling Ave., Ottawa, ON K1A 0C6 Canada
| | - Henri Goulet
- Department of Integrative Biology and the Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Paul D. N. Hebert
- Department of Integrative Biology and the Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1 Canada
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Hosoishi S, Ogata K. Description and DNA barcoding of Crematogaster fraxatrix Forel, 1911 and two new closely related species from Cambodia and Indonesia (Hymenoptera, Formicidae). Zookeys 2014:57-68. [PMID: 24493965 PMCID: PMC3909812 DOI: 10.3897/zookeys.374.5874] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 01/06/2014] [Indexed: 11/12/2022] Open
Abstract
Crematogaster fraxatrix Forel, 1911 and two new species, C. chhangisp. n. and C. simbolonisp. n., are described from Cambodia and Indonesia, respectively. DNA sequences were generated for C. fraxarix and the two newly described species using 3 amplications of two regions of the mitochondrial gene COI with a total of 1129 bp. The mean interspecific divergences are 9.4% and 23.5% for C. fraxatrix vs. C. chhangi, C. simboloni, respectively. DNA sequences reveal that C. simboloni is found to be genetically distinct from the other two species, but C. chhangi is not distinct from C. fraxatrix.
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Affiliation(s)
- Shingo Hosoishi
- Institute of Tropical Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 Japan
| | - Kazuo Ogata
- Institute of Tropical Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 Japan
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Touchard A, Dauvois M, Arguel MJ, Petitclerc F, Leblanc M, Dejean A, Orivel J, Nicholson GM, Escoubas P. Elucidation of the unexplored biodiversity of ant venom peptidomes via MALDI-TOF mass spectrometry and its application for chemotaxonomy. J Proteomics 2014; 105:217-31. [PMID: 24456813 DOI: 10.1016/j.jprot.2014.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/06/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED The rise of integrative taxonomy, a multi-criteria approach used in characterizing species, fosters the development of new tools facilitating species delimitation. Mass spectrometric (MS) analysis of venom peptides from venomous animals has previously been demonstrated to be a valid method for identifying species. Here we aimed to develop a rapid chemotaxonomic tool for identifying ants based on venom peptide mass fingerprinting. The study focused on the biodiversity of ponerine ants (Hymenoptera: Formicidae: Ponerinae) in French Guiana. Initial experiments optimized the use of automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to determine variations in the mass profiles of ant venoms using several MALDI matrices and additives. Data were then analyzed via a hierarchical cluster analysis to classify the venoms of 17 ant species. In addition, phylogenetic relationships were assessed and were highly correlated with methods using DNA sequencing of the mitochondrial gene cytochrome c oxidase subunit 1. By combining a molecular genetics approach with this chemotaxonomic approach, we were able to improve the accuracy of the taxonomic findings to reveal cryptic ant species within species complexes. This chemotaxonomic tool can therefore contribute to more rapid species identification and more accurate taxonomies. BIOLOGICAL SIGNIFICANCE This is the first extensive study concerning the peptide analysis of the venom of both Pachycondyla and Odontomachus ants. We studied the venoms of 17 ant species from French Guiana that permitted us to fine-tune the venom analysis of ponerine ants via MALDI-TOF mass spectrometry. We explored the peptidomes of crude ant venom and demonstrated that venom peptides can be used in the identification of ant species. In addition, the application of this novel chemotaxonomic method combined with a parallel genetic approach using COI sequencing permitted us to reveal the presence of cryptic ants within both the Pachycondyla apicalis and Pachycondyla stigma species complexes. This adds a new dimension to the search for means of exploiting the enormous biodiversity of venomous ants as a source for novel therapeutic drugs or biopesticides. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Axel Touchard
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France.
| | - Mélodie Dauvois
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
| | | | - Frédéric Petitclerc
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France
| | - Mathieu Leblanc
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
| | - Alain Dejean
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France; Université de Toulouse, UPS, INP, Laboratoire Écologie Fonctionnelle et Environnement (ECOLAB), 118 route de Narbonne, 31062 Toulouse, France
| | - Jérôme Orivel
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France
| | - Graham M Nicholson
- Neurotoxin Research Group, School of Medical & Molecular Biosciences, University of Technology, Sydney, NSW, Australia
| | - Pierre Escoubas
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
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Smith MA, Fernandez-Triana J, Roughley R, Hebert PDN. DNA barcode accumulation curves for understudied taxa and areas. Mol Ecol Resour 2013; 9 Suppl s1:208-16. [PMID: 21564980 DOI: 10.1111/j.1755-0998.2009.02646.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment - parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.
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Affiliation(s)
- M Alex Smith
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1, Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
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Stahlhut JK, Fernández-Triana J, Adamowicz SJ, Buck M, Goulet H, Hebert PDN, Huber JT, Merilo MT, Sheffield CS, Woodcock T, Smith MA. DNA barcoding reveals diversity of Hymenoptera and the dominance of parasitoids in a sub-arctic environment. BMC Ecol 2013; 13:2. [PMID: 23351160 PMCID: PMC3565895 DOI: 10.1186/1472-6785-13-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/21/2012] [Indexed: 12/03/2022] Open
Abstract
Background Insect diversity typically declines with increasing latitude, but previous studies have shown conflicting latitude-richness gradients for some hymenopteran parasitoids. However, historical estimates of insect diversity and species richness can be difficult to confirm or compare, because they may be based upon dissimilar methods. As a proxy for species identification, we used DNA barcoding to identify molecular operational taxonomic units (MOTUs) for 7870 Hymenoptera specimens collected near Churchill, Manitoba, from 2004 through 2010. Results We resolved 1630 MOTUs for this collection, of which 75% (1228) were ichneumonoids (Ichneumonidae + Braconidae) and 91% (1484) were parasitoids. We estimate the total number of Hymenoptera MOTUs in this region at 2624-2840. Conclusions The diversity of parasitoids in this sub-Arctic environment implies a high diversity of potential host species throughout the same range. We discuss these results in the contexts of resolving interspecific interactions that may include cryptic species, and developing reproducible methods to estimate and compare species richness across sites and between surveys, especially when morphological specialists are not available to identify every specimen.
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Affiliation(s)
- Julie K Stahlhut
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.
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Sarnat EM, Blanchard B, Guénard B, John Fasi, Evan P Economo. Checklist of the ants (Hymenoptera, Formicidae) of the Solomon Islands and a new survey of Makira Island. Zookeys 2013; 257:47-88. [PMID: 23653494 PMCID: PMC3591739 DOI: 10.3897/zookeys.257.4156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/17/2012] [Indexed: 12/02/2022] Open
Abstract
The intent of this paper is to facilitate future research of the Solomon Islands ant fauna by providing the first comprehensively researched species inventory in over 75 years. The species list presented here includes the names of all ant species recorded from the islands that are available in the literature together with specimen records from several museum collections and new records from our 2008 Makira field expedition. All the names of described species presented are valid in accordance with the most recent Formicidae classification. In total, the checklist is composed of 237 species and subspecies (including 30 morphospecies) in 59 genera representing nine subfamilies. We report that the recent field expedition added 67 new species records to Makira and 28 new species records to the Solomon Islands. Our research recovered species occurrence records for 32 individual islands and five island groups. The five islands with the highest number of recorded species are: Makira (142 spp.), Guadalcanal (107 spp.), Malaita (70 spp.), Santa Isabel (68 spp.), and Rennell (66 spp.). Based on our results, we discuss the taxonomic composition of the archipelago's ant fauna, which islands are most in need of additional sampling, and the importance of establishing biodiversity baselines before environmental threats such as the invasive ant Wasmannia auropunctata cause irrevocable harm to the native biodiversity.
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Affiliation(s)
- Eli M Sarnat
- Antwork Consulting, LLC, PO Box 563 Happy Camp, CA 96039 USA ; Department of Entomology, University of Illinois, Urbana, Illinois 61801
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Smith MA, Bertrand C, Crosby K, Eveleigh ES, Fernandez-Triana J, Fisher BL, Gibbs J, Hajibabaei M, Hallwachs W, Hind K, Hrcek J, Huang DW, Janda M, Janzen DH, Li Y, Miller SE, Packer L, Quicke D, Ratnasingham S, Rodriguez J, Rougerie R, Shaw MR, Sheffield C, Stahlhut JK, Steinke D, Whitfield J, Wood M, Zhou X. Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS One 2012; 7:e36514. [PMID: 22567162 PMCID: PMC3342236 DOI: 10.1371/journal.pone.0036514] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 04/02/2012] [Indexed: 01/28/2023] Open
Abstract
Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.
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Affiliation(s)
- M Alex Smith
- Department of Integrative Biology and the Biodiversity, Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
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Yoshimura M, Fisher BL. A revision of male ants of the Malagasy Amblyoponinae (Hymenoptera: Formicidae) with resurrections of the genera Stigmatomma and Xymmer. PLoS One 2012; 7:e33325. [PMID: 22496722 PMCID: PMC3320654 DOI: 10.1371/journal.pone.0033325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/07/2012] [Indexed: 11/17/2022] Open
Abstract
In a male-based revision of ants of the subfamily Amblyoponinae from the Southwest Indian Ocean islands (SWIO: Comoros, Madagascar, Mauritius, Mayotte, Reunion, and Seychelles), we explore and reconsider male morphological characters that distinguish genera within the group. Our investigation redefines Amblyopone Erichson sensu Brown (1960), here referred to as Amblyopone sensu lato, into three genera: Xymmer Santschi stat. rev.,Amblyopone sensu stricto, Stigmatomma Roger stat. rev. All species names under Amblyopone s. l. reassign into Xymmer and Amblyopone s. s., which are small, well-defined genera, and Stigmatomma, a large group with a generic delimitation that still needs further refinement. Based on a study of male mandible characters and our scenario for mandibular evolution of the worker caste within Amblyopone s. l, we conclude that Amblyopone s. s. nests outside of XMAS (Xymmer+Mystrium+Adetomyrma+Stigmatomma) clade. The following names are transferred from Amblyopone s. l. to Xymmer as comb. rev.: muticus. The following names are transferred from Amblyopone s. l. to Stigmatomma as comb. rev.: amblyops, armigerum, bellii, bierigi, bruni, celata, chilense, denticulatum, elongatum, emeryi, feae, impressifrons, luzonicum, minuta, normandi, oregonense, pallipes, quadratum, reclinatum, rothneyi, santschii, saundersi, silvestrii, zwaluwenburgi; as comb. nov.: agostii, annae, besucheti, boltoni, caliginosum, cleae, crenatum, degeneratum, egregium, electrinum, eminia, exiguum, falcatum, ferrugineum, fulvidum, gaetulicum, gingivalis, glauerti, gnoma, gracile, groehni, heraldoi, lucidum, lurilabes, monrosi, mystriops, noonadan, octodentatum, ophthalmicum, orizabanum, papuanum, pertinax, pluto, punctulatum, rubiginoum, sakaii, smithi, trigonignathum, trilobum, wilsoni, zaojun, and testaceum. A male-based key to the genera of Malagasy amblyoponine ants, their diagnoses, and a discussion of the evolution of the morphological character of males in the subfamily are given, and the distinguishing characters of each are illustrated. In addition, our results predict that Paraprionopelta belongs in the XMAS clade and that Concoctio should have males with two mandibular teeth.
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Affiliation(s)
- Masashi Yoshimura
- Department of Entomology, California Academy of Sciences, San Francisco, California, United States of America.
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Fournier D, Tindo M, Kenne M, Mbenoun Masse PS, Van Bossche V, De Coninck E, Aron S. Genetic structure, nestmate recognition and behaviour of two cryptic species of the invasive big-headed ant Pheidole megacephala. PLoS One 2012; 7:e31480. [PMID: 22371822 PMCID: PMC3284284 DOI: 10.1371/journal.pone.0031480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 01/10/2012] [Indexed: 11/28/2022] Open
Abstract
Background Biological invasions are recognized as a major cause of biodiversity decline and have considerable impact on the economy and human health. The African big-headed ant Pheidole megacephala is considered one of the world's most harmful invasive species. Methodology/Principal Findings To better understand its ecological and demographic features, we combined behavioural (aggression tests), chemical (quantitative and qualitative analyses of cuticular lipids) and genetic (mitochondrial divergence and polymorphism of DNA microsatellite markers) data obtained for eight populations in Cameroon. Molecular data revealed two cryptic species of P. megacephala, one inhabiting urban areas and the other rainforests. Urban populations belong to the same phylogenetic group than those introduced in Australia and in other parts of the world. Behavioural analyses show that the eight populations sampled make up four mutually aggressive supercolonies. The maximum distance between nests from the same supercolony was 49 km and the closest distance between two nests belonging to two different supercolonies was 46 m. The genetic data and chemical analyses confirmed the behavioural tests as all of the nests were correctly assigned to their supercolony. Genetic diversity appears significantly greater in Africa than in introduced populations in Australia; by contrast, urban and Australian populations are characterized by a higher chemical diversity than rainforest ones. Conclusions/Significance Overall, our study shows that populations of P. megacephala in Cameroon adopt a unicolonial social structure, like invasive populations in Australia. However, the size of the supercolonies appears several orders of magnitude smaller in Africa. This implies competition between African supercolonies and explains why they persist over evolutionary time scales.
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Affiliation(s)
- Denis Fournier
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium.
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Carolan JC, Murray TE, Fitzpatrick Ú, Crossley J, Schmidt H, Cederberg B, McNally L, Paxton RJ, Williams PH, Brown MJF. Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex. PLoS One 2012; 7:e29251. [PMID: 22238595 PMCID: PMC3253071 DOI: 10.1371/journal.pone.0029251] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 11/23/2011] [Indexed: 11/25/2022] Open
Abstract
Cryptic diversity within bumblebees (Bombus) has the potential to undermine crucial conservation efforts designed to reverse the observed decline in many bumblebee species worldwide. Central to such efforts is the ability to correctly recognise and diagnose species. The B. lucorum complex (Bombus lucorum, B. cryptarum and B. magnus) comprises one of the most abundant and important group of wild plant and crop pollinators in northern Europe. Although the workers of these species are notoriously difficult to diagnose morphologically, it has been claimed that queens are readily diagnosable from morphological characters. Here we assess the value of colour-pattern characters in species identification of DNA-barcoded queens from the B. lucorum complex. Three distinct molecular operational taxonomic units were identified each representing one species. However, no uniquely diagnostic colour-pattern character state was found for any of these three molecular units and most colour-pattern characters showed continuous variation among the units. All characters previously deemed to be unique and diagnostic for one species were displayed by specimens molecularly identified as a different species. These results presented here raise questions on the reliability of species determinations in previous studies and highlights the benefits of implementing DNA barcoding prior to ecological, taxonomic and conservation studies of these important key pollinators.
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Affiliation(s)
- James C Carolan
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland.
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Delsinne T, Sonet G, Nagy ZT, Wauters N, Jacquemin J, Leponce M. High species turnover of the ant genus Solenopsis (Hymenoptera : Formicidae) along an altitudinal gradient in the Ecuadorian Andes, indicated by a combined DNA sequencing and morphological approach. INVERTEBR SYST 2012. [DOI: 10.1071/is12030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Solenopsis is a widespread ant genus and the identification of its species is notoriously difficult. Hence, investigation of their distribution along elevational gradients is challenging. Our aims were (1) to test the complementarity of the morphological and DNA barcoding approaches for Solenopsis species identification, and (2) to assess species diversity and distribution along an altitudinal gradient in the Ecuadorian Andes. Ants were collected in five localities between 1000 and 3000 m above sea level. In total, 24 morphospecies were identified along the gradient and 14 of them were barcoded. Seven morphospecies were confirmed by the molecular approach. Three others, occurring sympatrically and possessing clear diagnostic characters, showed low genetic divergence. Representatives of a further four morphospecies were split into nine clusters by COI and nuclear wingless genetic markers, suggesting the existence of cryptic species. Examination of gynes revealed potential diagnostic characters for morphological discrimination. Solenopsis species were found up to an altitudinal record of 3000 m. Most morphospecies (20 of 24) were found at a single elevation. Our results suggest a high species turnover along the gradient, and point to the use of morphological and DNA barcoding approaches as necessary for differentiating among Solenopsis species.
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Li QQ, Li DY, Ye H, Liu XF, Shi W, Cao N, Duan YQ. Using COI gene sequence to barcode two morphologically alike species: the cotton bollworm and the oriental tobacco budworm (Lepidoptera: Noctuidae). Mol Biol Rep 2011; 38:5107-13. [PMID: 21181271 DOI: 10.1007/s11033-010-0658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 12/04/2010] [Indexed: 11/30/2022]
Abstract
Due to limited morphological difference, the two closely related sister species, the cotton bollworm, Helicoverpa armigera (Hübner) and the oriental tobacco budworm, H. assulta (Guenée) (Lepidoptera: Noctuidae), are very difficult to distinguish, especially at the larvae stage. Recently, DNA sequence has been widely used as a bio-barcode for species identification. In this study, we attempted to distinguish H. armigera and H. assulta using the mitochondrial cytochrome C oxidase subunit I gene (COI) gene sequence as the barcode. We determined a 658 bp segment of the COI gene for 28 individuals of H. armigera, 8 individuals of H. assulta, and 10 individuals of Mamestra brassicae (as the outgroup) in Yunnan Province, southwest of P. R. China, together with one H. assulta and two H. armigera reported sequences from GenBank. Twenty-three haplotypes were identified in all 49 samples. As expected, network analysis of the haplotypes of the three species presented a clustering pattern consistent with the respective species status. Haplotypes of the same species differed from each other by no more than three nucleotide substitutions. However, each haplotype of H. armigera differed from that of H. assulta by at least 22 nucleotide substitutions. Both species differed from M. brassicae by more than 50 nucleotide substitutions. 17 unique diagnostic nucleotides were also used to discriminate the two species. The finding of large COI sequence differences between H. armigera and H. assulta suggested that it could be used to distinguish the two morphologically alike species and be employed for quick species identification during pest control.
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Affiliation(s)
- Qing-Qing Li
- Life Science College, Yunnan Normal University, 650092 Kunming, Yunnan, China
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Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, Page RDM, Pyle RL. Aggregating, tagging and integrating biodiversity research. PLoS One 2011; 6:e19491. [PMID: 21829594 PMCID: PMC3148223 DOI: 10.1371/journal.pone.0019491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/07/2011] [Indexed: 12/04/2022] Open
Affiliation(s)
- David P Mindell
- California Academy of Sciences, San Francisco, California, United States of America.
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Schilthuizen M, Scholte C, van Wijk RE, Dommershuijzen J, van der Horst D, zu Schlochtern MM, Lievers R, Groenenberg DS. Using DNA-barcoding to make the necrobiont beetle family Cholevidae accessible for forensic entomology. Forensic Sci Int 2011; 210:91-5. [DOI: 10.1016/j.forsciint.2011.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 12/17/2010] [Accepted: 02/06/2011] [Indexed: 10/18/2022]
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Penev L, Hagedorn G, Mietchen D, Georgiev T, Stoev P, Sautter G, Agosti D, Plank A, Balke M, Hendrich L, Erwin T. Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID. Zookeys 2011:1-12. [PMID: 21594104 PMCID: PMC3084489 DOI: 10.3897/zookeys.90.1369] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 04/14/2011] [Indexed: 11/16/2022] Open
Abstract
Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.
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Affiliation(s)
- Lyubomir Penev
- Institute of Biodiversity and Ecosystem Research, Sofia, Bulgaria
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Goldstein PZ, DeSalle R. Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description. Bioessays 2010; 33:135-47. [DOI: 10.1002/bies.201000036] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Park DS, Suh SJ, Oh HW, Hebert PDN. Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers. BMC Genomics 2010; 11:423. [PMID: 20615258 PMCID: PMC2996951 DOI: 10.1186/1471-2164-11-423] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 07/09/2010] [Indexed: 12/03/2022] Open
Abstract
Background DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI) gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Results Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1) to produce a cocktail which generated a barcode amplicon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to amplify with standard primers. Conclusions A cocktail of two tRNA-W forward primers coupled with a standard reverse primer amplifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the amplification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.
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Affiliation(s)
- Doo-Sang Park
- Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Korea
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Penev L, Agosti D, Georgiev T, Catapano T, Miller J, Blagoderov V, Roberts D, Smith VS, Brake I, Ryrcroft S, Scott B, Johnson NF, Morris RA, Sautter G, Chavan V, Robertson T, Remsen D, Stoev P, Parr C, Knapp S, Kress WJ, Thompson CF, Erwin T. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. Zookeys 2010:1-16. [PMID: 21594113 PMCID: PMC3088020 DOI: 10.3897/zookeys.50.538] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022] Open
Abstract
The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.
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Affiliation(s)
- Lyubomir Penev
- Bulgarian Academy of Sciences & Pensoft Publishers, 13a Geo Milev Str., Sofia, Bulgaria
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