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DeSanctis ML, Soranno EA, Messner E, Wang Z, Turner EM, Falco R, Appiah-Madson HJ, Distel DL. Greater than pH 8: The pH dependence of EDTA as a preservative of high molecular weight DNA in biological samples. PLoS One 2023; 18:e0280807. [PMID: 36689492 PMCID: PMC9870144 DOI: 10.1371/journal.pone.0280807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is a divalent cation chelator and chemical preservative that has been shown to be the active ingredient of the popular DNA preservative DESS. EDTA may act to reduce DNA degradation during tissue storage by sequestering divalent cations that are required by nucleases naturally occurring in animal tissues. Although EDTA is typically used between pH 7.5 and 8 in preservative preparations, the capacity of EDTA to chelate divalent cations is known to increase with increasing pH. Therefore, increasing the pH of EDTA-containing preservative solutions may improve their effectiveness as DNA preservatives. To test this hypothesis, we stored tissues from five aquatic species in 0.25 M EDTA adjusted to pH 8, 9, and 10 for 12 months at room temperature before DNA isolation. For comparison, tissues from the same specimens were also stored in 95% ethanol. DNA extractions performed on tissues preserved in EDTA pH 9 or 10 resulted in as great or greater percent recovery of high molecular weight DNA than did extractions from tissues stored at pH 8. In all cases examined, percent recovery of high molecular weight DNA from tissues preserved in EDTA pH 10 was significantly better than that observed from tissues preserved in 95% ethanol. Our results support the conclusion that EDTA contributes to DNA preservation in tissues by chelating divalent cations and suggest that preservative performance can be improved by increasing the pH of EDTA-containing DNA preservative solutions.
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Affiliation(s)
- Mia L. DeSanctis
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elizabeth A. Soranno
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ella Messner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ziyu Wang
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elena M. Turner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Rosalia Falco
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
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Mitochondrial genes as strong molecular markers for species identification. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00393-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Crandall RS, Lombardo JA, Elkinton JS. Top-down regulation of hemlock woolly adelgid (Adelges tsugae) in its native range in the Pacific Northwest of North America. Oecologia 2022; 199:599-609. [PMID: 35796819 DOI: 10.1007/s00442-022-05214-8] [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] [Received: 02/12/2022] [Accepted: 06/15/2022] [Indexed: 12/01/2022]
Abstract
The density of insect herbivores is regulated by top-down factors (e.g., natural enemies), bottom-up effects (e.g., plant defenses against herbivory), or a combination of both. As such, understanding the relative importance of these factors can have important implications for the establishment of effective management options for invasive species. Here, we compared the relative importance of top-down and bottom-up factors on the abundance of hemlock woolly adelgid (HWA), Adelges tsugae. HWA is invasive in eastern North America, but its native range includes the Pacific Northwest of North America where it has co-evolved with western hemlock, Tsuga heterophylla. Eastern hemlock, Tsuga canadensis, can also be found planted in city and park settings in the Pacific Northwest and the presence of both host species allowed us to directly compare the importance of predators (top-down) and host plant resistance (bottom-up) on HWA abundance by placing mesh exclusion bags on branches of both species and monitoring HWA abundance over two years. We found no evidence for bottom-up control of HWA on western hemlock (a native host). HWA established more readily on that species than on eastern hemlock on which it is a major pest in eastern North America. We found strong evidence for top-down control in that both summer and winter-active predators significantly reduced HWA densities on the branches of both tree species where predators were allowed access. These findings support the validity of the biological control program for HWA, the goal of which is to reduce outbreak populations of HWA in eastern North America.
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Affiliation(s)
- Ryan S Crandall
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Jeffrey A Lombardo
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Biology, Hood College, Frederick, MD, 21701, USA
| | - Joseph S Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, 01003, USA
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Dancewicz K, Gabryś B, Morkunas I, Samardakiewicz S. Probing behavior of Adelges laricis Vallot (Hemiptera: Adelgidae) on Larix decidua Mill: Description and analysis of EPG waveforms. PLoS One 2021; 16:e0251663. [PMID: 34003844 PMCID: PMC8130970 DOI: 10.1371/journal.pone.0251663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/29/2021] [Indexed: 01/10/2023] Open
Abstract
Adelgidae are a sister group of Aphididae and Phylloxeridae within Hemiptera, Aphidoidea and occur exclusively on Pinaceae. The piercing-sucking mouthparts of Adelgidae are similar to those of aphids and it is believed that adelgids ingest sap from both the non-vascular and vascular (phloem) tissues. The aim of the present study was to identify and characterize the adelgid stylet activities during their penetration in plant tissues. The probing behavior of Adelges laricis Vallot (Hemiptera: Adelgidae) on European larch Larix decidua Mill. and sucrose diets was monitored using the DC-EPG (Electrical Penetration Graph technique = electropenetrography). The EPG waveforms were described based on amplitude, frequency, voltage level, and electrical origin of the observed traces, and associated with putative behavioral activities based on analogy with aphid activities. Waveform frequency, duration, and sequence were analysed as well. A. laricis generated EPG signals at two clearly distinct voltage levels positive and negative, suggesting extracellular and intracellular stylet penetration, respectively. The adelgid EPG patterns were ascribed to four behavioral phases, which were non-probing, pathway, phloem, and xylem phases. Non-probing referred to the position of the stylets outside the plant tissues. Pathway phase was represented by three waveform patterns that visualized extracellular stylet penetration in non-vascular tissues without potential drops (AC1), with serial short (1.2–1.5 s) potential drops (AC2), and with ‘aphid-like’ (5–10 s) potential drops (AC3). Phloem phase comprised three waveform patterns at intracellular level, which in all probability represented phloem salivation (AE1), and phloem sap passive (AE2) and active ingestion (AE3). AE3 was a newly described waveform, previously unreported from Hemiptera. Waveform AG represented the ingestion of xylem sap. The comparative analysis demonstrated that the gymnosperm-associated adelgids show certain similarities in probing behavior typical of aphids and phylloxerids on angiosperm plants. The present work is the first detailed analysis of specific adelgid stylet activities on gymnosperms.
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Affiliation(s)
- Katarzyna Dancewicz
- Department of Botany and Ecology, University of Zielona Góra, Zielona Góra, Poland
- * E-mail:
| | - Beata Gabryś
- Department of Botany and Ecology, University of Zielona Góra, Zielona Góra, Poland
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Sławomir Samardakiewicz
- Laboratory of Electron and Confocal Microscopy, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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Savage J, Sorokina VS. Review of the North American fauna of Drymeia Meigen (Diptera, Muscidae) and evaluation of DNA barcodes for species-level identification in the genus. Zookeys 2021; 1024:31-89. [PMID: 33776521 PMCID: PMC7985133 DOI: 10.3897/zookeys.1024.60393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/04/2021] [Indexed: 11/29/2022] Open
Abstract
The North American fauna of Drymeia Meigen was studied. Four new species are described (Drymeiahuckettisp. nov., Drymeiapontisp. nov., Drymeiavockerothisp. nov., Drymeiawoodorumsp. nov.), and three new synonymies are proposed: Drymeiaamnicola (Huckett, 1966) (= Drymeiarivalis (Huckett, 1966), syn. nov.); Drymeiaglacialis (Rondani, 1866) (= Drymeiaalpicola (Rondani, 1871), syn. nov.); and Drymeiaspinitarsis (Aldrich, 1918) (= Drymeialongiseta Sorokina & Pont, 2015, syn. nov.). An annotated checklist, DNA barcodes (when available), and keys for each sex of the 24 named species of North American Drymeia are provided. The utility of DNA barcodes for the identification of Drymeia species across a wide geographical range was explored using sequences from five countries. A match between morphology and DNA barcodes was found for 71% (22/31) of species studied (including three unnamed taxa). The remaining nine species clustered into two groups of taxa with very little interspecific variation within clusters (groups of two and seven species). Caution is advised against using DNA barcoding as the only determination tool for Drymeia material without prior knowledge of its limitations for certain species groups.
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Affiliation(s)
- Jade Savage
- Bishop's University, Sherbrooke, Quebec, Canada Bishop's University Sherbrooke Canada
| | - Vera S Sorokina
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630091, Russia Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences Novosibirsk Russia
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Lee Y, Thieme T, Kim H. Complex evolution in Aphis gossypii group (Hemiptera: Aphididae), evidence of primary host shift and hybridization between sympatric species. PLoS One 2021; 16:e0245604. [PMID: 33539375 PMCID: PMC7861460 DOI: 10.1371/journal.pone.0245604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Aphids provide a good model system to understand the ecological speciation concept, since the majority of the species are host-specific, and they spend their entire lifecycle on certain groups of host plants. Aphid species that apparently have wide host plant ranges have often turned out to be complexes of host-specialized biotypes. Here we investigated the various host-associated populations of the two recently diverged species, Aphis gossypii and A. rhamnicola, having multiple primary hosts, to understand the complex evolution with host-associated speciation. Using mitochondrial DNA marker and nine microsatellite loci, we reconstructed the haplotype network, and analyzed the genetic structure and relationships. Approximate Bayesian computation was also used to infer the ancestral primary host and host-associated divergence, which resulted in Rhamnus being the most ancestral host for A. gossypii and A. rhamnicola. As a result, Aphis gossypii and A. rhamnicola do not randomly use their primary and secondary host plants; rather, certain biotypes use only some secondary and specific primary hosts. Some biotypes are possibly in a diverging state through specialization to specific primary hosts. Our results also indicate that a new heteroecious race can commonly be derived from the heteroecious ancestor, showing strong evidence of ecological specialization through a primary host shift in both A. gossypii and A. rhamnicola. Interestingly, A. gossypii and A. rhamnicola shared COI haplotypes with each other, thus there is a possibility of introgression by hybridization between them by cross-sharing same primary hosts. Our results contribute to a new perspective in the study of aphid evolution by identifying complex evolutionary trends in the gossypii sensu lato complex.
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Affiliation(s)
- Yerim Lee
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan, Republic of Korea
| | - Thomas Thieme
- BTL Bio-Test Labor GmbH Sagerheide, RG Phyto-Entomology, Gross Lüsewitz, Germany
| | - Hyojoong Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan, Republic of Korea
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Yeh HT, Ko CC, Wu LW. The first complete mitochondrial genome of Adelges tsugae Annand (Hemiptera: Adelgidae). Mitochondrial DNA B Resour 2020; 5:2288-2290. [PMID: 33367011 PMCID: PMC7510656 DOI: 10.1080/23802359.2020.1772682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/16/2020] [Indexed: 11/05/2022] Open
Abstract
Hemlock wooly adelgid (HWA), Adelgests ugae Annand (Hemiptera: Adelgidae), is a species native to Asia but later ravages Endangered hemlock forests (Tsuga spp.) in eastern North America. In this study, we obtained the first complete mitochondrial genome of HWA (16,509 bp in length) using meta-genomic sequencing method. The HWA mitogenome has a general gene annotation as other aphids, comprising 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Our phylogenetic result showed Aphidoidea is sister to Coccoidea and the newly sequenced mitogenome is put on the correct position, sister to Adelgeslaricis.
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Affiliation(s)
- Hsin-Ting Yeh
- The Experimental Forest, National Taiwan University, Nantou County, Taiwan
| | - Chiun-Cheng Ko
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Li-Wei Wu
- The Experimental Forest, National Taiwan University, Nantou County, Taiwan
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DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative? PLoS One 2020; 15:e0237356. [PMID: 32817618 PMCID: PMC7440624 DOI: 10.1371/journal.pone.0237356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 01/20/2023] Open
Abstract
DESS is a formulation widely used to preserve DNA in biological tissue samples. Although it contains three ingredients, dimethyl sulfoxide (DMSO), ethylenediaminetetraacetic acid (EDTA) and sodium chloride (NaCl), it is frequently referred to as a DMSO-based preservative. The effectiveness of DESS has been confirmed for a variety of taxa and tissues, however, to our knowledge, the contributions of each component of DESS to DNA preservation have not been evaluated. To address this question, we stored tissues of three aquatic taxa, Mytilus edulis (blue mussel), Faxonius virilis (virile crayfish) and Alitta virens (clam worm) in DESS, each component of DESS individually and solutions containing all combinations of two components of DESS. After storage at room temperature for intervals ranging from one day to six months, we extracted DNA from each tissue and measured the percentage of high molecular weight (HMW) DNA recovered (%R) and normalized HMW DNA yield (nY). Here, HMW DNA is defined as fragments >10 kb. For comparison, we also measured the %R and nY of HMW DNA from extracts of fresh tissues and those stored in 95% EtOH over the same time intervals. We found that in cases where DESS performed most effectively (yielding ≥ 20%R of HMW DNA), all solutions containing EDTA were as or more effective than DESS. Conversely, in cases where DESS performed more poorly, none of the six DESS-variant storage solutions provided better protection of HMW DNA than DESS. Moreover, for all taxa and storage intervals longer than one day, tissues stored in solutions containing DMSO alone, NaCl alone or DMSO and NaCl in combination resulted in %R and nY of HMW DNA significantly lower than those of fresh tissues. These results indicate that for the taxa, solutions and time intervals examined, only EDTA contributed directly to preservation of high molecular weight DNA.
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Li M, Zhao Q, Chen R, He J, Peng T, Deng W, Che Y, Wang Z. Species diversity revealed in Sigmella Hebard, 1929 (Blattodea, ectobiidae) based on morphology and four molecular species delimitation methods. PLoS One 2020; 15:e0232821. [PMID: 32520927 PMCID: PMC7286484 DOI: 10.1371/journal.pone.0232821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
Cockroaches are one of the major decomposers involved in biogeochemical cycles. Cockroaches have an amazing amount of diversity, but most of them remain unknown due to the shortage of the trained taxonomists and the limitations of morphology-based identification. We obtained 49 COI sequences (including 42 novel sequences) and 32 novel 28S sequences for 5 Sigmella morphospecies collected from 11 localities. Three are new to science: Sigmella digitalis sp. nov., Sigmella exserta sp. nov. and Sigmella normalis sp. nov. Based on four species delimitation methods (ABGD, GMYC, BINs and bPTP), a total of 6 molecular operational taxonomic units (MOTUs) were recovered for 5 morphospecies. These were then confirmed by tree building methods using COI and combined data (COI and 28S). We detected more than one MOTU in the morphospecies S. digitalis sp. nov., which can indicate genetic diversity. Detailed morphological evidence for each MOTU is provided to confirm these slight variations and we conclude that natural barriers are likely the main cause of genetic diversity.
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Affiliation(s)
- Meng Li
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Qiongyao Zhao
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Rong Chen
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Jiajun He
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Tao Peng
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Wenbo Deng
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Yanli Che
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Zongqing Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing, China
- * E-mail:
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Aphids of the family Adelgidae in Lithuania: distribution, host specificity and molecular (mitochondrial COI and nuclear EF-1α) diversity. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00365-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Chan‐Chable RJ, Martínez‐Arce A, Mis‐Avila PC, Ortega‐Morales AI. DNA barcodes and evidence of cryptic diversity of anthropophagous mosquitoes in Quintana Roo, Mexico. Ecol Evol 2019; 9:4692-4705. [PMID: 31031936 PMCID: PMC6476762 DOI: 10.1002/ece3.5073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/11/2019] [Accepted: 02/22/2019] [Indexed: 11/08/2022] Open
Abstract
Culicidae mosquitoes are potential vectors of pathogens that affect human health. The correct species identification, as well as the discovery and description of cryptic species, is important in public health for the control and management of specific vectors. In the present study, the diversity of anthropophagous mosquitoes in Quintana Roo, at the border between Mexico and Belize, was evaluated using morphological and molecular data (COI-DNA Barcoding). A total of 1,413 adult female specimens were collected, belonging to eight genera and 31 morphospecies. Most species formed well-supported clades. Intraspecific Kimura 2 parameters (K2P) distance average was 0.75%, and a maximum distance of 4.40% was observed for Anopheles crucianss.l. ABGD method identified 28 entities, while 32 entities were identified with the BIN system. In Culex interrogator and Culex nigripalpus a low interspecific genetic distance of 0.1% was observed. One undescribed species belonging to the genus Aedes (Aedesn. sp.) was discovered, but no clear genetic divergence was found between this species and the closely related species Aedes angustivittatus. An intraspecific K2P distance greater than 2.7% was observed in Aedes serratus(3.9%), Anopheles crucianss.l. (4.4%), Culex taeniopus (3.7%), Haemagogus equinus (3.9%), Culex erraticus (5.0%), Psorophora ferox (4.5%), and in Anopheles apicimacula(8.10%); therefore, evidences of cryptic diversity are shown in these species. This study showed that DNA barcodes offer a reliable framework for mosquito species identification in Quintana Roo, except for some closely related species for which it is recommended to use additional nuclear genetic markers such as ITS2, in order to resolve these small discrepancies.
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Affiliation(s)
- Rahuel J. Chan‐Chable
- Departamento de Sistemática y Ecología AcuáticaUnidad Chetumal, El Colegio de la Frontera SurChetumalQuintana RooMéxico
| | - Arely Martínez‐Arce
- Departamento de Sistemática y Ecología AcuáticaUnidad Chetumal, El Colegio de la Frontera SurChetumalQuintana RooMéxico
| | - Pedro C. Mis‐Avila
- Departamento de Enfermedades Transmitidas por Vector y ZoonosisServicios Estatales de Salud de Quintana RooChetumalQuintana RooMéxico
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Foottit RG, Maw HEL, Kits JH, Scudder GGE. Hemiptera of Canada. Zookeys 2019; 819:277-290. [PMID: 30713446 PMCID: PMC6355760 DOI: 10.3897/zookeys.819.26574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/10/2018] [Indexed: 11/27/2022] Open
Abstract
The Canadian Hemiptera (Sternorrhyncha, Auchenorrhyncha, and Heteroptera) fauna is reviewed, which currently comprises 4011 species, including 405 non-native species. DNA barcodes available for Canadian specimens are represented by 3275 BINs. The analysis was based on the most recent checklist of Hemiptera in Canada (Maw et al. 2000) and subsequent collection records, literature records and compilation of DNA barcode data. It is estimated that almost 600 additional species remain to be discovered among Canadian Hemiptera.
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Affiliation(s)
- Robert G. Foottit
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre and Canadian National Collection of Insects, Arachnids and Nematodes, K. W. Neatby Bldg., 960 Carling Ave., Ottawa, Ontario, K1A 0C6, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - H. Eric L. Maw
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre and Canadian National Collection of Insects, Arachnids and Nematodes, K. W. Neatby Bldg., 960 Carling Ave., Ottawa, Ontario, K1A 0C6, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - Joel H. Kits
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre and Canadian National Collection of Insects, Arachnids and Nematodes, K. W. Neatby Bldg., 960 Carling Ave., Ottawa, Ontario, K1A 0C6, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - Geoffrey G. E. Scudder
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, CanadaUniversity of British ColumbiaVancouverCanada
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Liu J, Zhang H. DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1165-1173. [PMID: 29334293 DOI: 10.1080/24701394.2018.1424843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0-1.41%) when excluding Pliocardia sp.10 cf. venusta (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (Abyssogena southwardae and Calyptogena rectimargo-starobogatovi). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.
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Affiliation(s)
- Jun Liu
- a Institute of Deep-Sea Science and Engineering , Chinese Academy of Sciences , Sanya, China
| | - Haibin Zhang
- a Institute of Deep-Sea Science and Engineering , Chinese Academy of Sciences , Sanya, China
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von Dohlen CD, Spaulding U, Patch KB, Weglarz KM, Foottit RG, Havill NP, Burke GR. Dynamic Acquisition and Loss of Dual-Obligate Symbionts in the Plant-Sap-Feeding Adelgidae (Hemiptera: Sternorrhyncha: Aphidoidea). Front Microbiol 2017; 8:1037. [PMID: 28659877 PMCID: PMC5468457 DOI: 10.3389/fmicb.2017.01037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/23/2017] [Indexed: 11/29/2022] Open
Abstract
Sap-sucking insects typically engage in obligate relationships with symbiotic bacteria that play nutritional roles in synthesizing nutrients unavailable or in scarce supply from the plant-sap diets of their hosts. Adelgids are sap-sucking insects with complex life cycles that involve alternation between conifer tree species. While all adelgid species feed on spruce during the sexual phase of their life cycle, each adelgid species belongs to a major lineage that feeds on a distinct genus of conifers as their alternate host. Previous work on adelgid symbionts had discovered pairs of symbionts within each host species, and unusual diversity across the insect family, but left several open questions regarding the status of bacterial associates. Here, we explored the consistency of symbionts within and across adelgid lineages, and sought evidence for facultative vs. obligate symbiont status. Representative species were surveyed for symbionts using 16S ribosomal DNA gene sequencing, confirming that different symbiont pairs were consistently present within each major adelgid lineage. Several approaches were used to establish whether symbionts exhibited characteristics of long-term, obligate mutualists. Patterns of symbiont presence across adelgid species and diversification with host insects suggested obligate relationships. Fluorescent in situ hybridization and electron microscopy localized symbionts to bacteriocyte cells within the bacteriome of each species (with one previously known exception), and detection of symbionts in eggs indicated their vertical transmission. Common characteristics of long-term obligate symbionts, such as nucleotide compositional bias and pleomorphic symbiont cell shape were also observed. Superimposing microbial symbionts on the adelgid phylogeny revealed a dynamic pattern of symbiont gains and losses over a relatively short period of time compared to other symbionts associated with sap-sucking insects, with each adelgid species possessing an older, “senior” symbiont and a younger “junior” symbiont. A hypothesis relating adelgid life cycles to relaxed constraints on symbionts is proposed, with the degradation of senior symbionts and repeated acquisition of more junior symbionts creating opportunities for repeated colonization of new alternate-conifer hosts by adelgids.
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Affiliation(s)
| | - Usha Spaulding
- Department of Biology, Utah State University, LoganUT, United States
| | - Kistie B Patch
- Department of Biology, Utah State University, LoganUT, United States
| | - Kathryn M Weglarz
- Department of Biology, Utah State University, LoganUT, United States
| | | | - Nathan P Havill
- United States Forest Service, Northern Research Station, HamdenCT, United States
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, AthensGA, United States
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15
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Havill NP, Shiyake S, Lamb Galloway A, Foottit RG, Yu G, Paradis A, Elkinton J, Montgomery ME, Sano M, Caccone A. Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia. Mol Ecol 2016; 25:2065-80. [PMID: 26880353 DOI: 10.1111/mec.13589] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/15/2023]
Abstract
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and two each in Taiwan and Japan, with the Japanese lineages specializing on different Tsuga species. Adelgid life cycles varied at local and continental scales with different sexual, obligately asexual and facultatively asexual lineages. Adelgids in western North America exhibited very high microsatellite heterozygosity, which suggests ancient asexuality. The earliest lineages diverged in Asia during Pleistocene glacial periods, as estimated using approximate Bayesian computation. Colonization of western North America was estimated to have occurred prior to the last glacial period by adelgids directly ancestral to those in southern Japan, perhaps carried by birds. The modern invasion from southern Japan to eastern North America caused an extreme genetic bottleneck with just two closely related clones detected throughout the introduced range. Both colonization events to North America involved host shifts to unrelated hemlock species. These results suggest that genetic diversity, host specialization and host phylogeny are not predictive of adelgid invasion. Monitoring non-native sentinel host trees and focusing on invasion pathways might be more effective methods of preventing invasion than making predictions using species traits or evolutionary history.
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Affiliation(s)
- Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, Connecticut 06514, USA
| | | | - Ashley Lamb Galloway
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Robert G Foottit
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Guoyue Yu
- Institute of Plant & Environmental Protection, Beijing Academy of Agricultural & Forestry Science, Beijing 100097, China
| | - Annie Paradis
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Joseph Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | - Masakazu Sano
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Hokkaido, Japan
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
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16
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Cocuzza GEM, Silvestro SD, Giordano R, Rapisarda C. Congruence between cytochrome oxidase I (COI) and morphological data in Anuraphis spp. (Hemiptera, Aphididae) with a comparison between the utility of the 5' barcode and 3' COI regions. Zookeys 2015; 529:123-44. [PMID: 26692796 PMCID: PMC4668903 DOI: 10.3897/zookeys.529.6081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
The discrimination of species in the genus Anuraphis is particularly difficult due to the overlap of morphological characters. In this study, we used the 5' (barcode) and 3' regions of cytochrome oxidase I (COI) to test their utility in the identification of species in this genus as well as closely related species. Both regions were useful to discriminate all the species tested. However the non-barcode 3' region resulted in higher resolution and support for species relationships when the data were analyzed using both Maximum Likelihood and MrBayes. We propose the development of an integrated database that encompasses morphological, molecular, life-cycle, host plant and bibliographic information to facilitate and increase the accuracy of aphid identification.
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Affiliation(s)
- Giuseppe E. Massimino Cocuzza
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, via S. Sofia 100, 95123 Catania, Italy
| | - Silvia Di Silvestro
- Centro di Ricerca per l’Agrumicoltura e le Colture Mediterranee, Corso Savoia 190, 95024 Acireale, Italy
| | - Rosanna Giordano
- Department of Biology, University of Puerto Rico, San Juan, PR 00931, USA
| | - Carmelo Rapisarda
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, via S. Sofia 100, 95123 Catania, Italy
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17
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Foottit RG, Maw E, Hebert PDN. DNA barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera). PLoS One 2014; 9:e101385. [PMID: 25004106 PMCID: PMC4087040 DOI: 10.1371/journal.pone.0101385] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 06/06/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Many studies have shown the suitability of sequence variation in the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. METHODOLOGY/PRINCIPAL FINDINGS Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%. CONCLUSIONS/SIGNIFICANCE This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage.
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Affiliation(s)
- Robert G. Foottit
- Agriculture and Agri-Food Canada, Invertebrate Biodiversity – National Environmental Health Program, and Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, Canada
| | - Eric Maw
- Agriculture and Agri-Food Canada, Invertebrate Biodiversity – National Environmental Health Program, and Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, Ontario, Canada
| | - P. D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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18
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Shariff S, Ibrahim NJ, Md-Zain BM, Idris AB, Suhana Y, Roff MN, Yaakop S. Multiplex PCR in determination of Opiinae parasitoids of fruit flies, Bactrocera sp., infesting star fruit and guava. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:7. [PMID: 25373154 PMCID: PMC4199358 DOI: 10.1093/jis/14.1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/11/2012] [Indexed: 06/04/2023]
Abstract
Malaysia is a tropical country that produces commercial fruits, including star fruits, Averrhoa carambola L. (Oxalidales: Oxalidaceae), and guavas, Psidium guajava L. (Myrtales: Myrtaceae). There is a high demand for these fruits, and they are planted for both local consumption and export purposes. Unfortunately, there has been a gradual reduction of these fruits, which has been shown to be related to fruit fly infestation, especially from the Bactrocera species. Most parasitic wasps (Hymenoptera: Braconidae: Opiinae) are known as parasitoids of fruit fly larvae. In this study, star fruits and guavas infested by fruit fry larvae were collected from the Malaysian Agricultural Research and Development Institute. The parasitized larvae were reared under laboratory conditions until the emergence of adult parasitoids. Multiplex PCR was performed to determine the braconid species using two mitochondrial DNA markers, namely cytochrome oxidase subunit I and cytochrome b. Two benefits of using multiplex PCR are the targeted bands can be amplified simultaneously using the same reaction and the identification process of the braconid species can be done accurately and rapidly. The species of fruit flies were confirmed using the COI marker. The results obtained from our study show that Diachasmimorpha longicaudata (Ashmead) (Hymenoptera: Braconidae), Fopius arisanus (Sonan), and Pysttalia incisi (Silvestri) were parasitoids associated with Bactrocera carambolae (Drew and Hancock) (Diptera: Tephritidae) infested star fruits. Fopius arisanus was also the parasitoid associated with Bactrocera papayae (Drew and Hancock) infested guavas. Maximum parsimony was been constructed in Opiinae species to compare tree resolution between these two genes in differentiating among closely related species. The confirmation of the relationship between braconids and fruit fly species is very important, recognized as preliminary data, and highly necessary in biological control programs.
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Affiliation(s)
- S Shariff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - N J Ibrahim
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - B M Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - A B Idris
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Y Suhana
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia
| | - M N Roff
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia
| | - S Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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19
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Huang J, Zhang A, Mao S, Huang Y. DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera). PLoS One 2013; 8:e82400. [PMID: 24376533 PMCID: PMC3869712 DOI: 10.1371/journal.pone.0082400] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/22/2013] [Indexed: 11/26/2022] Open
Abstract
We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.
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Affiliation(s)
- Jianhua Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
- College of Life Sciences, Guangxi Normal University, Guilin, People's Republic of China
| | - Aibing Zhang
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - Shaoli Mao
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
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20
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Massimino Cocuzza GE, Cavalieri V. Identification of aphids ofAphis frangulae-group living on Lamiaceae species through DNA barcode. Mol Ecol Resour 2013; 14:447-57. [DOI: 10.1111/1755-0998.12199] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/11/2013] [Accepted: 10/18/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Giuseppe E. Massimino Cocuzza
- Department of Agri-Food and Environmental Systems Management; University of Catania; via Santa Sofia 100 95123 Catania Italy
| | - Vincenzo Cavalieri
- Department of Agri-Food and Environmental Systems Management; University of Catania; via Santa Sofia 100 95123 Catania Italy
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21
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Michalik A, Gołas A, Kot M, Wieczorek K, Szklarzewicz T. Endosymbiotic microorganisms in Adelges (Sacchiphantes) viridis (Insecta, Hemiptera, Adelgoidea: Adelgidae): Molecular characterization, ultrastructure and transovarial transmission. ARTHROPOD STRUCTURE & DEVELOPMENT 2013; 42:531-538. [PMID: 24100000 DOI: 10.1016/j.asd.2013.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/20/2013] [Accepted: 09/20/2013] [Indexed: 05/15/2023]
Abstract
The aim of this paper was to identify endosymbiotic microorganisms living in the body cavity of a Polish population of an aphid, Adelges (Sacchiphantes) viridis, as well as to describe their ultrastructure and mode of transmission between generations. Molecular data (amplification and sequencing of 16S rRNA genes) indicated that endosymbionts of A. (S.) viridis are Betaproteobacteria of the species "Candidatus Vallotia virida". Endosymbiotic bacteria are rod-shaped and localized in the cytoplasm of specific cells, termed bacteriocytes, of host insects. Endosymbionts sharing the same bacteriocytes differ in the density of their cytoplasm. There are two morphotypes of endosymbiotic bacteria: with electron-dense cytoplasm and electron-translucent cytoplasm. Since only bacteria containing electron-dense cytoplasm were observed in the binary fusion stage, differences in density of the cytoplasm are probably due to changes in the cytoskeleton of bacteria during division. Endosymbionts of A. (S.) viridis are transovarially (i.e. via oocytes) transmitted from the mother to the offspring.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Aniela Gołas
- Department of Genetics and Evolution, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Marta Kot
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Karina Wieczorek
- Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
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22
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Affiliation(s)
- G B Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1 Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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23
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von Dohlen CD, Spaulding U, Shields K, Havill NP, Rosa C, Hoover K. Diversity of proteobacterial endosymbionts in hemlock woolly adelgid (Adelges tsugae) (Hemiptera: Adelgidae) from its native and introduced range. Environ Microbiol 2013; 15:2043-62. [PMID: 23452267 DOI: 10.1111/1462-2920.12102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/21/2012] [Accepted: 01/23/2013] [Indexed: 01/19/2023]
Abstract
Knowledge of intraspecific variation in symbioses may aid in understanding the ecology of widespread insects in different parts of their range. We investigated bacterial symbionts of Adelges tsugae, a pest of hemlocks in eastern North America introduced from Asia. Amplification, cloning, and sequencing of bacterial 16S rDNA, in situ hybridizations, and electron microscopy revealed that A. tsugae harbours up to five bacterial phylotypes, according to population. Three Gammaproteobacteria species are maternally transmitted. The first, designated 'Ca. Pseudomonas adelgestsugas' resides in the haemocoel, and was detected in all populations except Taiwan. The second phylotype, 'Ca. Serratia symbiotica', resides in bacteriocytes of populations on Tsuga sieboldii in Japan and in E. North America. The third phylotype, designated 'Ca. Annandia adelgestsuga', clustered within a lineage of several insect endosymbionts that included Buchnera aphidicola. It was detected in bacteriocytes in all populations, and in salivary glands of first instars. Two Betaproteobacteria phylotypes were detected in some Japanese T. sieboldii and eastern North America populations, and were observed only in salivary glands with no evidence of maternal transmission. Our results support the ideas that symbiont gain and loss has been volatile in adelgids, and that symbionts may help to trace the source of invasive species.
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Affiliation(s)
- Carol D von Dohlen
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA.
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24
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Liu QH, Jiang LY, Qiao GX. DNA barcoding of Greenideinae (Hemiptera : Aphididae) with resolving taxonomy problems. INVERTEBR SYST 2013. [DOI: 10.1071/is13014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Species of the Greenideinae are distributed mainly throughout South-east Asia and include some important agricultural and horticultural pests. Rapid and accurate species circumscription and identification in this subfamily are very difficult because similar morphological traits are shared among congeneric species. Here, we test the efficiency of DNA barcoding in the Greenideinae by analysing 214 samples covering 42 species belonging to nine genera using two mitochondrial gene fragments (COI barcode fragment and Cytb gene fragment). The results show that DNA barcoding is a useful species identification method in this subfamily. Both genes can correctly identify most species using neighbour-joining tree analyses and distance-based analyses. Based on the molecular and morphological evidence, we question the validity of two species, Mollitrichosiphum rhusae Ghosh, 1917 and Schoutedenia emblica (Patel & Kulkarni, 1953). Further analysis of the COI barcode fragment shows that Greenidea psidii van der Goot, 1917, an invasive species in Hawaii, is possibly from China. This is a preliminary DNA barcoding study in Greenideinae, and comprehensive sampling is needed to rigorously test the usefulness of DNA barcoding in this subfamily.
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25
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Leite LAR. Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue. BIOTA NEOTROPICA 2012. [DOI: 10.1590/s1676-06032012000300029] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes.
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26
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Toenshoff ER, Gruber D, Horn M. Co-evolution and symbiont replacement shaped the symbiosis between adelgids (Hemiptera: Adelgidae) and their bacterial symbionts. Environ Microbiol 2012; 14:1284-95. [DOI: 10.1111/j.1462-2920.2012.02712.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Taylor HR, Harris WE. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 2012; 12:377-88. [PMID: 22356472 DOI: 10.1111/j.1755-0998.2012.03119.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.
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Affiliation(s)
- H R Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, PO Box 600 Wellington, New Zealand.
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28
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Piffaretti J, Vanlerberghe-Masutti F, Tayeh A, Clamens AL, D’Acier AC, Jousselin E. Molecular phylogeny reveals the existence of two sibling species in the aphid pest Brachycaudus helichrysi (Hemiptera: Aphididae). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00531.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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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: 57] [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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Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae). ISME JOURNAL 2011; 6:384-96. [PMID: 21833037 DOI: 10.1038/ismej.2011.102] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Adelgids (Insecta: Hemiptera: Adelgidae) are known as severe pests of various conifers in North America, Canada, Europe and Asia. Here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. Three geographically distant populations of members of the Adelges nordmannianae/piceae complex, identified based on coI and ef1alpha gene sequences, were investigated. Electron and light microscopy revealed two morphologically different endosymbionts, coccoid or polymorphic, which are located in distinct bacteriocytes. Phylogenetic analyses of their 16S and 23S rRNA gene sequences assigned both symbionts to novel lineages within the Gammaproteobacteria sharing <92% 16S rRNA sequence similarity with each other and showing no close relationship with known symbionts of insects. Their identity and intracellular location were confirmed by fluorescence in situ hybridization, and the names 'Candidatus Steffania adelgidicola' and 'Candidatus Ecksteinia adelgidicola' are proposed for tentative classification. Both symbionts were present in all individuals of all investigated populations and in different adelgid life stages including eggs, suggesting vertical transmission from mother to offspring. An 85 kb genome fragment of 'Candidatus S. adelgidicola' was reconstructed based on a metagenomic library created from purified symbionts. Genomic features including the frequency of pseudogenes, the average length of intergenic regions and the presence of several genes which are absent in other long-term obligate symbionts, suggested that 'Candidatus S. adelgidicola' is an evolutionarily young bacteriocyte-associated symbiont, which has been acquired after diversification of adelgids from their aphid sister group.
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Seabra S, Pina-Martins F, Marabuto E, Yurtsever S, Halkka O, Quartau J, Paulo O. Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species. Mol Phylogenet Evol 2010; 56:462-7. [DOI: 10.1016/j.ympev.2010.03.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 03/15/2010] [Accepted: 03/17/2010] [Indexed: 11/26/2022]
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Hubert N, Delrieu-Trottin E, Irisson JO, Meyer C, Planes S. Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Mol Phylogenet Evol 2010; 55:1195-203. [PMID: 20188843 DOI: 10.1016/j.ympev.2010.02.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
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