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Saran C, Genç HY. Genetic diversity of diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae) populations in Türkiye. Mol Biol Rep 2024; 51:146. [PMID: 38236331 DOI: 10.1007/s11033-023-08928-x] [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: 09/21/2023] [Accepted: 11/10/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), is an important worldwide pest of plants belonging to the Brassicaceae family. In this study, we investigated genetic diversity of DBM populations in Brassicaceae production areas in Türkiye using the partial mtDNA CO1 gene region. METHODS We determined 43 samples from 11 different populations for haplotype variations using the partial mitochondrial DNA sequences a 684 bp fragment of the CO1 gene. RESULTS The results indicated that, the average haplotype diversity (Hd) was determined as 0.962 and nucleotide diversity (π) was determined as 0.557%. In neutrality tests, negative values were obtained in Tajima's D and Fu' Fs tests (Fu' Fs=-0.40, Tajima's D=-0.01). Tajima's D test was not found significant (p > 0.05). Fst value among DBM population estimates ranged from 0 to 0.631. Barcode gap distance was determined as 1.6%, but the intraspecies of genetic distance were found to be 0.15%. CONCLUSION In conclusion, the presented study provided detailed and fundamental information about the genetic diversity of DBM populations in Türkiye. Further studies are needed to develop alternative pest management strategies for DBM populations integrating genetic approaches.
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Affiliation(s)
- Ceren Saran
- Faculty of Agriculture, Department of Agricultural Biotechnology, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey
| | - Hanife Yandayan Genç
- Faculty of Agriculture, Department of Agricultural Biotechnology, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey.
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Zhang P, Cai Y, Ma L, Chai J, Zhou Z. DNA barcoding of the genus Gampsocleis (Orthoptera, Tettigoniidae) from China. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22070. [PMID: 38288484 DOI: 10.1002/arch.22070] [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: 08/04/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 02/01/2024]
Abstract
DNA barcoding is a useful addition to the traditional morphology-based taxonomy. A ca. 650 bp fragment of the 5' end of mitochondrial cytochrome c oxidase subunit I (hereafter COI-5P) DNA barcoding was sued as a practical tool for Gampsocleis species identification. DNA barcodes from 889 specimens belonging to 8 putative Gampsocleis species was analyzed, including 687 newly generated DNA barcodes. These barcode sequences were clustered/grouped into Operational Taxonomic Units (OTUs) using the criteria of five algorithms, namely Barcode Index Number (BIN) System, Assemble Species by Automatic Partitioning (ASAP), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP). The Taxon ID Tree grouped sequences of morphospecies and almost all MOTUs in distinct nonoverlapping clusters. Both long- and short-winged Gampsocleis species are reciprocally monophyletic in the Taxon ID Tree. In BOLD, 889 barcode sequences are assigned to 17 BINs. The algorithms ASAP, jMOTU, bPTP and GMYC clustered the barcode sequences into 6, 13, 10, and 23 MOTUs, respectively. BIN, ASAP, and bPTP algorithm placed three long-winged species, G. sedakovii, G. sinensis and G. ussuriensis within the same MOTU. All species delimitation algorithms split two short-winged species,G. fletcheri and G. gratiosa into at least two MOTUs each, except for ASAP algorithm. More detailed molecular and morphological integrative studies are required to clarify the status of these MOTUs in the future.
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Affiliation(s)
- Pu Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Yuting Cai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Lan Ma
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Jinyan Chai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
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Molecular Species Delimitation Using COI Barcodes of Mealybugs (Hemiptera: Pseudococcidae) from Coffee Plants in Espírito Santo, Brazil. DIVERSITY 2023. [DOI: 10.3390/d15020305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Mealybugs are insects belonging to the family Pseudococcidae. This family includes many plant-pest species with similar morphologies, which may lead to errors in mealybug identification and delimitation. In the present study, we employed molecular-species-delimitation approaches based on distance (ASAP) and coalescence (GMYC and mPTP) methods to identify mealybugs collected from coffee and other plant hosts in the states of Espírito Santo, Bahia, Minas Gerais, and Pernambuco, Brazil. We obtained 171 new COI sequences, and 565 from the BOLD Systems database, representing 26 candidate species of Pseudococcidae. The MOTUs estimated were not congruent across different methods (ASAP-25; GMYC-30; mPTP-22). Misidentifications were revealed in the sequences from the BOLD Systems database involving Phenacoccus solani × Ph. solenopsis, Ph. tucumanus × Ph. baccharidis, and Planacoccus citri × Pl. minor species. Ten mealybug species were collected from coffee plants in Espírito Santo. Due to the incorrect labeling of the species sequences, the COI barcode library of the dataset from the database needs to be carefully analyzed to avoid the misidentification of species. The systematics and taxonomy of mealybugs may be improved by integrative taxonomy which may facilitate the integrated pest management of these pests.
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Gopurenko D, Bellis G, Pengsakul T, Siriyasatien P, Thepparat A. DNA Barcoding of Culicoides Latreille (Diptera: Ceratopogonidae) From Thailand Reveals Taxonomic Inconsistencies and Novel Diversity Among Reported Sequences. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1960-1970. [PMID: 36189978 DOI: 10.1093/jme/tjac142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 06/16/2023]
Abstract
Recent focus on Culicoides species diversity in Thailand was prompted by a need to identify vectors responsible for the transmission of African Horse Sickness in that country. To assist rapid genetic identification of species, we sampled mitochondrial cytochrome c oxidase subunit I (COI) DNA barcodes (N = 78) from 40 species of Culicoides biting midge from Thailand, including 17 species for which DNA barcodes were previously unavailable. The DNA barcodes were assigned to 39 Barcode Identification Numbers (BINs) representing terminal genetic clusters at the Barcode of Life Data systems (BOLD). BINs assisted with comparisons to published conspecific DNA barcodes and allowed partial barcodes obtained from seven specimens to be associated with BINs by their similarity. Some taxonomic issues were revealed and attributed to the possible misidentification of earlier reported specimens as well as a potential synonymy of C. elbeli Wirth & Hubert and C. menglaensis Chu & Liu. Comparison with published BINs also revealed genetic evidence of divergent population processes and or potentially cryptic species in 16 described taxa, flagged by their high levels of COI sequence difference among conspecifics. We recommend the BOLD BIN system to researchers preparing DNA barcodes of vouchered species for public release. This will alert them to taxonomic incongruencies between their records and publicly released DNA barcodes, and also flag genetically deep and potentially novel diversity in described species.
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Affiliation(s)
- David Gopurenko
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Glenn Bellis
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Theerakamol Pengsakul
- Faculty of Medical Technology, Prince of Songkla University, Songkla 90110, Thailand
| | - Padet Siriyasatien
- Center of Excellence in Vector Biology and Vector Borne Diseases, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Arunrat Thepparat
- Department of Agricultural Technology, Ramkhamhaeng University, Bangkok, Thailand
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Zhao Y, Wang H, Huang H, Zhou Z. A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China. Zookeys 2022; 1123:147-171. [PMID: 36762040 PMCID: PMC9836636 DOI: 10.3897/zookeys.1123.86704] [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: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.
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Affiliation(s)
- Yizheng Zhao
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Hui Wang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Huimin Huang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, ChinaHebei UniversityBaodingChina
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Timm VF, Gonçalves LT, Valente V, Deprá M. The efficiency of the COI gene as a DNA barcode and an overview of Orthoptera (Caelifera and Ensifera) sequences in the BOLD System. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2022-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orthoptera, among the oldest and most numerous insect lineages, is an excellent model for evolutionary studies but has numerous taxonomic problems. To mitigate these issues, the cytochrome c oxidase subunit I (COI), standardized with the DNA barcode for Metazoa, is increasingly used for specimen identification and species delimitation. We tested the performance of COI as a DNA barcode in Orthoptera, using two analyses based on intra- and interspecific distances, barcode gap and Probability of Correct Identification (PCI); and estimated species richness through Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP). We filtered all sequences of Orthoptera available in Barcode of Life Data System (BOLD) and used 11,605 COI sequences, covering 1,132 species, 226 genera, and 18 families. The overall average PCI was 73.86%. For 82.2% of genera the barcode gap boxplots were classified as good or intermediate, indicating that COI can be effective as a DNA barcode in Orthoptera, although with varying efficiency depending on the need for more information. ABGD and ASAP inferred species richness similar to labels informed by BOLD for the suborders Caelifera and Ensifera. The representation of Orthoptera in the BOLD database and the results of these analyses are discussed.
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Affiliation(s)
- Vítor Falchi Timm
- Universidade Federal do Rio Grande do Sul, 28124, Departamento de Genética, Porto Alegre, RS, Brazil
| | | | - V.l.S. Valente
- Universidade Federal do Rio Grande do Sul, 28124, Departamento de Genética, Porto Alegre, RS, Brazil,
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Zhu Q, Wang H, Zhou Z, Shi F. Phylogeny and Integrative Taxonomy of the Genera Gymnaetoides and Pseudotachycines (Orthoptera: Rhaphidophoridae). INSECTS 2022; 13:insects13070628. [PMID: 35886804 PMCID: PMC9322046 DOI: 10.3390/insects13070628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/29/2022]
Abstract
The genera Gymnaetoides and Pseudotachycines are endemic to China and are morphologically homogeneous. The few available diagnostic characters make species identification particularly challenging. Species cannot be classified according to the given generic diagnosis, and phylogenetic analyses have not been reported. Here, we reconstruct the phylogeny using Bayesian inference and maximum likelihood and employ four approaches to delimit species. The results suggest that both Gymnaetoides and Pseudotachycines are paraphyletic. Therefore, we revise their taxonomy based on the combination of morphological characters and molecular data. A new genus Homotachycines Zhu & Shi gen. nov. is erected, and six new combinations are proposed. Species delimitation identifies 15 new species and one new subspecies: Gymnaetoides huangshanensis, G. petalus, G. yangmingensis, G. lushanensis, Pseudotachycines procerus, P. procerus guizhouensis, P. zhengi, P. nephrus, P. sagittus, P. fengyangshanensis, Homotachycines triangulus, H. quadratus, H. baokangensis, H. fusus, H. concavus, and H. qinlingensis sp. nov. Moreover, we find that the shapes of the dorsal lateral lobes and the dorsal median lobe of the male genitalia are also important characters for identifying these genera and that the shapes of the dorsal and lateral sclerites of the male genitalia are suitable for the classifications of species.
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Affiliation(s)
- Qidi Zhu
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Haijian Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China;
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
- Correspondence: (Z.Z.); (F.S.)
| | - Fuming Shi
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
- Correspondence: (Z.Z.); (F.S.)
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Abstract
Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that the selected regions, even small, gave enough informative positions for both species’ identification and phylogenetic studies. Analyses of both DNA regions have unveiled their use as species identification characters, with special emphasis on Acari mitochondrial COI for Tetranychidae and Phytoseiidae species in comparison with the Folmer fragment, which has been universally used as a barcode marker. We demonstrated that the Acari mitochondrial COI region is also a suitable marker to establish a barcode dataset for Acari identification. Our phylogenetic analyses are congruent with other recent works, showing that Acari is a monophyletic group, of which Astigmata, Ixodida, Mesostigmata, Oribatida, and Prostigmata are also monophyletic.
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Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, Manzoor F, Sones J, Perez K, Sarwar G, Khan AA, Akhter M, Saeed S, Sultana R, Tahir HM, Rafi MA, Iftikhar R, Naseem MT, Masood M, Tufail M, Kumar S, Afzal S, McKeown J, Samejo AA, Khaliq I, D’Souza ML, Mansoor S, Hebert PDN. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 2022; 10:e13267. [PMID: 35497186 PMCID: PMC9048642 DOI: 10.7717/peerj.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 01/15/2023] Open
Abstract
Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- Centre for Animal Sciences and Fisheries, University of Swat, Mingora, Pakistan
| | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Naila Nazir
- Department of Entomology, University of Poonch, Rawalakot, Azad Kashmir, Pakistan
| | - Nazeer Ahmed
- Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azhar A. Khan
- College of Agriculture, Bahauddin Zakariya University Bahadur Campus, Layyah, Pakistan
| | - Muhammad Akhter
- Pulses Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shafqat Saeed
- Faculty of Agriculture and Environmental Sciences, MNS University of Agriculture, Multan, Pakistan
| | - Riffat Sultana
- Department of Zoology, University of Sindh, Jamshoro, Pakistan
| | | | - Muhammad A. Rafi
- National Insect Museum, National Agricultural Research Center, Islamabad, Pakistan
| | - Romana Iftikhar
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Mariyam Masood
- Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Santosh Kumar
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Sabila Afzal
- Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | | | | | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
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FREYHOF JÖRG, KAYA CÜNEYT, GEIGER MATTHIASF. A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae). Zootaxa 2022; 5128:151-194. [DOI: 10.11646/zootaxa.5128.2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 11/04/2022]
Abstract
The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis.
The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.0–1.8% while the distances between molecular clades ranges from 0.6–5.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.0–2.4% while the interspecific K2P distance ranges from 1.2–20.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kızılırmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Büyük Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Elekçi in northern Anatolia, is also widespread in the Yeşilırmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeşilırmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.
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Catzim VV, Elías-Gutiérrez M, Pérez-Lachaud G. Contribution to the lady beetle fauna of the Yucatan Peninsula and integrative taxonomy for species delimitation. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2017060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vannesa V. Catzim
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Manuel Elías-Gutiérrez
- Departamento de Ecología y Sistemática Acuática, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Gabriela Pérez-Lachaud
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
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Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
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Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
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13
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A dearth of data: fitting parasitoids into ecological networks. Trends Parasitol 2021; 37:863-874. [PMID: 34030983 DOI: 10.1016/j.pt.2021.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022]
Abstract
Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.
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14
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Onn Chan K, Hutter CR, Wood PL, Su YC, Brown RM. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). Syst Biol 2021; 71:40-57. [PMID: 33964168 DOI: 10.1093/sysbio/syab034] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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15
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Kundu S, Kumar H, Tyagi K, Chandra K, Kumar V. DNA barcoding of selected short-horned grasshoppers (Orthoptera: Acrididae) from Indian Himalayan region. Mitochondrial DNA B Resour 2020; 5:3618-3623. [PMID: 33367033 PMCID: PMC7594861 DOI: 10.1080/23802359.2020.1830725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/25/2020] [Indexed: 12/03/2022] Open
Abstract
In the context of Indian zoogeography, the DNA barcode data of short-horned grasshoppers (family Acrididae) are limited in global databases. Hence, the present study was aimed to collect selected Acridid species from the Indian Himalayan regions and generate DNA barcode data to enrich the global database. The estimated K2P genetic distances, Bayesian analysis (BA) topology and multiple species delimitation methods (ABGD, bPTP, and GMYC) clearly discriminate all the studied species. Based on high genetic distance (7.5%), multiple clades, and more than one molecular operational taxonomic unit, the present study elucidates the allopatric speciation and presence of possible cryptic diversity of Oxya japonica within India, China, and Russia. The present study suggests the collection of multiple specimens from different geographical locations and the generation of more DNA barcode data would facilitate the actual diversity of this insect group.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hirdesh Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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16
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Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, Butt A, Mansoor S, Hebert PDN. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One 2019; 14:e0217086. [PMID: 31116764 PMCID: PMC6530854 DOI: 10.1371/journal.pone.0217086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/04/2019] [Indexed: 01/16/2023] Open
Abstract
Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Abida Butt
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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