1
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Gorring PS, Farrell BD. Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles. Mol Phylogenet Evol 2023; 184:107777. [PMID: 36990304 DOI: 10.1016/j.ympev.2023.107777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 02/18/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Plant-feeding beetle species are diverse and often individually highly variable. Accurate classifications can be difficult to establish yet are essential for study of evolutionary patterns and processes. Molecular data are key to further characterizing morphologically difficult groups and defining genus and species boundaries. Monochamus Dejean species are ecologically and economically significant, and in coniferous forests they vector the nematode that causes Pine Wilt Disease. This study uses nuclear and mitochondrial genes to test the monophyly and relationships of Monochamus and applies coalescent methods to further delimit the conifer-feeding species. Monochamus has also included approximately 120 Old World species associated with diverse angiosperm tree species. We sample from these additional morphologically diverse species to determine their placement in the Lamiini. Through supermatrix and coalescent methods, the higher-level relationships of Monochamus show that conifer-feeders are a monophyletic group that includes the type species and has split into Nearctic and Palearctic clades. Molecular dating indicates a single dispersal of conifer-feeders to North America over the second Bering Land Bridge circa 5.3 Ma. All other Monochamus sampled fall in different parts of the Lamiini tree. Small-bodied angiosperm-feeding Monochamus group with the monotypic genus Microgoes Casey. The African Monochamus subgenera sampled are distantly related to the conifer-feeding clade. The multispecies coalescent delimitation methods BPP and STACEY delimit 17 conifer-feeding Monochamus species for a total of 18 species, and supports the retention of all current species. An interrogation with nuclear gene allele phasing reveals that unphased data can be unreliable for accurate delimitations and divergence times. The delimited species are discussed with integrative evidence, highlighting real-world challenges in recognizing the completion of speciation trajectories.
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Affiliation(s)
- Patrick S Gorring
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St. Cambridge, MA, USA.
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St. Cambridge, MA, USA
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2
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Sanchez-Rojas JC, Aguirre-Obando OA. Dispersion routes of the main vectors of human malaria in the Americas: Genetic evidence from the mitochondrial COI gene. J Vector Borne Dis 2022; 59:363-374. [PMID: 36751768 DOI: 10.4103/0972-9062.361173] [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: 12/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES In America, of the 44 species of Anopheles, nine are main vectors of malaria and, of these, genetic information exists for seven. Hence, this study sought to know the gene flow and diversity of the seven principal vectors of malaria at the Americas level. METHODS For the seven species and the sequences of the mitochondrial cytochrome c oxidase I (COI) gene obtained from the GenBank and Bold System, genetic analyzes of populations and genetic structure were performed and haplotype networks and phylogenetic trees were obtained. RESULTS For the seven species, 1440 sequences were analyzed and 519 haplotypes were detected. The Hd and π values were higher within a continental context than by countries. Neutrality tests indicated positive and negative values with most of these being significant (p < 0.05). Phylogenetic analyses for all the species recovered three clades with no geographic pattern among them. INTERPRETATION & CONCLUSION Studies suggest that native species of Anopheles from the Americas have greater haplotype diversity and low genetic differentiation due to the lack of physical barriers to impede gene flow among these populations. Moreover, all the species are interconnected by roadways. This scenario complicates the epidemiological picture of malaria in the Americas.
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Affiliation(s)
- Jean Carlos Sanchez-Rojas
- School of Biomathematical Research; Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío. Carrera 15 Calle 12 Norte, Armenia, Colombia
| | - Oscar Alexander Aguirre-Obando
- School of Biomathematical Research; Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío. Carrera 15 Calle 12 Norte, Armenia, Colombia
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3
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Schultz JA, Hebert PDN. Do pseudogenes pose a problem for metabarcoding marine animal communities? Mol Ecol Resour 2022; 22:2897-2914. [PMID: 35700118 DOI: 10.1111/1755-0998.13667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.
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Affiliation(s)
- Jessica A Schultz
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
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4
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Lucas T, Vincent B, Eric P. Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211888. [PMID: 35719890 PMCID: PMC9198517 DOI: 10.1098/rsos.211888] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.
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Affiliation(s)
- Torres Lucas
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
| | - Bretagnolle Vincent
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
| | - Pante Eric
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
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5
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Vargas-Espinosa JH, Aguirre-Obando OA. Global phylogeography of the flood mosquito, Aedes vexans (Diptera: Culicidae), from mitochondrial DNA. ZOOLOGIA 2022. [DOI: 10.1590/s1984-4689.v39.e21029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Hansen S, Addison P, Benoit L, Haran JM. Barcoding pest species in a biodiversity hot-spot: the South African polyphagous broad-nosed weevils (Coleoptera, Curculionidae, Entiminae). Biodivers Data J 2021; 9:e66452. [PMID: 34257510 PMCID: PMC8263552 DOI: 10.3897/bdj.9.e66452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022] Open
Abstract
Polyphagous broad nosed weevils (Curculionidae: Entiminae) constitute a large and taxonomically challenging subfamily that contains economically significant agricultural pests worldwide. South Africa is a hot-spot for biodiversity and several species of indigenous and endemic genera of Entiminae have shifted on to cultivated plants, with some being phytosanitary pests. The sporadic pest status of many species (where the species has an occasional economic impact on the agricultural industry, but is not encountered often enough that is is readily recognisable by researchers and agricultural extension workers) and the presence of pest complexes and cryptic species represent an identification challenge to non-specialists. Furthermore, no comprehensive identification tools exist to identify immature stages that may be found in crops/soil. In this paper, a curated barcoding database with 70 COI sequences from 41 species (39 Entiminae, 2 Cyclominae) is initiated, to assist with the complexity of identification of species in this group.
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Affiliation(s)
- Steffan Hansen
- Stellenbosch University, Stellenbosch, South AfricaStellenbosch UniversityStellenboschSouth Africa
| | - Pia Addison
- University of Stellenbosch, Stellenbosch, South AfricaUniversity of StellenboschStellenboschSouth Africa
| | - Laure Benoit
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier University, Montpellier, FranceCBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier UniversityMontpellierFrance
| | - Julien M Haran
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier University, Montpellier, FranceCBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Montpellier UniversityMontpellierFrance
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7
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Javal M, Terblanche JS, Conlong DE, Delahaye N, Grobbelaar E, Benoit L, Lopez-Vaamonde C, Haran JM. DNA barcoding for bio-surveillance of emerging pests and species identification in Afrotropical Prioninae (Coleoptera, Cerambycidae). Biodivers Data J 2021; 9:e64499. [PMID: 33967581 PMCID: PMC8099841 DOI: 10.3897/bdj.9.e64499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/11/2021] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been succesfully used for bio-surveillance of forest and agricultural pests in temperate areas, but has few applications in the tropics and particulary in Africa. Cacoscelesnewmannii (Coleoptera: Cerambycidae) is a Prioninae species that is locally causing extensive damage in commercially-grown sugarcane in the KwaZulu-Natal Province in South Africa. Due to the risk of spread of this species to the rest of southern Africa and to other sugarcane growing regions, clear and easy identification of this pest is critical for monitoring and for phytosanitary services. The genus Cacosceles Newman, 1838 includes four species, most being very similar in morphology. The damaging stage of the species is the larva, which is inherently difficult to distinguish morphologically from other Cerambycidae species. A tool for rapid and reliable identification of this species was needed by plant protection and quarantine agencies to monitor its potential abundance and spread. Here, we provide newly-generated barcodes for C.newmannii that can be used to reliably identify any life stage, even by non-trained taxonomists. In addition, we compiled a curated DNA barcoding reference library for 70 specimens of 20 named species of Afrotropical Prioninae to evaluate DNA barcoding as a valid tool to identify them. We also assessed the level of deeply conspecific mitochondrial lineages. Sequences were assigned to 42 different Barcode Index Numbers (BINs), 28 of which were new to BOLD. Out of the 20 named species barcoded, 11 (52.4%) had their own unique Barcode Index Number (BIN). Eight species (38.1%) showed multiple BINs with no morphological differentiation. Amongst them, C.newmannii showed two highly divergent genetic clusters which co-occur sympatrically, but further investigation is required to test whether they could represent new cryptic species.
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Affiliation(s)
- Marion Javal
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | - John S Terblanche
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | - Desmond E Conlong
- South African Sugarcane Research Institute, Mount Edgecombe, South Africa South African Sugarcane Research Institute Mount Edgecombe South Africa.,Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University Stellenbosch South Africa
| | | | - Elizabeth Grobbelaar
- Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X134, Queenswood, Pretoria, South Africa Biosystematics Division, ARC-Plant Protection Research Institute, Private Bag X134, Queenswood Pretoria South Africa
| | - Laure Benoit
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier Montpellier France
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orleans, France INRAE, URZF Orleans France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France IRBI, UMR 7261, CNRS-Université de Tours Tours France
| | - Julien M Haran
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier Montpellier France
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8
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Tuda M, Iwase SI, Kébé K, Haran J, Skuhrovec J, Sanaei E, Tsuji N, Podlussány A, Merkl O, El-Heneidy AH, Morimoto K. Diversification, selective sweep, and body size in the invasive Palearctic alfalfa weevil infected with Wolbachia. Sci Rep 2021; 11:9664. [PMID: 33958611 PMCID: PMC8102540 DOI: 10.1038/s41598-021-88770-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 04/15/2021] [Indexed: 11/21/2022] Open
Abstract
The alfalfa weevil Hypera postica, native to the Western Palearctic, is an invasive legume pest with two divergent mitochondrial clades in its invading regions, the Western clade and the Eastern/Egyptian clade. However, knowledge regarding the native populations is limited. The Western clade is infected with the endosymbiotic bacteria Wolbachia that cause cytoplasmic incompatibility in host weevils. Our aim was to elucidate the spatial genetic structure of this insect and the effect of Wolbachia on its population diversity. We analyzed two mitochondrial and two nuclear genes of the weevil from its native ranges. The Western clade was distributed in western/central Europe, whereas the Eastern/Egyptian clade was distributed from the Mediterranean basin to central Asia. Intermediate mitotypes were found from the Balkans to central Asia. Most Western clade individuals in western Europe were infected with an identical Wolbachia strain. Mitochondrial genetic diversity of the infected individuals was minimal. The infected clades demonstrated a higher nonsynonymous/synonymous substitution rate ratio than the uninfected clades, suggesting a higher fixation of nonsynonymous mutations due to a selective sweep by Wolbachia. Trans-Mediterranean and within-European dispersal routes were supported. We suggest that the ancestral populations diversified by geographic isolation due to glaciations and that the diversity was reduced in the west by a recent Wolbachia-driven sweep(s). The intermediate clade exhibited a body size and host plant that differed from the other clades. Pros and cons of the possible use of infected-clade males to control uninfected populations are discussed.
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Affiliation(s)
- Midori Tuda
- Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan. .,Laboratory of Insect Natural Enemies, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
| | - Shun-Ichiro Iwase
- Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan.,Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Japan
| | - Khadim Kébé
- GRBA-BE, LE3PI Laboratory, Department of Chemical Engineering and Applied Biology, Polytechnic Higher School of Dakar, Dakar, Senegal
| | - Julien Haran
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France
| | - Jiri Skuhrovec
- Group Function of Invertebrate and Plant Biodiversity in Agro-Ecosystems, Crop Research Institute, Drnovska, Praha, Czech Republic
| | - Ehsan Sanaei
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Naomichi Tsuji
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | | | - Ottó Merkl
- Hungarian Natural History Museum, Budapest, Hungary
| | - Ahmed H El-Heneidy
- Department of Biological Control, Plant Protection Research Institute, Agricultural Research Center, Giza, Egypt
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9
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Postic E, Outreman Y, Derocles S, Granado C, Le Ralec A. Genetics of wild and mass-reared populations of a generalist aphid parasitoid and improvement of biological control. PLoS One 2021; 16:e0249893. [PMID: 33848317 PMCID: PMC8043399 DOI: 10.1371/journal.pone.0249893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/28/2021] [Indexed: 11/19/2022] Open
Abstract
Due to their ability to parasitize various insect species, generalist parasitoids are widely used as biological control agents. They can be mass-reared and released in agroecosystems to control several pest species in various crops. However, the existence of genetic differentiation among populations of generalist parasitoid species is increasingly recognized and this can be associated with an adaptation to local conditions or to a reduced range of host species. Moreover, constraints of mass-rearing conditions can alter genetic variation within parasitoid populations released. These features could be associated with a reduced efficiency of the control of targeted pest species. Here, we focused on strawberry greenhouses where the control of aphids with the generalist parasitoid Aphidius ervi appears to be inefficient. We investigated whether this inefficiency may have both genetic and ecological bases comparing wild and commercial populations of A. ervi. We used two complementary genetic approaches: one based on the mitochondrial marker COI and one based on microsatellite markers. COI analysis showed a genetic differentiation within the A. ervi species, but the structure was neither associated with the commercial/wild status nor with host species factors. On the other hand, using microsatellite markers, we showed a genetic differentiation between commercial and wild A. ervi populations associated with a loss of genetic diversity within the mass-reared populations. Our ecological genetics study may potentially explain the weak efficiency of biological control of aphids in protected strawberry crops and enable to provide some insights to improve biological control.
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Affiliation(s)
- Estelle Postic
- IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- AOPn Fraises de France, Estillac, France
| | | | | | | | - Anne Le Ralec
- IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- * E-mail:
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10
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Pereira RJ, Ruiz‐Ruano FJ, Thomas CJ, Pérez‐Ruiz M, Jiménez‐Bartolomé M, Liu S, Torre J, Bella JL. Mind the
numt
: Finding informative mitochondrial markers in a giant grasshopper genome. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Francisco J. Ruiz‐Ruano
- Department of Genetics University of Granada Granada Spain
- Department of Ecology and Genetics – Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Callum J.E. Thomas
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Mar Pérez‐Ruiz
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Miguel Jiménez‐Bartolomé
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Shanlin Liu
- Department of Entomology College of Plant Protection China Agricultural University Beijing China
| | - Joaquina Torre
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
| | - José L. Bella
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
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11
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Haran J, Ndzana Abanda RFX, Benoit L, Bakoumé C, Beaudoin-Ollivier L. Multilocus phylogeography of the world populations of Elaeidobius kamerunicus (Coleoptera, Curculionidae), pollinator of the palm Elaeis guineensis. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:654-662. [PMID: 32381154 DOI: 10.1017/s0007485320000218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Elaeidobius kamerunicus Faust (Coleoptera, Curculionidae) is one of the specific pollinators on inflorescences of the African oil palm Elaeis guineensis Jacquin. This derelomine weevil is native to tropical Africa. During the late 20th century, it was introduced into all tropical regions where E. guineensis is grown, in order to improve its pollination and fruit set. Despite an overall success, a decline in pollination efficiency has been documented in several regions. In this study, we reconstructed a multilocus phylogeography of the world populations of E. kamerunicus, in order to explore its genetic diversity in its native and introduced ranges. Our results showed that African populations of E. kamerunicus are forming two differentiated mitochondrial clusters in West and central Africa, forming a contact zone along the Cameroon Volcanic Line. The existence of this sharp contact zone along this weak altitudinal barrier suggests that other parameters, such as climate, may be driving the distribution of populations. A differential genetic structure between mitochondrial and nuclear genes, and the strong level of genetic structure of the mitochondrial gene, also suggest sex-biased dispersal in this species, with males dispersing more than females. The genetic structure inferred from Asian and South American populations suggests that they originate from populations of both western and central tropical Africa and that a bottleneck has probably been experienced by these populations.
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Affiliation(s)
- Julien Haran
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | - Laure Benoit
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
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12
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Ricardo PC, Françoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion 2020; 53:243-254. [PMID: 32569843 DOI: 10.1016/j.mito.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/28/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
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13
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Blattner L, Gerecke R, von Fumetti S. Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia). Parasit Vectors 2019; 12:492. [PMID: 31639027 PMCID: PMC6805402 DOI: 10.1186/s13071-019-3750-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/12/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library. METHODS We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels. RESULTS A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6-6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels. CONCLUSIONS Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.
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Affiliation(s)
- Lucas Blattner
- Department of Environmental Sciences, Geoecology Research Group, University of Basel, St. Johanns-Vorstadt 10, 4056 Basel, Switzerland
| | - Reinhard Gerecke
- Department of Biology, University of Tübingen, Auf der Morgenstelle 28E, 72076 Tübingen, Germany
| | - Stefanie von Fumetti
- Department of Environmental Sciences, Geoecology Research Group, University of Basel, St. Johanns-Vorstadt 10, 4056 Basel, Switzerland
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14
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Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
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15
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Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
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Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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16
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Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding. Sci Rep 2018; 8:6158. [PMID: 29670192 PMCID: PMC5906601 DOI: 10.1038/s41598-018-24382-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/15/2018] [Indexed: 11/26/2022] Open
Abstract
Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite’s epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene’s barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first complete Mansonella genus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placed M. ozzardi in the Onchocercidae “ONC5” clade and suggested that Mansonella parasites are more closely related to Wuchereria and Brugia genera parasites than they are to Loa genus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing that M. ozzardi from the Amazon and Caribbean regions are near-identical and that previously reported Peruvian M. ozzardi CO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to the Mansonella genus’s molecular tool-kit and providing evidence that some M. ozzardi CO1 sequence deposits are pseudogenes, our results suggest that all Neotropical M. ozzardi parasites are closely related.
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17
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Galan M, Pons JB, Tournayre O, Pierre É, Leuchtmann M, Pontier D, Charbonnel N. Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Mol Ecol Resour 2018; 18:474-489. [PMID: 29288544 DOI: 10.1111/1755-0998.12749] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/29/2017] [Accepted: 12/23/2017] [Indexed: 12/26/2022]
Abstract
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.
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Affiliation(s)
- Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | - Jean-Baptiste Pons
- LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France
| | - Orianne Tournayre
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | - Éric Pierre
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | | | - Dominique Pontier
- LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France.,CNRS, Laboratoire de Biométrie et Biologie Évolutive, UMR5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Nathalie Charbonnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
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18
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Hazkani-Covo E, Martin WF. Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health. Genome Biol Evol 2017; 9:1190-1203. [PMID: 28444372 PMCID: PMC5570036 DOI: 10.1093/gbe/evx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 12/28/2022] Open
Abstract
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health.
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Affiliation(s)
- Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
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19
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Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene 2017; 628:63-71. [DOI: 10.1016/j.gene.2017.07.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022]
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20
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De JesÚs-Bonilla VS, Barrientos-Lozano L, ZaldÍvar-RiverÓn A. Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera, Romaleidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1313792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Vladimir Salvador De JesÚs-Bonilla
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito exterior s/n Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C.P 04510, D.F., México
| | - Ludivina Barrientos-Lozano
- Instituto Tecnológico de Cd. Victoria. Blvd., Emilio Portes Gil No. 1301, C. P. 87010, Ciudad Victoria, Tamaulipas, México
| | - Alejandro ZaldÍvar-RiverÓn
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito exterior s/n Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C.P 04510, D.F., México
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21
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Complex patterns of global spread in invasive insects: eco-evolutionary and management consequences. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1082-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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22
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Drag L, Hauck D, Bérces S, Michalcewicz J, Šerić Jelaska L, Aurenhammer S, Cizek L. Genetic differentiation of populations of the threatened saproxylic beetle Rosalia longicorn,Rosalia alpina(Coleoptera: Cerambycidae) in Central and South-east Europe. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12624] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lukas Drag
- Faculty of Science; University of South Bohemia; Branisovska 31 37005 Ceske Budejovice Czech Republic
- Biology Centre CAS, v. v. i.; Institute of Entomology; Branisovska 31 37005 Ceske Budejovice Czech Republic
| | - David Hauck
- Biology Centre CAS, v. v. i.; Institute of Entomology; Branisovska 31 37005 Ceske Budejovice Czech Republic
| | - Sándor Bérces
- Duna-Ipoly National Park Directorate; Kolto utca 21 1121 Budapest Hungary
| | - Jakub Michalcewicz
- Institute of Forest Ecosystem Protection; Faculty of Forestry; University of Agriculture; Al. 29 Listopada 46 31-425 Kraków Poland
| | - Lucija Šerić Jelaska
- Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| | - Sandra Aurenhammer
- Institute for Animal Ecology and Landscape Planning; Bergmanngasse 22 8010 Graz Austria
| | - Lukas Cizek
- Faculty of Science; University of South Bohemia; Branisovska 31 37005 Ceske Budejovice Czech Republic
- Biology Centre CAS, v. v. i.; Institute of Entomology; Branisovska 31 37005 Ceske Budejovice Czech Republic
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