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Thipphet K, Horpaopan S, Jaturas N, Thanchomnang T, Moophayak K, Chaiwong T, Hongsrichan N, Nakhonkam W, Phuwanatsarunya P, Dumidae A, Bunthong S, Kaewbungkord T, Sanit S, Ruankham W, Vitta A, Kurahashi H, Sukontason KL, Bunchu N. Molecular identification and genetic variation of forensically important fly species (Order: Diptera) in Thailand using DNA barcoding. Acta Trop 2024; 258:107366. [PMID: 39179166 DOI: 10.1016/j.actatropica.2024.107366] [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: 06/22/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Forensic entomology plays a crucial role in criminal investigations by providing vital insights into minimum postmortem interval (PMImin) and corpse relocation by identifying insect species that colonize in decomposing remains. This study aimed to identify and analyze the genetic variation of forensically significant fly species in Thailand, using DNA barcoding of the mitochondrial cytochrome c oxidase subunit I COI gene. A total of 3,220 fly specimens were collected from 18 provinces across six regions of Thailand from October 2017 to September 2022. These specimens were classified by morphological identification into 21 species among three Dipteran families: Calliphoridae, Muscidae, and Sarcophagidae, with Chrysomya megacephala Diptera: Calliphoridae being the most abundant species. DNA barcoding confirmed the morphological identifications with 100 % accuracy, showing low intraspecific K2P distances0.0 to 1.1 %) and significant interspecific K2P distances 2.5 % to 17.2 %. A Neighbour-Joining (NJ) analysis was conducted to assess the molecular identification capabilities of the barcoding region. This analysis successfully recovered nearly all species as distinct monophyletic groups. The species groupings obtained were generally consistent with both morphological and molecular identifications. These findings underscore the effectiveness of DNA barcoding for precise species identification and contribute to a comprehensive database of forensically important flies in Thailand, thus facilitating improved forensic investigations and biodiversity studies.
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Affiliation(s)
- Ketsarin Thipphet
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medicine, Chaing Mai University, Muang, Chaing Mai 50200, Thailand
| | - Narong Jaturas
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | | | - Kittikhun Moophayak
- Nakhonsawan Campus, Mahidol University, Khaothong subdistrict, Phayuhakiri district, Nakhonsawan 60130, Thailand
| | - Tarinee Chaiwong
- College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Nuttanan Hongsrichan
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wannacha Nakhonkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Pluemkamon Phuwanatsarunya
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Abdulhakam Dumidae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Suthawan Bunthong
- Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | | | - Sangob Sanit
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Watcharapong Ruankham
- Faculty of Public Health, Chiang Rai Rajabhat University, Chiang Rai 57100, Thailand
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Hiromu Kurahashi
- International Department of Dipterology (IDD), Hikawadai 1-2-21, Higashikurume City, Tokyo 203-0004 Japan
| | - Kabkaew L Sukontason
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nophawan Bunchu
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand.
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2
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Kaila L, Huemer P. Elachistadimicatella sensu auctt.-a complex of neglected species diversity (Lepidoptera, Elachistidae) from European mountain systems. Zookeys 2024; 1212:179-194. [PMID: 39318677 PMCID: PMC11420535 DOI: 10.3897/zookeys.1212.126598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/15/2024] [Indexed: 09/26/2024] Open
Abstract
Elachistadimicatella Rebel, 1903, has so far been considered a species in Europe with restricted distribution from Ukraine to western France. The species occurs on mountainous regions. However, the in-depth analysis of a taxonomically uncertain species of Elachista from the Cottian Alps (Italy), especially through DNA barcoding and subsequent morphological studies, led to the realization that individuals previously identified as E.dimicatella from the Cottian Alps and the Pyrenees were misidentified. According to our research, a total of three species can be differentiated: E.dimicatella from Carpathians and its former junior synonym E.niphadophanes Meyrick, 1937, sp. rev., from the Pyrenees, as well as the newly described E.cottiella sp. nov. from southwestern Alps, hitherto incorrectly identified as E.dimicatella. Diagnostic features of the three species are discussed and illustrated. Elachistadimicatella and E.niphadophanes are redescribed.
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Affiliation(s)
- Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, P.O.Box 17, FI-00014, Helsinki, Finland University of Helsinki Helsinki Finland
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Natural History Collections, Krajnc-Str. 1, A-6060 Hall in Tirol, Austria Tiroler Landesmuseen Betriebsges.m.b.H., Natural History Collections Hall in Tirol Austria
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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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Wierer A, von Hoermann C, Benbow ME, Büchner C, Feldhaar H, Fiderer C, Mitesser O, Rietz J, Schlüter J, Zeitzler J, Lackner T, Bässler C, Heurich M, Müller J. Mechanisms determining the multi-diversity of carrion visiting species along a gradient of carrion body mass. Oecologia 2024:10.1007/s00442-024-05611-1. [PMID: 39251421 DOI: 10.1007/s00442-024-05611-1] [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: 03/26/2024] [Accepted: 08/21/2024] [Indexed: 09/11/2024]
Abstract
Resource availability and habitat heterogeneity are essential drivers of biodiversity, but their individual roles often remain unclear since both factors are often correlated. Here, we tested the more-individuals hypothesis (MIH) and the habitat-heterogeneity hypothesis (HHH) for bacteria, fungi, dipterans, coleopterans, birds, and mammals on 100 experimentally exposed carcasses ranging by three orders of magnitude in body mass. At the level of each carcass we found marginal or significant support for the MIH for bacteria, fungi, and beetles in spring and significant support for fungi, dipterans, and mammals in summer. The HHH was supported only for bacteria in spring, while it was supported for all groups except mammals in summer. Overall multidiversity always increased with body mass, with a steeper increase in summer. Abundance based rarefaction-extrapolation curves for three classes of body mass showed the highest species richness for medium-sized carcasses, particular for dipterans and microbes, supporting the HHH also among carcasses. These findings complement existing necromass studies of deadwood, showing there are more niches associated with larger resource amounts and an increasing habitat heterogeneity between carcasses most pronounced for medium-sized species. Higher resource amount led to increased diversity of carrion-consuming organisms in summer, particularly due to the increasing number of niches with increasing size. Our findings underline the importance of distributed large carrion as well as medium-sized carrion in ecosystems supporting overall biodiversity of carrion-consumers. Furthermore, the different responses in spring and summer may inform strategies of carrion enrichment management schemes throughout the year.
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Affiliation(s)
- Amelie Wierer
- Chair of Conservation Biology and Forest Ecology, Biocenter University of Würzburg, Glashüttenstr. 5, 96181, Rauhenebrach, Germany
| | - Christian von Hoermann
- Chair of Conservation Biology and Forest Ecology, Biocenter University of Würzburg, Glashüttenstr. 5, 96181, Rauhenebrach, Germany
- Department of Conservation and Research, Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - M Eric Benbow
- Department of Entomology, Department of Osteopathic Medical Specialties; Ecology, Evolution and Behavior Program, AgBioResearch, Michigan State University, East Lansing, MI, USA
| | - Christiane Büchner
- Animal Ecology I, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95440, Bayreuth, Germany
| | - Heike Feldhaar
- Animal Ecology I, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95440, Bayreuth, Germany
| | - Christian Fiderer
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Freyunger Straße 2, 94481, Grafenau, Germany
| | - Oliver Mitesser
- Chair of Conservation Biology and Forest Ecology, Biocenter University of Würzburg, Glashüttenstr. 5, 96181, Rauhenebrach, Germany
| | - Janine Rietz
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Freyunger Straße 2, 94481, Grafenau, Germany
| | - Jens Schlüter
- Department of Conservation and Research, Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Johannes Zeitzler
- Weihenstephan-Triesdorf University of Applied Sciences, Am Hofgarten 4, 85354, Freising, Germany
| | - Tomáš Lackner
- Department of Conservation and Research, Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Claus Bässler
- Department of Conservation and Research, Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
- Fungal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95440, Bayreuth, Germany
| | - Marco Heurich
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Freyunger Straße 2, 94481, Grafenau, Germany
- Institute of Forestry and Wildlife Management, Inland Norway University of Applied Science, NO-2480, Koppang, Norway
| | - Jörg Müller
- Chair of Conservation Biology and Forest Ecology, Biocenter University of Würzburg, Glashüttenstr. 5, 96181, Rauhenebrach, Germany.
- Department of Conservation and Research, Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany.
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5
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Schmidt LA, Brix S, Rossel S, Forster S, Eichsteller A. Unveiling ophiuroid biodiversity across North Atlantic habitats via an integrative perspective. Sci Rep 2024; 14:20405. [PMID: 39223179 PMCID: PMC11369278 DOI: 10.1038/s41598-024-71178-9] [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: 06/07/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
The depths of the North Atlantic Ocean host a species-rich fauna providing heterogeneous habitats from thermal vent fields to cold-water coral reefs. With the increasing threat of destruction of deep-sea habitats due to human impacts, such as demersal fishing and the beginning of deep-sea mining, an analysis of the diversity and distribution of species is crucial for conservation efforts. Brittle stars occur in high biomasses, contributing to the biodiversity of the seafloor. Specimens were collected during several scientific expeditions to gain a more detailed insight into the brittle star diversity in the North Atlantic Ocean. An integrative approach to identify the species with DNA barcoding (mtCOI) in combination with morphological studies revealed 24 species. Most species have been previously identified in the North Atlantic, but sequences for 13 species are newly added to public repositories. Additionally, the MALDI-TOF-MS proteomic analysis was successfully applied for 197 specimens with known COI barcodes. Results are congruent with other molecular species delimitations demonstrating the functionality of proteomics for the identification of brittle stars. This dataset significantly expands our understanding of the taxonomic and genetic diversity of brittle stars and contributes to publicly available data. It emphasizes the importance of considering habitat heterogeneity for large scale patterns of biodiversity.
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Affiliation(s)
- Lydia Anastasia Schmidt
- Institute of Biological Science, University of Rostock, Albert-Einsteinstraße 3, 18059, Rostock, Germany.
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Stefan Forster
- Institute of Biological Science, University of Rostock, Albert-Einsteinstraße 3, 18059, Rostock, Germany
| | - Angelina Eichsteller
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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Lavrador AS, Amaral FG, Moutinho J, Vieira PE, Costa FO, Duarte S. Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach. MARINE ENVIRONMENTAL RESEARCH 2024; 200:106660. [PMID: 39088889 DOI: 10.1016/j.marenvres.2024.106660] [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: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), in particular using filtered seawater. However, comprehensive detection of all NIS may require a diversity of sampling substrates. To assess the effectiveness of 5 sample types (hard and artificial substrates, water, zooplankton) on the recovery of invertebrates' diversity, two marinas were monitored over three time points, using COI and 18S rRNA genes as DNA metabarcoding markers. We detected a total of 628 species and 23 NIS, with only up to 9% species and 17% of NIS detected by all sample types. Hard and artificial substrates were similar to each other but displayed the most significant difference in invertebrate recovery when compared to water eDNA and zooplankton. Five NIS are potential first records for Portugal. No NIS were detected in all sample types and seasons, highlighting the need for varied sampling approaches, and consideration of temporal variation for comprehensive marine NIS surveillance.
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Affiliation(s)
- Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Fábio G Amaral
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jorge Moutinho
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Ferreira AO, Azevedo OM, Barroso C, Duarte S, Egas C, Fontes JT, Ré P, Santos AMP, Costa FO. Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples. Sci Rep 2024; 14:19772. [PMID: 39187534 PMCID: PMC11347574 DOI: 10.1038/s41598-024-69963-7] [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: 06/18/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.
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Affiliation(s)
- André O Ferreira
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Olga M Azevedo
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Cristina Barroso
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Biocant-Transfer Technology Association, 3060-197, Cantanhede, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Biocant-Transfer Technology Association, 3060-197, Cantanhede, Portugal
| | - João T Fontes
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Ré
- MARE-Marine and Environmental Sciences Centre and ARNET-Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - A Miguel P Santos
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Portuguese Institute for the Sea and the Atmosphere (IPMA), 1749-077, Lisboa, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Landers E, Claridge B, Kuhn W, Seymour V, Peek H, Fluet S, Ramgren J, Phelps J, Paulk B, Cordner L, Blaschke J. Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park. ENVIRONMENTAL ENTOMOLOGY 2024; 53:730-739. [PMID: 38853372 DOI: 10.1093/ee/nvae058] [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: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.
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Affiliation(s)
- Emerie Landers
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brandon Claridge
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA
| | - Will Kuhn
- Discover Life in America, 1316 Cherokee Orchard Road, Gatlinburg, TN, 37738, USA
| | - Victoria Seymour
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Hettie Peek
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Scout Fluet
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Ramgren
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Phelps
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brayden Paulk
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Lydia Cordner
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jeremy Blaschke
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
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Knorrn AH, Beuck L, Barros-García D, Fernández-Peralta L, Freiwald A. Gaidropsarus mauritanicus (Gadiformes, Gaidropsaridae) a new three-bearded rockling from a deep-water coral ecosystem with a genetically verified biogeographical distribution of the genus and notes to its ecology and behavior. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39150971 DOI: 10.1111/jfb.15859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 08/18/2024]
Abstract
Gaidropsarus mauritanicus sp. nov. is described from one specimen collected using a grab sample from the Tanoûdêrt Canyon (ca. 20° N) off Mauritania at a depth of 595 m. The new species was further observed during eight remotely operated vehicle (ROV) dives along the Mauritanian slope southwards down to the Tiguent Coral Mound Complex (~17° N) in a bathymetric range between 613 and 416 m. It can be distinguished from congeners by a combination of characteristics, including large eyes (38.1% head length [HL]), large head (25.8% standard length [SL]), elongated pelvic fins (35.7% SL), low number of vertebrae (44), and coloration (pinkish with a dorsal darker brownish hue and bright blotches along the dorsal-fin base). A species-delimitation analysis performed with available cytochrome c oxidase subunit 1 (COI) sequences affiliated to the genus Gaidropsarus additionally supported the validity of the new species. Video analyses showed a deep-water coral-associated and protection-seeking behavior, which may explain why the species has remained undescribed until now. Additional ROV footage from separate deep-water coral sites in the North Atlantic and Mediterranean Sea further highlights the ecological behavior and hidden diversity of bathyal three-bearded rocklings. Here, we additionally discuss the biogeographical distribution of all genetically verified Gaidropsarus spp. in combination with genetic data and morphological characters. G. mauritanicus sp. nov. is closely related to a species from Tasmania (43° S), a geographical point furthest among the studied samples, which may hint to an important influence of (paleo-) oceanography on the distributions of Gaidropsarus species.
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Affiliation(s)
- Alexander H Knorrn
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
- MARUM, University of Bremen, Bremen, Germany
| | - Lydia Beuck
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
| | - David Barros-García
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Matosinhos, Portugal
| | - Lourdes Fernández-Peralta
- Instituto Español de Oceanografía (IEO), Fuengirola, Spain
- Department of Animal Biology, Faculty of Science, University of Málaga, Málaga, Spain
| | - André Freiwald
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
- MARUM, University of Bremen, Bremen, Germany
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10
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Yamamoto T, Tachihara K, Toda M. Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding. Biodivers Data J 2024; 12:e126744. [PMID: 39184369 PMCID: PMC11342385 DOI: 10.3897/bdj.12.e126744] [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: 05/07/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.
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Affiliation(s)
- Takumi Yamamoto
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, JapanGraduate School of Engineering and Science, University of the RyukyusNishihara, OkinawaJapan
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, JapanLaboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the RyukyusNishihara, OkinawaJapan
| | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, JapanTropical Biosphere Research Center, University of the RyukyusNishihara, OkinawaJapan
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11
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Ibalim S, Toko PS, Segar ST, Sagata K, Koane B, Miller SE, Novotny V, Janda M. Phylogenetic structure of moth communities (Geometridae, Lepidoptera) along a complete rainforest elevational gradient in Papua New Guinea. PLoS One 2024; 19:e0308698. [PMID: 39133743 PMCID: PMC11318904 DOI: 10.1371/journal.pone.0308698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
We use community phylogenetics to elucidate the community assembly mechanisms for Geometridae moths (Lepidoptera) collected along a complete rainforest elevational gradient (200-3700 m a.s.l) on Mount Wilhelm in Papua New Guinea. A constrained phylogeny based on COI barcodes for 604 species was used to analyse 1390 species x elevation occurrences at eight elevational sites separated by 500 m elevation increments. We obtained Nearest Relatedness Index (NRI), Nearest Taxon Index (NTI) and Standardised Effect Size of Faith's Phylogenetic Diversity (SES.PD) and regressed these on temperature, plant species richness and predator abundance as key abiotic and biotic predictors. We also quantified beta diversity in the moth communities between elevations using the Phylogenetic Sorensen index. Overall, geometrid communities exhibited phylogenetic clustering, suggesting environmental filters, particularly at higher elevations at and above 2200 m a.s.l and no evidence of overdispersion. NRI, NTI and SES.PD showed no consistent trends with elevation or the studied biotic and abiotic variables. Change in community structure was driven by turnover of phylogenetic beta-diversity, except for the highest 2700-3200 m elevations, which were characterised by nested subsets of lower elevation communities. Overall, the elevational signal of geometrid phylogeny was weak-moderate. Additional insect community phylogeny studies are needed to understand this pattern.
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Affiliation(s)
- Sentiko Ibalim
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Pagi S. Toko
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Simon T. Segar
- Department of Crop and Environment Sciences, Harper Adams University, Newport, United Kingdom
| | - Katayo Sagata
- PNG Institute of Biological Research, Madang, Papua New Guinea
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Scott E. Miller
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Vojtech Novotny
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Milan Janda
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
- Faculty of Science, Department of Zoology, Palacky University Olomouc, Olomouc, Czech Republic
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12
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Leong JV, Mezzomo P, Kozel P, Volfová T, de Lima Ferreira P, Seifert CL, Butterill PT, Freiberga I, Michálek J, Matos-Maraví P, Weinhold A, Engström MT, Salminen JP, Segar ST, Sedio BE, Volf M. Effects of individual traits vs. trait syndromes on assemblages of various herbivore guilds associated with central European Salix. Oecologia 2024; 205:725-737. [PMID: 38829402 DOI: 10.1007/s00442-024-05569-0] [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: 10/04/2023] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Plants employ diverse anti-herbivore defences that can covary to form syndromes consisting of multiple traits. Such syndromes are hypothesized to impact herbivores more than individual defences. We studied 16 species of lowland willows occurring in central Europe and explored if their chemical and physical traits form detectable syndromes. We tested for phylogenetic trends in the syndromes and explored whether three herbivore guilds (i.e., generalist leaf-chewers, specialist leaf-chewers, and gallers) are affected more by the detected syndromes or individual traits. The recovered syndromes showed low phylogenetic signal and were mainly defined by investment in concentration, richness, or uniqueness of structurally related phenolic metabolites. Resource acquisition traits or inducible volatile organic compounds exhibited a limited correlation with the syndromes. Individual traits composing the syndromes showed various correlations to the assemblages of herbivores from the three studied guilds. In turn, we found some support for the hypothesis that defence syndromes are composed of traits that provide defence against various herbivores. However, individual traits rather than trait syndromes explained more variation for all studied herbivore assemblages. The detected negative correlations between various phenolics suggest that investment trade-offs may occur primarily among plant metabolites with shared metabolic pathways that may compete for their precursors. Moreover, several traits characterizing the recovered syndromes play additional roles in willows other than defence from herbivory. Taken together, our findings suggest that the detected syndromes did not solely evolve as an anti-herbivore defence.
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Affiliation(s)
- Jing V Leong
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic.
| | - Priscila Mezzomo
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Petr Kozel
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Tereza Volfová
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Paola de Lima Ferreira
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Carlo L Seifert
- Department of Forest Nature Conservation, Faculty of Forest Sciences and Forest Ecology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Phillip T Butterill
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Inga Freiberga
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Jan Michálek
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Institute of Microbiology, Centre Algatech Czech Academy of Sciences, Trebon, Czech Republic
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Marica T Engström
- Bioanalytical Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Juha-Pekka Salminen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, Turku, Finland
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, United Kingdom
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
- Smithsonian Tropical Research Institute, Ancón, Panama
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, Ceske Budejovice, Czech Republic
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13
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Doorenweerd C, San Jose M, Leblanc L, Barr N, Geib SM, Chung AYC, Dupuis JR, Ekayanti A, Fiegalan E, Hemachandra KS, Aftab Hossain M, Huang CL, Hsu YF, Morris KY, Maryani A Mustapeng A, Niogret J, Pham TH, Thi Nguyen N, Sirisena UGAI, Todd T, Rubinoff D. Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies. Mol Ecol Resour 2024; 24:e13987. [PMID: 38956928 DOI: 10.1111/1755-0998.13987] [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: 03/07/2024] [Revised: 05/14/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.
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Affiliation(s)
- Camiel Doorenweerd
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Michael San Jose
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | - Arthur Y C Chung
- Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Arni Ekayanti
- Niogret Ecology Consulting LLC, Wotu, Luwu Timor, Sulawesi Seleaton, Indonesia
| | - Elaida Fiegalan
- Department of Crop Protection, College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines
| | | | - Mohammad Aftab Hossain
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka, Bangladesh
| | - Chia-Lung Huang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, ROC
| | - Kimberly Y Morris
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | | | - Jerome Niogret
- Centre for Tropical Environmental & Sustainability Science, Nguma-Bada Campus, James Cook University, Smithfield, Queensland, Australia
| | - Thai Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology (VAST), Hue, Vietnam
- Vietnam National Museum of Nature & Graduate School of Science and Technology, VAST, Hanoi, Vietnam
| | - Nhien Thi Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Uda G A I Sirisena
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Terrence Todd
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Daniel Rubinoff
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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14
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Renner SS, Scherz MD, Schoch CL, Gottschling M, Vences M. Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains. Syst Biol 2024; 73:486-494. [PMID: 37956405 DOI: 10.1093/sysbio/syad068] [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: 05/16/2023] [Revised: 08/21/2023] [Accepted: 11/11/2023] [Indexed: 11/15/2023] Open
Abstract
Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.
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Affiliation(s)
- Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Mark D Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Marc Gottschling
- Faculty of Biology, GeoBio-Center, Ludwig-Maximilians-University, Munich 80333, Germany
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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15
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Khumalo N, Chaisi M, Magoro R, Mwale M. An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance. Genome 2024. [PMID: 39018572 DOI: 10.1139/gen-2024-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.
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Affiliation(s)
- Nozipho Khumalo
- Foundational Biodiversity Science, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
| | - Mamohale Chaisi
- Foundational Biodiversity Science, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
- Department of Veterinary Tropical Diseases, University of Pretoria, P/Bag X04, Onderstepoort 0001, Pretoria, South Africa
| | - Rebecca Magoro
- Foundational Biodiversity Science, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
| | - Monica Mwale
- Foundational Biodiversity Science, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
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16
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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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17
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Quicke DLJ, Ranjith AP, Loncle MK, Van Achterberg C, Long KD, Butcher BA. Revision of Troporhogas Cameron (Hymenoptera, Braconidae, Rogadinae) with six new species from India and Thailand. Zookeys 2024; 1206:99-136. [PMID: 39006403 PMCID: PMC11245641 DOI: 10.3897/zookeys.1206.120824] [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: 02/13/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024] Open
Abstract
The genus Troporhogas Cameron, 1905 from the Indo-Malayan region is reviewed. Six new species, Troporhogasalboniger Quicke, Loncle & Butcher, sp. nov., T.benjamini Quicke, Loncle & Butcher, sp. nov., T.hugoolseni Quicke, Loncle & Butcher, sp. nov., T.rafaelnadali Quicke, Loncle & Butcher, sp. nov., and T.rogerfedereri Quicke, Loncle & Butcher, sp. nov. from Thailand, and T.anamikae Ranjith, sp. nov. from India are described and illustrated photographically, bringing the total number of species of the genus known from the Indo-Malayan Region to 19. Troporhogas is recorded for the first time from India. A key is included to differentiate Troporhogas species. A four-gene ML tree based on COI, Cytb, 16S and 28S is reconstructed, representing the six new species. Troporhogascontrastus Long, 2014, originally described from Vietnam, is recorded from Thailand for the first time. The holotypes of the type species, Troporhogastricolor Cameron, 1905 and that of its junior synonym Iporhogas are illustrated, and photographs are presented of all the species known only from China and Sri Lanka. Sexual colour dimorphism of males of several species is described for the first time. Drawings summarising the different patterns of black marks on the metasoma that aid species recognition are presented.
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Affiliation(s)
- Donald L J Quicke
- Integrative Insect Ecology Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
| | - A P Ranjith
- Integrative Insect Ecology Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore 560064, India Ashoka Trust for Research in Ecology and the Environment (ATREE) Bangalore India
| | - Marisa K Loncle
- Integrative Insect Ecology Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
| | - Cornelis Van Achterberg
- Department of Terrestrial Zoology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, Netherlands Naturalis Biodiversity Centre Leiden Netherlands
- Zhejiang University, Hangzhou 310058, China Zhejiang University Hangzhou China
| | - Khuat Dang Long
- Institute of Ecology & Biological Resources (IEBR), Vietnam Academy of Science & Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, Vietnam Institute of Ecology & Biological Resources (IEBR), Vietnam Academy of Science & Technology (VAST) Hanoi Vietnam
| | - Buntika A Butcher
- Integrative Insect Ecology Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand Chulalongkorn University Bangkok Thailand
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18
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Douglas HB, Renkema J, Smith TW, Konstantinov AS, Moisan-De Serres J. Palearctic flea beetle and pest of hops and Cannabis, Psylliodesattenuata (Coleoptera, Chrysomelidae, Galerucinae), new to North America. Biodivers Data J 2024; 12:e120340. [PMID: 39015798 PMCID: PMC11249851 DOI: 10.3897/bdj.12.e120340] [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: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 07/18/2024] Open
Abstract
Background The univoltine leaf beetle Psylliodesattenuata (Koch, 1803) is a pest of Cannabis and Humulus (Cannabaceae) and native to the Palaearctic Region, known from eastern Asia to western Europe. New information First North American records are presented for P.attenuata from Canada: Ontario and Québec. Adult beetle feeding damage to hops Humuluslupulus L. (Cannabacaea) plants is recorded from Québec. Diagnostic information is presented to distinguish P.attenuata from other North American Chrysomelidae and a preliminary assessment of its potential to spread in North America is presented. While our climate analysis is limited by a lack of data, it appears P.attenuata is physiologically capable of persisting throughout the range of Humulus in North America.The United States of America and Canada are now known to be home to 71 or more species of adventive Chrysomelidae.
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Affiliation(s)
- Hume B Douglas
- Agriculture and Agri-Food Canada, Ottawa, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - Justin Renkema
- Agriculture and Agri-Food Canada, Vineland, CanadaAgriculture and Agri-Food CanadaVinelandCanada
| | - Tyler W Smith
- Agriculture and Agri-Food Canada, Ottawa, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - Alexander S Konstantinov
- Systematic Entomology Laboratory, USDA, ARS, Smithsonian Institution, National Museum of Natural History, MRC-168 Washington, United States of AmericaSystematic Entomology Laboratory, USDA, ARS, Smithsonian InstitutionNational Museum of Natural History, MRC-168 WashingtonUnited States of America
| | - Joseph Moisan-De Serres
- Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec, Québec, CanadaMinistère de l'Agriculture, des Pêcheries et de l'Alimentation du QuébecQuébecCanada
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19
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Janko Š, Rok Š, Blaž K, Danilo B, Andrej G, Denis K, Klemen Č, Matjaž G. DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors. Mol Ecol Resour 2024; 24:e13953. [PMID: 38523561 DOI: 10.1111/1755-0998.13953] [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: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.
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Affiliation(s)
- Šet Janko
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Šturm Rok
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Koderman Blaž
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Bevk Danilo
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Gogala Andrej
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Kutnjak Denis
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Čandek Klemen
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Gregorič Matjaž
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
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20
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Mejia E, Buckup PA. Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species. JOURNAL OF FISH BIOLOGY 2024; 105:288-313. [PMID: 38747127 DOI: 10.1111/jfb.15780] [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] [Received: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 07/19/2024]
Abstract
Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided.
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Affiliation(s)
- Eduardo Mejia
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo A Buckup
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Slusher EK, Cottrell T, Gariepy T, Acebes-Doria A, Querejeta Coma M, Toledo PFS, Schmidt JM. A molecular approach to unravel trophic interactions between parasitoids and hyperparasitoids associated with pecan aphids. JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:5. [PMID: 38989842 PMCID: PMC11237992 DOI: 10.1093/jisesa/ieae071] [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: 11/16/2023] [Revised: 05/31/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
Advances in molecular ecology can overcome many challenges in understanding host-parasitoid interactions. Genetic characterization of the key-players in systems helps to confirm species and identify trophic linkages essential for ecological service delivery by biological control agents; however, relatively few agroecosystems have been explored using this approach. Pecan production consists of a large tree perennial system containing an assortment of seasonal pests and natural enemies. As a first step to characterizing host-parasitoid associations in pecan food webs, we focus on aphid species and their parasitoids. Based on DNA barcoding of field-collected and reared specimens, we confirmed the presence of 3 species of aphid, one family of primary parasitoids, and 5 species of hyperparasitoids. By applying metabarcoding to field-collected aphid mummies, we were able to identify multiple species within each aphid mummy to unravel a complex food web of 3 aphids, 2 primary parasitoids, and upward of 8 hyperparasitoid species. The results of this study demonstrate that multiple hyperparasitoid species attack a single primary parasitoid of pecan aphids, which may have negative consequences for successful aphid biological control. Although further research is needed on a broader spatial scale, our results suggest multiple species exist in this system and may suggest a complex set of interactions between parasitoids, hyperparasitoids, and the 3 aphid species. This was the first time that many of these species have been characterized and demonstrates the application of novel approaches to analyze the aphid-parasitoid food webs in pecans and other tree crop systems.
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Affiliation(s)
- Eddie K Slusher
- Department of Entomology, University of Georgia, Tifton, GA, USA
- USDA-ARS Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, USA
- Texas A&M Agrilife Research and Extension Center, Stephenville, TX, USA
| | - Ted Cottrell
- USDA-ARS Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, USA
| | - Tara Gariepy
- Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Marina Querejeta Coma
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), Université de Tours, Tours, France
- Department of Functional Biology, University of Oviedo, Asturias, Spain
| | - Pedro F S Toledo
- Department of Entomology, University of Georgia, Tifton, GA, USA
| | - Jason M Schmidt
- Department of Entomology, University of Georgia, Tifton, GA, USA
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22
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Macko P, Derka T, Čiamporová-Zaťovičová Z, Grabowski M, Čiampor F. Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries. Mol Ecol Resour 2024; 24:e13954. [PMID: 38520175 DOI: 10.1111/1755-0998.13954] [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: 06/19/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
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Affiliation(s)
- Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Derka
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
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23
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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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24
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Svenningsen CS, Schigel D. Sharing insect data through GBIF: novel monitoring methods, opportunities and standards. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230104. [PMID: 38705176 PMCID: PMC11070266 DOI: 10.1098/rstb.2023.0104] [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: 06/16/2023] [Accepted: 03/12/2024] [Indexed: 05/07/2024] Open
Abstract
Technological advancements in biological monitoring have facilitated the study of insect communities at unprecedented spatial scales. The progress allows more comprehensive coverage of the diversity within a given area while minimizing disturbance and reducing the need for extensive human labour. Compared with traditional methods, these novel technologies offer the opportunity to examine biological patterns that were previously beyond our reach. However, to address the pressing scientific inquiries of the future, data must be easily accessible, interoperable and reusable for the global research community. Biodiversity information standards and platforms provide the necessary infrastructure to standardize and share biodiversity data. This paper explores the possibilities and prerequisites of publishing insect data obtained through novel monitoring methods through GBIF, the most comprehensive global biodiversity data infrastructure. We describe the essential components of metadata standards and existing data standards for occurrence data on insects, including data extensions. By addressing the current opportunities, limitations, and future development of GBIF's publishing framework, we hope to encourage researchers to both share data and contribute to the further development of biodiversity data standards and publishing models. Wider commitments to open data initiatives will promote data interoperability and support cross-disciplinary scientific research and key policy indicators. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Cecilie S. Svenningsen
- Global Biodiversity Information Facility, Universitetsparken 15, 2100 København Ø, Denmark
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Universitetsparken 15, 2100 København Ø, Denmark
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25
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Li R, Ratnasingham S, Zarubiieva I, Somervuo P, Taylor GW. PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230124. [PMID: 38705180 PMCID: PMC11070247 DOI: 10.1098/rstb.2023.0124] [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: 10/31/2023] [Accepted: 12/23/2023] [Indexed: 05/07/2024] Open
Abstract
DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Roy Li
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- Department of Computer Science, University of Toronto, Toronto, Canada M5S 2E4
| | | | - Iuliia Zarubiieva
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
| | - Panu Somervuo
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Graham W. Taylor
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
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26
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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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27
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Tedersoo L, Hosseyni Moghaddam MS, Mikryukov V, Hakimzadeh A, Bahram M, Nilsson RH, Yatsiuk I, Geisen S, Schwelm A, Piwosz K, Prous M, Sildever S, Chmolowska D, Rueckert S, Skaloud P, Laas P, Tines M, Jung JH, Choi JH, Alkahtani S, Anslan S. EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database (Oxford) 2024; 2024:baae043. [PMID: 38865431 PMCID: PMC11168333 DOI: 10.1093/database/baae043] [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: 10/26/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]
Abstract
Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala 75651, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, Göteborg 40530, Sweden
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
- Department of Environment, Soils and Land-Use, Teagasc, Oak Park House, Wexford R93 XE12, Ireland
| | - Kasia Piwosz
- National Marine Fisheries Research Institute, Kołłątaja 1, Gdynia 81332, Poland
| | - Marko Prous
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Ecology and Genetics Research Unit, University of Oulu, Box 8000, Oulu 90014, Finland
| | - Sirje Sildever
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
| | - Dominika Chmolowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, Kraków 31016, Poland
| | - Sonja Rueckert
- Eukaryotic Microbiology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 1, Essen, Nordrhein-Westfalen 45141, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Praha 12800, Czech Republic
| | - Peeter Laas
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50400, Estonia
| | - Marco Tines
- Department for Biological Sciences, Institute for Ecology, Evolution, and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
- Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Straße 14-16, Frankfurt am Main 60325, Germany
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Ji Hye Choi
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
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Lopes-Lima M, Geist J, Egg S, Beran L, Bikashvili A, Van Bocxlaer B, Bogan AE, Bolotov IN, Chelpanovskaya OA, Douda K, Fernandes V, Gomes-Dos-Santos A, Gonçalves DV, Gürlek ME, Johnson NA, Karaouzas I, Kebapçı Ü, Kondakov AV, Kuehn R, Lajtner J, Mumladze L, Nagel KO, Neubert E, Österling M, Pfeiffer J, Prié V, Riccardi N, Sell J, Schneider LD, Shumka S, Sîrbu I, Skujienė G, Smith CH, Sousa R, Stöckl K, Taskinen J, Teixeira A, Todorov M, Trichkova T, Urbańska M, Välilä S, Varandas S, Veríssimo J, Vikhrev IV, Woschitz G, Zając K, Zając T, Zanatta D, Zieritz A, Zogaris S, Froufe E. Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications. Mol Phylogenet Evol 2024; 195:108046. [PMID: 38447924 DOI: 10.1016/j.ympev.2024.108046] [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: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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Affiliation(s)
- M Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - J Geist
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany
| | - S Egg
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany; Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - L Beran
- Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration, Nature Conservation Agency of the Czech Republic, Česká 149, CZ-27601 Mělnik, Czech Republic
| | - A Bikashvili
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - B Van Bocxlaer
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - A E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - I N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - O A Chelpanovskaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - K Douda
- Department of Zoology and Fisheries, FAFNR, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500 Prague, Czech Republic
| | - V Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - A Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - D V Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - M E Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Türkiye
| | - N A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - I Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - Ü Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - A V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - R Kuehn
- Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - L Mumladze
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - K-O Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - E Neubert
- Natural History Museum, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - M Österling
- Institution of Environmental and Life Sciences, Karlstad University, Biology, 65188 Karlstad, Sweden
| | - J Pfeiffer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue, Washington, DC, USA
| | - V Prié
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - N Riccardi
- CNR Water Research Institute, Largo Tonolli 50, 28922 Verbania, Italy
| | - J Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - L D Schneider
- The Rural Economy and Agricultural Society, 305 96 Eldsberga, Sweden
| | - S Shumka
- Faculty Of Biotechnology and Food, Agricultural University of Tirana, Koder Kamez, Tirana 2029, Albania
| | - I Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania
| | - G Skujienė
- Department of Zoology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223 Vilnius, Lithuania
| | - C H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - R Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - K Stöckl
- Bavarian Academy for Nature Conservation and Landscape Management, Seethalerstrasse 6, 83410 Laufen, Germany
| | - J Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - A Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - M Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - T Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - M Urbańska
- Department of Zoology, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637 Poznań, Poland
| | - S Välilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - S Varandas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; CITAB-UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, Portugal
| | - J Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - I V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - G Woschitz
- IFIS - Ichthyological Research Initiative Styria, 1160 Vienna, Austria
| | - K Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - T Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - D Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - A Zieritz
- School of Geography, University of Nottingham, University Park, Sir Clive Granger Building, Nottingham NG7 2RD, United Kingdom
| | - S Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - E Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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29
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Lima RC, de Lima SR, Rocha MS, Dos Anjos HDB, Dantas YCA, Benites IDN, Queiroz CDCS, Fraga EDC, Batista JDS. Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding. JOURNAL OF FISH BIOLOGY 2024; 104:1924-1939. [PMID: 38551122 DOI: 10.1111/jfb.15721] [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] [Received: 07/08/2023] [Revised: 12/03/2023] [Accepted: 02/25/2024] [Indexed: 06/27/2024]
Abstract
The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.
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Affiliation(s)
- Renato Corrêia Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Sabrina Rufino de Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Marcelo Salles Rocha
- Coordenação de Ciências Biológicas, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
| | | | | | | | | | - Elmary da Costa Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão (UEMA), Caxias, Brazil
| | - Jacqueline da 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, Brazil
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30
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Bañón R, Barros-García D, Baldó F, Cojan M, de Carlos A. Unveiling taxonomic diversity in the deep-sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp. JOURNAL OF FISH BIOLOGY 2024; 104:1910-1923. [PMID: 38513288 DOI: 10.1111/jfb.15734] [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] [Received: 08/11/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.
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Affiliation(s)
- Rafael Bañón
- Grupo de Estudo do Medio Mariño (GEMM), Ribeira, Spain
| | - David Barros-García
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Matosinhos, Portugal
| | - Francisco Baldó
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Cádiz, Spain
| | - Miguel Cojan
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Cádiz, Spain
| | - Alejandro de Carlos
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
- Centro de Investigación Mariña da Universidade de Vigo (CIM-UVIGO), Vigo, Spain
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31
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Drozdova PB, Madyarova EV, Gurkov AN, Saranchina AE, Romanova EV, Petunina JV, Peretolchina TE, Sherbakov DY, Timofeyev MA. Lake Baikal amphipods and their genomes, great and small. Vavilovskii Zhurnal Genet Selektsii 2024; 28:317-325. [PMID: 38952708 PMCID: PMC11214899 DOI: 10.18699/vjgb-24-36] [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: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 07/03/2024] Open
Abstract
Endemic amphipods (Crustacea: Amphipoda) of Lake Baikal represent an outstanding example of large species flocks occupying a wide range of ecological niches and originating from a handful of ancestor species. Their development took place at a restricted territory and is thus open for comprehensive research. Such examples provide unique opportunities for studying behavioral, anatomic, or physiological adaptations in multiple combinations of environmental conditions and thus attract considerable attention. The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. The studies of allozymes and marker genes have revealed a significant cryptic diversity in Baikal amphipods, as well as a large variance in genetic diversity within some morphological species. Crossing experiments conducted so far for two morphological species suggest that the differences in the mitochondrial marker (cytochrome c oxidase subunit I gene) can potentially be applied for making predictions about reproductive isolation. For about one-tenth of the Baikal amphipod species, nuclear genome sizes and chromosome numbers are known. While genome sizes vary within one order of magnitude, the karyotypes are relatively stable (2n = 52 for most species studied). Moreover, analysis of the diversity of repeated sequences in nuclear genomes showed significant between-species differences. Studies of mitochondrial genomes revealed some unusual features, such as variation in length and gene order, as well as duplications of tRNA genes, some of which also underwent remolding (change in anticodon specificity due to point mutations). The next important steps should be (i) the assembly of whole genomes for different species of Baikal amphipods, which is at the moment hampered by complicated genome structures with high repeat content, and (ii) updating species taxonomy taking into account all the data.
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Affiliation(s)
- P B Drozdova
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - A N Gurkov
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - E V Romanova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - J V Petunina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - D Y Sherbakov
- Irkutsk State University, Irkutsk, Russia Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia Novosibirsk State University, Novosibirsk, Russia
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32
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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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33
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Ferreira S, Corley MFV, Nunes J, Rosete J, Vasconcelos S, Mata VA, Veríssimo J, Silva TL, Sousa P, Andrade R, Grosso-Silva JM, Pinho CJ, Chaves C, Martins FMS, Pinto J, Puppo P, Muñoz-Mérida A, Archer J, Pauperio J, Beja P. The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths. Biodivers Data J 2024; 12:e117169. [PMID: 38903959 PMCID: PMC11188589 DOI: 10.3897/bdj.12.e117169] [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: 12/11/2023] [Accepted: 02/19/2024] [Indexed: 06/22/2024] Open
Abstract
Background The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. New information The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).
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Affiliation(s)
- Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões,
Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Martin F. V. Corley
- Pucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP,
U.K, Oxfordshire, United KingdomPucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP, U.KOxfordshireUnited Kingdom
| | - João Nunes
- Rua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647,
Valongo, PortugalRua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647ValongoPortugal
| | - Jorge Rosete
- Urbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote
16, 2. frente, P-3105-165 Louriçal, Pombal, PortugalUrbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote 16, 2. frente,
P-3105-165 LouriçalPombalPortugal
| | - Sasha Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
- Department of Ecology, Swedish University of Agricultural
Sciences, PO Box 7044, 750 07, Uppsala, SwedenDepartment of Ecology, Swedish University of Agricultural Sciences, PO Box
7044, 750 07UppsalaSweden
| | - Vanessa A. Mata
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Teresa L Silva
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pedro Sousa
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- International Union for Conservation of Nature (IUCN),
Species Survival Commission (SSC), Spider and Scorpion Specialist Group, Gland,
SwitzerlandInternational Union for Conservation of Nature (IUCN), Species Survival
Commission (SSC), Spider and Scorpion Specialist GroupGlandSwitzerland
| | - Rui Andrade
- Rua Calouste Gulbenkian 237 4H3, 4050-145, Porto,
PortugalRua Calouste Gulbenkian 237 4H3, 4050-145PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do
Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Catarina J. Pinho
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Filipa MS Martins
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences,
Huntington, West Virginia, United States of AmericaMarshall University, Department of Biological SciencesHuntington, West VirginiaUnited States of America
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pauperio
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto,,
4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairão, Universidade do Porto,4485–661 Vairão, Vila do CondePortugal
- European Molecular Biology Laboratory, European
Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics
InstituteHinxton, CambridgeUnited Kingdom
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
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Bušić N, Klobučar A, Landeka N, Žitko T, Vignjević G, Turić N, Sudarić Bogojević M, Merdić E, Kučinić M, Bruvo Mađarić B. A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species. Parasit Vectors 2024; 17:216. [PMID: 38734639 PMCID: PMC11088778 DOI: 10.1186/s13071-024-06291-9] [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: 01/30/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species. METHODS Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs. RESULTS A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna. CONCLUSION We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.
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Affiliation(s)
- Nataša Bušić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia.
| | - Ana Klobučar
- Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
| | - Nediljko Landeka
- Teaching Institute for Public Health of the Istrian County, Pula, Croatia
| | - Toni Žitko
- Teaching Institute for Public Health, Split-Dalmatia County, Split, Croatia
| | - Goran Vignjević
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Nataša Turić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
- Teaching Institute for Public Health of the Osijek-Baranja County, Osijek, Croatia
| | | | - Enrih Merdić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Mladen Kučinić
- Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia
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35
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Seymour M, Roslin T, deWaard JR, Perez KHJ, D'Souza ML, Ratnasingham S, Ashfaq M, Levesque-Beaudin V, Blagoev GA, Bukowski B, Cale P, Crosbie D, Decaëns T, deWaard SL, Ekrem T, El-Ansary HO, Evouna Ondo F, Fraser D, Geiger MF, Hajibabaei M, Hallwachs W, Hanisch PE, Hausmann A, Heath M, Hogg ID, Janzen DH, Kinnaird M, Kohn JR, Larrivée M, Lees DC, León-Règagnon V, Liddell M, Lijtmaer DA, Lipinskaya T, Locke SA, Manjunath R, Martins DJ, Martins MB, Mazumdar S, McKeown JTA, Anderson-Teixeria K, Miller SE, Milton MA, Miskie R, Morinière J, Mutanen M, Naik S, Nichols B, Noguera FA, Novotny V, Penev L, Pentinsaari M, Quinn J, Ramsay L, Rochefort R, Schmidt S, Smith MA, Sobel CN, Somervuo P, Sones JE, Staude HS, St Jaques B, Stur E, Telfer AC, Tubaro PL, Wardlaw TJ, Worcester R, Yang Z, Young MR, Zemlak T, Zakharov EV, Zlotnick B, Ovaskainen O, Hebert PDN. Global arthropod beta-diversity is spatially and temporally structured by latitude. Commun Biol 2024; 7:552. [PMID: 38720028 PMCID: PMC11078949 DOI: 10.1038/s42003-024-06199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.
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Affiliation(s)
- Mathew Seymour
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Ulls väg 18B, Uppsala, 75651, Sweden
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Michelle L D'Souza
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Gergin A Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Belén Bukowski
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Peter Cale
- Australian Landscape Trust, Renmark, SA, SA5341, Australia
| | | | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Hosam O El-Ansary
- Plant Production Department, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fidèle Evouna Ondo
- Agence Nationale des Parcs Nationaux, Departement de la Recherche Scientifique, Libreville, Gabon
| | - David Fraser
- BC Conservation Data Centre, Ministry of Environment, Box 9338, Station Prov Govt, Victoria, BC, V8W 9M1, Canada
| | - Matthias F Geiger
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113, Bonn, Germany
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Priscila E Hanisch
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
- Department of Animal Ecology and Tropical Biology, Biocenter - University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | | | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Joshua R Kohn
- Section of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0116, USA
| | - Maxim Larrivée
- Insectarium, Montréal Space for Life, Montréal, QC, Canada
| | - David C Lees
- Department of Science, Natural History Museum, South Kensington, London, United Kingdom
| | - Virginia León-Règagnon
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 21, C.P, 48980, San Patricio, Jalisco, Mexico
| | - Michael Liddell
- Centre for Tropical, Environmental, and Sustainability Sciences, James Cook University, Cairns, Queensland, Australia
| | - Darío A Lijtmaer
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Tatsiana Lipinskaya
- Laboratory of Hydrobiology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sean A Locke
- Departamento de Biología, University of Puerto Rico at Mayagüez, Mayagüez, 00680, Puerto Rico
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dino J Martins
- Mpala Research Centre and Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Marlúcia B Martins
- Laboratório de Ecologia de Invertebrados, Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Avenida Perimetral 1901, Terra Firma, CEP, 66077 530, Belém, Pará, Brazil
| | - Santosh Mazumdar
- Department of Zoology, University of Chittagong, 4331, Chittagong, Bangladesh
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Scott E Miller
- National Museum of Natural History, Smithsonian Institution, Washington, WA, USA
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Becky Nichols
- US National Park Service, 1316 Cherokee Orchard Road, Great Smoky Mountains National Park, Gatlinburg, TN, USA
| | - Felipe A Noguera
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 21, C.P, 48980, San Patricio, Jalisco, Mexico
| | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Lyubomir Penev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113, Sofia, Bulgaria
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jenna Quinn
- Rare Charitable Research Reserve, Cambridge, ON, Canada
| | - Leah Ramsay
- BC Conservation Data Centre, Ministry of Environment, Box 9338, Station Prov Govt, Victoria, BC, V8W 9M1, Canada
| | - Regina Rochefort
- North Cascades National Park Service Complex, 810 State Route 20, Sedro-Woolley, WA, 98284, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Brianne St Jaques
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Pablo L Tubaro
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Tim J Wardlaw
- ARC Centre for Forest Values, University of Tasmania, Hobart, TAS, Australia
| | - Robyn Worcester
- Stanley Park Ecology Society, P.O. Box 5167, Vancouver, BC, V6B 4B2, Canada
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Tyler Zemlak
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014, Jyväskylä, Finland
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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36
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Crabo LG. A new noctuid genus and species (Lepidoptera, Noctuidae, Amphipyrinae, Psaphidini, Triocnemidina) from New Mexico and Texas, United States of America. Zookeys 2024; 1200:199-213. [PMID: 38756345 PMCID: PMC11096726 DOI: 10.3897/zookeys.1200.117772] [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: 12/23/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Pooleagen. nov. is described for two noctuid species from southwestern United States: Pooleagrandimacula Barnes & McDunnough, comb. nov., previously in Oxycnemis Grote, and Pooleapsaphidoidessp. nov.Poolea is compared to Oxycnemis (Amphipyrinae, Psaphidini, Triocnemidina) and is retained in the same subtribe. Adult moths and male and female genitalia of Poolea species are illustrated along with those of Oxycnemisadvena Grote, the genus type species. Pertinent recent taxonomic changes to Amphipyrinae classification are reviewed.
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Affiliation(s)
- Lars G. Crabo
- Adjunct Faculty, Washington State University, Pullman, Washington, USAWashington State UniversityPullmanUnited States of America
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Munian K, Ramli FF, Othman N, Mahyudin NAA, Sariyati NH, Abdullah-Fauzi NAF, Haris H, Ilham-Norhakim ML, Abdul-Latiff MAB. Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool. Mol Ecol Resour 2024; 24:e13936. [PMID: 38419264 DOI: 10.1111/1755-0998.13936] [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: 10/19/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.
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Affiliation(s)
- Kaviarasu Munian
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
- Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Farah Farhana Ramli
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nur Aina Amira Mahyudin
- Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Hidayah Haris
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Mohd Lokman Ilham-Norhakim
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
- Kim Ichthyologist Centre, Kg Parit Samsu, Jalan Temenggong Ahmad, Parit Jawa, Muar, Johor, Malaysia
- Akim Fishes Enterprise, Muar, Johor, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
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38
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Vella A, Vella N. The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses. Animals (Basel) 2024; 14:1107. [PMID: 38612346 PMCID: PMC11010884 DOI: 10.3390/ani14071107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.
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Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, MSD 2080 Msida, Malta
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39
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Ge X, Wang C, Pei W, Tang Y, Liu W, Yan C. New descriptions of the larval and pupal stages of Orthocladiusnitidoscutellatus and Psectrocladiusnevalis from Xizang, China (Diptera, Chironomidae). Biodivers Data J 2024; 12:e121952. [PMID: 38617833 PMCID: PMC11016161 DOI: 10.3897/bdj.12.e121952] [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: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024] Open
Abstract
Background Tibetan Plateau is one of the most typical areas of biodiversity in the world because of its unique environmental and regional units, which breed unique biological communities and concentrate on many unique and rare wild animals and plants. Research on Chironomidae in the Tibetan Plateau is relatively weak. At present, the identification of Chironomidae species mainly depends on male adults, while identification of larvae and pupae is relatively difficult and there is less research on them. New information During the investigations of insect diversity in the Tibetan Plateau, larval and pupal stages of Orthocladiusnitidoscutellatus Lundström, 1915 and Psectrocladiusnevalis Akhrorov, 1977 were described and illustrated. Matching and identification of larval and pupal stages were based on DNA barcodes. Neighbour-joining trees were reconstructed, based on known Orthocladius and Psectrocladius COI DNA barcodes, respectively.
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Affiliation(s)
- Xinyu Ge
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
| | - Chengyan Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
| | - Wenxuan Pei
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
| | - Yaning Tang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
| | - Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University Tianjin China
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40
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Finnie S, Butterill P, Novotny V, Redmond C, Jorge LR, Abe T, Lamarre GPA, Maicher V, Sam K. Vertical stratification and defensive traits of caterpillars against parasitoids in a lowland tropical forest in Cameroon. Oecologia 2024; 204:915-930. [PMID: 38613574 PMCID: PMC11062930 DOI: 10.1007/s00442-024-05542-x] [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: 11/08/2023] [Accepted: 03/12/2024] [Indexed: 04/15/2024]
Abstract
Insect herbivores and their parasitoids play a crucial role in terrestrial trophic interactions in tropical forests. These interactions occur across the entire vertical gradient of the forest. This study compares how caterpillar communities, and their parasitism rates, vary across vertical strata and between caterpillar defensive strategies in a semi deciduous tropical forest in Nditam, Cameroon. Within a 0.1 ha plot, all trees with a diameter at breast height (DBH) ≥ 5 cm were felled and systematically searched for caterpillars. We divided the entire vertical gradient of the forest into eight, five-metre strata. All caterpillars were assigned to a stratum based on their collection height, reared, identified, and classified into one of three defensive traits: aposematic, cryptic and shelter-building. Caterpillar species richness and diversity showed a midstory peak, whereas density followed the opposite pattern, decreasing in the midstory and then increasing towards the highest strata. This trend was driven by some highly dense shelter-building caterpillars in the upper canopy. Specialisation indices indicated decreasing levels of caterpillar generality with increasing height, a midstory peak in vulnerability, and increasing connectance towards the upper canopy, although the latter was likely driven by decreasing network size. Both aposematic and shelter-building caterpillars had significantly higher parasitism rates than cryptic caterpillars. Our results highlight nuanced changes in caterpillar communities across forest strata and provide evidence that defences strategies are important indicators of parasitism rates in caterpillars and that both aposematic and shelter-building caterpillars could be considered a "safe haven" for parasitoids.
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Affiliation(s)
- Sam Finnie
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Philip Butterill
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vojtech Novotny
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Conor Redmond
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Leonardo Ré Jorge
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomokazu Abe
- Department of Biology, Faculty of Science, Chiba University, Chiba, 263-8522, Japan
| | - Greg P A Lamarre
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Ancon, Panama
| | - Vincent Maicher
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- The Nature Conservancy (TNC), Libreville, Gabon
| | - Katerina Sam
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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41
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Lai Y, Li K, Liu X. Comprehensive DNA barcode reference library and optimization of genetic divergence threshold facilitate the exploration of species diversity of green lacewings (Neuroptera: Chrysopidae). INSECT SCIENCE 2024; 31:613-632. [PMID: 37479953 DOI: 10.1111/1744-7917.13254] [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] [Received: 03/21/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/23/2023]
Abstract
Chrysopidae are a family of Neuroptera of significant importance in biocontrol against agricultural pests because of their predatory larvae. Currently, the taxonomy of Chrysopidae lacks a comprehensive revision, which impedes the exploration of species diversity as well as the selection and the conservation of green lacewings as biocontrol agents. We have established a DNA barcode reference library of the Chinese green lacewings based on an approximately complete sampling (95.63%) in 25 of the 34 provincial regions in China, comprising 1 119 barcodes of 25 genera and 197 species (representing 85% genera and 43.62% species from China). Combining other 1 049 high quality green lacewing DNA barcodes, we first inferred the optimal threshold of interspecific genetic divergence (1.87%) for successful species identification in multiple simulated scenarios based on present data. We further inferred the threshold of genetic divergence (7.77%) among genera with biocontrol significance. The inference and performance of the threshold appears to be mainly associated with the completeness of sampling, the proportion of closely related species, and the analytical approaches. Six new combinations, Apertochrysa platypa (Yang & Yang, 1991) comb. nov., Apertochrysa shennongana (Yang & Wang, 1990) comb. nov., Apertochrysa pictifacialis (Yang, 1988) comb. nov., Apertochrysa helana (Yang, 1993) comb. nov., Plesiochrysa rosulata (Yang & Yang, 2002) comb. nov., and Signochrysa hainana (Yang & Yang, 1991), are proposed according to integrative species delimitation. Our library and optimal threshold will effectively facilitate the exploration of species diversity of green lacewings. Our study also provides a methodological reference in molecular delimitation of other insects.
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Affiliation(s)
- Yan Lai
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Kaiyu Li
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xingyue Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
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42
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Mejia E, Reis RE. Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages. JOURNAL OF FISH BIOLOGY 2024; 104:1042-1053. [PMID: 38149310 DOI: 10.1111/jfb.15639] [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] [Received: 07/19/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/28/2023]
Abstract
Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.
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Affiliation(s)
- Eduardo Mejia
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Vertebrados, Programa de Pós-graduação em Ciências Biológicas (Zoologia), Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brazil
| | - Roberto E Reis
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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Teixeira MAL, Fourreau CJL, Sempere-Valverde J, Carvalho S. Two new records and description of a new Perinereis (Annelida, Nereididae) species for the Saudi Arabian Red Sea region. Zookeys 2024; 1196:331-354. [PMID: 38726099 PMCID: PMC11079592 DOI: 10.3897/zookeys.1196.115260] [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: 11/05/2023] [Accepted: 01/26/2024] [Indexed: 05/12/2024] Open
Abstract
Annelid biodiversity studies in the Red Sea are limited and integrative taxonomy is needed to accurately improve reference libraries in the region. As part of the bioblitz effort in Saudi Arabia to assess the invertebrate biodiversity in the northern Red Sea and Gulf of Aqaba, Perinereis specimens from intertidal marine and lagoon-like rocky environments were selected for an independent assessment, given the known taxonomic ambiguities in this genus. This study used an integrative approach, combining molecular with morphological and geographic data. Our results demonstrate that specimens found mainly in the Gulf of Aqaba are not only morphologically different from other five similar Perinereis Group I species reported in the region, but phylogenetic analysis using available COI sequences from GenBank revealed different molecular operational taxonomic units, suggesting an undescribed species, P.kaustianasp. nov. The new species is genetically close and shares a similar paragnath pattern to the Indo-Pacific distributed P.helleri, in particular in Area III and Areas VII-VIII. Therefore, we suggest it may belong to the same species complex. However, P.kaustianasp. nov. differs from the latter mainly in the shorter length of the postero-dorsal tentacular cirri, median parapodia with much longer dorsal Tentacular cirri, posteriormost parapodia with much wider and greatly expanded dorsal ligules. Additionally, two new records are reported for the Saudi Neom area belonging to P.damietta and P.suezensis, previously described only for the Egyptian coast (Suez Canal) and are distributed sympatrically with the new species, but apparently not sympatric with each other.
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Affiliation(s)
- Marcos A. L. Teixeira
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Juan Sempere-Valverde
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Laboratorio de Biología Marina/Estación de Biología Marina del Estrecho (Ceuta), Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain
| | - Susana Carvalho
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM. Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity. Sci Rep 2024; 14:7432. [PMID: 38548880 PMCID: PMC10978826 DOI: 10.1038/s41598-024-58071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.
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Affiliation(s)
- Maurício Moraes Zenker
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil.
| | - Tatiana Pineda Portella
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe Arley Costa Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus, Brazil
| | - Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, 412 96, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), Gothenburg, Sweden
| | - Pedro Manoel Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
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45
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van Nieukerken EJ, Davis DR, Swain SV, Epstein ME. A new North American species of Etainia (Lepidoptera, Nepticulidae), feeding on Arbutus and Arctostaphylos species (Ericaceae). Zookeys 2024; 1193:195-218. [PMID: 38496800 PMCID: PMC10940862 DOI: 10.3897/zookeys.1193.116982] [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: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 03/19/2024] Open
Abstract
Etainiathoraceleuca van Nieukerken, Epstein & Davis, sp. nov. is the second native American species of Etainia Beirne, 1945, and the second known Etainia species feeding on Ericaceae. The species is known from light-collected adults in the USA (California, Arizona) and Canada (Ontario). These were linked via DNA barcodes to larvae that make short leafmines on Arbutus and Arctostaphylos species, then continue feeding in stems and branches, causing damage in nurseries and planted trees in Sonoma and Marin Counties, California. The holotype was accidentally reared from Arbutusarizonica, without observing the damage. Life history and damage are described in detail. Damage in Arctostaphylosuva-ursi found in Washington State probably belongs to E.thoraceleuca, which is a sister species to the European E.albibimaculella (Larsen, 1927).
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Affiliation(s)
- Erik J. van Nieukerken
- Naturalis Biodiversity Center, PO Box 9557, NL-2300 RA Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Donald R. Davis
- Department of Entomology, National Museum of Natural History, MRC 105, Smithsonian Institution, PO Box 37012, Washington, DC 20013–7012, USANational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Steven V. Swain
- Environmental Horticulture Advisor Marin & Sonoma Counties, 1682 Novato Blvd., Suite 150-B, Novato, CA 94947, USAEnvironmental Horticulture Advisor Marin & Sonoma CountiesNovato, CAUnited States of America
| | - Marc E. Epstein
- Plant Pest Diagnostics Center, California Department of Food & Agriculture, 3294 Meadowview Rd., Sacramento, CA 95832, USAPlant Pest Diagnostics Center, California Department of Food & AgricultureSacramentoUnited States of America
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Ho CW, Chen PY, Liao YT, Cheng YF, Tsou HH, Liu TY, Liang KH. Uncovering the microbiome landscape in sashimi delicacies. Sci Rep 2024; 14:5454. [PMID: 38443405 PMCID: PMC10914738 DOI: 10.1038/s41598-024-55938-1] [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: 12/08/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.
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Affiliation(s)
- Cheng-Wei Ho
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Pei-Ying Chen
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Yi-Ting Liao
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Han-Hsing Tsou
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Tsung-Yun Liu
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Kung-Hao Liang
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming Chiao-Tung University, Taipei, Taiwan.
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.
- Institute of Biomedical Informatics, National Yang-Ming Chiao-Tung University, Taipei, Taiwan.
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Kelly S, Dong Y, Wang W, Matthee S, Wentzel JM, Durden LA, Shao R. Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species. MEDICAL AND VETERINARY ENTOMOLOGY 2024; 38:112-117. [PMID: 37850372 DOI: 10.1111/mve.12699] [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] [Received: 05/17/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.
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Affiliation(s)
- Sarah Kelly
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Yalun Dong
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wei Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, South Africa
| | - Jeanette M Wentzel
- Hans Hoheisen Research Station, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
- Department of Veterinary Tropical Disease, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
- Centre for Veterinary Wildlife Research, University of Pretoria, Onderstepoort, South Africa
| | - Lance A Durden
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Renfu Shao
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Hartig F, Abrego N, Bush A, Chase JM, Guillera-Arroita G, Leibold MA, Ovaskainen O, Pellissier L, Pichler M, Poggiato G, Pollock L, Si-Moussi S, Thuiller W, Viana DS, Warton DI, Zurell D, Yu DW. Novel community data in ecology-properties and prospects. Trends Ecol Evol 2024; 39:280-293. [PMID: 37949795 DOI: 10.1016/j.tree.2023.09.017] [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: 04/25/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.
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Affiliation(s)
- Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland
| | - Alex Bush
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki 00014, Finland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland; Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
| | | | - Giovanni Poggiato
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Laura Pollock
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Sara Si-Moussi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | | | | | | | - Douglas W Yu
- Kunming Institute of Zoology; Yunnan, China; University of East Anglia, Norfolk, UK
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49
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Rodrigues BL, da Silva Costa G, Godoy RE, Pereira Júnior AM, Cella W, Ferreira GEM, de Medeiros JF, Shimabukuro PHF. Molecular and morphometric study of Brazilian populations of Psychodopygus davisi. MEDICAL AND VETERINARY ENTOMOLOGY 2024; 38:83-98. [PMID: 37867259 DOI: 10.1111/mve.12701] [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] [Received: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
In this study, we analysed the molecular and morphometric differences of several populations of the putative sand fly vector Psychodopygus davisi (Root, 1934) (Diptera, Psychodidae, Phlebotominae) in Brazil. We amplified the 658 base pair fragments of the DNA barcoding region-cytochrome c oxidase subunit 1 (COI) gene-for 57 specimens of P. davisi and three specimens of Psychodopygus claustrei (Abonnenc, Léger & Fauran, 1979). We merged our data with public sequences of the same species available from GenBank. Then, the combined dataset-87 sequences and 20 localities-was analysed using population structure analysis and different species delimitation approaches. Geometric morphometry of wings was performed for 155 specimens of P. davisi populations from the North, Midwest and Southeast Brazilian regions, analysing the differences in centroid sizes and canonical variates. Molecular analysis indicated high intraspecific genetic distance values for P. davisi (maximum p distance = 5.52%). All algorithms identified P. davisi and P. claustrei as distinct molecular taxonomic units, despite the low interspecific distance (p distance to the nearest neighbour = 4.79%). P. davisi sequences were split into four genetic clusters by population structure analysis and at least five genetic lineages using intermediate scenarios of the species delimitation algorithms. The species validation analysis of BPP strongly supported the five-species model in our dataset. We found high genetic diversity in this taxon, which is in agreement with its wide geographic distribution in Brazil. Furthermore, the wing analysis showed that specimens from the Southeast Region of Brazil are different from those in the North and the Midwest. The evolutionary patterns of P. davisi populations in Brazil suggest the presence of candidate species, which need to be validated in future studies using a more comprehensive approach with both genomic data and morphological characters.
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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), São Paulo, Brazil
| | - Glaucilene da Silva Costa
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório Central de Saúde Pública do Estado de Rondônia, LACEN-RO, Porto Velho, Brazil
| | | | | | - Wilsandrei Cella
- Programa de Pós Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense, Paraná, Brazil
- Universidade do Estado do Amazonas (UEA), Tefé, Brazil
| | - Gabriel Eduardo Melim Ferreira
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Epidemiologia Genética, Fiocruz Rondônia, Porto Velho, Brazil
| | - Jansen Fernandes de Medeiros
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Entomologia, Fiocruz Rondônia, Porto Velho, Brazil
| | - Paloma Helena Fernandes Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- Coleção de Flebotomíneos (Fiocruz/COLFLEB), Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
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50
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Kaishian P, Layug CRK, Anderson M, Berg DR, Aime MC. Rust HUBB: DNA barcode-based identification of Pucciniales. IMA Fungus 2024; 15:3. [PMID: 38402196 PMCID: PMC10894486 DOI: 10.1186/s43008-023-00132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/06/2023] [Indexed: 02/26/2024] Open
Abstract
Rust fungi (Pucciniales, Basidiomycota) are a species-rich (ca. 8000 species), globally distributed order of obligate plant pathogens. Rust species are host-specific, and as a group they cause disease on many of our most economically and/or ecologically significant plants. As such, the ability to accurately and rapidly identify these fungi is of particular interest to mycologists, botanists, agricultural scientists, farmers, quarantine officials, and associated stakeholders. However, the complexities of the rust life cycle, which may include production of up to five different spore types and alternation between two unrelated host species, have made standard identifications, especially of less-documented spore states or alternate hosts, extremely difficult. The Arthur Fungarium (PUR) at Purdue University is home to one of the most comprehensive collections of rust fungi in the world. Using material vouchered in PUR supplemented with fresh collections we generated DNA barcodes of the 28S ribosomal repeat from > 3700 rust fungal specimens. Barcoded material spans 120 genera and > 1100 species, most represented by several replicate sequences. Barcodes and associated metadata are hosted in a publicly accessible, BLAST searchable database called Rust HUBB (Herbarium-based Universal Barcode Blast) and will be continuously updated.
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Affiliation(s)
- Patricia Kaishian
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
- New York State Museum, 3140 Cultural Education Center, Albany, NY, 12230, USA
| | - Christopher R K Layug
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Mark Anderson
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Diane R Berg
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA.
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