1
|
Bursali F, Simsek FM. Population Genetics of Culex tritaeniorhynchus (Diptera: Culicidae) in Türkiye. Acta Parasitol 2024; 69:1157-1171. [PMID: 38592372 PMCID: PMC11182820 DOI: 10.1007/s11686-024-00844-9] [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: 11/14/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024]
Abstract
PURPOSE Mosquitoes are important vectors of pathogens that can affect humans and animals. Culex tritaeniorhynchus is an important vector of arboviruses such as Japanese encephalitis virus, West Nile virus among various human and animal communities. These diseases are of major public health concern and can have huge economic and health burdens in prevalent countries. Although populations of this important mosquito species have been detected in the Mediterranean and Aegean regions of Türkiye; little is known about its population structure. Our study is to examine the population genetics and genetic composition of Cx. tritaeniorhynchus mosquitoes collected from several localities using cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 5 genes (ND5). This is the first extensive study of Cx. tritaeniorhynchus in the mainland Türkiye with sampling spanning many of provinces. METHODS In this study, DNA extraction, amplification of mitochondrial COI and ND5 genes and population genetic analyses were performed on ten geographic populations of Culex tritaeniorhynchus in the Aegean and Mediterranean region of Türkiye. RESULTS Between 2019 and 2020, 96 samples were collected from 10 geographic populations in the Aegean and Mediterranean regions; they were molecularly analyzed and 139 sequences (50 sequence for COI and 89 sequence for ND5) were used to determine the population structure and genetic diversity. For ND5 gene region, the samples produced 24 haplotypes derived from 15 variable sites and for COI gene region, 43 haplotypes were derived from 17 variable sites. The haplotype for both gene regions was higher than nucleotide diversity. Haplotype phylogeny revealed two groups present in all populations. AMOVA test results show that the geographical populations were the same for all gene regions. Results suggest that Cx. tritaeniorhynchus is a native population in Türkiye, the species is progressing towards speciation and there is no genetic differentiation between provinces and regions. CONCLUSION This study provides useful information on the molecular identifcation and genetic diversity of Cx. tritaeniorhynchus; these results are important to improve mosquito control programs.
Collapse
Affiliation(s)
- Fatma Bursali
- Faculty of Science, Department of Biology, Aydın Adnan Menderes University, Aydın, 09100, Türkiye.
| | - Fatih Mehmet Simsek
- Faculty of Science, Department of Biology, Aydın Adnan Menderes University, Aydın, 09100, Türkiye
| |
Collapse
|
2
|
Hussain A, Kakar A, Naseem M, Kamran K, Ullah Z, Shehla S, Obaid MK, Ahmed N, Khan Q, Liaqat I. Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan. PLoS One 2024; 19:e0300903. [PMID: 38598453 PMCID: PMC11006193 DOI: 10.1371/journal.pone.0300903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/05/2024] [Indexed: 04/12/2024] Open
Abstract
The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).
Collapse
Affiliation(s)
- Abid Hussain
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Asmatullah Kakar
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Mahrukh Naseem
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Kashif Kamran
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Zafar Ullah
- Department of Zoology, University of Loralai, Balochistan, Pakistan
| | - Shehla Shehla
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Kashif Obaid
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Nazeer Ahmed
- Balochistan University of Information Technology, Engineering and Management Sciences, Balochistan, Pakistan
| | - Qaiser Khan
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Iram Liaqat
- Department of Zoology, Government College University, Lahore, Punjab, Pakistan
| |
Collapse
|
3
|
Li SY, Yao Y, Sun L, Ling HN, Jin WD, Lin XL. DNA barcodes and morphology reveal new species within the Rheotanytarsus guineensis species group from China (Diptera: Chironomidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:e22060. [PMID: 37919838 DOI: 10.1002/arch.22060] [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: 08/14/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
The Rheotanytarsus guineensis species group (Diptera: Chironomidae) is a species diverse and taxonomically difficult group. Using DNA barcodes, we found five new species within the R. guineensis species group and reviewed the species group based on adult males from China. Rheotanytarsus guoae Lin & Yao sp. n., Rheotanytarsus miaoae Lin & Yao sp. n., Rheotanytarsus qiangi Lin & Yao sp. n., Rheotanytarsus yueqingensis Lin & Yao sp. n., and Rheotanytarsus yui Lin & Yao sp. n. are all described and figured. A key to known adult males of the R. guineensis species group worldwide is provided for the first time.
Collapse
Affiliation(s)
- Shu-Yi Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Yuan Yao
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Li Sun
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Hai-Ning Ling
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Wei-Dong Jin
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xiao-Long Lin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
4
|
Savaris M, Saldanha AV, Corrêa AS, Rainho HL, Scarpare Filho JA, Silveira Neto S, Zucchi RA. Establishment of Sinoxylon anale Lesne (Coleoptera, Bostrichidae) in Brazil: Identification, Host Plants, Distribution, and Damage. NEOTROPICAL ENTOMOLOGY 2023; 52:1144-1154. [PMID: 37819481 DOI: 10.1007/s13744-023-01087-5] [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: 05/04/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Damage from Sinoxylon anale Lesne, a woodboring beetle not previously known to be established in Brazil, was observed in young jabuticaba trees (Plinia cauliflora, Myrtaceae) in a nursery in the municipality of Laranjal Paulista, state of São Paulo. We immediately advised MAPA ("Ministério da Agricultura, Pecuária e Abastecimento") and collected samples from the nursery and from different hosts in nearby areas, to identify the specimens and investigate the dynamics of the infestation in the jabuticaba trees. Sinoxylon anale was also collected in ethanol-baited and ultraviolet-light traps and in dry branches of the native species pau-jacaré (Piptadenia gonoacantha, Fabaceae) and inga (Inga vera, Fabaceae), and the exotic pau-d'água (Dracaena fragrans, Asparagaceae) in the municipality of Piracicaba, state of São Paulo. These collections established that S. anale larvae and adults develop in dead branches of four new host plants. Taxonomic studies using morphological parameters and DNA barcoding confirmed the identification of S. anale. An illustrated key to the three Sinoxylon species now recorded in Brazil is provided, and the COI gene sequences have been made available in a public database. Sinoxylon anale probably attacked the young jabuticaba trees after they were killed by larvae of long-horned beetles (Cerambycidae). So far, S. anale has been found established only in two locations in the same area of the state of São Paulo.
Collapse
Affiliation(s)
- Marcoandre Savaris
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
| | - Alan Valdir Saldanha
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alberto Soares Corrêa
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Hugo Leoncini Rainho
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - João Alexio Scarpare Filho
- Departament of Crop Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Sinval Silveira Neto
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Roberto Antonio Zucchi
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| |
Collapse
|
5
|
da Silva FL, Pinho LC, Stur E, Nihei SS, Ekrem T. DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America. Ecol Evol 2023; 13:e10602. [PMID: 37841227 PMCID: PMC10568203 DOI: 10.1002/ece3.10602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/04/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.
Collapse
Affiliation(s)
- Fabio Laurindo da Silva
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Present address:
Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Luiz Carlos Pinho
- Laboratory of Systematic of Diptera, Department of Ecology and ZoologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Elisabeth Stur
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Silvio Shigueo Nihei
- Laboratory of Systematic and Biogeography of Insecta, Department of Zoology, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Torbjørn Ekrem
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| |
Collapse
|
6
|
Silva FLDA. Connecting the dots: DNA barcoding and lectotype designation shedding light on Labrundinia longipalpis (Goetghebuer, 1921), an intriguing non-biting midge (Chironomidae, Tanypodinae). Zootaxa 2023; 5346:151-162. [PMID: 38221346 DOI: 10.11646/zootaxa.5346.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Indexed: 01/16/2024]
Abstract
Accurate taxonomic classification is deemed paramount for gaining an understanding of the diversity and distribution of insect species. In this study, an essential stride was made towards advancing the taxonomy of the non-biting midge Labrundinia longipalpis (Chironomidae, Tanypodinae), which serves as the type species of the genus. The distribution of L. longipalpis is particularly intriguing as it contrasts with the predominantly tropical distribution of the genus, with this species being found across the Holarctic region. The main goal of this investigation was to designate a lectotype and several paralectotypes, which was achieved through a comprehensive reexamination of the original material, alongside additional specimens obtained from the type-locality in Flanders. Furthermore, the distribution of L. longipalpis across Europe and North America was examined, and the proposed synonymization of L. maculata with the latter was challenged using the analysis of molecular data. Through the comparison of DNA barcodes, it was revealed that the North American population of L. longipalpis clustered together with the European population, which alludes to a considerable level of genetic similarity between these two populations. These results provide valuable insights into the behavior, ecological dynamics and biogeography of L. longipalpis, while also raising interesting questions about colonization and distribution patterns attributed to its adaptability and potential for long-distance dispersal.
Collapse
Affiliation(s)
- Fabio Laurindo DA Silva
- Laboratory of Aquatic Insect Biodiversity and Ecology; Department of Zoology; Institute of Biosciences; University of So Paulo; So Paulo; Brazil.
| |
Collapse
|
7
|
Alsarraf M, Carretón E, Ciuca L, Diakou A, Dwużnik-Szarek D, Fuehrer HP, Genchi M, Ionică AM, Kloch A, Kramer LH, Mihalca AD, Miterpáková M, Morchón R, Papadopoulos E, Pękacz M, Rinaldi L, Alsarraf M, Topolnytska M, Vismarra A, Zawistowska-Deniziak A, Bajer A. Diversity and geographic distribution of haplotypes of Dirofilaria immitis across European endemic countries. Parasit Vectors 2023; 16:325. [PMID: 37700369 PMCID: PMC10498598 DOI: 10.1186/s13071-023-05945-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Dirofilaria immitis, also known as heartworm, is one of the most important parasitic nematodes of domestic dogs, causing a potentially serious disease, cardiopulmonary dirofilariosis, which can be lethal. This species seems to be less 'expansive' than its sister species Dirofilaria repens, and it is believed that climate change facilitates the spread of this parasite to new non-endemic regions. METHODS In total, 122 heartworm isolates were analysed from nine endemic countries in Europe (Portugal, Spain, Italy, Greece, Hungary, Romania, Slovakia, and Ukraine) and a single isolate from Bangladesh by amplification and sequencing of two mitochondrial (mt) DNA markers: cytochrome c oxidase subunit 1 (COI) and dehydrogenase subunit 1 (NADH). The main aim of the current study was to determine the genetic diversity of D. immitis and compare it with D. repens haplotype diversity and distribution. DNA was extracted from adult heartworms or microfilariae in blood. Most isolates originated from dogs (Canis lupus familiaris) while 10 isolates originated from wildlife species from Romania, including eight isolates from golden jackals (Canis aureus), one isolate from a Eurasian otter (Lutra lutra) and one isolate from a red fox (Vulpes vulpes). RESULTS Median spanning network analysis was based on the combined sequence (1721 bp) obtained from two mt markers and successfully delineated nine haplotypes (Di1-Di9). Haplotype Di1 was the dominant haplotype encompassing 91 out of the 122 sequences (75%) from all nine countries and four host species. Haplotype Di2 was the second most common haplotype, formed solely by 13 isolates from Italy. The remaining sequences were assigned to Di3-Di9 haplotypes, differing by 1-4 SNPs from the dominant Di1 haplotype. There was evidence for geographical segregation of haplotypes, with three unique haplotypes associated with Italy and four others associated with certain countries (Di4 and Di7 with Slovakia; Di8 with Greece; Di6 with Hungary). CONCLUSION Diversity in D. immitis mt haplotypes was lower by half than in D. repens (9 vs. 18 haplotypes in D. immitis and D. repens, respectively), which may be associated with the slower expansion of heartworm in Central and NE Europe. NADH gene appears to be conserved in Dirofilaria sp. by showing lower genetic diversity than the analysed COI gene.
Collapse
Affiliation(s)
- Mustafa Alsarraf
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Elena Carretón
- Internal Medicine, Faculty of Veterinary Medicine, University of Las Palmas de Gran Canaria, Campus Arucas, Arucas, 35413 Las Palmas, Spain
| | - Lavinia Ciuca
- Department of Veterinary Medicine and Animal Production, University of Napoli Federico II, Via Delpino 1, 80137 Naples, Italy
| | - Anastasia Diakou
- Laboratory of Parasitology and Parasitic Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dorota Dwużnik-Szarek
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Marco Genchi
- Department of Veterinary Science, Parasitology Unit, University of Parma, strada del Taglio, 10, 43126 Parma, Italy
| | - Angela Monica Ionică
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania
| | - Agnieszka Kloch
- Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Laura Helen Kramer
- Department of Veterinary Science, Parasitology Unit, University of Parma, strada del Taglio, 10, 43126 Parma, Italy
| | - Andrei D. Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania
| | - Martina Miterpáková
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01 Košice, Slovakia
| | - Rodrigo Morchón
- Zoonotic Diseases and One Health Group, IBSAL-CIETUS (Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases University of Salamanca), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain
| | - Elias Papadopoulos
- Laboratory of Parasitology and Parasitic Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Mateusz Pękacz
- Division of Parasitology, Department of Preclinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Napoli Federico II, Via Delpino 1, 80137 Naples, Italy
| | - Mohammed Alsarraf
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Mariia Topolnytska
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Alice Vismarra
- Department of Veterinary Science, Parasitology Unit, University of Parma, strada del Taglio, 10, 43126 Parma, Italy
| | - Anna Zawistowska-Deniziak
- Department of Parasitology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
- Department of Immunology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Bajer
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| |
Collapse
|
8
|
Velásquez-Rodríguez K, Lin XL, Sánchez-Vendizú P, Loayza-Muro R, Huamantinco A, Prat N. DNA Barcode of symbiotic chironomids: Findings in the genus Symbiocladius (Diptera: Chironomidae). Zootaxa 2023; 5319:48-56. [PMID: 37518251 DOI: 10.11646/zootaxa.5319.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Chironomidae of symbiotic habits have been recorded in different parts of the world, among commensals and parasites. There are different genera reported at the moment, however questions such as the origin of commensal or parasitic life, which occurred first or what are their benefits remain debatable. In order to contribute with information to elucidate the above mentioned issues, the present study reports the finding of immature stages of Symbiocladius (Acletus) wygodzinskyi Roback, 1965 in the Churup stream located in the Andes Cordillera (Peru), living on nymphs of Leptophlebiidae (Ephemeroptera). We present a morphological description of immature stages of this species and for the first time the sequence of COX1 gene S. (A.) wygodzinskyi. The genetic result also supports differences between the morphospecies of Symbiocladius (Symbiocladius) rhithrogenae Zavřel, 1924 and S. (A.) wygodzinskyi in 23%.
Collapse
Affiliation(s)
- Karen Velásquez-Rodríguez
- Facultad de Ciencias de la Vida y de la Salud; Perú; Universidad Científica del Sur; Lima; Perú; Laboratorio de Ecotoxicología; San Martín de Porres 15102; Peru.
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment; Shanghai Ocean University; Shanghai 201306; China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution; Shanghai Ocean University; Shanghai 201306; China.
| | - Pamela Sánchez-Vendizú
- Programa de Doctorado en Ciencias mención Ecología y Evolución; Escuela Graduados; Facultad de Ciencias; Universidad Austral de Chile; Valdivia; Chile; Departamento de Mastozoología; Museo de Historia Natural; Universidad Nacional Mayor de San Marcos; Lima; Peru.
| | - Raúl Loayza-Muro
- Universidad Peruana Cayetano Heredia; Facultad de Ciencias e Ingeniería; Laboratorio de Ecotoxicología; San Martín de Porres 15102; Peru.
| | - Ana Huamantinco
- Laboratorio de Invertebrados Acuáticos; Facultad de Ciencias Biológicas; Universidad Nacional Mayor de San Marcos; Lima; Perú.
| | - Narcís Prat
- Grupo de Investigación FEHM (Freshwater Ecology Hydrology and Management); Departamento de Biología; Evolutiva; Ecología y Ciencias Ambientales; Facultad de Biología; Universidad de Barcelona; Barcelona; Spain.
| |
Collapse
|
9
|
Pava-Ripoll M, Miller AK, Ziobro GC. Development of A Multiplex Polymerase Chain Reaction (PCR) Assay for the Potential Detection of Insect Contaminants in Food. J Food Prot 2023:100120. [PMID: 37348561 DOI: 10.1016/j.jfp.2023.100120] [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: 02/01/2023] [Revised: 05/01/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
Molecular methods can potentially be used to detect insect contaminants of food products. In this study, we used three sets of group-specific primers, two of them targeting the amplification of two regions of the insect's mitochondrial cytochrome c oxidase subunit I (COI-Fa and COI-Fb) and the other targeting a region of the nuclear protein-coding wingless (wg) gene. Using singleplex and multiplex polymerase chain reaction (PCR), we evaluated the three set of primers using genomic DNA (gDNA) from 48 insect species including food-storage insect pests and known vectors of foodborne pathogens. Seven plant-based food matrices were also evaluated for exclusivity testing. Additionally, we spiked fragments from five insect species in a selected food matrix (whole wheat flour). Singleplex and multiplex PCR amplified single specific bands (401-449 bp), corresponding to the wg gene, from insect species belonging to families Blattidae and Formicidae, and in Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae). The COI-Fa primers amplified specific bands (171-188 bp) in all Dipteran species and the COI-Fb primers amplified a specific band (∼140 bp) in DNA from Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) and P. interpunctella. However, the presence of specific bands in most Coleopterans was not consistent. No amplicon bands were observed in any of the food matrixes tested and the expected pattern of amplicon bands was seen in multiplex reactions using gDNA from spiked food samples. Our multiplex PCR assay targeted specific groups of insects that commonly contaminate foods without amplifying bands from the food matrixes tested; thus, molecular methods may be suitable for detecting insects or their fragments in foods.
Collapse
Affiliation(s)
- Monica Pava-Ripoll
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD.
| | - Amy K Miller
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD
| | - George C Ziobro
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD
| |
Collapse
|
10
|
Chimeno C, Rulik B, Manfrin A, Kalinkat G, Hölker F, Baranov V. Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach. PeerJ 2023; 11:e15336. [PMID: 37250705 PMCID: PMC10211366 DOI: 10.7717/peerj.15336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample's contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
Collapse
Affiliation(s)
- Caroline Chimeno
- Bavarian State Collection of Zoology (SNSB-ZSM), Munich, Germany
| | - Björn Rulik
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alessandro Manfrin
- Institute for Environmental Sciences, iES Landau, RPTU University of Kaiserslautern-Landau, Landau, Germany
| | - Gregor Kalinkat
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Viktor Baranov
- Estación Biológica de Doñana-CSIC/Doñana Biological Station-CSIC, Seville, Spain
| |
Collapse
|
11
|
Liu WB, Wang Y, Zhao KZ, Wang CY, Zhang JY, Yan CC, Lin XL. New species, a new combination, and DNA barcodes of Parachironomus Lenz, 1921 (Diptera, Chironomidae). Zookeys 2023; 1153:121-140. [DOI: 10.3897/zookeys.1153.98542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The genus Parachironomus has a cosmopolitan distribution including 85 valid described species worldwide. Species records and studies of the genus in the Tibetan Plateau are scarce. In this study, the genus Parachironomus from China is revised and two new species, Parachironomus wangi Liu & Lin, sp. nov. and Parachironomus nankaiensis Liu & Lin, sp. nov., are described based on adult morphology and molecular data. Paracladopelma demissum Yan, Wang & Bu is placed in the genus Parachironomus as a new combination. A neighbor-joining tree was reconstructed based on all known ParachironomusCOI DNA barcodes. A key to adult males of the genus Parachironomus from China is also provided.
Collapse
|
12
|
Song C, Wang L, Lei T, Qi X. New Color-Patterned Species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a Deep Intraspecific Divergence of Species by DNA Barcodes. INSECTS 2023; 14:227. [PMID: 36975912 PMCID: PMC10054112 DOI: 10.3390/insects14030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The genus Microtendipes Kieffer (Diptera: Chironomidae) has a nearly worldwide distribution, comprising more than 60 species, which are further divided into two species groups based on larval stage. However, species delimitation and identification among the adults of this genus are controversial and uncertain. For instance, previous studies have provided many synonymies based on conspecific color pattern variations in Microtendipes species. Here, we used DNA barcode data to address Microtendipes species delimitation as well as to test whether color pattern variations can be diagnostic characters for interspecific identification. The 151 DNA barcodes used, 51 of which were contributed by our laboratory, represent 21 morphospecies. Species with specific color patterns could be accurately separated based on DNA barcodes. Consequently, the color patterns of adult males could be important diagnostic characters. The average intraspecific and interspecific sequence divergences were 2.8% and 12.5%, respectively, and several species exhibited deep intraspecific divergences higher than 5%. Molecular operational taxonomic units (OTUs) ranged from 21 to 73, based on methods including phylogenetic trees, the assemble species by automatic partitioning method, the Poisson tree process (PTP), and the general mixed Yule-coalescent (GMYC) method. As a result of these analyses, five new species were recognized (M. baishanzuensis sp. nov., M. bimaculatus sp. nov., M. nigrithorax sp. nov., M. robustus sp. nov., and M. wuyiensis sp. nov.).
Collapse
Affiliation(s)
- Chao Song
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Le Wang
- Nanjing Institute of Environmental Sciences under Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Xin Qi
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| |
Collapse
|
13
|
Dos Santos FAA, Duarte MD, Carvalho CL, Monteiro M, Carvalho P, Mendonça P, Valente PCLG, Sheikhnejad H, Waap H, Gomes J. Genetic and morphological identification of filarial worm from Iberian hare in Portugal. Sci Rep 2022; 12:9310. [PMID: 35661130 PMCID: PMC9166702 DOI: 10.1038/s41598-022-13354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
The Iberian hare (Lepus granatensis) is an endemic species of the Iberian Peninsula and the only hare species found in Portugal, although also being present in some areas of Spain. The reduction of wild hare populations due to several ecological and sanitary factors, has been raising growing concerns in the recent years. Despite different helminth species were already described in Iberian hares in Portugal, to this date, no filarial worms have been identified in this species. Furthermore, only a few studies on lagomorphs' onchocercid worms are available, referring to other hosts species of hares and/or rabbits. In this study, we describe the presence of filarial worms in the blood vessels of two adult Iberian hares collected in 2019 in continental Portugal. Morphology and sequencing data from the 12S rRNA, coxI, 18S rRNA, myoHC, hsp70 and rbp1 genes, showed that the filaroid species were genetically related with Micipsella numidica. However, the extension of the genetic differences found with M. numidica suggests that the filaroids specimens under study belong to a new species, that we provisionally named Micipsella iberica n. sp.. The body location of this putative new parasite species and its physiological implications indicate that it may constitute a potential menace to the already fragile Iberian hare justifying, therefore, further investigation regarding the morphological characterization, prevalence and real clinical impact of this new parasite in hares.
Collapse
Affiliation(s)
- F A Abade Dos Santos
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal.
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal.
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal.
| | - M D Duarte
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal
| | - C L Carvalho
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| | - M Monteiro
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| | - P Carvalho
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| | - P Mendonça
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| | - P C L G Valente
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - H Sheikhnejad
- InnovPlantProtect Collaborative Laboratory, Department of Protection of Specific Crops, 7350-478, Elvas, Portugal
| | - H Waap
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| | - J Gomes
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
- Instituto Nacional de Investigação Agrária E Veterinária (INIAV, I.P.), Quinta Do Marquês, Av. da República, 2780-157, Oeiras, Portugal
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Ballesteros I, Bravo-Castro M, Villamarín-Cortez S, Jijón G, Prat N, Ríos-Touma B, Villamarín C. Genetic Variability of Polypedilum (Diptera: Chironomidae) from Southwest Ecuador. INSECTS 2022; 13:insects13040382. [PMID: 35447824 PMCID: PMC9028585 DOI: 10.3390/insects13040382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary Polypedilum is a genus of aquatic non-biting midges in the family Chironomidae. This genus is widely distributed in neotropical rivers from lowlands to Andean highlands. Nevertheless, making species identification based on morphology is quite complex, even more so in the Neotropics, since systematic studies of this group are scarce. DNA barcoding can help to overcome this problem using a short DNA sequence as a barcode for species delimitation. A fragment of the mitochondrial gene cytochrome c oxidase I (CO1) has been successfully employed as a barcode in the genus Polypedilum. In this study, our aim was to understand the effect of environmental characteristics on Polypedilum diversity and distribution. We examined the CO1 sequence of 68 Polypedilum specimens from rivers with different environmental conditions located in an important biogeographic area of Ecuador. We identified five morphotypes and seven putative species which revealed high genetic variability among them. Polypedilum distribution seems to be affected mainly by two environmental factors, dissolved oxygen, and temperature. Our study is the first evidence of richness within the genus in Ecuador, highlighting the importance of developing taxonomic studies along with ecological assessments to further describe and identify new species. Abstract Chironomids show a wide distribution and can occupy several habitats due to their high adaptive capacity in different freshwater environments. The genus Polypedilum is found along a wide elevational and environmental gradient in the neotropics, and its genetic variability could help to elucidate factors determining its distribution and tolerance to the environmental changes of different species or populations. This study examines the genetic variability of Polypedilum in an important biogeographic area that acts as a geographical barrier of biodiversity at the border of the Choco and Tumbes biomes. We identified five Polypedilum morphotypes using classic taxonomic methods. We examined 68 Polypedilum individuals from eight sampling sites in El Oro Province, Ecuador, analyzing the putative molecular species using the cytochrome c oxidase subunit 1 (CO1) mitochondrial gene fragment. Then, we calculated molecular diversity indices, Haplotype diversity (Hd), and θs and θπ estimators. Seven Polypedilum OTUs were determined from which a high molecular diversity was registered. A CCA was conducted to understand the population composition in relation to environmental characteristics. Results indicated that dissolved oxygen and temperature are the main environmental factors affecting Polypedilum distribution across elevational gradients and between basins.
Collapse
Affiliation(s)
- Isabel Ballesteros
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Universidad de Las Américas, Quito 170503, Ecuador; (I.B.); (M.B.-C.); (G.J.); (B.R.-T.)
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Mishell Bravo-Castro
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Universidad de Las Américas, Quito 170503, Ecuador; (I.B.); (M.B.-C.); (G.J.); (B.R.-T.)
| | - Santiago Villamarín-Cortez
- Department of Biology, Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV 89557, USA;
- Instituto Nacional de Biodiversidad–INABIO, Rumipamba 341 y Av. Shyris, Quito 170135, Ecuador
| | - Gabriela Jijón
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Universidad de Las Américas, Quito 170503, Ecuador; (I.B.); (M.B.-C.); (G.J.); (B.R.-T.)
| | - Narcís Prat
- Grupo de Investigación Freshwater, Hydrology and Ecology Management (FHEM), Departamento de Ecología, Universidad de Barcelona, 08014 Barcelona, Spain;
| | - Blanca Ríos-Touma
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Universidad de Las Américas, Quito 170503, Ecuador; (I.B.); (M.B.-C.); (G.J.); (B.R.-T.)
| | - Christian Villamarín
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Universidad de Las Américas, Quito 170503, Ecuador; (I.B.); (M.B.-C.); (G.J.); (B.R.-T.)
- Correspondence:
| |
Collapse
|
16
|
Kang HJ, Baek MJ, Kang JH, Bae YJ. Diversity and DNA Barcode Analysis of Chironomids (Diptera: Chironomidae) from Large Rivers in South Korea. INSECTS 2022; 13:insects13040346. [PMID: 35447788 PMCID: PMC9032365 DOI: 10.3390/insects13040346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023]
Abstract
Most large rivers in South Korea run through major cities, which often experience many environmental problems, including outbreaks of non-biting midges (Diptera: Chironomidae). However, chironomid species inhabiting large rivers have not been thoroughly investigated. We aimed to identify chironomid species collected from the four main large rivers in South Korea, construct a corresponding DNA barcode library, and examine the distribution and community structure of the identified riverine species. Adult chironomids were collected from nine sites along the rivers by using sweep nets and light traps during June and August 2015. Adults were morphologically identified, and COI nucleotide sequences were generated to verify the species identification and construct a DNA barcode library. The distribution and community structure of the identified species were also analyzed. A total of 124 COI sequences were established from 37 species belonging to 19 genera, and the resulting DNA barcode library effectively discriminated >90% of riverine Chironomidae in South Korea. Ten species, which are considered indicator species for large rivers, were collected from all four rivers. In addition, members of the subfamily Chironominae were collected more frequently than members of other subfamilies, with Tanytarsus tamagotoi being the most common and widespread chironomid species in South Korea. The DNA barcode library developed in this study will facilitate environmental studies of large rivers, such as biomonitoring chironomid larvae.
Collapse
Affiliation(s)
- Hyo Jeong Kang
- Department of Life Science, Graduate School, Korea University, Seoul 02841, Korea;
| | - Min Jeong Baek
- National Institute of Biological Resources, Incheon 22689, Korea;
| | - Ji Hyoun Kang
- Korean Entomological Institute, Korea University, Seoul 02841, Korea;
| | - Yeon Jae Bae
- Department of Life Science, Graduate School, Korea University, Seoul 02841, Korea;
- Korean Entomological Institute, Korea University, Seoul 02841, Korea;
- Division of Environmental Science and Ecological Engineering, College of Life Sciences, Korea University, Seoul 02841, Korea
- Correspondence: ; Tel.: +82-2-3290-3408
| |
Collapse
|
17
|
Gadawski P, Montagna M, Rossaro B, Giłka W, Pešić V, Grabowski M, Magoga G. DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Affiliation(s)
- Piotr Gadawski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Matteo Montagna
- Department of Agricultural Sciences University of Naples Federico II Portici Italy
- BAT Center ‐ Interuniversity Center for Studies on Bioinspired Agro‐environmental Technology University of Napoli Federico II Portici Italy
| | - Bruno Rossaro
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
| | - Wojciech Giłka
- Laboratory of Systematic Zoology Department of Invertebrate Zoology and Parasitology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Vladimir Pešić
- Department of Biology Faculty of Science University of Montenegro Podgorica Montenegro
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Giulia Magoga
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
| |
Collapse
|
18
|
Xie GL, Ma XR, Liu QY, Meng FX, Li C, Wang J, Guo YH. Genetic structure of Culex tritaeniorhynchus (Diptera: Culicidae) based on COI DNA barcodes. Mitochondrial DNA B Resour 2022; 6:1411-1415. [PMID: 35174283 PMCID: PMC8843312 DOI: 10.1080/23802359.2021.1911711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Culex tritaeniorhynchus Gile is a major vector of Japanese encephalitis in China. The population genetics study is crucial as it helps understanding the epidemiological aspects of mosquito-brone diseases and improving vector control measures. Here, the genetic population structure of C. tritaeniorhynchus in the mainland China were estimated using the cytochrome c oxidase subunit 1 (COI) DNA barcodes region. 485 individuals of C. tritaeniorhynchus were collected from 38 sampling sites in 21 geographic populations in the mainland China. In total, 485 sequences were used to explore the population structure and genetic diversity. The results showed that the populations of C. tritaeniorhynchus had high haplotype diversity (Hd = 0.98, with 303 haplotypes), low nucleotide diversity (p = 0.02245) and high gene flow (Nm = 47.11) with two maternal lineages and four groups. An AMOVA indicated that 98.8% of the total variation originated from variation within populations. In addition, the population genetic structure exhibited by C. tritaeniorhynchus filling the vacant of the genetic structure in the mainland China. Human activities may also assist mosquito movement and migration. Gene flow among the populations of C. tritaeniorhynchus can facilitate the spread of insecticide resistance genes over geographical areas, and it will be a challenging for controlling the populations.
Collapse
Affiliation(s)
- Gui-Lin Xie
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Xin-Ran Ma
- College of Life Science, Northeast Agricultural University, Harbin, China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qi-Yong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Feng-Xia Meng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chao Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu-Hong Guo
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
19
|
Song C, Martin J, Wang S, Qi X. Redescription and New Record of Chironomus novosibiricus (Diptera, Chironomidae) from Northern China. ANN ZOOL FENN 2022. [DOI: 10.5735/086.059.0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Chao Song
- College of Life Sciences, Taizhou University, Taizhou, CN-318000 Zhejiang, China
| | - Jon Martin
- Genetics, Genomics and Development, School of Biosciences, The University of Melbourne, VIC 3010, Australia
| | - Song Wang
- Taizhou Forestry Extension Station, Taizhou, CN-318000 Zhejiang, China
| | - Xin Qi
- College of Life Sciences, Taizhou University, Taizhou, CN-318000 Zhejiang, China
| |
Collapse
|
20
|
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
| |
Collapse
|
21
|
Langat SK, Eyase F, Bulimo W, Lutomiah J, Oyola SO, Imbuga M, Sang R. Profiling of RNA Viruses in Biting Midges ( Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis. mSphere 2021; 6:e0055121. [PMID: 34643419 PMCID: PMC8513680 DOI: 10.1128/msphere.00551-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022] Open
Abstract
Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 700,000 deaths each year. A significant number of these VBDs are caused by RNA virus pathogens. Here, we used metagenomics and metabarcoding analysis to characterize RNA viruses and their insect hosts among biting midges from Kenya. We identified a total of 15 phylogenetically distinct insect-specific viruses. These viruses fall into six families, with one virus falling in the recently proposed negevirus taxon. The six virus families include Partitiviridae, Iflaviridae, Tombusviridae, Solemoviridae, Totiviridae, and Chuviridae. In addition, we identified many insect species that were possibly associated with the identified viruses. Ceratopogonidae was the most common family of midges identified. Others included Chironomidae and Cecidomyiidae. Our findings reveal a diverse RNA virome among Kenyan midges that includes previously unknown viruses. Further, metabarcoding analysis based on COI (cytochrome c oxidase subunit 1 mitochondrial gene) barcodes reveal a diverse array of midge species among the insects used in the study. Successful application of metagenomics and metabarcoding methods to characterize RNA viruses and their insect hosts in this study highlights a possible simultaneous application of these two methods as cost-effective approaches to virus surveillance and host characterization. IMPORTANCE The majority of the viruses that currently cause diseases in humans and animals are RNA viruses, and more specifically arthropod-transmitted viruses. They cause diseases such as dengue, West Nile infection, bluetongue disease, Schmallenberg disease, and yellow fever, among others. Several sequencing investigations have shown us that a diverse array of RNA viruses among insect vectors remain unknown. Some of these could be ancient lineages that could aid in comprehensive studies on RNA virus evolution. Such studies may provide us with insights into the evolution of the currently pathogenic viruses. Here, we applied metagenomics to field-collected midges and we managed to characterize several RNA viruses, where we recovered complete and nearly complete genomes of these viruses. We also characterized the insect host species that are associated with these viruses. These results add to the currently known diversity of RNA viruses among biting midges as well as their associated insect hosts.
Collapse
Affiliation(s)
- Solomon K. Langat
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Fredrick Eyase
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate—Africa, Nairobi, Kenya
| | - Wallace Bulimo
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Joel Lutomiah
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Mabel Imbuga
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Rosemary Sang
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| |
Collapse
|
22
|
Lue CH, Buffington ML, Scheffer S, Lewis M, Elliott TA, Lindsey ARI, Driskell A, Jandova A, Kimura MT, Carton Y, Kula RR, Schlenke TA, Mateos M, Govind S, Varaldi J, Guerrieri E, Giorgini M, Wang X, Hoelmer K, Daane KM, Abram PK, Pardikes NA, Brown JJ, Thierry M, Poirié M, Goldstein P, Miller SE, Tracey WD, Davis JS, Jiggins FM, Wertheim B, Lewis OT, Leips J, Staniczenko PPA, Hrcek J. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol Ecol Resour 2021; 21:2437-2454. [PMID: 34051038 DOI: 10.1111/1755-0998.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.
Collapse
Affiliation(s)
- Chia-Hua Lue
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sonja Scheffer
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Matthew Lewis
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Amy Driskell
- Laboratories of Analytical Biology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Anna Jandova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | | | - Yves Carton
- "Évolution, Génomes, Comportement, Écologie", CNRS et Université Paris-Saclay, Paris, France
| | - Robert R Kula
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Mariana Mateos
- Wildlife and Fisheries Sciences Department, Texas A&M University, College Station, TX, USA
| | - Shubha Govind
- The Graduate Center of the City University of New York, New York, NY, USA
| | - Julien Varaldi
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Emilio Guerrieri
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Massimo Giorgini
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kim Hoelmer
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Nicholas A Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Joel J Brown
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Melanie Thierry
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Marylène Poirié
- INRAE, CNRS. and Evolution and Specificity of Multitrophic Interactions (ESIM) Sophia Agrobiotech Institute, Université "Côte d'Azur", Sophia Antipolis, France
| | - Paul Goldstein
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Scott E Miller
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - W Daniel Tracey
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Gill Center for Biomolecular Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jeremy S Davis
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Biology Department, University of Kentucky, Lexington, KY, USA
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| |
Collapse
|
23
|
Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
Collapse
Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
| |
Collapse
|
24
|
|
25
|
Lin XL, Yu HJ, Wang XH, Bu WJ, Yan CC, Liu WB. New or little-known Boreoheptagyia (Diptera, Chironomidae) in China inferred from morphology and DNA barcodes. Zookeys 2021; 1040:187-200. [PMID: 34135660 PMCID: PMC8178290 DOI: 10.3897/zookeys.1040.66527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/07/2021] [Indexed: 11/12/2022] Open
Abstract
The male adult of Boreoheptagyiazhengi Lin & Liu, sp. nov. is described and illustrated based on material collected in China. Associated morphological characteristics and reference to its DNA barcode are provided. Boreoheptagyiakurobebrevis (Sasa & Okazawa, 1992) is newly recorded from China based on both a male and female, with additional associated data on the DNA barcode of the male adult. A neighbor-joining tree based on available Boreoheptagyia DNA barcodes and a key to the adults of Boreoheptagyia from China are given.
Collapse
Affiliation(s)
- Xiao-Long Lin
- College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China
| | - Hai-Jun Yu
- Center of Animal husbandry and Fisheries, Bijiang Agriculture and Rural affairs Bureau, Tongren, Guizhou, 554300, China Center of Animal husbandry and Fisheries, Bijiang Agriculture and Rural affairs Bureau Guizhou China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China
| | - Wen-Jun Bu
- College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China
| | - Chun-Cai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China
| | - Wen-Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China
| |
Collapse
|
26
|
Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
Collapse
Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| |
Collapse
|
27
|
Liu WB, Yao Y, Duan X, Lin XL, Yan CC. New Record, COI Barcode and Redescription of Xylotopus amamiapiatus (Sasa, 1990) (Diptera, Chironomidae) from China. ANN ZOOL FENN 2021. [DOI: 10.5735/086.058.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Wen-Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, CN-300387 Tianjin, P. R. China
| | - Yuan Yao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, CN-300387 Tianjin, P. R. China
| | - Xin Duan
- College of Horticulture and Landscape Architecture, Tianjin Agricultural University, CN-300382 Tianjin, P. R. China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, CN-300071 Tianjin, P. R. China
| | - Chun-Cai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, CN-300387 Tianjin, P. R. China
| |
Collapse
|
28
|
Kong FQ, Wang XH, Lin XL. Bryophaenocladius huadingensis (Diptera: Orthocladiinae), a New Species from China. ANN ZOOL FENN 2021. [DOI: 10.5735/086.058.0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fan-Qing Kong
- Ecological Environment Monitoring and Scientific Research Center of Haihe River Basin and Beihai Sea Area, Ministry of Ecological Environment, CN-300170 Tianjin, China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, CN-300071 Tianjin, China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, CN-300071 Tianjin, China
| |
Collapse
|
29
|
Liu WB, Yao Y, Yan CC, Wang XH, Lin XL. A new species of Polypedilum ( Cerobregma) (Diptera, Chironomidae) from Oriental China. Zookeys 2021; 1011:139-148. [PMID: 33568962 PMCID: PMC7847467 DOI: 10.3897/zookeys.1011.59554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/15/2020] [Indexed: 11/29/2022] Open
Abstract
Polypedilum (Cerobregma) huapingensis Liu & Lin, sp. nov. is described and illustrated based on an adult male from Huaping National Nature Reserve, Guangxi, China. A DNA barcode analysis, including the known partial COI sequences of species in the Cerobregma subgenus, was conducted. An updated key to adult males of the subgenus Cerobregma is provided.
Collapse
Affiliation(s)
- Wen-Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China
| | - Yuan Yao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China
| | - Chun-Cai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China
| |
Collapse
|
30
|
Lin X, Mo L, Bu W, Wang X. The first comprehensive DNA barcode reference library of Chinese
Tanytarsus
(Diptera: Chironomidae) for environmental DNA metabarcoding. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiao‐Long Lin
- College of Life Sciences Nankai University Tianjin China
- Department of Natural History NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Lidong Mo
- Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland
| | - Wen‐Jun Bu
- College of Life Sciences Nankai University Tianjin China
| | - Xin‐Hua Wang
- College of Life Sciences Nankai University Tianjin China
| |
Collapse
|
31
|
Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour 2020; 21:609-620. [PMID: 33058550 DOI: 10.1111/1755-0998.13281] [Citation(s) in RCA: 375] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Collapse
Affiliation(s)
- Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sophie Brouillet
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,SMILE Group, CIRB, UMR 7241, Collège de France, CNRS, INSERM, Paris, France.,Éco-anthropologie, Muséum National d'Histoire Naturelle, CNRS UMR 7206, Université de Paris, Paris, France
| |
Collapse
|
32
|
Shimizu S, Broad GR, Maeto K. Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. Zookeys 2020; 990:1-144. [PMID: 33269011 PMCID: PMC7674391 DOI: 10.3897/zookeys.990.55542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
The predominantly tropical ophionine genus Enicospilus Stephens, 1835 is one of the largest genera of Darwin wasps (Hymenoptera, Ichneumonidae), with more than 700 extant species worldwide that are usually crepuscular or nocturnal and are parasitoids of Lepidoptera larvae. In the present study, the Japanese species of Enicospilus are revised using an integrative approach (combined morphology and DNA barcoding). On the basis of 3,110 specimens, 47 Enicospilus species are recognised in Japan, eight of which are new species (E.acutus Shimizu, sp. nov., E.kunigamiensis Shimizu, sp. nov., E.limnophilus Shimizu, sp. nov., E.matsumurai Shimizu, sp. nov., E.pseudopuncticulatus Shimizu, sp. nov., E.sharkeyi Shimizu, sp. nov., E.takakuwai Shimizu, sp. nov., and E.unctus Shimizu, sp. nov.), seven are new records from Japan (E.jilinensis Tang, 1990, E.laqueatus (Enderlein, 1921), E.multidens Chiu, 1954, stat. rev., E.puncticulatus Tang, 1990, E.stenophleps Cushman, 1937, E.vestigator (Smith, 1858), and E.zeugos Chiu, 1954, stat. rev.), 32 had already been recorded in Japan; three (E.biharensis Townes, Townes & Gupta, 1961, E.flavicaput (Morley, 1912), and E.merdarius (Gravenhorst, 1829)) have been erroneously recorded from Japan based on misidentifications, and four names that were previously on the Japanese list are deleted through synonymy. The following taxonomic changes are proposed: E.vacuus Gauld & Mitchell, 1981, syn. nov. (= E.formosensis (Uchida, 1928)); E.multidensstat. rev.; E.striatus Cameron, 1899, syn. nov. = E.lineolatus (Roman, 1913), syn. nov. = E.uniformis Chiu, 1954, syn. nov. = E.flatus Chiu, 1954, syn. nov. = E.gussakovskii Viktorov, 1957, syn. nov. = E.striolatus Townes, Townes & Gupta, 1961, syn. nov. = E.unicornis Rao & Nikam, 1969, syn. nov. = E.unicornis Rao & Nikam, 1970, syn. nov. (= E.pungens (Smith, 1874)); E.iracundus Chiu, 1954, syn. nov. (= E.sakaguchii (Matsumura & Uchida, 1926)); E.sigmatoides Chiu, 1954, syn. nov. (= E.shikokuensis (Uchida, 1928)); E.yamanakai (Uchida, 1930), syn. nov. (= E.shinkanus (Uchida, 1928)); E.ranunculus Chiu, 1954, syn. nov. (= E.yezoensis (Uchida, 1928)); and E.zeugosstat. rev. = E.henrytownesi Chao & Tang, 1991, syn. nov. In addition, the following new regional and country records are also provided: E.flavocephalus (Kirby, 1900), E.puncticulatus, and E.vestigator from the Eastern Palaearctic region, E.laqueatus from the Eastern Palaearctic and Oceanic regions, and E.maruyamanus (Uchida, 1928) from the Oriental region; E.abdominalis (Szépligeti, 1906) from Nepal, E.flavocephalus from Laos, E.formosensis from Laos and Malaysia, E.insinuator (Smith, 1860) from Taiwan, E.maruyamanus from India and Philippines, E.nigronotatus Cameron, 1903, E.riukiuensis (Matsumura & Uchida, 1926), and E.sakaguchii from Indonesia, E.pungens from 14 countries (Australia, Bhutan, Brunei, Indonesia, Laos, Malaysia, Nepal, New Caledonia, Papua New Guinea, Philippines, Solomon Islands, Sri Lanka, Tajikistan, and Taiwan), and E.yezoensis from South Korea. An identification key to all Japanese species of Enicospilus is proposed. Although 47 species are recognised in the present study, approximately 55 species could potentially be found in Japan based on ACE and Chao 1 estimators. The latitudinal diversity gradient of Enicospilus species richness is also tested in the Japanese archipelago based on the constructed robust taxonomic framework and extensive samples. Enicospilus species richness significantly increases towards the south, contrary to the ‘anomalous’ pattern of some other ichneumonid subfamilies.
Collapse
Affiliation(s)
- So Shimizu
- Laboratory of Insect Biodiversity and Ecosystem Science, Graduate School of Agricultural Science, Kôbe University, Rokkôdaichô 1-1, Nada, Kôbe, Hyôgo 657-8501, Japan Kôbe University Kôbe Japan.,DC and Overseas Challenge Program for Young Researchers, Japan Society for the Promotion of Science, Tôkyô, Japan The Natural History Museum London United Kingdom.,Depertment of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK Japan Society for the Promotion of Science Tokyo Japan
| | - Gavin R Broad
- Depertment of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK Japan Society for the Promotion of Science Tokyo Japan
| | - Kaoru Maeto
- Laboratory of Insect Biodiversity and Ecosystem Science, Graduate School of Agricultural Science, Kôbe University, Rokkôdaichô 1-1, Nada, Kôbe, Hyôgo 657-8501, Japan Kôbe University Kôbe Japan
| |
Collapse
|
33
|
Fontes JT, Vieira PE, Ekrem T, Soares P, Costa FO. BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries. Mol Ecol Resour 2020; 21:573-583. [PMID: 33000878 DOI: 10.1111/1755-0998.13262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023]
Abstract
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
Collapse
Affiliation(s)
- João T Fontes
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Pedro E Vieira
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Pedro Soares
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Filipe O Costa
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| |
Collapse
|
34
|
Yu HJ, Lin XL, Zhang RL, Wang Q, Wang XH. Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes. Zookeys 2020; 975:79-86. [PMID: 33117065 PMCID: PMC7572518 DOI: 10.3897/zookeys.957.54668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/08/2020] [Indexed: 11/12/2022] Open
Abstract
The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerusakamusi (Tokunaga, 1938), Propsilocerusparadoxus (Lundström, 1915), Propsilocerussaetheri Wang, Liu et Paasivirta, 2007, Propsilocerussinicus Sæther et Wang, 1996, and Propsilocerustaihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P.akamusi and P.taihuensis are provided.
Collapse
|
35
|
Bhunjun CS, Dong Y, Jayawardena RS, Jeewon R, Phukhamsakda C, Bundhun D, Hyde KD, Sheng J. A polyphasic approach to delineate species in Bipolaris. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00446-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
36
|
The Chironomidae (Diptera) of Svalbard and Jan Mayen. INSECTS 2020; 11:insects11030183. [PMID: 32183077 PMCID: PMC7143642 DOI: 10.3390/insects11030183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 11/27/2022]
Abstract
Non-biting midges of the fly family Chironomidae are extremely abundant and diverse in Arctic regions and are essential components of Arctic ecosystems. Modern identification tools based on documented records of Arctic chironomid species are therefore important for ecological research and environmental monitoring in the region. Here, we provide an updated review of the chironomid fauna of the Svalbard archipelago and the island of Jan Mayen, Norway. Our results show that a total of 73 species distributed across 24 genera in four subfamilies are known from these areas. Our review treats 109 taxa, including nomina dubia and misidentifications. It includes morphological identification keys to all known species as well as photographs of most taxa and DNA barcodes of 66 species. Taxonomic remarks are given for selected taxa, including previous misidentifications and erroneous records. Chironomus islandicus, Tvetenia bavarica, Limnophyes schnelli, Metriocnemus brusti and Metriocnemus fuscipes as well as the genera Allocladius, Corynoneura and Bryophaenocladius are reported from Svalbard for the first time, while Procladius (Holotanypus) frigidus, Stictochironomus psilopterus, Chaetocladius incertus, Orthocladius (Orthocladius) mixtus and Smittia longicosta, previously considered as junior synonyms or nomina dubia, are revived as valid species based on examination of type material or literature. Twenty species within eleven genera are introduced with interim names. Metriocnemus similis is regarded as a junior synonym of Metriocnemus ursinus, and Smittia incerta, Smittia flexinervis and Smittia spitzbergensis are regarded as nomina dubia. Valid taxa no longer considered as part of the Svalbard fauna are Parochlus kiefferi, Arctopelopia barbitarsis, Procladius (Holotanypus) crassinervis, Diamesa lindrothi, Diamesa incallida, Diamesa lundstromi, Chironomus hyperboreus, Sergentia coracina, Camptocladius stercorarius, Chaetocladius dissipatus, Chaetocladius dentiforceps, Chaetocladius laminatus, Chaetocladius perennis, Cricotopus (Cricotopus) humeralis, Cricotopus (Cricotopus) polaris, Hydrosmittia ruttneri, Limnophyes edwardsi, Metriocnemus picipes, Metriocnemus tristellus, Orthocladius (Eudactylocladius) gelidus, Orthocladius (Euorthocladius) thienemanni, Orthocladius (Orthocladius) obumbratus, Orthocladius (Orthocladius) rhyacobius, Paralimnophyes, Paraphaenocladius impensus, Psectrocladius (Monopsectrocladius) calcaratus, Psectrocladius (Psectrocladius) psilopterus, Psectrocladius (Psectrocladius) ventricosus, Smittia lasiophthalma, Smittia lasiops and Zalutschia tatrica.
Collapse
|
37
|
Back from the Past: DNA Barcodes and Morphology Support Ablabesmyia americana Fittkau as a Valid Species (Diptera: Chironomidae). DIVERSITY 2019. [DOI: 10.3390/d11090173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Short, standardized gene fragments for species identification (DNA barcodes) have proven effective in delineating closely-related insect species, and can be critical characters to include in taxonomic studies. This is also the case for the species-rich and widely distributed fly family Chironomidae (non-biting midges). Inspired by observed genetic differences in partial COI gene sequences between North American and European populations of the chironomid Ablabesmyia monilis sensu lato, we investigated whether or not the morphology of male and female adults supported the distinction of more than one species. Our results support that the junior synonym Ablabesmyia americana is a valid species separate from A. monilis, and that A. monilis sensu stricto is distributed both in the Palearctic region and in North America. We provide re-descriptions of all of the major life stages of A. americana and of the adult female of A. monilis.
Collapse
|
38
|
Sun Z, Majaneva M, Sokolova E, Rauch S, Meland S, Ekrem T. DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds. Ecol Evol 2019; 9:9712-9722. [PMID: 31534687 PMCID: PMC6745668 DOI: 10.1002/ece3.5503] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/01/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity.Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure.DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data.The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management. OPEN PRACTICES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.
Collapse
Affiliation(s)
- Zhenhua Sun
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Markus Majaneva
- Department of Natural HistoryNorwegian University of Science and Technology, NTNU University MuseumTrondheimNorway
| | - Ekaterina Sokolova
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Sebastien Rauch
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Sondre Meland
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
- Norwegian Institute for Water Research (NIVA)OsloNorway
| | - Torbjørn Ekrem
- Department of Natural HistoryNorwegian University of Science and Technology, NTNU University MuseumTrondheimNorway
| |
Collapse
|
39
|
Lee TRC, Anderson SJ, Tran-Nguyen LTT, Sallam N, Le Ru BP, Conlong D, Powell K, Ward A, Mitchell A. Towards a global DNA barcode reference library for quarantine identifications of lepidopteran stemborers, with an emphasis on sugarcane pests. Sci Rep 2019; 9:7039. [PMID: 31065024 PMCID: PMC6504866 DOI: 10.1038/s41598-019-42995-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/05/2019] [Indexed: 11/09/2022] Open
Abstract
Lepidopteran stemborers are among the most damaging agricultural pests worldwide, able to reduce crop yields by up to 40%. Sugarcane is the world’s most prolific crop, and several stemborer species from the families Noctuidae, Tortricidae, Crambidae and Pyralidae attack sugarcane. Australia is currently free of the most damaging stemborers, but biosecurity efforts are hampered by the difficulty in morphologically distinguishing stemborer species. Here we assess the utility of DNA barcoding in identifying stemborer pest species. We review the current state of the COI barcode sequence library for sugarcane stemborers, assembling a dataset of 1297 sequences from 64 species. Sequences were from specimens collected and identified in this study, downloaded from BOLD or requested from other authors. We performed species delimitation analyses to assess species diversity and the effectiveness of barcoding in this group. Seven species exhibited <0.03 K2P interspecific diversity, indicating that diagnostic barcoding will work well in most of the studied taxa. We identified 24 instances of identification errors in the online database, which has hampered unambiguous stemborer identification using barcodes. Instances of very high within-species diversity indicate that nuclear markers (e.g. 18S, 28S) and additional morphological data (genitalia dissection of all lineages) are needed to confirm species boundaries.
Collapse
Affiliation(s)
- Timothy R C Lee
- Department of Entomology, Australian Museum Research Institute, 1 William St, Darlinghurst, NSW, 2010, Australia.
| | - Stacey J Anderson
- Biosecurity Operations, NAQS, Department of Agriculture and Water Resources, 1 Pederson Road, Eaton, NT, 0812, Australia
| | - Lucy T T Tran-Nguyen
- Northern Territory Department of Primary Industry and Resources, GPO Box 3000, Darwin, NT, 0801, Australia
| | - Nader Sallam
- Department of Agriculture and Water Resources, 114 Catalina Crescent, Airport Business Park, Cairns Airport, Cairns, QLD, 4870, Australia
| | - Bruno P Le Ru
- African Insect Science for Food and Health (ICIPE), PO Box 30772-00100, Nairobi, Kenya.,IRD/CNRS, UMR IRD 247 EGCE, Laboratoire Evolution Génomes Comportement et Ecologie, Avenue de la terrasse, BP1, 91198, Gif-sur-Yvette, France and Université Paris-Sud 11, 91405, Orsay, France
| | - Desmond Conlong
- Department of Conservation Ecology and Entomology, Faculty of AgriSciences, University of Stellenbosch, Private Bag X1, Matieland, Western Cape, 7602, South Africa.,South African Sugarcane Research Institute, 170 Flanders Drive, Mount Edgecombe, KwaZulu-Natal, 4300, South Africa
| | - Kevin Powell
- Sugar Research Australia, 71378 Bruce Highway, Gordonvale, QLD, 4865, Australia
| | - Andrew Ward
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Andrew Mitchell
- Department of Entomology, Australian Museum Research Institute, 1 William St, Darlinghurst, NSW, 2010, Australia
| |
Collapse
|
40
|
Litman J, Chittaro Y, Birrer S, Praz C, Wermeille E, Fluri M, Stalling T, Schmid S, Wyler S, Gonseth Y. A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation. PLoS One 2018; 13:e0208639. [PMID: 30576327 PMCID: PMC6303096 DOI: 10.1371/journal.pone.0208639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/20/2018] [Indexed: 11/19/2022] Open
Abstract
Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.
Collapse
Affiliation(s)
- Jessica Litman
- Museum of Natural History of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
| | | | - Stefan Birrer
- Hintermann & Weber AG, Reinach, Switzerland
- Biodiversity Monitoring Switzerland, Bern, Switzerland
| | - Christophe Praz
- Laboratory of Evolutive Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Markus Fluri
- Hintermann & Weber AG, Reinach, Switzerland
- Biodiversity Monitoring Switzerland, Bern, Switzerland
| | - Thomas Stalling
- Hintermann & Weber AG, Reinach, Switzerland
- Biodiversity Monitoring Switzerland, Bern, Switzerland
| | - Sarah Schmid
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
41
|
Ekrem T, Stur E, Orton MG, Adamowicz SJ. DNA barcode data reveal biogeographic trends in Arctic non-biting midges. Genome 2018; 61:787-796. [DOI: 10.1139/gen-2018-0100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic – West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland – North American affinity, comparisons using Chao’s dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ∼4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.
Collapse
Affiliation(s)
- Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Matthew G. Orton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
42
|
Ants in Australia’s Monsoonal Tropics: CO1 Barcoding Reveals Extensive Unrecognised Diversity. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
43
|
Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 2018; 6:e4577. [PMID: 29736329 PMCID: PMC5936072 DOI: 10.7717/peerj.4577] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
Collapse
Affiliation(s)
- Nadine Havemann
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Lars Hendrich
- Sektion Insecta varia, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Jèrôme Morinière
- Taxonomic coordinator-German Barcode of Life (GBOL), SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Rolf Niedringhaus
- Department of Biology, Earth and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Peter Schäfer
- B.U.G.S. (Biologische Umwelt-Gutachten Schäfer), Telgte, North-Rhine Westphalia, Germany
| | - Michael J Raupach
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| |
Collapse
|
44
|
Song C, Lin XL, Wang Q, Wang XH. DNA barcodes successfully delimit morphospecies in a superdiverse insect genus. ZOOL SCR 2018. [DOI: 10.1111/zsc.12284] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chao Song
- College of Life Sciences; Nankai University; Tianjin China
| | - Xiao-Long Lin
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Qian Wang
- Tianjin key Laboratory of Aqua-Ecology & Aquaculture; Fisheries of College; Tianjin Agricultural University; Tianjin China
| | - Xin-Hua Wang
- College of Life Sciences; Nankai University; Tianjin China
| |
Collapse
|
45
|
Lin XL, Stur E, Ekrem T. Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges. ZOOL SCR 2018. [DOI: 10.1111/zsc.12280] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Xiao-Long Lin
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Elisabeth Stur
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Torbjørn Ekrem
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| |
Collapse
|
46
|
Rodrigues MS, Morelli KA, Jansen AM. Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species. Parasit Vectors 2017; 10:488. [PMID: 29037251 PMCID: PMC5644147 DOI: 10.1186/s13071-017-2457-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The DNA barcoding system using the cytochrome c oxidase subunit 1 mitochondrial gene (cox1 or COI) is highly efficient for discriminating vertebrate and invertebrate species. In the present study, we examined the suitability of cox1 as a marker for Trypanosoma cruzi identification from other closely related species. Additionally, we combined the sequences of cox1 and the nuclear gene glucose-6-phosphate isomerase (GPI) to evaluate the occurrence of mitochondrial introgression and the presence of hybrid genotypes. METHODS Sixty-two isolates of Trypanosoma spp. obtained from five of the six Brazilian biomes (Amazon Forest, Atlantic Forest, Caatinga, Cerrado and Pantanal) were sequenced for cox1 and GPI gene fragments. Phylogenetic trees were reconstructed using neighbor-joining, maximum likelihood, parsimony and Bayesian inference methods. Molecular species delimitation was evaluated through pairwise intraspecific and interspecific distances, Automatic Barcode Gap Discovery, single-rate Poisson Tree Processes and multi-rate Poisson Tree Processes. RESULTS Both cox1 and GPI genes recognized and differentiated T. cruzi, Trypanosoma cruzi marinkellei, Trypanosoma dionisii and Trypanosoma rangeli. Cox1 discriminated Tcbat, TcI, TcII, TcIII and TcIV. Additionally, TcV and TcVI were identified as a single group. Cox1 also demonstrated diversity in the discrete typing units (DTUs) TcI, TcII and TcIII and in T. c. marinkellei and T. rangeli. Cox1 and GPI demonstrated TcI and TcII as the most genetically distant branches, and the position of the other T. cruzi DTUs differed according to the molecular marker. The tree reconstructed with concatenated cox1 and GPI sequences confirmed the separation of the subgenus Trypanosoma (Schizotrypanum) sp. and the T. cruzi DTUs TcI, TcII, TcIII and TcIV. The evaluation of single nucleotide polymorphisms (SNPs) was informative for DTU differentiation using both genes. In the cox1 analysis, one SNP differentiated heterozygous hybrids from TcIV sequences. In the GPI analysis one SNP discriminated Tcbat from TcI, while another SNP distinguished TcI from TcIII. CONCLUSIONS DNA barcoding using the cox1 gene is a reliable tool to distinguish T. cruzi from T. c. marinkellei, T. dionisii and T. rangeli and identify the main T. cruzi genotypes.
Collapse
Affiliation(s)
- Marina Silva Rodrigues
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Karina Alessandra Morelli
- Department of Ecology, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Maria Jansen
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| |
Collapse
|
47
|
Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 2017; 33:1630-1638. [PMID: 28108445 PMCID: PMC5447239 DOI: 10.1093/bioinformatics/btx025] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/27/2016] [Accepted: 01/17/2017] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. RESULTS We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. AVAILABILITY AND IMPLEMENTATION mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . CONTACT : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- P Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - S Lutteropp
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J Zhang
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - K Kobert
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - P Pavlidis
- Foundation for Research and Technology, Hellas Institute of Computer Science GR, Heraklion, Crete, Greece
| | - A Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T Flouri
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| |
Collapse
|
48
|
Abstract
The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species. Through this hands-on approach, they participated in a learning exercise that conveys a real sense of scientific discovery. As well, the students contributed valuable data to the largest biodiversity genomics initiative ever undertaken: the International Barcode of Life project. To date, the SMTP has sequenced over 80,000 insect specimens, which includes representatives of 7,990 different species, nearly a tenth of the Canadian fauna. Both surprisingly and importantly, the collections generated the first DNA barcode records for 1,288 Canadian species.
Collapse
|
49
|
Geiger MF, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert PDN, Rulik B. Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany? Biodivers Data J 2016:e10671. [PMID: 27932930 PMCID: PMC5136679 DOI: 10.3897/bdj.4.e10671] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: “Nationalpark Bayerischer Wald” in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. New information In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.
Collapse
Affiliation(s)
| | | | | | | | - Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| |
Collapse
|
50
|
Barreto SB, Nunes LA, da Silva AT, Jucá-Chagas R, Diniz D, Sampaio I, Schneider H, Affonso PRADM. Is Nematocharax (Actinopterygii, Characiformes) a monotypic fish genus? Genome 2016; 59:851-865. [PMID: 27608265 DOI: 10.1139/gen-2015-0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The combination of DNA barcodes and geometric morphometrics is useful to discriminate taxonomically controversial species, providing more precise estimates of biodiversity. Therefore, our goal was to assess the genetic and morphometric diversity in Nematocharax, a controversial monotypic and sexually dimorphic genus of Neotropical fish, based on sequencing of cytochrome c oxidase subunit I (COI) and morphometric analyses in seven populations of N. venustus from coastal rivers in Brazil. The average pairwise intrapopulation divergence in COI ranged from 0 to 2.2%, while the average pairwise interpopulation divergence varied from 0 to 7.5%. The neighbour-joining (NJ) tree resulted in five genetic groups (bootstrap ≥ 97%), which correspond to the five clusters delimited by the BIN System, GMYC, and bPTP, indicating that there might be at least five species (or OTUs) within Nematocharax. Morphometric differences among these genetic lineages were also identified. Apparently, sexual selection, restricted dispersal, and geographic isolation might have acted synergistically to cause the evolutionary split of populations. These data challenge the current view that Nematocharax is a monotypic genus inasmuch as evolutionarily significant units or even distinguished species were identified. Therefore, we recommend that the highly impacted coastal basins in northeastern Brazil should be prioritized in conservation plans.
Collapse
Affiliation(s)
- Silvia Britto Barreto
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Lorena Andrade Nunes
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - André Teixeira da Silva
- b Department of Zoology, Biosciences Institute, Universidade Estadual Paulista Júlio de Mesquita Filho, Av. 24-A, 1515, Bela Vista, 13506970, Rio Claro, São Paulo, Brazil
| | - Ricardo Jucá-Chagas
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Débora Diniz
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| | - Iracilda Sampaio
- c Coastal Studies Institute, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Aldeia, 68600000, Bragança, Pará, Brazil
| | - Horacio Schneider
- c Coastal Studies Institute, Universidade Federal do Pará, Alameda Leandro Ribeiro, s/n, Aldeia, 68600000, Bragança, Pará, Brazil
| | - Paulo Roberto Antunes de Mello Affonso
- a Department of Biological Sciences, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, 45206190, Jequié, Bahia, Brazil
| |
Collapse
|