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Yeo H, Lin J, Yeoh TX, Puniamoorthy N. Resolution of cryptic mosquito species through wing morphometrics. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105647. [PMID: 39067583 DOI: 10.1016/j.meegid.2024.105647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Mosquitoes are medically important insects, and accurate species identification is crucial to understanding vector biology, forming the cornerstone of successful vector control programs. Identification is difficult owing to morphologically similar species. Wing morphometrics can provide a simple, fast, and accurate way to classify species, and using it as a method to differentiate vector species among its cryptic congeners has been underexplored. Using a total of 227 mosquitoes and 20 landmarks per specimen, we demonstrated the utility of wing morphometrics in differentiating species two groups occurring in sympatry - Culex (Culex) vishnui group and Culex (Lophoceraomyia) subgenus, as well as explored population-level variation in the wing shape of Aedes albopictus across habitats. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Procrustes ANOVA regression and CVA based on wing shape reflected that the wing landmarks across all species differed significantly, and leave-one-out cross validation revealed an overall high accuracy of >97% for the two Culex groups. Wing morphometrics uncovered population-level variation within Aedes albopictus, but cross validation accuracy was low. Overall, we show that wing geomorphometric analysis is able to resolve cryptic Culex species (including vectors) occurring sympatrically, and is a robust tool for identifying mosquitoes reliably.
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Affiliation(s)
- Huiqing Yeo
- Department of Biological Sciences, National University of Singapore, Singapore.
| | - Jiawei Lin
- Department of Biological Sciences, National University of Singapore, Singapore.
| | - Tze Xuan Yeoh
- Department of Biological Sciences, National University of Singapore, Singapore.
| | - Nalini Puniamoorthy
- Department of Biological Sciences, National University of Singapore, Singapore.
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Massip-Veloso Y, Hoagstrom CW, McMahan CD, Matamoros WA. Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses. Biol Rev Camb Philos Soc 2024; 99:901-927. [PMID: 38205676 DOI: 10.1111/brv.13050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.
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Affiliation(s)
- Yibril Massip-Veloso
- Programa de Doctorado en Ciencias en Biodiversidad y Conservación de Ecosistemas Tropicales, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
| | | | | | - Wilfredo A Matamoros
- Programa de Doctorado en Ciencias en Biodiversidad y Conservación de Ecosistemas Tropicales, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
- Field Museum of Natural History, Chicago, IL, 60605, USA
- Laboratorio de Diversidad Acuática y Biogeografía, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Libramiento Norte Poniente 1150, C.P. 29039, Tuxtla Gutiérrez, Chiapas, Mexico
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Mejia E, Reis RE. Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages. JOURNAL OF FISH BIOLOGY 2024; 104:1042-1053. [PMID: 38149310 DOI: 10.1111/jfb.15639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/28/2023]
Abstract
Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.
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Affiliation(s)
- Eduardo Mejia
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Vertebrados, Programa de Pós-graduação em Ciências Biológicas (Zoologia), Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brazil
| | - Roberto E Reis
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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Modeel S, Negi RK, Sharma M, Dolkar P, Yadav S, Siwach S, Yadav P, Negi T. A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas. Sci Rep 2024; 14:2763. [PMID: 38307873 PMCID: PMC10837433 DOI: 10.1038/s41598-024-52519-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.
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Affiliation(s)
- Sonakshi Modeel
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India.
| | - Monika Sharma
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Padma Dolkar
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sheetal Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sneha Siwach
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Pankaj Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Tarana Negi
- Department of Zoology, Govt. College Dujana, District Jhajjar, Beri, Haryana, India
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Lam TTH, Dinh QM, Truong VTB, Truong NT, Tran NS, Nguyen THD. The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam. Heliyon 2023; 9:e20139. [PMID: 37809956 PMCID: PMC10559908 DOI: 10.1016/j.heliyon.2023.e20139] [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: 02/11/2022] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90-100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.
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Affiliation(s)
- Tran Thi Huyen Lam
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
- Institute of High Quality Biotechnology - Food Technology, Cuu Long University, National Road 1A, Phu Quoi Ward, Long Ho District, Vinh Long, 850000, Viet Nam
| | - Quang Minh Dinh
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Van Thi Bich Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Ngon Trong Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Nam Sy Tran
- Department of Environmental Sciences, College of Environment and Natural Resources, Can Tho University, Can Tho, 900000, Viet Nam
| | - Ton Huu Duc Nguyen
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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DNA barcoding provides insights into Fish Diversity and Molecular Taxonomy of the Amundsen Sea. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01273-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abdulmalik-Labe OP, Picart NMR, Francisco MEM, Castillo RMG, Quilang JP. DNA barcoding of Glossogobius species (Teleostei: Gobiidae) from major lakes in the Philippines reveals the presence of cryptic species and species complexes. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01278-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Turan D, Kaya C, Aksu İ, Bektaş Y. Paracapoeta, a new genus of the Cyprinidae from Mesopotamia, Cilicia and Levant (Teleostei, Cypriniformes). ZOOSYST EVOL 2022. [DOI: 10.3897/zse.98.81463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular and morphological studies carried out within the scope of this study revealed that the scrapers, known as the Mesopotamian group, belong to a different genus. The Paracapoetagen. nov., from the Mesopotomia and Levant, is distinguished from Capoeta and Luciobarbus species by the presence of a strong ligament between the base of the last simple and the first branched rays of the dorsal-fin (vs. no or a very weak ligament). The Paracapoeta further differs from Capoeta by the last simple dorsal-fin ray strongly ossified in adult specimens (more than 75%, vs. less than 75%). The Paracapoeta further differs from Luciobarbus by the lower lip with horny layer (vs. fleshy lips). The molecular phylogeny based on the combined dataset (COI + Cytb, 1312 bp.) showed that the genus Paracapoeta was recovered from the other groups in the subfamily Barbinae with high bootstrap and posterior probability values (BP: 94%, PP: 0.96). Also, Paracapoeta and Capoeta are well differentiated by an average genetic distance of 8.02±0.78%. The morphological and molecular findings have largely overlapped each other. Besides, Capoeta turani is treated as a synonym of Capoeta erhani.
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Rodríguez-Machado S, Rodríguez-Cabrera TM, Chakrabarty P. Identity of Fish Fry from the “Tetí” Fishery in Eastern Cuba. CARIBB J SCI 2021. [DOI: 10.18475/cjos.v51i2.a6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sheila Rodríguez-Machado
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, U.S.A
| | | | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, U.S.A
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Ahmed MS, Datta SK, Saha T, Hossain Z. Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes. Ecol Evol 2021; 11:3696-3709. [PMID: 33976769 PMCID: PMC8093680 DOI: 10.1002/ece3.7355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
This study describes the molecular characterization of marine and coastal fishes of Bangladesh based on the mitochondrial cytochrome c oxidase subunit I (COI) gene as a marker. A total of 376 mitochondrial COI barcode sequences were obtained from 185 species belonging to 146 genera, 74 families, 21 orders, and two classes of fishes. The mean length of the sequences was 652 base pairs. In Elasmobranchii (Sharks and rays), the average Kimura two parameter (K2P) distances within species, genera, families, and orders were 1.20%, 6.07%, 11.08%, and 14.68%, respectively, and for Actinopterygii, the average K2P distances within species, genera, families, and orders were 0.40%, 6.36%, 14.10%, and 24.07%, respectively. The mean interspecies distance was 16-fold higher than the mean intraspecies distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species in accordance with their taxonomic position. A total of 21 species were newly recorded in Bangladesh. High efficiency and fidelity in species identification and discrimination were demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used as an authentic identification marker for Bangladesh marine fish species.
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Affiliation(s)
| | | | - Tonmoy Saha
- Department of ZoologyJagannath UniversityDhakaBangladesh
| | - Zarif Hossain
- Department of OceanographyUniversity of DhakaDhakaBangladesh
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Rapid in-situ detection kit (RisK): Development of loop-mediated isothermal amplification (LAMP) assay for the rapid identification of selected invasive alien fish in Malaysian freshwaters. Mol Cell Probes 2020; 55:101683. [PMID: 33259896 DOI: 10.1016/j.mcp.2020.101683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 11/22/2022]
Abstract
Invasive alien fish species have become a silent treat towards the ecosystem especially the native fish population in Malaysia. There has been a need to develop rapid identification methods that can aid management teams in identifying fish species that are not native to our ecosystem. Current visual identification methods are highly tedious and require time, delaying action towards curbing the invasion. The LAMP assay successfully identified six popular invasive fish species in Malaysia. None of the LAMP assays showed false positives and the Limit of Detection of the LAMP primers were highly sensitive and could detect DNA samples up to 1 × 10-15 ng/μl. The LAMP primers designed were highly specific to the target species and did not amplify non target species. DNA sequencing was done to ensure the accuracy of LAMP assay results. This study demonstrates that LAMP is a suitable tool in species identification efforts of invasive fish species in Malaysia.
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Ghouri MZ, Ismail M, Javed MA, Khan SH, Munawar N, Umar AB, Mehr-un-Nisa, Aftab SO, Amin S, Khan Z, Ahmad A. Identification of Edible Fish Species of Pakistan Through DNA Barcoding. FRONTIERS IN MARINE SCIENCE 2020. [DOI: https://doi.org/10.3389/fmars.2020.554183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jiang KW, Zhang R, Zhang ZF, Pan B, Tian B. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage. PLANT DIVERSITY 2020; 42:376-385. [PMID: 33134622 PMCID: PMC7584798 DOI: 10.1016/j.pld.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.
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Affiliation(s)
- Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Fu Zhang
- Department of Wetland, Southwest Forestry University, Kunming, 650224, China
| | - Bo Pan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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Rebelo H, Ferreira S, Amorim F, Horta P, Raposeira H, Santos H, Beja P, Mata VA. Hidden in our pockets: building of a DNA barcode library unveils the first record of Myotis alcathoe for Portugal. Biodivers Data J 2020; 8:e54479. [PMID: 32821211 PMCID: PMC7403162 DOI: 10.3897/bdj.8.e54479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 11/12/2022] Open
Abstract
Background The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (Chiroptera) dataset containing DNA sequences of 63 specimens representing the 25 bat species currently known for continental Portugal. For that, we sequenced tissues samples obtained in a vast array of projects spanning the last two decades. New information We added four new Barcoding Index Numbers (BINs) to existing Chiroptera barcodes on BOLD, two belonging to Myotisescalerai, one to Plecotusauritus and the other to Rhinolophushipposideros. Surprisingly, one of the samples initially identified in the field as Myotismystacinus turned out to be Myotisalcathoe, which represents the first record of this species for Portugal. The presence of Nyctalusnoctula in Portugal was also genetically confirmed for the first time. This case study shows the power and value of DNA barcoding initiatives to unravel new data that may be hidden on biological collections.
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Affiliation(s)
- Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia Lisboa Portugal
| | - Sónia Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Francisco Amorim
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Pedro Horta
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto Porto Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Helena Raposeira
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto Porto Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Helena Santos
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Pedro Beja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia Lisboa Portugal
| | - Vanessa A Mata
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
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Hernández D, Møller PR, Casane D, García-Machado E. A new species of the cave-fish genus Lucifuga (Ophidiiformes, Bythitidae), from eastern Cuba. Zookeys 2020; 946:17-35. [PMID: 32728339 PMCID: PMC7358250 DOI: 10.3897/zookeys.946.51373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/03/2020] [Indexed: 11/22/2022] Open
Abstract
Recently, a barcoding study and a molecular phylogenetic analysis of the Cuban species of the cave-fish genus Lucifuga Poey, 1858 revealed the existence of different evolutionary lineages that were previously unknown or passed unnoticed by morphological scrutiny (i.e., cryptic candidate species). In the present study, Lucifugagibarensis is described as a new species restricted to anchialine caves in the northeastern karst region of the main island. The species was earlier described as a variety of Lucifugadentata, but since the name was introduced as a variety after 1960, it is deemed to be infrasubspecific and unavailable according to the International Code of Zoological Nomenclature Art. 15.2. The new species differs from L.dentata by pigmented eyes vs. eyes absent and lack of palatine teeth vs. present. Lucifugagibarensis seems to be most similar to the Bahamian species L.lucayana by showing pigmented eyes, 13 or 14 precaudal vertebrae and ten caudal fin rays. However, differs from it by a larger size of the pigmented eye (1.1–1.9 vs. 0.9–1.0% SL) and number of posterior lateral line neuromasts (30–33 vs. 34–35).
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Affiliation(s)
- Damir Hernández
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, Ciudad Habana 11300, Cuba Centro de Investigaciones Marinas, Universidad de La Habana Havana Cuba
| | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Natural History Museum of Denmark Copenhagen Denmark
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France Université Paris-Saclay Gif-sur-Yvette France.,Université Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas-Mann, 75205 Paris, France Université Paris Diderot, Sorbonne Paris France
| | - Erik García-Machado
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, Ciudad Habana 11300, Cuba Centro de Investigaciones Marinas, Universidad de La Habana Havana Cuba.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada Institut de Biologie Intégrative et des Systèmes, Université Laval Québec Canada
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18
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Garcia-Vazquez E, Ardura A, Planes S. DNA mtCOI Barcodes for Maritime Biosecurity: A Proof of Concept in French Polynesia Ports. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01155-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractWithin Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.
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20
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Inconspicuous genetic and morphological patterns challenge the taxonomic status of endemic species Bodianus insularis (Labridae). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Tatarenkov A, Earley RL, Taylor DS, Davis WP, Avise JC. Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: Ramifications for species concepts and taxonomy. J Evol Biol 2020; 34:49-59. [PMID: 32242998 DOI: 10.1111/jeb.13624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/23/2020] [Accepted: 03/15/2020] [Indexed: 01/31/2023]
Abstract
Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a 'Central clade' closely related to K. hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K. marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K. marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.
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Affiliation(s)
- Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ryan L Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | | | - John C Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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22
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Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history. Mol Phylogenet Evol 2019; 144:106712. [PMID: 31862460 DOI: 10.1016/j.ympev.2019.106712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/22/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022]
Abstract
The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.
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23
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Jardim de Queiroz L, Cardoso Y, Jacot-des-Combes C, Bahechar IA, Lucena CA, Rapp Py-Daniel L, Sarmento Soares LM, Nylinder S, Oliveira C, Parente TE, Torrente-Vilara G, Covain R, Buckup P, Montoya-Burgos JI. Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol Phylogenet Evol 2019; 145:106711. [PMID: 31857199 DOI: 10.1016/j.ympev.2019.106711] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/20/2019] [Accepted: 12/14/2019] [Indexed: 10/25/2022]
Abstract
With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Yamila Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque S/N, B1900FWA, La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Cécile Jacot-des-Combes
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Ilham Anne Bahechar
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Carlos Alberto Lucena
- Museu de Ciências e Tecnologia, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil
| | - Lucia Rapp Py-Daniel
- Coordenação de Biodiversidade, Programa de Coleções Científicas e Biológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, 69060-001 Manaus, AM, Brazil
| | - Luisa Maria Sarmento Soares
- Museu de Biologia Professor Mello Leitão, Instituto Nacional da Mata Atlântica, Av. José Ruschi 4, 29650-000 Santa Teresa, ES, Brazil
| | - Stephan Nylinder
- Department of Psychology, University of Gothenburg. Haraldsgatan 1, 413 14 Gothenburg, Sweden
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual de São Paulo, Rua Professor Doutor Antonio Celso Wagner Zanin 250, 18618-689 Botucatu, SP, Brazil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Laboratório de Genética Molecular de Microrganismos, Fundação Oswaldo Cruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Gislene Torrente-Vilara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Av. Doutor Carvalho de Mendonça 144, 11070-100 Santos, SP, Brazil
| | - Raphaël Covain
- Department of Herpertology and Ichthyology, Museum of Natural History of Geneva, Route de Malagnou 1, 1211 Geneva, Switzerland
| | - Paulo Buckup
- Departamento de Vertebrados, Vista Museu Nacional do Rio de Janeiro/Universidade Federal do Rio de Janeiro, Quinta da Boa, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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24
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Rabaoui L, Yacoubi L, Sanna D, Casu M, Scarpa F, Lin YJ, Shen KN, Clardy TR, Arculeo M, Qurban MA. DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf. JOURNAL OF FISH BIOLOGY 2019; 95:1286-1297. [PMID: 31469430 DOI: 10.1111/jfb.14130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.
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Affiliation(s)
- Lotfi Rabaoui
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- Geosciences Department, College of Petroleum Engineering & Geosciences, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | | | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Yu-Jia Lin
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | - Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Todd R Clardy
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| | - Marco Arculeo
- Dipartimento STEBICEF, Università degli Studi di Palermo, Palermo, Italy
| | - Mohammad A Qurban
- Center for Environment & Water, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
- Geosciences Department, College of Petroleum Engineering & Geosciences, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
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25
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Arroyave J, Martinez CM, Stiassny MLJ. DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes). JOURNAL OF FISH BIOLOGY 2019; 95:379-392. [PMID: 31001832 DOI: 10.1111/jfb.13987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.
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Affiliation(s)
- Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | | | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
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26
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Chan AFO, Luczon AU, Fontanilla IKC, Ong PS, Santos MD, Willette DA, Quilang JP. DNA barcoding cannot discriminate between Sardinella tawilis and S. hualiensis (Clupeiformes: Clupeidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2499-2503. [PMID: 33365600 PMCID: PMC7687547 DOI: 10.1080/23802359.2019.1638839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sardinella tawilis, the only known freshwater sardinella in the world, is endemic to Taal Lake, Philippines. Previous studies found the Taiwan sardinella, S. hualiensis, to be morphologically very similar to S. tawilis and identified it as the marine sister species of S. tawilis. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was carried out to analyze species demarcation in the Sardinella genus, focusing primarily on the relationship between S. tawilis and S. hualiensis. The neighbour-joining (NJ) tree that was constructed using Kimura 2-parameter (K2P) model showed a single clade for the two species with 100% bootstrap support. K2P interspecific genetic divergence ranged from 0% to 0.522%, which is clearly below the suggested 3–3.5% cutoff for species discrimination. Recombination activating gene 1 (RAG1), mitochondrial control region (CR), cytochrome b, 16S rRNA, and S7 markers were used to further validate the results. Sardinella tawilis and S. hualiensis clustered together with a bootstrap support of 99–100% in each of the NJ trees. Low interspecific genetic distances between S. tawilis and S. hualiensis for all the markers except CR could be attributed to incipient allopatric speciation.
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Affiliation(s)
- Alison Faye O Chan
- Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines.,DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Adrian U Luczon
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Ian Kendrich C Fontanilla
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Perry S Ong
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | | | - Demian A Willette
- Biology Department, Loyola Marymount University, Los Angeles, CA, USA
| | - Jonas P Quilang
- Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
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27
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Rahman MM, Norén M, Mollah AR, Kullander SO. Building a DNA barcode library for the freshwater fishes of Bangladesh. Sci Rep 2019; 9:9382. [PMID: 31253861 PMCID: PMC6599201 DOI: 10.1038/s41598-019-45379-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/03/2019] [Indexed: 01/24/2023] Open
Abstract
We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the country, and include about 30 undescribed or potentially undescribed species. Several of the taxa that we could not sample represent erroneous records for the country, or sporadic occurrences. Species identifications were classified at confidence levels 1(best) to 3 (worst). We propose the new term Operational Barcode Unit (OBU) to simplify references to would-be DNA barcode sequences and sequence clusters. We found one case where there were two mitochondrial lineages present in the same species, several cases of cryptic species, one case of introgression, one species yielding a pseudogene to standard barcoding primers, and several cases of taxonomic uncertainty and need for taxonomic revision. Large scale national level DNA barcode prospecting in high diversity regions may suffer from lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.
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Affiliation(s)
- Md Mizanur Rahman
- University of Dhaka, Department of Zoology, Dhaka, Dhaka, 1000, Bangladesh
| | - Michael Norén
- Swedish Museum of Natural History, Department of Zoology, SE-104 05, Stockholm, Sweden
| | - Abdur Rob Mollah
- University of Dhaka, Department of Zoology, Dhaka, Dhaka, 1000, Bangladesh
| | - Sven O Kullander
- Swedish Museum of Natural History, Department of Zoology, SE-104 05, Stockholm, Sweden.
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Fish diversity of the largest deltaic formation in the Americas - a description of the fish fauna of the Parnaíba Delta using DNA Barcoding. Sci Rep 2019; 9:7530. [PMID: 31101898 PMCID: PMC6525184 DOI: 10.1038/s41598-019-43930-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/03/2019] [Indexed: 01/29/2023] Open
Abstract
Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.
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de Borba RS, Mariotto S, Centofante L, Henrique Zawadzki C, Pasquali Parise-Maltempi P. Molecular discrimination of Ancistrus lineages (Siluriformes: Loricariidae) using barcode DNA tool. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:602-608. [PMID: 30983442 DOI: 10.1080/24701394.2019.1597071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although several species of Ancistrus have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected Ancistrus lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of Ancistrus from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the Ancistrus lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.
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Affiliation(s)
| | | | - Liano Centofante
- c Institute of Biosciences, Mato Grosso Federal University , Cuiabá , Brazil
| | - Claudio Henrique Zawadzki
- d Department of Biology, Center for Research in Limnology, Ichthyology and Aquaculture (Nupélia), Maringá State University , Paraná , Brazil
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Labrador K, Agmata A, Palermo JD, Follante J, Pante MJ. Authentication of processed Philippine sardine products using Hotshot DNA extraction and minibarcode amplification. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.11.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rathipriya A, Karal Marx K, Jeyashakila R. Molecular identification and phylogenetic relationship of flying fishes of Tamil Nadu coast for fishery management purposes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:500-510. [PMID: 30691341 DOI: 10.1080/24701394.2018.1558220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The partial sequences of cytochrome c oxidase subunit I (COI) mitochondrial gene were analysed for developing species specific molecular signatures and phylogenetic relationship among the commercially important flying fishes (Cheilopogon cyanopterus, Cheilopogon furcatus and Hirundichthys coromandelensis) distributed in Tamil Nadu coast. Accurate identification of these species is important for fishery management as its morphological characters are very similar. Since the morphological features are very similar, accurate identification using molecular tools is essential for sustainable utilization and management of these species across their distributional range. The estimated transition/transversion bias (R) is 3.45. The average nucleotide sequences calculated were A = 30.00%, T/U = 26.40%, C = 17.00% and G = 26.60%. Using COI data analysis, the intraspecies genetic distance ranged from 0.00 to 0.05, while it varied from 0.06 to 0.08 for interspecies. Partial sequences of the genes provided sufficient phylogenetic information to distinguish the three flying fishes indicating the usefulness of mtDNA-based approach in species identification.
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Affiliation(s)
- A Rathipriya
- a Tamil Nadu Dr. J. Jayalalithaa Fisheries University , Nagapattinam , India
| | - K Karal Marx
- b Institute of Postgraduate Studies, OMR Campus , Chennai , India
| | - R Jeyashakila
- c Fisheries College and Research Institute , Thoothukudi , India
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Zhou A, Xie S, Liu S, Sun Z, Wang Z, Zhang Y, Chen Y, Luo M, Zou J. Genetic diversity of Northern snakehead ( Channa argus) based on complete mitochondrial COI gene sequences. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1561222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Aiguo Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shaolin Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shulin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhuolin Sun
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhenlu Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yue Zhang
- Departments of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Yanfeng Chen
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mingfei Luo
- Zhuhai Modern Agriculture Development Center, Zhuhai, China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Jacobina UP, Lima SMQ, Maia DG, Souza G, Batalha-Filho H, Torres RA. DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras. Genetica 2018; 146:505-515. [DOI: 10.1007/s10709-018-0043-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 10/09/2018] [Indexed: 02/04/2023]
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Molecular characterization of small indigenous fish species (SIS) of Bangladesh through DNA barcodes. Gene 2018; 684:53-57. [PMID: 30359742 DOI: 10.1016/j.gene.2018.10.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 10/04/2018] [Accepted: 10/19/2018] [Indexed: 11/23/2022]
Abstract
The mitochondrial DNA gene cytochrome oxidase subunit I (COI) has been adopted as a global bioidentification system for animals. This study represents the comprehensive molecular identification of small indigenous fish species (SIS) of Bangladesh assessed by DNA barcoding. DNA barcodes were generated from 81 SIS species belongs to the orders Clupeiformes, Cypriniforms, Siluriformes, Perciformes, Synbranchiformes, Beloniformes and Tetraodontiformes representing 55 genera and 24 families. For all the samples, %G were significantly lowered compared to other nucleotides and %GC compared to %AT. Also, a significantly lowered GC content was observed in second and third codon position compared to the first codon position in all samples. The average Kimura two-parameter (K2P) distances within genera, families, and orders were 15.83%, 19.14%, and 25.07%, respectively. The minimum and maximum K2P distance based genetic divergences were 0.19% and 57.14% respectively. Members of Cypriniformes, Siluriformes, and Perciformes were clustered separately in the neighbour-joining (NJ) tree. Nucleotide composition, GC distribution across codon positions, K2P distance, genetic divergence, and phylogenetic analyses reveal that these freshwater SIS fishes are genetically very diverse. Along with morphological data, we have confirmed the existence of seven new records of SIS fishes in Bangladesh using such barcode approach. These findings suggest that fishes can be discriminated using these barcode data without any confusion.
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Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding. Sci Rep 2018; 8:10787. [PMID: 30018357 PMCID: PMC6050249 DOI: 10.1038/s41598-018-29049-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/26/2018] [Indexed: 11/15/2022] Open
Abstract
Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.
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Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 2018; 13:e0198109. [PMID: 29856794 PMCID: PMC5983523 DOI: 10.1371/journal.pone.0198109] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/14/2018] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.
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Affiliation(s)
- Xing Bingpeng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Lin Heshan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Zhang Zhilan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Chunguang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Yanguo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Jianjun
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
- * E-mail:
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Schmidt RE, Shoobs NF, McMullin ER. Occurrence of the large ostracod, Chlamydotheca unispinosa (Baird, 1862), in temporary waters of Montserrat, Lesser Antilles. Zookeys 2018:89-95. [PMID: 29674916 PMCID: PMC5904454 DOI: 10.3897/zookeys.748.22323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/09/2018] [Indexed: 11/12/2022] Open
Abstract
Four populations of the large freshwater ostracod, Chlamydotheca unispinosa (Baird, 1862), were discovered on the Caribbean island of Montserrat. These are the first records of the species on Montserrat and extend its known distribution approximately 113 km northwest and 63 km southeast of the closest known populations on Îles des Saintes (Guadeloupe) and Nevis, respectively. We provide the first DNA barcode for C. unispinosa, a 686 bp fragment of the COI gene which may be used for future comparative studies of this widely distributed species.
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Affiliation(s)
- Robert E Schmidt
- Bard College at Simon's Rock, 84 Alford Rd., Great Barrington, Massachusetts, 01230, USA
| | - Nathaniel F Shoobs
- Academy of Natural Sciences of Drexel University, Department of Malacology, 1900 Ben Franklin Parkway, Philadelphia, Pennsylvania, 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, 3201 Arch Street, Suite 240, Philadelphia. Pennsylvania, 19104, USA
| | - Erin R McMullin
- Bard College at Simon's Rock, 84 Alford Rd., Great Barrington, Massachusetts, 01230, USA
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Paixão RV, Ribolli J, Zaniboni-Filho E. Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae). Front Genet 2018. [PMID: 29520295 PMCID: PMC5827538 DOI: 10.3389/fgene.2018.00048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank. S. scriptum from the UUR and the UPR were assigned in two distinct molecular operational taxonomic units (MOTUs) with higher inter-specific K2P distance than the optimum threshold (OT = 0.0079). The COI Intra-MOTU distances of S. scriptum specimens from the UUR ranged from 0.0000 to 0.0100. The control region indicated a high number of haplotypes and low nucleotide diversity, compatible with a new population in recent expansion process. Genetic structure was observed, with high differentiation between UUR and UPR basins, identified by BAPS, haplotype network, AMOVA (FST = 0.78, p < 0.05) and Mantel test. S. scriptum from the UUR showed a slight differentiation (FST = 0.068, p < 0.05), but not isolation-by-distance. Negative values of Tajima’s D and Fu’s Fs suggest recent demographic oscillations. The Bayesian skyline plot analysis indicated possible population expansion from beginning 2,500 years ago and a recent reduction in the population size. Low nucleotide diversity, spatial population structure, and the reduction of effective population size should be considered for the planning of strategies aimed at the conservation and rehabilitation of this important fisheries resource.
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Affiliation(s)
- Rômulo V Paixão
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Evoy Zaniboni-Filho
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Nirchio M, Paim FG, Milana V, Rossi AR, Oliveira C. Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes). Front Genet 2018; 9:17. [PMID: 29459882 PMCID: PMC5807406 DOI: 10.3389/fgene.2018.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/15/2018] [Indexed: 11/13/2022] Open
Abstract
Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.
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Affiliation(s)
- Mauro Nirchio
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador
| | - Fabilene G. Paim
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Anna R. Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
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Fisch-Muller S, Mol JHA, Covain R. An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex. PLoS One 2018; 13:e0189789. [PMID: 29298344 PMCID: PMC5752014 DOI: 10.1371/journal.pone.0189789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/03/2017] [Indexed: 11/29/2022] Open
Abstract
Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and two subspecies), as well as a source of dispersal of G. brevispinis toward the other main basins of the Eastern Guianas.
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Affiliation(s)
- Sonia Fisch-Muller
- Natural History Museum, Department of Herpetology and Ichthyology, Geneva, Switzerland
| | - Jan H. A. Mol
- Center for Agricultural Research in Suriname (CELOS) and Department of Biology, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Raphaël Covain
- Natural History Museum, Department of Herpetology and Ichthyology, Geneva, Switzerland
- * E-mail:
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Page TJ, Stevens MI, Adams M, Foster R, Velasco-Castrillón A, Humphreys WF. Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei). AUST J ZOOL 2018. [DOI: 10.1071/zo18008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Australia was once thought to be a biodiversity desert when considering the subterranean world; however, recent work has revealed a fascinating collection of cave creatures, many with surprising biogeographic histories. This has especially been so in the karstic regions of north-western Australia (Cape Range peninsula, Barrow Island, Pilbara), which is home not only to a diverse collection of subterranean invertebrates, but also to the continent’s only known underworld-adapted vertebrates, which includes the cave fish in the genus Milyeringa. These cave gudgeons have recently been in a state of taxonomic flux, with species being both split and lumped, but this was done with limited data (incomplete geographic sampling and no nuclear DNA sequence data). Therefore, we have revisited the systematic status of Milyeringa in a total-evidence molecular approach by integrating all existing data (mitochondrial, allozymes) with new DNA sequences from nuclear and mitochondrial loci and new multilocus allozyme data. Our conclusion, that there are two species, matches the most recent taxonomic treatment, with Milyeringa veritas present on both the eastern and western sides of the Cape Range peninsula, and Milyeringa justitia on Barrow Island. This has implications for future research in the linked fields of biogeography and conservation.
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Duarte L, Oliveira E, Amorim A, Silva D, Carvalho E, Mazzoni R, Amaral C. DNA Barcoding and Atlantic reef fishes: The molecular identification of a reef fish community from the Todos os Santos Bay, Bahia, Brazil. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hou G, Chen WT, Lu HS, Cheng F, Xie SG. Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity. Mol Ecol Resour 2017; 18:137-146. [DOI: 10.1111/1755-0998.12718] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/14/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Gang Hou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
- Guangdong Ocean University; Zhanjiang China
| | - Wei-Tao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | | | - Fei Cheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Song-Guang Xie
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Huai'an Research Center; Institute of Hydrobiology; Chinese Academy of Sciences; Huai'an China
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Tatarenkov A, Lima SMQ, Earley RL, Berbel-Filho WM, Vermeulen FBM, Taylor DS, Marson K, Turner BJ, Avise JC. Deep and concordant subdivisions in the self-fertilizing mangrove killifishes (Kryptolebias) revealed by nuclear and mtDNA markers. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Cong Q, Shen J, Borek D, Robbins RK, Opler PA, Otwinowski Z, Grishin NV. When COI barcodes deceive: complete genomes reveal introgression in hairstreaks. Proc Biol Sci 2017; 284:20161735. [PMID: 28179510 PMCID: PMC5310595 DOI: 10.1098/rspb.2016.1735] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/09/2017] [Indexed: 12/24/2022] Open
Abstract
Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
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Affiliation(s)
- Qian Cong
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Jinhui Shen
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Dominika Borek
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Robert K Robbins
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, NHB Stop 105, Washington, DC, USA
| | - Paul A Opler
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Zbyszek Otwinowski
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
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de Sousa TP, Marques DKS, Vitorino CDA, Faria KDC, Braga GDSF, Ferreira DC, Venere PC. Cytogenetic and Molecular Data Support the Occurrence of Three Gymnotus Species (Gymnotiformes: Gymnotidae) Used as Live Bait in Corumbá, Brazil: Implications for Conservation and Management of Professional Fishing. Zebrafish 2017; 14:177-186. [PMID: 28151699 DOI: 10.1089/zeb.2016.1356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
In the Pantanal of Mato Grosso do Sul, electric fish (Gymnotus spp.) are the primary source of live bait, accounting for more than three-quarters of total sales. Based on chromosomal and molecular markers, the present study attempted to identify the Gymnotus species used as bait in the region of Corumbá, Mato Grosso do Sul, Brazil. Three species were detected, based on their distinct karyotypes: G. paraguensis (2n = 54), G. sylvius (2n = 40), and G. pantanal (2n = 39-40, X1X2Y/X1X1X2X2), with no evidence being found of interspecific hybrids. All three species presented a single nucleolar organizer regions (NOR) (heterochromatin CMA3+/DAPI-) and pericentromeric heterochromatin in almost all chromosomes, with a few distal and/or interstitial blocks. G. sylvius and G. pantanal had one and two pairs of chromosomes with 5S rDNA sites, respectively, while G. paraguensis had 17 chromosome pairs with these markers. The three species formed well-defined clusters in the DNA barcoding analysis. The integrated analysis of the cytogenetic and DNA barcoding data confirmed that the diversity of Gymnotus species exploited as live bait in the study region has been underestimated. These findings indicate that the markers analyzed represent valuable tools for the conservation and fishery management of the Gymnotus stocks exploited.
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Affiliation(s)
- Tatiane Pires de Sousa
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | | | - Carla de Andrade Vitorino
- 3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Karina de Cassia Faria
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | - Gisele da Silva Ferreira Braga
- 3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Daniela Cristina Ferreira
- 4 Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Paulo Cesar Venere
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil .,3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil .,4 Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
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Sánchez-Pinedo G, Díaz-Viloria N, Ortiz-Galindo JL, Ferreira-Fontoura N, Perez-Enriquez R, Sánchez-Velasco L, De La Cruz-Agüero J. Proposed synonymy for Micropogonias altipinnis (Günther 1864), Micropogonias ectenes (Jordan & Gilbert 1882), and Micropogonias megalops (Gilbert 1890). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:136-146. [PMID: 28116960 DOI: 10.1080/24701394.2016.1258405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Within the Sciaenidae family, the genus Micropogonias is composed of three recognized species along the Pacific coast of Mexico: Micropogonias altipinnis, M. ectenes, and M. megalops. These species exhibit overlapping diagnostic characters, which make species identification difficult. This study ties morphological differences (meristic, morphometry of body, and otolith) with DNA sequences (CO1 and 16S fractions of mtDNA and 28S of nDNA) among Micropogonias species in the Pacific. Meristic analysis showed a latitudinal variation among the three species in the number of rays, the number of gill rakers, and length of the longest spine of the dorsal fin. Discriminant analysis of morphometric characters (body and otolith) showed three morphological entities (p < 0.001). However, the mean genetic divergences among the three species with partial sequences of mtDNA (CO1 and 16S), and nuclear (28S) were lower than those reported at the interspecific level (>2%). Genetic results suggest that the three species are one species and that the differences in meristics and morphometry could be the result of phenotypic plasticity or incipient speciation. In this sense, M. ectenes and M. megalops are proposed as junior synonyms of M. altipinnis.
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Affiliation(s)
- Geremías Sánchez-Pinedo
- a Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR) , La Paz , B.C.S , Mexico
| | - Noé Díaz-Viloria
- a Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR) , La Paz , B.C.S , Mexico
| | - José L Ortiz-Galindo
- a Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR) , La Paz , B.C.S , Mexico
| | - Nelson Ferreira-Fontoura
- b Faculdade de Biociências-Pontifícia Universidade Católica do Rio Grande do Sul (FaBio-PUCRS) , Porto Alegre , RS , Brazil
| | | | - Laura Sánchez-Velasco
- a Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR) , La Paz , B.C.S , Mexico
| | - José De La Cruz-Agüero
- a Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR) , La Paz , B.C.S , Mexico
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Rossini BC, Oliveira CAM, de Melo FAG, Bertaco VDA, de Astarloa JMD, Rosso JJ, Foresti F, Oliveira C. Highlighting Astyanax Species Diversity through DNA Barcoding. PLoS One 2016; 11:e0167203. [PMID: 27992537 PMCID: PMC5167228 DOI: 10.1371/journal.pone.0167203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.
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Affiliation(s)
- Bruno César Rossini
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Instituto de Biotecnologia da UNESP, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Carlos Alexandre Miranda Oliveira
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Paraná, Brazil
| | | | - Vinicius de Araújo Bertaco
- Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Juan M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Karthika P, Krishnaveni N, Vadivalagan C, Murugan K, Nicoletti M, Benelli G. DNA barcoding and evolutionary lineage of 15 insect pests of horticultural crops in South India. KARBALA INTERNATIONAL JOURNAL OF MODERN SCIENCE 2016. [DOI: 10.1016/j.kijoms.2016.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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de Carvalho Lima TP, do Egito AA, Feijó GLD, de Arruda Mauro R, Ferraz ALJ. Molecular identification and phylogenetic analysis of Siluriformes from the Paraguay River basin, Brazil. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:536-543. [PMID: 27246435 DOI: 10.3109/24701394.2016.1149825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The objective of this study was to identify, through the DNA barcode, fishable Siluriformes which were collected from the Paraguay River basin in Pantanal. It was analyzed for genetic distance calculation using the Kimura-two-model parameters and the dendrogram was builtusing the Neighbour-Joining algorithm. The average genetic distance within species, genus and families were 0.2%, 1.6% and 4.2%, respectively. These values were lower than those reported in studies from other continents, probably due to the recent radiation process undergone by Neotropical fish. The dendrogram revealed two possible cases of hybridization, one individual Pseudoplatystoma corruscans, it was not possible to identify whether it was a natural event or commercial production exhaust and other of Pimelodus cf. argenteus leading to the assumption that the aspects of reproductive isolation cannot be clearly defined. Besides, the populations of the species Hemisorubim platyrhynchos and e Platydora armatulus may be undergoing a substructuring process, with genetic differences 3% and 4%, respectively.
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