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Salis R, Sunde J, Gubonin N, Franzén M, Forsman A. Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity. Mol Ecol Resour 2024; 24:e14018. [PMID: 39285627 DOI: 10.1111/1755-0998.14018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/25/2024] [Accepted: 08/06/2024] [Indexed: 10/03/2024]
Abstract
For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.
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Affiliation(s)
- Romana Salis
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Johanna Sunde
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Nikolaj Gubonin
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Markus Franzén
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
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2
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Chomphuphuang N, Leamyongyai C, Songsangchote C, Piraonapicha K, Pojprasat N, Piyatrakulchai P. Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand. Acta Trop 2024; 260:107424. [PMID: 39369928 DOI: 10.1016/j.actatropica.2024.107424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/03/2024] [Accepted: 10/04/2024] [Indexed: 10/08/2024]
Abstract
The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.
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Affiliation(s)
- Narin Chomphuphuang
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; Spider Excellence Center of Thailand, Khon Kaen University, Khon Kaen 40002, Thailand.
| | | | - Chaowalit Songsangchote
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; Spider Excellence Center of Thailand, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kanyakorn Piraonapicha
- Entomology Section, Queen Sirikit Botanic Garden, The Botanical Garden Organization, Chiang Mai 50180, Thailand
| | - Nirun Pojprasat
- Spider Excellence Center of Thailand, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Paveen Piyatrakulchai
- Spider Excellence Center of Thailand, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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3
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Dettner K, Kovács Z, Rewicz T, Csabai Z. Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae). Zookeys 2024; 1212:153-177. [PMID: 39318675 PMCID: PMC11420541 DOI: 10.3897/zookeys.1212.130039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/22/2024] [Indexed: 09/26/2024] Open
Abstract
A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.
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Affiliation(s)
- Konrad Dettner
- Universität Bayreuth, Chair of Evolutionary Animal Ecology, D-95440 Bayreuth, Hohereuth 17b, D-95448 Bayreuth, GermanyUniversität BayreuthBayreuthGermany
| | - Zsolt Kovács
- University of Pécs, Department of Hydrobiology, Ifjúság útja 6, H-7624 Pécs, HungaryUniversity of PécsPécsHungary
| | - Tomasz Rewicz
- University of Lodz, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, PolandUniversity of LodzŁódźPoland
| | - Zoltán Csabai
- University of Pécs, Department of Hydrobiology, Ifjúság útja 6, H-7624 Pécs, HungaryUniversity of PécsPécsHungary
- HUN-REN Balaton Limnological Research Institute, Klebelsberg Kuno 3, H-8237, Tihany, HungaryHUN-REN Balaton Limnological Research InstituteTihanyHungary
- HUN-REN Centre for Ecological Research, Institute of Aquatic Ecology, Bem square 18/C, H-4026, Debrecen, HungaryHUN-REN Centre for Ecological Research, Institute of Aquatic EcologyDebrecenHungary
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4
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Ma J, Dong X, Xu K, Zeng J, Wang Z, Li J. The Characterization of the Mitochondrial Genome of Fulgoraria rupestris and Phylogenetic Considerations within the Neogastropoda. Genes (Basel) 2024; 15:1076. [PMID: 39202435 PMCID: PMC11353978 DOI: 10.3390/genes15081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Fulgoraria rupestris is a predatory marine gastropod belonging to Neogastropoda and possessing considerable taxonomic significance. However, research on this species remains limited. We acquired the complete mitochondrial genome of F. rupestris through second-generation sequencing and conducted an analysis of its genome structural features. The mitochondrial genome of F. rupestris spans a total length of 16,223 bp and encompasses 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs). Notably, most tRNAs exhibit the typical cloverleaf structure, but there is an absence of the Dihydrouridine (DHU) arm in the trnS1 and trnS2 genes. The A + T content is 68.67%, indicating a pronounced AT bias. Additionally, we conducted a selection pressure analysis on the mitochondrial genomes of four species within Volutidae, revealing that all PCGs are subjected to purifying selection. In comparison to other species within Neogastropoda, F. rupestris shares an identical gene arrangement. Additionally, based on mitochondrial genome sequences of the 13 PCGs from 50 species within Neogastropoda, we constructed a phylogenetic tree. The phylogenetic tree indicates F. rupestris forms a clade with species within the family Volutidae (Cymbium olla, Neptuneopsis gilchristi, and Melo melo). This study serves as a valuable reference for future research on F. rupestris, offering insights for the upcoming phylogenetic and taxonomic classification within Neogastropoda. Furthermore, the findings provide valuable information for the development of genetic resources in this context.
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Affiliation(s)
- Jiale Ma
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Xiangli Dong
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Kaida Xu
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiaying Zeng
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Zhongming Wang
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
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Múrria C, Wangensteen OS, Somma S, Väisänen L, Fortuño P, Arnedo MA, Prat N. Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173243. [PMID: 38761946 DOI: 10.1016/j.scitotenv.2024.173243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 04/04/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.
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Affiliation(s)
- Cesc Múrria
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Owen S Wangensteen
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Simona Somma
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Leif Väisänen
- Stream Ecology Research Group, Department of Ecology and Genetics, University of Oulu, Finland
| | - Pau Fortuño
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Narcís Prat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
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6
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Ren J, Ren L, Zhang R. Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding. Ecol Evol 2024; 14:e11592. [PMID: 38979006 PMCID: PMC11229427 DOI: 10.1002/ece3.11592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.
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Affiliation(s)
- Jinliang Ren
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Li Ren
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
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Rewicz A, Monzalvo R, Myśliwy M, Tończyk G, Desiderato A, Ruchisansakun S, Rewicz T. Pollination biology of Impatiens capensis Meerb. in non-native range. PLoS One 2024; 19:e0302283. [PMID: 38900825 PMCID: PMC11189253 DOI: 10.1371/journal.pone.0302283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/02/2024] [Indexed: 06/22/2024] Open
Abstract
Pollination biology in the widespread species Impatiens capensis Meerb. has only been studied in America, specifically in zones of the U.S.A. and Canada. In this study, we investigated the pollination biology of I. capensis using an integrative identification approach using morphological and molecular tools in four populations of Northwest Poland. We also determined and compared the functional characteristics of the pollinators of the introduced species from the study sites and the native ones reported, for the latter collecting information from bibliographic sources. Visitors were identified using standard morphological keys, including identifying and classifying insect mouthparts. Molecular identification was carried out using mitochondrial DNA's cytochrome oxidase subunit I (COI). We morphologically identified 20 species of visitors constituted by 17 pollinators and three nectar robbers. DNA barcoding of 59 individuals proved the identification of 18 species (also 18 BINs). The frequency of pollinator species was primarily made up of representatives of both Hymenoptera (75%) and Diptera (21%). The morphological traits, such as the chewing and sucking mouthparts, small and big body height, and robber and pollinator behavior explained mainly the native and introduced visitors' arrangements that allow pollination success. However, to understand the process comprehensively, further investigation of other causalities in pollination success and understanding the diversity of pollinators in outer native ranges are necessary.
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Affiliation(s)
- Agnieszka Rewicz
- Department of Geobotany and Plant Ecology, University of Lodz, Łódź, Poland
| | - René Monzalvo
- Molecular Systematics Laboratory, Autonomous University of Hidalgo State, Biological Research Center., Carboneras, Mineral de la Reforma, Hidalgo, México
| | - Monika Myśliwy
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Grzegorz Tończyk
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Andrea Desiderato
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Saroj Ruchisansakun
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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Samreen KB, Manzoor F. Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan. PeerJ 2024; 12:e17420. [PMID: 38832046 PMCID: PMC11146329 DOI: 10.7717/peerj.17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.
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Affiliation(s)
- Khush Bakhat Samreen
- Department of Zoology, Lahore College for Women University, Lahore, Lahore, Pakistan
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9
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Main DC, Taft JM, Geneva AJ, Jansenvan Vuuren B, Tolley KA. The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons. PeerJ 2024; 12:e17076. [PMID: 38708350 PMCID: PMC11067893 DOI: 10.7717/peerj.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 05/07/2024] Open
Abstract
Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
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Affiliation(s)
- Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Jody M. Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Anthony J. Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Bettine Jansenvan Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
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10
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Rios-Willars E, Chirinos-Arias MC. Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. PLANTA 2024; 259:134. [PMID: 38671234 DOI: 10.1007/s00425-024-04420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
MAIN CONCLUSION Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.
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Affiliation(s)
- Ernesto Rios-Willars
- Faculty of Systems, Autonomous University of Coahuila (UAdeC), 25350, Saltillo, Coahuila, México.
| | - Michelle C Chirinos-Arias
- Molecular Biology and Bioinformatics Area, Instituto de Genetica Barbara McClintock (IGBM), Lima, 15022, Peru
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Wei P, Li Y, Ke M, Hou Y, Aikebaier A, Wu Z. Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis. Genes (Basel) 2024; 15:546. [PMID: 38790176 PMCID: PMC11121282 DOI: 10.3390/genes15050546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.
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Affiliation(s)
- Peng Wei
- Grassland Research Institute, Xinjiang Academy of Animal Sciences, Urumqi 830000, China; (M.K.); (Y.H.); (A.A.)
| | - Youzheng Li
- College of Grassland Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Mei Ke
- Grassland Research Institute, Xinjiang Academy of Animal Sciences, Urumqi 830000, China; (M.K.); (Y.H.); (A.A.)
| | - Yurong Hou
- Grassland Research Institute, Xinjiang Academy of Animal Sciences, Urumqi 830000, China; (M.K.); (Y.H.); (A.A.)
| | - Abudureyimu Aikebaier
- Grassland Research Institute, Xinjiang Academy of Animal Sciences, Urumqi 830000, China; (M.K.); (Y.H.); (A.A.)
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010011, China
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12
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Mejías-Alpízar MJ, Porras-Silesky C, Rodríguez EJ, Quesada J, Alfaro-Segura MP, Robleto-Quesada J, Gutiérrez R, Rojas A. Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance. Parasit Vectors 2024; 17:77. [PMID: 38378676 PMCID: PMC10880205 DOI: 10.1186/s13071-023-06113-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/26/2023] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Nematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show. METHODS Nuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed. RESULTS The 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively. CONCLUSIONS The use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups.
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Affiliation(s)
- María José Mejías-Alpízar
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Catalina Porras-Silesky
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Esteban José Rodríguez
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Joban Quesada
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - María Paula Alfaro-Segura
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Joby Robleto-Quesada
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Ricardo Gutiérrez
- National Reference Center for Bacteriology, Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA), Tres Rios, Costa Rica
- Ross University School of Veterinary Medicine, West Farm, Basseterre, Saint Kitts and Nevis
| | - Alicia Rojas
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica.
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica.
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13
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Hew YX, Ya'cob Z, Chen CD, Lau KW, Sofian-Azirun M, Muhammad-Rasul AH, Putt QY, Tan TK, Hadi UK, Suana IW, Takaoka H, Low VL. Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line. Acta Trop 2024; 250:107097. [PMID: 38097150 DOI: 10.1016/j.actatropica.2023.107097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.
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Affiliation(s)
- Yan Xin Hew
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Zubaidah Ya'cob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chee Dhang Chen
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Koon Weng Lau
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Qi Yan Putt
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Tiong Kai Tan
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Upik Kesumawati Hadi
- Entomology Laboratory, Division of Parasitology and Medical Entomology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia
| | - I Wayan Suana
- Faculty of Mathematics and Natural Science, University of Mataram (UNRAM), Mataram, Indonesia
| | - Hiroyuki Takaoka
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia.
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14
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Vanderpool DD, Wilcox TM, Young MK, Pilgrim KL, Schwartz MK. Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study. Ecol Evol 2024; 14:e11020. [PMID: 38371866 PMCID: PMC10870330 DOI: 10.1002/ece3.11020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non-destructive and suitable for the detection of endangered species where "no take" restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.
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Affiliation(s)
- Daniel D. Vanderpool
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Taylor M. Wilcox
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Young
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Kristine L. Pilgrim
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Schwartz
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
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15
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Hein N, Astrin JJ, Beckers N, Giebner H, Langen K, Löffler J, Misof B, Fonseca VG. Arthropod diversity in the alpine tundra using metabarcoding: Spatial and temporal differences in alpha- and beta-diversity. Ecol Evol 2024; 14:e10969. [PMID: 38343576 PMCID: PMC10857931 DOI: 10.1002/ece3.10969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/05/2023] [Accepted: 01/02/2024] [Indexed: 10/28/2024] Open
Abstract
All ecosystems face ecological challenges in this century. Therefore, it is becoming increasingly important to understand the ecology and degree of local adaptation of functionally important Arctic-alpine biomes by looking at the most diverse taxon of metazoans: the Arthropoda. This is the first study to utilize metabarcoding in the Alpine tundra, providing insights into the effects of micro-environmental parameters on alpha- and beta-diversity of arthropods in such unique environments. To characterize arthropod diversity, pitfall traps were set at three middle-alpine sampling sites in the Scandinavian mountain range in Norway during the snow-free season in 2015. A metabarcoding approach was then used to determine the small-scale biodiversity patterns of arthropods in the Alpine tundra. All DNA was extracted directly from the preservative EtOH from 27 pitfall traps. In order to identify the controlling environmental conditions, all sampling locations were equipped with automatic data loggers for permanent measurement of the microenvironmental conditions. The variables measured were: air temperature [°C] at 15 cm height, soil temperature [°C] at 15 cm depth, and soil moisture [vol.%] at 15 cm depth. A total of 233 Arthropoda OTUs were identified. The number of unique OTUs found per sampling location (ridge, south-facing slope, and depression) was generally higher than the OTUs shared between the sampling locations, demonstrating that niche features greatly impact arthropod community structure. Our findings emphasize the fine-scale heterogeneity of arctic-alpine ecosystems and provide evidence for trait-based and niche-driven adaptation. The spatial and temporal differences in arthropod diversity were best explained by soil moisture and soil temperature at the respective locations. Furthermore, our results show that arthropod diversity is underestimated in alpine-tundra ecosystems using classical approaches and highlight the importance of integrating long-term functional environmental data and modern taxonomic techniques into biodiversity research to expand our ecological understanding of fine- and meso-scale biogeographical patterns.
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Affiliation(s)
- Nils Hein
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
- Department of GeographyUniversity of BonnBonnGermany
| | - Jonas J. Astrin
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
| | | | - Hendrik Giebner
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
| | - Kathrin Langen
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
| | - Jörg Löffler
- Department of GeographyUniversity of BonnBonnGermany
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
| | - Vera G. Fonseca
- Centre for Environment Fisheries and Aquaculture Science (Cefas)WeymouthUK
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16
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Taniguchi K, Miyaguchi H. COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics. J Proteome Res 2024; 23:377-385. [PMID: 38091499 DOI: 10.1021/acs.jproteome.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.
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Affiliation(s)
- Kei Taniguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
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17
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Selcuk MA, Celik F, Simsek S, Ahmed H, Kesik HK, Kilinc SG, Cao J. Genetic, haplotype and phylogenetic analysis of Ligula intestinalis by using mt-CO1 gene marker: ecological implications, climate change and eco-genetic diversity. BRAZ J BIOL 2024; 84:e258626. [DOI: 10.1590/1519-6984.258626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/01/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Ligula intestinalis is a cestode parasite that affects freshwater fish in different countries of the world. The current study aims to reveal the phylogenetic, genetic and haplotype diversity of mt-CO1 gene sequences sent to the NCBI database from different countries by using in-silico analysis. The 105 mt-CO1 (371 bp) gene sequences of L. intestinalis obtained from NCBI were used for bioinformatics analyses. Sequences were subjected to phylogenetic and haplotype analysis. As a result of the haplotype analysis of L. intestinalis, 38 haplotypes were obtained from 13 different countries. Hap24 constituted 44.76% of the obtained haplotype network. Changes in nucleotides between haplotypes occurred at 1-84 different points. China and Turkey have highest fixation index (Fst) values of 0.59761, while the lowest (-0.10526) was found between Russia and Turkey. This study provides a baseline for future studies on extensive scale on the epidemiology, ecological aspects, distribution pattern, transmission dynamics and population dispersion of L. intestinalis worldwide.
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Affiliation(s)
- M. A. Selcuk
- Siirt University, Turkey; University of Firat, Turkey
| | | | | | - H. Ahmed
- COMSATS University Islamabad, Pakistan
| | | | | | - J. Cao
- National Health Commission of People’s Republic of China, China; National Institute of Parasitic Diseases, China; Shanghai Jiao Tong University School of Medicine, China; World Health Organization Collaborating Centre for Tropical Diseases, China
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18
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Bevilaqua DR, Batista JS, da Mota AJ, da Silva ACV, da Mota AMS, Formiga KM, de Carvalho Freitas CE. FishDNAIDs: DNA barcoding as a tool in the development and validation in silico and in vitro of detection systems to four species of Characiformes of commercial importance in the Brazilian Amazon. Mol Biol Rep 2023; 50:10657-10662. [PMID: 37962704 DOI: 10.1007/s11033-023-08872-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The COI mitochondrial gene has been chosen as the "DNA barcode in animals" and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system. METHODS AND RESULTS The present study aimed to develop a Specific Molecular Detection System (SMDS: FishDNAIDs) (primers and probe sets) for the following four target species: Prochilodus nigricans, Potamorhina altamazonica, Psectrogaster rutiloides and Triportheus angulatus, in qPCR assays. In silico and in vitro tests (using gDNA) were performed to test these sets. The database generated contained the cytochrome c oxidase subunit I (COI) nucleotide sequence for 183 specimens of Characiformes, distributed in 34 species representing eight families. In silico, primers designed for the target species amplified different species from the same genus, except for P. rutiloides, which amplified only the target species. In the in vitro test, using the SYBRGreentm and TaqMan® fluorescence systems, both sets detected the respective target species (P. nigricans, P. altamazonica, P. rutiloides and T. angulatus). In the qPCR assays using SYBRGreentm, species considered to be related were also detected, in addition to the target species, with the exception of P. amazonica and P. essequibensis (correlated to P. rutiloides). All target species were detected in the qPCR assays using the TaqMan® system; however, with the SMDS PALT, the target species P. altamazonica was detected with low CT values (22.21 ± 0.17) as well as the correlates of P. latior and P. pristigaster, though with high CT values (23.51 ± 0.19 and 30.21 ± 0.95). This assay uniquely identifies known adult tissue samples from all four species. CONCLUSIONS The primers and probe sets developed can act as powerful tools for detecting the target Characiformes species.
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Affiliation(s)
- Danniel Rocha Bevilaqua
- Instituto Federal de Educação Ciência e Tecnologia do Amazonas (IFAM), Campus Avançado, Highway Manoel Urbano, km 77 - Morada do Sol, Manacapuru, AM, CEP 69400-000, Brazil.
| | - Jacqueline Silva Batista
- Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Adolfo José da Mota
- Faculdade de Ciências Agrárias, Departamento de Ciências Fundamentais e Desenvolvimento Agrícola, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
| | - Ana Caroline Viana da Silva
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Andreza Mikeyne Silva da Mota
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais - PPG MBT, Universidade Estadual do Amazonas - UEA, Manaus, AM, Brazil
| | - Kyara Martins Formiga
- Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Carlos Edwar de Carvalho Freitas
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
- Faculdade de Ciências Agrárias, Departamento de Ciências Pesqueiras, Universidade Federal do Amazonas, Manaus, AM, Brazil
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19
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Tadmor‐Levi R, Feldstein‐Farkash T, Milstein D, Golani D, Leader N, Goren M, David L. Revisiting the species list of freshwater fish in Israel based on DNA barcoding. Ecol Evol 2023; 13:e10812. [PMID: 38125953 PMCID: PMC10731390 DOI: 10.1002/ece3.10812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity "hotspots." This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region.
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Affiliation(s)
- Roni Tadmor‐Levi
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Tamar Feldstein‐Farkash
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Dana Milstein
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Daniel Golani
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Noam Leader
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Menachem Goren
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Lior David
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
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20
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Amat E, Gómez GF, López-Rubio A, Gómez-Piñerez LM, Albertino Rafael J. A short fragment of mitochondrial DNA for the taxonomic identification of blow flies (Diptera: Calliphoridae) in northwestern South America. JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:931-943. [PMID: 37467349 DOI: 10.1093/jme/tjad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023]
Abstract
Blow flies are of medical, sanitary, veterinary, and forensic importance. Their accurate taxonomic identification is essential for their use in applied research. However, neotropical fauna has not been completely studied or described, and taxa identification without the required training is a difficult task. Additionally, the current morphological keys are not fitting to all extant taxa. Molecular-based approaches are widely used to overcome these issues, including the standard 5' COI barcode fragment (~650 base pairs [bp]) for identification at the species level. Here, a shorter sequence of 5' COI fragment (~342 bp) was assessed for the identification of 28 blow fly species inhabiting the northwest of South America. One tree-based (the generalized mixed Yule-coalescent-GMYC) and 3 distance-based approaches (automatic barcode gap discover - ABGD, the best close match - BCM, and the nearest neighbor - NN) analyses were performed. Noticeably, the amplification and sequencing of samples that had been preserved for up to 57 years were successful. The tree topology assigned 113 sequences to a specific taxon (70% effectiveness), while the distance approach assigned to 95 (59% effectiveness). The short fragment allowed the molecular identification of 19 species (60% of neotropical species except for the Lucilia species and Hemilucilia semidiaphana). According to these findings, the taxonomic and faunistic considerations of the blow fly fauna were provided. Overall, the short fragment approach constitutes an optimal species confirmation tool for the most common blow flies in northwestern South America.
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Affiliation(s)
- Eduardo Amat
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
- Programa de Pós-graduação em Entomologia - Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Giovan F Gómez
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
- Dirección Académica, Escuela de Pregrados, Universidad Nacional de Colombia Sede de La Paz, La Paz, Cesar, Colombia
| | - Andrés López-Rubio
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
| | - Luz M Gómez-Piñerez
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
| | - Jose Albertino Rafael
- Programa de Pós-graduação em Entomologia - Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
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Huang WC, Evacitas FC, Balisco RA, Nañola CL, Chou TK, Jhuang WC, Chang CW, Shen KN, Shao KT, Liao TY. DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle. Sci Rep 2023; 13:14867. [PMID: 37684303 PMCID: PMC10491795 DOI: 10.1038/s41598-023-41832-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.
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Affiliation(s)
- Wen-Chien Huang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Florence Chan Evacitas
- Department of Biology and Environmental Science, University of the Philippines Cebu, Cebu City, Philippines
| | - Rodulf Anthony Balisco
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- College of Fisheries and Aquatic Sciences, Western Philippines University, Puerto Princesa, Philippines
| | - Cleto L Nañola
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Davao City, Philippines
| | - Tak-Kei Chou
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wei-Cheng Jhuang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Chih-Wei Chang
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung, Taiwan
- Institute of Marine Ecology and Conservation, National Sun Yat-sen University, Kaohsiung, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Kang-Ning Shen
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung, Taiwan
| | - Kwang-Tsao Shao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan.
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22
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Van Caenegem W, Blondelle A, Dumolein I, Santamaria B, Dick CW, Hiller T, Liu J, Quandt CA, Villarreal Saucedo RV, Verbeken A, Haelewaters D. Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction. Mycologia 2023; 115:714-737. [PMID: 37589548 DOI: 10.1080/00275514.2023.2230114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023]
Abstract
This paper describes and illustrates five new species of Gloeandromyces (Ascomycota, Laboulbeniales) associated with tropical American bat flies (Diptera, Streblidae). These are Gloeandromyces cusucoensis sp. nov. from Trichobius uniformis in Costa Rica and Honduras, G. diversiformis sp. nov. from Strebla wiedemanni in Costa Rica, G. plesiosaurus sp. nov. from Trichobius yunkeri in Panama, G. pseudodickii sp. nov. from Trichobius longipes in Ecuador and Panama, and G. verbekeniae sp. nov. from Strebla galindoi in Ecuador and Panama. The description of these five species doubles the number of known species in the genus. Morphological characteristics, host association, and a three-locus (18S nuc rDNA, 28S nuc rDNA, TEF1) phylogenetic reconstruction support placement of these taxa in the genus Gloeandromyces. Three of the new species are polymorphic; they have multiple morphotypes that grow in specific positions on the host integument: G. diversiformis f. diversiformis, f. musiformis, and f. vanillicarpiformis; G. plesiosaurus f. asymmetricus and f. plesiosaurus; and G. verbekeniae f. verbekeniae and f. inflexus. Finally, a dichotomous key to all species and morphotypes is presented.
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Affiliation(s)
- Warre Van Caenegem
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Aimée Blondelle
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Iris Dumolein
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Brianna Santamaria
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Carl W Dick
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky 42101
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois 60605
| | - Thomas Hiller
- Department of Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart 70599, Germany
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | | | - Annemieke Verbeken
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent 9000, Belgium
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309
- Herbario UCH, Universidad Autónoma de Chiriquí, Apartado Postal 0427, David, Panama
- Centro de Investigaciones Micológicas, Universidad Autónoma de Chiriquí, Apartado Postal 0427, David, Panama
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Werner MJ, Hausmann A, Kostjuk I, Wanke D, Rajaei H. Integrative taxonomic revision of the genus Phaselia Guene, [1858] (Geometridae: Ennominae) in the Middle East and Central Asia. Zootaxa 2023; 5326:1-66. [PMID: 38220889 DOI: 10.11646/zootaxa.5326.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Indexed: 01/16/2024]
Abstract
In the past, the high intraspecific variation of wing pattern within the genus Phaselia Guene, [1858] repeatedly led to misidentifications. In this study, we applied an integrative approach using external and internal morphological characters, along with DNA barcoding and distribution data to review the taxonomy of the genus Phaselia in the Middle East and Central Asia. For this study, 710 specimens, including type specimens and 242 genitalia slides were prepared and examined. As a result, P. phaeoleucaria (Lederer, 1855) stat. rev. is reinstated from synonymy of P. serrularia; P. phaeoleucaria shurensis Wehrli 1941 comb. nov. is regarded as a subspecies of P. phaeoleucaria stat. rev. instead of a subspecies of P. serrularia; P. serrularia catharia Wehrli, 1941 syn. nov. is regarded as a junior synonym of P. phaeoleucaria shurensis comb. nov.; P. narynaria Oberthr, 1913 syn. nov. is regarded as a junior synonym of P. serrularia (Eversmann, 1847); P. pithana Wehrli, 1941 bona sp. is raised to species level from subspecies of P. serrularia. Furthermore, two species and two subspecies are described as new to science: P. smettboi sp. nov., P. sihvoneni sp. nov., P. erika jonubi ssp. nov. and P. erika sindhi ssp. nov. Wing pattern, and both male and female genitalia of all discussed taxa are illustrated, their distribution patterns are shown on a map and CO1 data is evaluated to confirm our taxonomic decisions.
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Affiliation(s)
- Maria Johanna Werner
- University of Hohenheim; Systematic Entomology (190n); Garbenstr. 30; D-70599 Stuttgart; Germany; State Museum of Natural History Stuttgart; Entomology; Rosenstein 1; D-70191 Stuttgart; Germany.
| | - Axel Hausmann
- SNSB-ZSM; Bavarian State Collection of Zoology; Mnchhausenstr. 21; D-81247 Munich; Germany.
| | - Igor Kostjuk
- Zoological museum; Kyiv National Taras Shevchenko University; Volodymyrska str. 60; UA-01601 Kyiv; Ukraine.
| | - Dominic Wanke
- University of Hohenheim; Systematic Entomology (190n); Garbenstr. 30; D-70599 Stuttgart; Germany; State Museum of Natural History Stuttgart; Entomology; Rosenstein 1; D-70191 Stuttgart; Germany.
| | - Hossein Rajaei
- State Museum of Natural History Stuttgart; Entomology; Rosenstein 1; D-70191 Stuttgart; Germany.
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24
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Kamdem MM, Ramoejane M, Voua Otomo P. Local-Scale DNA Barcoding of Afrotropical Hoverflies (Diptera: Syrphidae): A Case Study of the Eastern Free State of South Africa. INSECTS 2023; 14:692. [PMID: 37623402 PMCID: PMC10455394 DOI: 10.3390/insects14080692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023]
Abstract
The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14-17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses.
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Affiliation(s)
- Michel Mathurin Kamdem
- Department of Zoology and Entomology, University of the Free State, Private Bag x13, Phuthaditjhaba 9866, South Africa; (M.R.); (P.V.O.)
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25
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Gutiérrez-López R, Egeter B, Paupy C, Rahola N, Makanga B, Jiolle D, Bourret V, Melo M, Loiseau C. Monitoring mosquito richness in an understudied area: can environmental DNA metabarcoding be a complementary approach to adult trapping? BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:456-468. [PMID: 37183666 DOI: 10.1017/s0007485323000147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Mosquito surveillance programmes are essential to assess the risks of local vector-borne disease outbreaks as well as for early detection of mosquito invasion events. Surveys are usually performed with traditional sampling tools (i.e., ovitraps and dipping method for immature stages or light or decoy traps for adults). Over the past decade, numerous studies have highlighted that environmental DNA (eDNA) sampling can enhance invertebrate species detection and provide community composition metrics. However, the usefulness of eDNA for detection of mosquito species has, to date, been largely neglected. Here, we sampled water from potential larval breeding sites along a gradient of anthropogenic perturbations, from the core of an oil palm plantation to the rainforest on São Tomé Island (Gulf of Guinea, Africa). We showed that (i) species of mosquitoes could be detected via metabarcoding mostly when larvae were visible, (ii) larvae species richness was greater using eDNA than visual identification and (iii) new mosquito species were also detected by the eDNA approach. We provide a critical discussion of the pros and cons of eDNA metabarcoding for monitoring mosquito species diversity and recommendations for future research directions that could facilitate the adoption of eDNA as a tool for assessing insect vector communities.
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Affiliation(s)
- Rafael Gutiérrez-López
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Animal Health Research Center, National Food and Agriculture Research and Technology Institute (INIA-CISA-CSIC), Valdeolmos, Spain
| | - Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Christophe Paupy
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Nil Rahola
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Boris Makanga
- Institut de Recherche en Écologie Tropicale/CENAREST, BP 13354 Libreville, Gabon
| | - Davy Jiolle
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Vincent Bourret
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- INRAE - Université de Toulouse UR 0035 CEFS, 31326 Castanet Tolosan, France
| | - Martim Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP - Natural History and Science Museum of the University of Porto, Porto, Portugal
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
| | - Claire Loiseau
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- CEFE, Université de Montpellier, CNRS, Montpellier, France
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Serrana JM, Watanabe K. Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis. PLoS One 2023; 18:e0289056. [PMID: 37486933 PMCID: PMC10365294 DOI: 10.1371/journal.pone.0289056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
Metabarcoding is a molecular-based tool capable of large quantity high-throughput species identification from bulk samples that is a faster and more cost-effective alternative to conventional DNA-sequencing approaches. Still, further exploration and assessment of the laboratory and bioinformatics strategies are required to unlock the potential of metabarcoding-based inference of haplotype information. In this study, we assessed the inference of freshwater macroinvertebrate haplotypes from metabarcoding data in a mock sample. We also examined the influence of DNA template concentration and PCR cycle on detecting true and spurious haplotypes. We tested this strategy on a mock sample containing twenty individuals from four species with known haplotypes based on the 658-bp Folmer region of the mitochondrial cytochrome c oxidase gene. We recovered fourteen zero-radius operational taxonomic units (zOTUs) of 421-bp length, with twelve zOTUs having a 100% match with the Sanger haplotype sequences. High-quality reads relatively increased with increasing PCR cycles, and the relative abundance of each zOTU was consistent for each cycle. This suggests that increasing the PCR cycles from 24 to 64 did not affect the relative abundance of each zOTU. As metabarcoding becomes more established and laboratory protocols and bioinformatic pipelines are continuously being developed, our study demonstrated the method's ability to infer intraspecific variability while highlighting the challenges that must be addressed before its eventual application for population genetic studies.
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Affiliation(s)
- Joeselle M Serrana
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
- Faculty of Engineering, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
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Filonzi L, Ardenghi A, Rontani PM, Voccia A, Ferrari C, Papa R, Bellin N, Nonnis Marzano F. Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species. Foods 2023; 12:2420. [PMID: 37372635 DOI: 10.3390/foods12122420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.
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Affiliation(s)
- Laura Filonzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessia Ardenghi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Pietro Maria Rontani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Voccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Riccardo Papa
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Nicolò Bellin
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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28
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Atencio GWG, Zanini R, Deprá M, Romanowski HP. Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae). AN ACAD BRAS CIENC 2023; 95:e20210503. [PMID: 37341269 DOI: 10.1590/0001-3765202320210503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 06/22/2023] Open
Abstract
Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.
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Affiliation(s)
- Guilherme Wagner G Atencio
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade de Lisboa, Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais, Edifício C2, 5.º piso, Sala 2.5.46, Código Postal 1749-016, Campo Grande, Lisboa, Portugal
| | - Rebeca Zanini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Universidade Nova de Lisboa, Faculdade de Ciências Médicas, Laboratório de Biomedicina Integrativa, Rua do Instituto Bacteriológico 5, Código Postal 1169-056, Lisboa, Portugal
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312 M, Caixa Postal 15053, Agronomia, 90650-001 Porto Alegre, RS, Brazil
| | - Helena P Romanowski
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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Guo L, Wang X, Wang R, Li P. Characterization and Comparative Analysis of Chloroplast Genomes of Medicinal Herb Scrophularia ningpoensis and Its Common Adulterants (Scrophulariaceae). Int J Mol Sci 2023; 24:10034. [PMID: 37373180 DOI: 10.3390/ijms241210034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Scrophularia ningpoensis, a perennial medicinal plant from the Scrophulariaceae family, is the original species of Scrophulariae Radix (SR) in the Chinese Pharmacopoeia. This medicine is usually deliberately substituted or accidentally contaminated with other closely related species including S. kakudensis, S. buergeriana, and S. yoshimurae. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete chloroplast genomes of the four mentioned Scrophularia species were sequenced and characterized. Comparative genomic studies revealed a high degree of conservation in genomic structure, gene arrangement, and content within the species, with the entire chloroplast genome spanning 153,016-153,631 bp in full length, encoding 132 genes, including 80 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 18 duplicated genes. We identified 8 highly variable plastid regions and 39-44 SSRs as potential molecular markers for further species identification in the genus. The consistent and robust phylogenetic relationships of S. ningpoensis and its common adulterants were firstly established using a total of 28 plastid genomes from the Scrophulariaceae family. In the monophyletic group, S. kakudensis was determined to be the earliest diverging species, succeeded by S. ningpoensis. Meanwhile, S. yoshimurae and S. buergeriana were clustered together as sister clades. Our research manifestly illustrates the efficacy of plastid genomes in identifying S. ningpoensis and its counterfeits and will also contribute to a deeper understanding of the evolutionary processes within Scrophularia.
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Affiliation(s)
- Lei Guo
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xia Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Razuvaeva AV, Ulyanova EG, Skolotneva ES, Andreeva IV. Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods. Vavilovskii Zhurnal Genet Selektsii 2023; 27:240-249. [PMID: 37293445 PMCID: PMC10244583 DOI: 10.18699/vjgb-23-30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/25/2022] [Accepted: 01/07/2022] [Indexed: 06/10/2023] Open
Abstract
Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Affiliation(s)
- A V Razuvaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Ulyanova
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
| | - E S Skolotneva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Andreeva
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
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Li M, Lei T, Wang G, Zhang D, Liu H, Zhang Z. Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China. Ecol Evol 2023; 13:e10031. [PMID: 37091562 PMCID: PMC10121320 DOI: 10.1002/ece3.10031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/25/2023] Open
Abstract
Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.
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Affiliation(s)
- Min Li
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Ting Lei
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Guobin Wang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Danli Zhang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Huaxi Liu
- Department of Life SciencesNatural History MuseumLondonUK
| | - Zhiwei Zhang
- College of Forestry, Shanxi Agricultural UniversityJinzhongChina
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Jossart Q, Bauman D, Moreau CV, Saucède T, Christiansen H, Brasier MJ, Convey P, Downey R, Figuerola B, Martin P, Norenburg J, Rosenfeld S, Verheye M, Danis B. A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula). ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:514. [PMID: 36973586 DOI: 10.1007/s10661-023-11066-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Marine Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- UMR CNRS 6282, Université de Bourgogne, Dijon, France.
| | - David Bauman
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, Montpellier, IRD, France
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Camille Ve Moreau
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Madeleine J Brasier
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, United Kingdom
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
| | - Rachel Downey
- Fenner School of Environment & Society, Australian National University, Canberra, Australia
| | | | - Patrick Martin
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Jon Norenburg
- Smithsonian Institution National Museum of Natural History, Washington, United States of America
| | - Sebastian Rosenfeld
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
- Laboratorio de Ecosistemas Marinos Antarticos y Subantarticos, Universidad de Magallanes, Punta Arenas, Chile
- Centro de Investigación Gaia‑Antártica, Universidad de Magallanes, Punta Arenas, Chile
| | - Marie Verheye
- Laboratory of Trophic and Isotopes Ecology (LETIS), Université de Liège, Liège, Belgium
- Laboratory of Evolutionary Ecology, Université de Liège, Liège, Belgium
| | - Bruno Danis
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Han W, Tang H, Wei L, Zhang E. The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecol Evol 2023; 13:e9849. [PMID: 36861023 PMCID: PMC9969238 DOI: 10.1002/ece3.9849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.
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Affiliation(s)
- Wu Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Hongqu Tang
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Lili Wei
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Enlou Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
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Rodrigues BL, Galati EAB. Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review. Acta Trop 2023; 238:106778. [PMID: 36435214 DOI: 10.1016/j.actatropica.2022.106778] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.
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Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904.
| | - Eunice Aparecida Bianchi Galati
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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Hadj-Henni L, Djerada Z, Millot C, Cousinat M, Lehrter V, Augot D. Wing morphology variations in Culicoides circumscriptus from France. Front Vet Sci 2023; 10:1089772. [PMID: 37168098 PMCID: PMC10164937 DOI: 10.3389/fvets.2023.1089772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/23/2023] [Indexed: 05/13/2023] Open
Abstract
The biting midge Culicoides circumscriptus Kieffer, 1918 is a European widespread vector of avian malaria throughout the continent and is a possible vector of Akabane virus and Bluetongue virus. This species populates a wide range of environments in contrasting ecological settings often exposed to strong seasonal fluctuations. The main goals of this study were to investigate C. circumscriptus phenotypic variation at three departments in France (Corsica Island, Moselle and Var) and to determine if its phenotypes vary with the environment. Culicoides circumscriptus wing phenotypes were analyzed using a geometric morphometric approach based on anatomical landmarks and outlines of the wing. Dendogram trees based on landmarks and the outlines-2 set (cell m4) showed similar topologies and separated populations of C. circumscriptus. In contrast, another set of outlines-1 (covering the r-m cross vein, M, radiale and arculus) presented a different hierarchical clustering tree. The phenotypic variation observed in C. circumscriptus indicated that these populations are exposed to environmental and ecological pressures. Our results suggest the presence of phenotypic plasticity in this species.
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Affiliation(s)
- Leila Hadj-Henni
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, Reims Cedex, France
| | - Zoubir Djerada
- Department of Medical Pharmacology, EA 3801, SFR Cap Santé, Reims University Hospital, Reims Cedex, France
| | - Christine Millot
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, Reims Cedex, France
- *Correspondence: Christine Millot, ; Denis Augot,
| | - Mireille Cousinat
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, Reims Cedex, France
| | - Véronique Lehrter
- Université de Reims Champagne-Ardenne, Unité BioSpecT, EA7506, SFR Cap Santé, UFR de Pharmacie, Reims, France
| | - Denis Augot
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, Reims Cedex, France
- ANSES, INRAe, ENVA, UMR-BIPAR, Laboratoire de Santé Animale, Maisons-Alfort Cedex, France
- *Correspondence: Christine Millot, ; Denis Augot,
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Nascimento BM, de Paula TS, Brito PMM. DNA barcode of tilapia fish fillet from the Brazilian market and a standardized COI haplotyping for molecular identification of Oreochromis spp. (Actinopterygii, Cichlidae). FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2022. [DOI: 10.1016/j.fsiae.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Howard A, Monadjem A, MacFadyen D, Chimimba CT. Testing the efficacy of bat monitoring methods for identification and species surveys in KwaZulu-Natal province, South Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2138722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alexandra Howard
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
| | - Ara Monadjem
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Duncan MacFadyen
- Department of Research and Conservation, Oppenheimer Generations, Johannesburg, South Africa
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- DSI-NRF Centre of Excellence for Invasion Biology (CIB), Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Šlapeta J, Halliday B, Chandra S, Alanazi AD, Abdel-Shafy S. Rhipicephalus linnaei (Audouin, 1826) recognised as the "tropical lineage" of the brown dog tick Rhipicephalus sanguineus sensu lato: Neotype designation, redescription, and establishment of morphological and molecular reference. Ticks Tick Borne Dis 2022; 13:102024. [PMID: 36063755 DOI: 10.1016/j.ttbdis.2022.102024] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/15/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022]
Abstract
We re-describe the adult stages of Rhipicephalus linnaei (Audouin, 1826), and characterise its diagnostic molecular traits. A male R. linnaei collected in Esna City, Luxor Governorate, Egypt is designated as the neotype. Rhipicephalus linnaei is re-established as a valid tick name and removed from the synonymy list of Rhipicephalus sanguineus (Latreille, 1806). Rhipicephalus linnaei is most similar to R. sanguineus and Rhipicephalus camicasi Morel, Mouchet & Rodhain, 1976 because they share similar elongated comma-like spiracula that are narrowly visible dorsally, and the dorsal prolongation is narrower than the width of the adjacent festoon. The male of R. camicasi is distinguished from R. linnaei by the non-tapering caudal widening of the spiracula. The male of R. sanguineus is distinguished from R. linnaei by shorter extension that does not taper into a long narrow extension of the spiracula. The genital pore atrium of female R. linnaei is broadly U-shaped, while it is a narrower U-shape in R. sanguineus. The remaining species within the R. sanguineus species complex - Rhipicephalus sulcatus Neumann, 1908, Rhipicephalus turanicus Pomerantsev, 1940, Rhipicephalus guilhoni Morel & Vassilades, 1963, Rhipicephalus secundus Feldman-Muhsam, 1952 and Rhipicephalus afranicus Bakkes, 2020, all exhibit spiracula with the dorsal prolongation as wide as the adjacent festoon. The DNA sequence of R. linnaei is most closely related to R. guilhoni. The phylogenetic analysis of mitogenome (mtDNA) sequences including assembled mtDNA from whole genome sequencing of the neotype supports R. linnaei as a well-defined taxon when compared with DNA sequences of other species of the R. sanguineus species complex, in particular: R. sanguineus, R. turanicus, R. secundus and R. camicasi. Molecularly, R. linnaei belongs to the so-called R. sanguineus s.l. "tropical lineage" distributed globally including the Americas, Africa, Europe, Asia and is the only species from R. sanguineus species complex in Australia.
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Affiliation(s)
- Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales 2006, Australia.
| | - Bruce Halliday
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Shona Chandra
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Abdullah D Alanazi
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, Ad-Dawadimi, Saudi Arabia
| | - Sobhy Abdel-Shafy
- Department of Parasitology and Animal Diseases, Veterinary Research Institute, National Research Centre, Dokki, Giza, Egypt
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Sofiev M, Sofieva S, Palamarchuk J, Šaulienė I, Kadantsev E, Atanasova N, Fatahi Y, Kouznetsov R, Kuula J, Noreikaite A, Peltonen M, Pihlajamäki T, Saarto A, Svirskaite J, Toiviainen L, Tyuryakov S, Šukienė L, Asmi E, Bamford D, Hyvärinen AP, Karppinen A. Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign. ENVIRONMENTAL RESEARCH 2022; 214:113798. [PMID: 35810819 DOI: 10.1016/j.envres.2022.113798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.
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Affiliation(s)
- Mikhail Sofiev
- Finnish Meteorological Institute, Helsinki, Finland; Vilnius University, Vilnius, Lithuania.
| | - Svetlana Sofieva
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Nina Atanasova
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | - Yalda Fatahi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Joel Kuula
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Martina Peltonen
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | - Julija Svirskaite
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Eija Asmi
- Finnish Meteorological Institute, Helsinki, Finland
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41
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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42
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Bonvicino CR, Lazar A, Povill C, Caramaschi FP, de Freitas TPT, Crisóstomo CF, Botelho ALM, D’Andrea PS. Phylogeny of Didelphid marsupials (Didelphimorphia) from Acre, western Amazonia. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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43
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Tadmor-Levi R, Cummings D, Borovski T, Shapira R, Marcos-Hadad E, David L. A method for quick and efficient identification of cichlid species by high resolution DNA melting analysis of minibarcodes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1010838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freshwater bodies are key in supporting aquatic and terrestrial life. Ecological balance of freshwater habitats is very vulnerable, hence, often significantly disrupted by climatic changes and anthropogenic acts. In Israel, due to its relatively arid climate, many freshwater resources have been disrupted and still are under great pressure. The Sea of Galilee is the largest surface freshwater body in the Middle East and a habitat to unique populations of several fishes, including six cichlid species. Studies on the ecology of these fish and their conservation require effective monitoring tools. In this study, a simple and efficient molecular method was developed to identify the species of these lake cichlids using high resolution melting analysis of mini DNA barcodes. The species of an individual sample can be identified by a single tube PCR reaction. This assay successfully identified sequence differences both among and within species. Here, this method identified the species for 279 small cichlid fry that could not be morphologically identified, allowing to estimate relative species abundance and map their distribution in time and location. The results are key to understand not only the ecology of young stages but also their recruitment potential to adult fish populations and their sustainability. This method can be readily implemented in further ecological studies and surveys related to these species, in the lake and its surroundings, as a tool to enhance understanding and protection of these species.
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Godunko RJ, Alba-Tercedor J, Grabowski M, Rewicz T, Staniczek AH. Cenozoic origins of the genus Calliarcys (Insecta, Ephemeroptera) revealed by Micro-CT, with DNA barcode gap analysis of Leptophlebiinae and Habrophlebiinae. Sci Rep 2022; 12:15228. [PMID: 36075938 PMCID: PMC9458648 DOI: 10.1038/s41598-022-18234-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Mayflies (Ephemeroptera) are among the oldest pterygote insects, with the earliest fossils dating back to the Late Carboniferous. Within mayflies, Leptophlebiidae are a highly diverse and widespread group, with approximately 140 genera and 640 species. Whereas taxonomy, systematics, and phylogeny of extant Leptophlebiidae are in the focus of extensive studies, little is known about leptophlebiid fossil taxa. Because fossil remains of Ephemeroptera in sedimentary rocks are relatively rare, inclusions of mayflies in amber are a unique source of information on their evolution and diversity in the past. Leptophlebiidae found in Cenozoic resins mostly belong to the subfamilies Leptophlebiinae (in Eocene Baltic amber) and Atalophlebiinae (in Miocene Dominican and Mexican ambers). In the present contribution, we confirm the first finding of the genus Calliarcys from Eocene Baltic amber by using Micro-CT, which allowed confirming its generic placement by visualizing diagnostic key characters otherwise hidden by a cloud of turbidity. Additionally, we present first molecular data on the extant species Calliarcys humilis Eaton, 1881 from the Iberian Peninsula and the barcode gap analysis for Leptophlebiinae and Habrophlebiinae.
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Affiliation(s)
- Roman J Godunko
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic. .,Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237, Łódź, Poland. .,State Museum of Natural History, NAS Ukraine, Teatralna 18, Lviv, 79008, Ukraine.
| | - Javier Alba-Tercedor
- Department of Zoology, Faculty of Sciences, University of Granada, Avenida de Fuente Nueva s/n, 18071, Granada, Spain
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237, Łódź, Poland
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237, Łódź, Poland
| | - Arnold H Staniczek
- Department of Entomology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany
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Yang H, Yang Z, Dong W. Morphological Identification and Phylogenetic Analysis of Laelapin Mite Species (Acari: Mesostigmata: Laelapidae) from China. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:273-279. [PMID: 36041489 PMCID: PMC9441453 DOI: 10.3347/kjp.2022.60.4.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/06/2022] [Indexed: 11/27/2022]
Abstract
Laelapinae mites are involved in transmission of microbial diseases between wildlife and humans, with an impact on public health. In this study, 5 mite members in the subfamily Laelapinae (laelapin mites; LM) were morphologically identified by light microscopy, and the phylogenetic relationship of LM was analyzed in combination with the sequence information of part of the LM cytochrome oxidase subunit I (cox1) gene. The morphological identification revealed that 5 mites belonged to the genera Laelaps and Haemolaelaps, respectively. Sequence analysis showed that the ratio of non-synonymous mutation rate to synonymous mutation rate of LM was less than 1, indicating that the LM cox1 gene had undergone purifying selection. Phylogenetic analysis showed that the Laelapinae is a monophyletic group. The genera Haemolaelaps and Hyperlaelaps did not separated into distinct clades but clustered together with species of the genus Laelaps. Our morphological and molecular analyses to describe the phylogenetic relationships among different genera and species of Laelapinae provide a reference for the improvement and revision of the LM taxonomy system.
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Affiliation(s)
- Huijuan Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, Yunnan 671000, China
| | - Zhihua Yang
- School of Public Health, Dali University, Dali, Yunnan 671000, China
| | - Wenge Dong
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, Yunnan 671000, China
- Corresponding author ()
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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] [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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Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:865606. [PMID: 35937320 PMCID: PMC9355515 DOI: 10.3389/fpls.2022.865606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/16/2022] [Indexed: 05/24/2023]
Abstract
Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.
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Affiliation(s)
- Qing Duan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfen Cui
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Wenjie Jia
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Ameliorative effects of Guilandina bonduc L. aqueous seed extract on letrozole induced polycystic ovary syndrome in female wistar albino rats. ADVANCES IN TRADITIONAL MEDICINE 2022. [DOI: 10.1007/s13596-022-00652-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Current Techniques to Study Beneficial Plant-Microbe Interactions. Microorganisms 2022; 10:microorganisms10071380. [PMID: 35889099 PMCID: PMC9317800 DOI: 10.3390/microorganisms10071380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
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