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Legault S, James PMA. Spatial patterns of hyperparasitism along a latitudinal gradient of forest genus diversity: insights from the spruce budworm-parasitoids community. Environ Entomol 2024; 53:116-126. [PMID: 38006330 DOI: 10.1093/ee/nvad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
High-order mobile predators are generally thought to increase ecosystem stability and resilience to natural perturbations. In many insect food-webs, higher trophic positions are occupied by parasitoids, which are themselves hosts for hyperparasitoids that can reduce primary parasitoids' efficiency in controlling insect pests. Hyperparasitoids can thus provide ecosystem disservices by facilitating pest outbreaks, or ecosystem services by stabilizing food web fluctuations over longer time periods. To better understand how hyperparasitism affects multitrophic forest systems, we examined for the first time spatial variations in hyperparasitism associated with the spruce budworm. We examined 2 common primary parasitoids of the spruce budworm during outbreaks (Apanteles fumiferanae and Glypta fumiferanae), and estimated their true and pseudohyperparasitism rates in 2014-2015 from 28 locations across a latitudinal gradient (over 450 km) of forest genus diversity. Hyperparasitoid cryptic diversity was also quantified using DNA-barcoding. We found that A. fumiferanae and G. fumiferanae share at least 2 of 5 common hyperparasitoid species, confirming the connected nature of the spruce budworm-parasitoid food web. Moreover, hyperparasitism is modulated by spatial context as we observed a positive correlation between forest genus diversity and hyperparasitism for A. fumiferanae, but not for G. fumiferanae. Further monitoring hyperparasitism holds significant potential to provide new insights into how forest composition affects multitrophic interactions and spatio-temporal outbreak dynamics.
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Affiliation(s)
- Simon Legault
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Patrick M A James
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
- Institute of Forestry and Conservation, University of Toronto, Toronto, ON, Canada
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2
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Piccoli C, Muñoz-Mérida A, Crottini A. PARSID: a Python script for automatic analysis of local BLAST results for a rapid molecular taxonomic identification. BMC Res Notes 2024; 17:35. [PMID: 38268047 PMCID: PMC10807118 DOI: 10.1186/s13104-024-06686-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVE A reliable taxonomic identification of species from molecular samples is the first step for many studies. For researchers unfamiliar with programming, running a BLAST analysis, filtering, and organizing results for hundreds of sequences through the BLAST web interface can be difficult. Additionally, sequences deposited in GenBank can have outdated taxonomic identification. The use of reliable Reference Sequences Library (RSL) containing accurate taxonomically-identified sequences facilitates this task. Pending the availability of a RSL with the user, we developed a tool that automates the molecular taxonomic identification of sequences. RESULTS We developed PARSID, a Python script running through the command-line that automates the routine workflow of blasting an input sequence file against the user's RSL, and retrieves the matches with the highest percentage of identity in five steps. PARSID accepts cut-off parameters and supplementary information in a.csv file for filtering the results. The final output is visualized in a spreadsheet. We tested its functioning using 10 input sequences simulating different situations of the molecular taxonomic identification of sequences against an example RSL containing 25 sequences. Step-by-step instructions and test files are publicly available at https://github.com/kokinide/PARSID.git .
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Affiliation(s)
- Costanza Piccoli
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Hübner JJ, Chemyreva V. Review of German Spilomicrus Westwood (Hymenoptera, Diapriidae, Spilomicrini). Biodivers Data J 2024; 12:e114515. [PMID: 38230309 PMCID: PMC10790369 DOI: 10.3897/bdj.12.e114515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Background This study provides an integrative taxonomy-based review for the genus Spilomicrus Westwood in Germany using DNA barcoding and classic morphology. New information Spilomicrussimplex Tomsik, 1947 is placed in synonymy with S.antennatus Jurine, 1807; Spilomicrusthomsoni Kieffer, 1911 is removed from synonymy with S.hemipterus Marshall, 1868. A lectotype is designated for Spilomicrusnigripes Thomson, 1858. Newly recorded for Germany are the following species: S.thomsoni Kieffer, 1911, S.crassiclavis Marshall, 1868, S.lusitanicus Kieffer, 1910 and S.diversus Chemyreva, 2021. Three species, Spilomicrusbrevimalaris sp. nov., S.flavecorpus sp. nov. and S.politus sp. nov. are described as new to science. The 23 DNA-barcodes with species identification present a substantial addition over the previous German checklist. This study aims to update the number of nationwide known Spilomicrus species from fifteen to twenty. Furthermore, a new key to identify all European Spilomicrus species is provided.
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Affiliation(s)
- Jeremy Joshua Hübner
- Zoologische Staatssammlung München, Munich, GermanyZoologische Staatssammlung MünchenMunichGermany
| | - Vasilisa Chemyreva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
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Hübner J, Chemyreva VG, Notton DG. Taxonomic and nomenclatural notes on Geodiaprialongiceps Kieffer, 1911 (Hymenoptera, Diapriidae) and synonymy of the genus Geodiapria Kieffer, 1910. Zookeys 2023; 1183:1-11. [PMID: 37915996 PMCID: PMC10616777 DOI: 10.3897/zookeys.1183.110952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
This paper reviews the status of Geodiapria and its nominotypical and only included species G.longiceps. Geodiapria was previously understood to be very similar to, and doubtfully separated from the genus Basalys. We use integrative taxonomy (morphology, DNA-barcoding, phylogenetic tree building) to show that the valid name for what was G.longiceps Kieffer, 1911 is now Basalysrufocinctus (Kiefer, 1911) and that Geodiapria is consequently a junior synonym of Basalyssyn. nov. The following taxa are new synonyms of B.rufocinctus: Loxotropalongiceps Wasmann, 1909, syn. nov., G.longiceps Kieffer, 1911, syn. nov., L.rufosignata Kieffer, 1911, syn. nov. Basalysrufocinctus is newly reported from Corsica, Germany, Norway and Spain.
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Affiliation(s)
- Jeremy Hübner
- Zoologische Staatssammlung München, Muenchhausenstr. 21, 81247 Munich, GermanyZoologische Staatssammlung MünchenMunichGermany
| | - Vasilisa G. Chemyreva
- Zoological Institute, Russian Academy of Sciences, 1 Universitetskaya Emb., St. Petersburg 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - David G. Notton
- Department of Natural Sciences, National Museums Collection Centre, 242 West Granton Road, Granton, Edinburgh EH5 1JA, UKNational Museums Collection CentreEdinburghUnited Kingdom
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Nascimbene J, Nimis PL, Klüßendorf J, Thüs H. Freshwater Lichens, Including New Species in the Genera Verrucaria, Placopyrenium and Circinaria, Associated with Lobothallia hydrocharis (Poelt & Nimis) Sohrabi & Nimis from Watercourses of Sardinia. J Fungi (Basel) 2023; 9:jof9030380. [PMID: 36983548 PMCID: PMC10051252 DOI: 10.3390/jof9030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
This work summarizes the results of the exploration of freshwater lichen biota on the island of Sardinia associated with the regional flagship species Lobothallia hydrocharis, a large-sized crustose lichen from the splash zone along mountain streams, so far known from Sardinia only. Molecular data were used to confirm its distinctiveness from other taxa and its systematic placement and to identify critical taxa among its associated lichen biota. We found 25 species of lichenized fungi, including three species new to science in the genera Verrucaria, Placopyrenium, and Circinaria, and seven species new to Sardinia (Hydropunctaria rheithrophila, Ionaspis chrysophana, I. odora, Verrucaria aquatilis, V. collematodes, V. pseudovirescens), or new to Southern Europe (V. devensis). Specific traits for the freshwater lichen biota of Sardinia were identified and compared to those reported from freshwater sites in the Alps and Carpathian mountains, e.g., a relative scarcity of subgelatinous lichens. Parasitic or epilichenic interactions were found frequently but only in the splash zone and not in the permanently submerged zone, i.e., two parasitic Placopyrenium species, and clearly lichenicolous thalli of Kuettlingeria atroflava and Lobothallia hydrocharis. Due to its specific trait profile and the great potential for the discovery of new species, we recommend the inclusion of Sardinian and further Mediterranean sites in continental-scale monitoring programs for freshwater lichens.
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Affiliation(s)
- Juri Nascimbene
- Biome-Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum, University of Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Pier Luigi Nimis
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, I-34127 Trieste, Italy
| | - Johanna Klüßendorf
- Department of Botany, State Museum of Natural History Stuttgart, Rosenstein 1, D-270191 Stuttgart, Germany
| | - Holger Thüs
- Department of Botany, State Museum of Natural History Stuttgart, Rosenstein 1, D-270191 Stuttgart, Germany
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L'Ambert G, Gendrot M, Briolant S, Nguyen A, Pages S, Bosio L, Palomo V, Gomez N, Benoit N, Savini H, Pradines B, Durand GA, Leparc-Goffart I, Grard G, Fontaine A. Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation. Mol Ecol Resour 2023; 23:410-423. [PMID: 36161270 PMCID: PMC10092573 DOI: 10.1111/1755-0998.13716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/02/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023]
Abstract
Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.
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Affiliation(s)
- Grégory L'Ambert
- Entente Interdépartementale Pour la Démoustication du Littoral Méditerranéen (EID Méditerranée), Montpellier, France
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | | | - Sylvain Pages
- Entente Interdépartementale Pour la Démoustication du Littoral Méditerranéen (EID Méditerranée), Montpellier, France
| | - Laurent Bosio
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Vincent Palomo
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Hélène Savini
- IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,Service des Maladies Infectieuses, Hôpital d'Instruction des Armées Laveran, Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Centre National de Référence du Paludisme, Marseille, France
| | - Guillaume André Durand
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Isabelle Leparc-Goffart
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.,Centre National de Référence des Arbovirus, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix Marseille Univ, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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Bolshakov V, Prokin A, Pavlov D, Akkizov A, Movergoz E. Karyotypes and COI Gene Sequences of Chironomus sp. Le1 (Kiknadze and Salova, 1996), Ch. laetus (Belyanina and Filinkova, 1996) and Their Hybrid from the Yamal Peninsula, Arctic Zone of Russia. Insects 2022; 13:1112. [PMID: 36555022 PMCID: PMC9784555 DOI: 10.3390/insects13121112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
The study of the biological diversity of the Arctic zone yields intriguing results. Initial research on the lakes of the Yamal Peninsula resulted in the identification of Chironomus laetus and the hybrid Ch. laetus × Ch. sp. Le1. To avoid misidentification, we used morphological, cytogenetic, and molecular genetic approaches. By cytogenetics, in Ch. sp. Le1, seven banding sequences were found: Le1A1, Le1B1, Le1C1, Le1D1, Le1E1, Le1F1, and Le1G1. The karyotype of Ch. laetus was mapped for the first time; it is the first species with the arm combinations AE BC DF G. We propose the name of a new cytocomplex-"laetus". DNA-barcoding of the COI gene was carried out for Ch. laetus and Ch. laetus × Ch. sp. Le1 for the first time. The estimated genetic distance between the sequences of Ch. laetus and Ch. riihimakiensis is 2.3-2.5%. The high similarity in morphology, banding sequences, and the possibility of hybridization indicate a close relationship between Ch. laetus and Ch. sp. Le1, which is assumed to be the northern variant of Ch. riihimakiensis. Molecular genetic data suggests the presence of a subgroup with Ch. laetus.
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Affiliation(s)
- Viktor Bolshakov
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz prov., Borok 152742, Russia
| | - Alexander Prokin
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz prov., Borok 152742, Russia
- Ecological-Analytical Laboratory, Cherepovets State University, Lunacharski 5, Cherepovets 162600, Russia
| | - Dmitry Pavlov
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz prov., Borok 152742, Russia
| | - Azamat Akkizov
- Department of Biology, Geoecology and Molecular Genetic Foundations of Living Systems, Kabardino-Balkarian State University Named after H. M. Berbekov, Chernyshevsky St., 173, Nalchik 360004, Russia
| | - Ekaterina Movergoz
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz prov., Borok 152742, Russia
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Trujillo-Argueta S, del Castillo RF, Velasco-Murguía A. Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods. PeerJ 2022; 10:e13771. [PMID: 35990900 PMCID: PMC9390329 DOI: 10.7717/peerj.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.
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Amorim PF, Katz AM, Ottoni FP, de Bragança PHN. Genetic Structure of the Mangrove Killifish Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations. Zool Stud 2022; 60:e4. [PMID: 35774256 PMCID: PMC9168499 DOI: 10.6620/zs.2022.61-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
The Kryptolebias marmoratus species group is composed of the only three vertebrate species that lack females. These species present only males and simultaneously hermaphroditic individuals; that are able to reproduce by allogamy, with males, or by autogamy, performing self-fertilization and generating clones of themselves. The proportion of males is variable among those species and even among their populations. Kryptolebias hermaphroditus has the smallest proportion of males. Indeed, no males have been recorded in most known populations. This is a mainly autogamous species, with small populations having a disjunct distribution along the eastern and northern coast of Brazil. Species presenting such adaptations would be expected to have an elevated rate of genetic population structure, reflecting any barriers that obstruct gene flow between populations. Partial sequences of the mitochondrial cytochrome c oxidase I (COI) gene from 335 individuals were sampled to perform a population analysis. Only a single haplotype of COI, widely distributed throughout all the sampled populations, was recovered for K. hermaphroditus. Here we hypothesize that the high degree of communication within populations is probably the main biological feature leading to this pattern.
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Affiliation(s)
- Pedro F Amorim
- Laboratory of Systematics and Evolution of Teleost Fishes, Genetic Graduation Program, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Rio de Janeiro, Brazil. E-mail: (Amorim)
| | - Axel Makay Katz
- Laboratory of Systematics and Evolution of Teleost Fishes, Biodiversity and Evolutionary Biology Graduation Program, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Rio de Janeiro, Brazil. E-mail: (Katz)
| | - Felipe Polivanov Ottoni
- Laboratory of Systematics and Ecology of Aquatic Organisms, Center for Agricultural and Environmental Sciences, Federal University of Maranhão, CEP 65500-000, BR-222, KM 04, Boa Vista, Chapadinha, MA, Brasil. E-mail: (Ottoni)
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O Attia A, A Ismail I, S Dessoky ED, S Aljuaid B. Using of DNA-Barcoding, SCoT and SDS-PAGE Protein to Assess Soma-Clonal Variation in Micro-Propagated Fig ( Ficus carica L.) Plant. Pak J Biol Sci 2022; 25:415-425. [PMID: 35638512 DOI: 10.3923/pjbs.2022.415.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
<b>Background and Objective:</b> <i>In vitro</i> propagation of fig (<i>Ficus carica</i> L.) is one of the possible approaches that may be used to maximize the diversity of plant species. The current work was carried out to evaluate genetic stability of micropropagated fig plantlets and to determine the effect of <i>in vitro </i>propagation on genomic content of Saudi fig. <b>Materials and Methods:</b> The start codon-targeted (SCoT), DNA-barcoding chloroplast gene RNA polymerase1 (<i>rpoC1</i> sequencing) and total protein profiling assays (SDS-PAGE) techniques were used to detect genetic stability in micropropagated fig plantlets. <b>Results:</b> The Scorable PCR bands were produced with 10 SCoT primers used, where the total number of bands was 135 bands. Twenty polymorphic bands were generated with 18.4% of a polymorphism percentage. According to the result, no visual unique bands were generated which confirmed the genetic homogeneity of micropropagated plantlets samples compared to the control sample (mother plant). Sequence analysis and phylogenetic tree generated using fig <i>rpoC1</i> sequence showed high similarity between control and plantlets samples of fig plant. The protein profiling results revealed no remarkable changes between micropropagated plantlets and the mother plant. <b>Conclusion:</b> The results indicate that using SCoT, DNA barcoding and protein profiling have demonstrated their utility to detect genetic homogeneity in micropropagated fig plantlets, which suggests using of micropropagation protocol of plants applied on the plantlets in the current study as a reliable protocol for <i>in vitro</i> culture and conservation of fig plant.
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11
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S Dessoky ED, Attia AO, A Ismail I, Alotaibi SS, S Aljuaid B. Molecular Assessment of Genetic Stability Using CDDP and DNA-barcoding Assays in Long-term Micropropagated Rose Plant. Pak J Biol Sci 2021; 23:1176-1183. [PMID: 32981248 DOI: 10.3923/pjbs.2020.1176.1183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Roses are the world's best-known garden plants, established as ornamental plants cultivated for their blooms. Taif rose (Rosa damascena trigintipetala) refers to the Damascus Rose species and is regarded one of Taif Governorate's most significant financial goods, which produces an extremely fragrant commercially precious essential oil. The objective of current study was to assess the genetic stability of micropropagated Taif rose and to assess the usefulness of Conserved DNA Derived Polymorphism (CDDP) and DNA-barcoding genes such as; rpoC1 (chloroplast gene RNA polymerase1) in the detection of somaclonal variation. MATERIALS AND METHODS Ten combinations of CDDP PCR primers were employed and the rpoC1 gene region was sequenced for mother plant (control) and micropropagated plantlets of Taif rose plant. RESULTS Based on CDDP data, phylogenetic divergence indicated that the distinct specimens of Taif rose micro-propagated plantlets and control were genetically differentiated by a difference of 1% of genetic dissimilarity. Phylogenetic tree which developed using rpoC1 DNA showed that rpoC1 DNA sequencing discovered a genetic difference between the control and micro-propagated plantlets of Taif rose. CONCLUSION Furthermore, CDDP and DNA barcoding using rpoC1 gene have demonstrated their usefulness in investigating the genetic history of Rosa species and their ability to explore genetic mutation.
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Wagner M, Kovačić M, Koblmüller S. Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra. J Fish Biol 2021; 98:64-88. [PMID: 32985685 PMCID: PMC7821206 DOI: 10.1111/jfb.14558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.
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Affiliation(s)
- Maximilian Wagner
- Institute of BiologyUniversity of GrazGrazAustria
- Department of BiologyUniversity of AntwerpAntwerpBelgium
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Martinsson S, Klinth M, Erséus C. Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation. BMC Evol Biol 2020; 20:116. [PMID: 32928097 PMCID: PMC7488859 DOI: 10.1186/s12862-020-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. RESULTS A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. CONCLUSION We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.
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Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.
| | - Mårten Klinth
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Christer Erséus
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
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Zangl L, Oberreiter H, Huss H, Stabentheiner E, Sturmbauer C, Koblmüller S. Discriminating larvae of two syntopic Cychramus species (Coleoptera, Nitidulidae) by means of bar-HRM analysis. Mol Biol Rep 2020; 47:8251-8257. [PMID: 32901359 PMCID: PMC7588358 DOI: 10.1007/s11033-020-05786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/28/2020] [Indexed: 11/03/2022]
Abstract
Molecular genetic methods are increasingly used to supplement or substitute classical morphology-based species identification. Here, we employ a COI mini-barcode coupled high-resolution melting analysis to quickly, cost-efficiently and reliably determine larvae of two closely related Cychramus (Coleoptera, Nitidulidae) species. Euclidean distance comparison (p < 0.01) and a Welch t-test of the melting point temperatures (p < 0.01) provide highly significant statistical evidence for species specific differences in melting and fluorescence curves, thus allowing the assignment of larvae to either of the two species. This protocol serves as a fast, low-cost and low-tech method to discriminate between pairs or groups of closely related species and can be adapted and applied to various ecological research questions.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria. .,Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045, Graz, Austria. .,ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010, Graz, Austria.
| | - Hannes Oberreiter
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | | | - Edith Stabentheiner
- Institute of Biology, University of Graz, Schubertstraße 51, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
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Rosińska J, Piotrowicz R, Celiński K, Dabert M, Rzymski P, Klimaszyk P. The Reappearance of An Extremely Rare and Critically Endangered Nitella translucens (Charophyceae) in Poland. J Phycol 2019; 55:1412-1415. [PMID: 31339181 DOI: 10.1111/jpy.12905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
We report the reappearance of the rare charophyte Nitella translucens in Poland. It was identified in the soft-water lobelian Lake Jeleń (North Poland) during 2013 and 2018 phytolittoral surveys. This species is considered critically endangered in various European countries and was previously classified as extinct in Poland. Its occurrence was confirmed using morphological and molecular data (ITS1-18S, ITS2-28S, rDNA, and rbcL). The N. translucens occupied ~20% of the lake bottom, at depths of 1.5-6.5 m, water pH 7.5-8.6, conductivity of 59-66 μS · cm-1 , and total nitrogen and phosphorus during growing season in the range of 1.1-1.4 mg · L-1 and 0.07-0.1 mg · L-1 , respectively. It co-occurred mainly with plant species typical for lobelia lakes: Isoetes lacustris, Littorella uniflora, and Myriophyllum alterniflorum, as well as Ceratophyllum demersum and Elodea canadensis, which are characteristic for eutrophicated waters. It appears that N. translucens may thrive in lobelia lakes during their transformation to more eutrophic states.
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Affiliation(s)
- Joanna Rosińska
- Department of Environmental Medicine, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznań, Poland
| | - Ryszard Piotrowicz
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Konrad Celiński
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Mirosława Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznań, Poland
| | - Piotr Klimaszyk
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
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Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
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Glowska E, Broda L, Dabert M. Insight into the species diversity of the quill mite genus Betasyringophiloidus Skoracki, 2011 (Prostigmata: Syringophilidae) on the basis of the DNA barcodes. Folia Parasitol (Praha) 2019; 66. [PMID: 31366736 DOI: 10.14411/fp.2019.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/17/2019] [Indexed: 11/19/2022]
Abstract
Betasyringophiloidus Skoracki, 2011 is a genus of quill mites (Prostigmata: Syringophilidae) that is believed to contain mono-, steno- and polyxenous parasites associated with a wide range of passerine birds (Passeriformes) across the world. In this work we applied the DNA-barcode marker (mitochondrial cytochrome c oxidase subunit I gene fragment, COI) to verify whether Betasyringophiloidus schoeniclus (Skoracki, 2002) and Betasyringophiloidus seiuri (Clark, 1964) are actual steno- and polyxenous species associated with the currently recognised host ranges, or their populations are highly host-specific, cryptic species. Our results revealed that a population living on the Tristram's bunting Emberiza tristrami Swinhoe (Emberizidae) in Russia, so far classified as B. schoeniclus, is a new cryptic species Betasyringophiloidus emberizae sp. nov. Both topologies of the neighbor-joining and maximum likelihood phylogenetic trees as well as genetic distance (11.9% Kimura 2-parameter distance) (K2P) support species status of the mite population from E. tristrami. The same data support previously established conspecific status of B. seiuri found on the ovenbird Seiurus aurocapilla (Linnaeus) (Parulidae) (type host) and the northern waterthrush Parkesia noveboracensis (Gmelin) (Parulidae) and expand its range with a population found on a new host species Icterus pustulatus (Wagler) (Icteridae) with intraspecific K2P distance up to 1.9% and interpopulation distances ranging from 1.3 to 3.1%.
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Affiliation(s)
- Eliza Glowska
- Adam Mickiewicz University in Poznan, Faculty of Biology, Department of Animal Morphology, Poznan, Poland
| | - Lukasz Broda
- Adam Mickiewicz University in Poznan, Faculty of Biology, Department of Animal Morphology, Poznan, Poland
| | - Miroslawa Dabert
- Adam Mickiewicz University in Poznan, Faculty of Biology, Molecular Biology Techniques Laboratory, Poznan, Poland
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Garcia-Salguero A, Delgado-Serra S, Sola J, Negre N, Miranda MA, Paredes-Esquivel C. Combined morphology and DNA-barcoding to identify Plagiorhynchus cylindraceus cystacanths in Atelerix algirus. Parasitol Res 2019; 118:1473-8. [PMID: 30927061 DOI: 10.1007/s00436-019-06299-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 10/27/2022]
Abstract
The acanthocephalan parasite Plagiorhynchus cylindraceus has a global distribution and utilizes isopods and birds as intermediate and definitive hosts, respectively. Occasionally, mammals of various orders can act as paratenic hosts. In hedgehogs, severe cases have been reported in juvenile specimens due to secondary infections, as a consequence of complete penetrations of the intestinal wall by cystacanths. In a 66-month study period, we found seven larvae of this parasite encysted in both, the peritoneal cavity and intestine of the Algerian hedgehog, Atelerix algirus in Majorca. Morphology alone was insufficient to identify the species, due to the lack of previous reports and taxonomy-informative characters. In the present report, we combined the use of morphology and the DNA-barcoding approach to confirm to identify cystacanths as P. cylindraceus. This is the first report of this parasite in this hedgehog species. The epidemiological implications will be discussed, including the risk of zoonosis and the importance of using modern approaches to identify immature acanthocephalan larvae in wildlife hosts.
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Liu SY, He K, Chen SD, Jin W, Murphy RW, Tang MK, Liao R, Li FJ. How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses. Zool Res 2018; 39:309-320. [PMID: 29955026 PMCID: PMC6102683 DOI: 10.24272/j.issn.2095-8137.2018.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/07/2018] [Indexed: 11/23/2022] Open
Abstract
Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.
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Affiliation(s)
- Shao-Ying Liu
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China; E-mail:
| | - Kai He
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Shun-De Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- College of Life Sciences, Sichuan Normal University, Chengdu Sichuan 610066, China
| | - Wei Jin
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Ming-Kun Tang
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China
| | - Rui Liao
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China
| | - Feng-Jun Li
- College of Life Sciences, Sichuan Normal University, Chengdu Sichuan 610066, China
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Jansson D, Wolterink A, Bergwerff L, Hough P, Geukens K, Åstot C. Source attribution profiling of five species of Amanita mushrooms from four European countries by high resolution liquid chromatography-mass spectrometry combined with multivariate statistical analysis and DNA-barcoding. Talanta 2018; 186:636-644. [PMID: 29784414 DOI: 10.1016/j.talanta.2018.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/15/2018] [Accepted: 03/22/2018] [Indexed: 01/25/2023]
Abstract
Source attribution profiling of five species of Amanita mushrooms from four European countries was performed using Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) combined with multivariate statistical analysis. Initially, species determination was carried out morphologically and was verified by DNA-analysis. This data was then combined with chemical profiling, generated from LC-HRMS full scan analysis. The untargeted data was processed and the 720 most abundant peaks in the LC-HRMS chromatogram were used to build a multivariate PLS-DA model. The two independent methods for species determination showed 100% correlation, indicating the potential use of chemical profiling as a supporting technique to genetic methods. When specimens of one species were studied, significant variation related to the region of growth was found. The potential of the geo-positioning was shown for A. phalloides from Sweden, Denmark and UK and A. virosa from Sweden and Denmark. Additionally, A. virosa specimens could be attributed to three geographically different regions of Sweden.
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Affiliation(s)
- Daniel Jansson
- Swedish Defence Research Agency, FOI CBRN Defence and Security, SE-901 82 Umeå, Sweden
| | - Arthur Wolterink
- Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - Leonie Bergwerff
- Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | | | - Kris Geukens
- DLD, Belgian Defence Laboratories, Martelarenstraat 181, B-1800 Vilvoorde, Belgium
| | - Crister Åstot
- Swedish Defence Research Agency, FOI CBRN Defence and Security, SE-901 82 Umeå, Sweden.
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Fernández-González S, Pérez-Rodríguez A, Proctor HC, De la Hera I, Pérez-Tris J. High diversity and low genetic structure of feather mites associated with a phenotypically variable bird host. Parasitology 2018; 145:1243-50. [PMID: 29338798 DOI: 10.1017/S0031182017002360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Obligate symbionts may be genetically structured among host individuals and among phenotypically distinct host populations. Such processes may in turn determine within-host genetic diversity of symbionts, which is relevant for understanding symbiont population dynamics. We analysed the population genetic structure of two species of feather mites (Proctophyllodes sylviae and Trouessartia bifurcata) in migratory and resident blackcaps Sylvia atricapilla that winter sympatrically. Resident and migratory hosts may provide mites with habitats of different qualities, what might promote specialization of mite populations. We found high genetic diversity of within-host populations for both mite species, but no sign of genetic structure of mites between migratory and resident hosts. Our results suggest that, although dispersal mechanisms between hosts during the non-breeding season are unclear, mite populations are not limited by transmission bottlenecks that would reduce genetic diversity among individuals that share a host. Additionally, there is no evidence that host phenotypic divergence (associated with the evolution of migration and residency) has promoted the evolution of host-specialist mite populations. Unrestricted dispersal among host types may allow symbiotic organisms to avoid inbreeding and to persist in the face of habitat heterogeneity in phenotypically diverse host populations.
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Yusseff-Vanegas SZ, Agnarsson I. DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region. PeerJ 2017; 5:e3516. [PMID: 28761780 PMCID: PMC5531032 DOI: 10.7717/peerj.3516] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/07/2017] [Indexed: 11/20/2022] Open
Abstract
Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.
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Affiliation(s)
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, United States of America
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Abstract
Three new species of the spider genus Leptonetela collected from caves in Greece are described: Leptonetela arvanitidisi sp. n. (male & female), Leptonetela paragamiani sp. n. (male & female) and Leptonetela penevi sp. n. (male & female). Detailed illustrations of the new species are provided. DNA barcodes were obtained for future use.
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Affiliation(s)
- Yi Wu
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Chunxia Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo Zheng
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Martinsson S, Rhodén C, Erséus C. Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:147-155. [PMID: 26709635 DOI: 10.3109/19401736.2015.1115487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's PAB and Rodrigo et al.'s P(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.
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Affiliation(s)
- Svante Martinsson
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Caroline Rhodén
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Christer Erséus
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
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