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Grzegorczyk E, Bézier L, Le‐Rest K, Caizergues A, Francesiaz C, Champagnon J, Guillemain M, Eraud C. Is hunting nonintentionally selective? A test using game bird capture‐dead recoveries. Ecol Evol 2022; 12:e9285. [PMID: 36188522 PMCID: PMC9486496 DOI: 10.1002/ece3.9285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Selective hunting has various impacts that need to be considered for the conservation and management of harvested populations. The consequences of selective harvest have mostly been studied in trophy hunting and fishing, where selection of specific phenotypes is intentional. Recent studies, however, show that selection can also occur unintentionally. With at least 52 million birds harvested each year in Europe, it is particularly relevant to evaluate the selectivity of hunting on this taxon. Here, we considered 211,806 individuals belonging to 7 hunted bird species to study unintentional selectivity in harvest. Using linear mixed models, we compared morphological traits (mass, wing, and tarsus size) and body condition at the time of banding between birds that were subsequently recovered from hunting during the same year as their banding, and birds that were not recovered. We did not find any patterns showing systematic differences between recovery categories, among our model species, for the traits we studied. Moreover, when a difference existed between recovery categories, it was so small that its biological relevance can be challenged. Hunting of birds in Europe therefore does not show any form of strong selectivity on the morphological and physiological traits that we studied and should hence not lead to any change of these traits either by plastic or by evolutionary response.
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Affiliation(s)
- Emilienne Grzegorczyk
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Villiers‐en‐Bois France
| | - Léa Bézier
- Institut français de recherche pour l'exploitation de la mer Nantes France
| | - Kévin Le‐Rest
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Nantes France
| | - Alain Caizergues
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Nantes France
| | - Charlotte Francesiaz
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Juvignac France
| | - Jocelyn Champagnon
- Tour du Valat, Research Institute for Conservation of Mediterranean Wetlands Arles France
| | - Matthieu Guillemain
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Arles France
| | - Cyril Eraud
- Office Français de la Biodiversité, Conservation et Gestion des Espèces à enjeux Villiers‐en‐Bois France
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Kinebuchi T, Idota N, Tsuboi H, Takaso M, Bando R, Ikegaya H. The genome profiling method can be applied for species identification of biological materials collected at crime scenes. BMC Genet 2019; 20:50. [PMID: 31182029 PMCID: PMC6558897 DOI: 10.1186/s12863-019-0753-9] [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: 09/11/2018] [Accepted: 05/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-amplified with universal primers to identify species. However, not all species can be identified using a single locus. In this study, DNA from 13 commonly handled taxa was analyzed to identify species by a genome profiling (GP) method, which involves random PCR and temperature gradient gel electrophoresis. RESULTS In a clustering analysis, we successfully obtained a single cluster for each species. CONCLUSION The GP method is cost-effective and does not require advanced techniques and knowledge in molecular biology. The random sampling of the whole genome using multiple primers provides substantial genomic information. Therefore, the method is effective for classifying a wide range of species, including animals, plants, and insects, and is useful for crime scene investigations.
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Affiliation(s)
- Takako Kinebuchi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Nozomi Idota
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hajime Tsuboi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Marin Takaso
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Risa Bando
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan.
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Zhao L, Dong J, Sun C, Tian Y, Hu J, Ye X. Phylogenetic analysis of sooty grunter and other major freshwater fishes in the suborder Percoidei based on mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:234-248. [PMID: 30451556 DOI: 10.1080/24701394.2018.1482283] [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: 10/27/2022]
Abstract
Perciformes is the largest order of fishes and vertebrates. Sooty grunter (Hephaestus fuliginosus) is an economic fish species in the Terapontidae family of Percoidei, a suborder within Perciformes. To conduct molecular-level analysis of the phylogenetic relationships between sooty grunter and major freshwater fishes in Percoidei, we analysed the entire sooty grunter mitochondrial genome sequence and obtained the mitochondrial genome information of 19 fishes from Terapontidae, Serranidae, and Centrarchidae families in Percoidei from GenBank. The complete length of the sooty grunter mitochondrial genome was 16,770 bp; it encoded 13 proteins, 2 rRNAs, 22 tRNAs, and a displacement loop (D-loop). Other than ND6 and eight tRNA genes that are encoded by the light strand, the majority of genes are encoded by the heavy strand. The sequence and distribution of sooty grunter mitochondrial-encoded genes and non-coding segment were similar to those of most vertebrates. The results of neighbour joining, maximum parsimony, and Bayesian inference analyses of the complete mitochondrial genome and six genes, including cytochrome oxidase I, cytochrome B, 12S rRNA, ND2, ND4, and ND5, were consistent. In the phylogenetic trees, fishes in Terapontidae and Centrarchidae formed monophyletic clades, whereas those in Serranidae were divided into two clades, each containing Lateolabrax and Siniperca species. Among the three freshwater fish species in Terapontidae, the freshwater Terapontidae were more closely related to jade perch than with silver perch, suggesting that freshwater Terapontidae fishes originate from marine fishes. In addition, the phylogenetic results indicated that Micropterus salmoides salmoides and Micropterus salmoides floridanus in Centrarchidae should be designated as two independent species, and Siniperca in Serranidae should be considered an independent family. The sooty grunter mitochondrial genome sequence obtained in this study could be used to conduct population genetic diversity and germplasm resource studies. Furthermore, the phylogenetic analysis results of freshwater fishes in Percoidei could provide a molecular basis for cross-breeding.
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Affiliation(s)
- Lixiang Zhao
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
| | - Junjian Dong
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Chengfei Sun
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
| | - Yuanyuan Tian
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Jie Hu
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Xing Ye
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
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Dysthe JC, Carim KJ, Ruggles M, McKelvey KS, Young MK, Schwartz MK. Environmental DNA assays for the sister taxa sauger (Sander canadensis) and walleye (Sander vitreus). PLoS One 2017; 12:e0176459. [PMID: 28441436 PMCID: PMC5404789 DOI: 10.1371/journal.pone.0176459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/11/2017] [Indexed: 11/23/2022] Open
Abstract
Sauger (Sander canadensis) and walleye (S. vitreus) are percid fishes that naturally co-occur throughout much of the eastern United States. The native range of sauger extends into the upper Missouri River drainage where walleye did not historically occur, but have been stocked as a sport fish. Sauger populations have been declining due to habitat loss, fragmentation, and competition with non-native species, such as walleye. To effectively manage sauger populations, it is necessary to identify areas where sauger occur, and particularly where they co-occur with walleye. We developed quantitative PCR assays that can detect sauger and walleye DNA in filtered water samples. Each assay efficiently detected low quantities of target DNA and failed to detect DNA of non-target species with which they commonly co-occur.
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Affiliation(s)
- Joseph C. Dysthe
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America
- * E-mail:
| | - Kellie J. Carim
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America
| | - Michael Ruggles
- Montana Department of Fish, Wildlife and Parks, Region 5, Billings, Montana, United States of America
| | - Kevin S. McKelvey
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America
| | - Michael K. Young
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America
| | - Michael K. Schwartz
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America
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de Brito MA, Schneider H, Sampaio I, Santos S. DNA barcoding reveals high substitution rate and mislabeling in croaker fillets (Sciaenidae) marketed in Brazil: The case of “pescada branca” (Cynoscion leiarchus and Plagioscion squamosissimus). Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.01.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Genetic diversity of ivory shell (Babylonia areolata) in Taiwan and identification of species using DNA-based assays. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Skog A, Vøllestad LA, Stenseth NC, Kasumyan A, Jakobsen KS. Circumpolar phylogeography of the northern pike (Esox lucius) and its relationship to the Amur pike (E. reichertii). Front Zool 2014. [DOI: 10.1186/s12983-014-0067-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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8
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Dávalos LM, Russell AL. Sex-biased dispersal produces high error rates in mitochondrial distance-based and tree-based species delimitation. J Mammal 2014. [DOI: 10.1644/14-mamm-a-107] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Iyengar A. Forensic DNA analysis for animal protection and biodiversity conservation: A review. J Nat Conserv 2014. [DOI: 10.1016/j.jnc.2013.12.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Wu L, Yang J. Identifications of captive and wild tilapia species existing in Hawaii by mitochondrial DNA control region sequence. PLoS One 2012; 7:e51731. [PMID: 23251613 PMCID: PMC3520857 DOI: 10.1371/journal.pone.0051731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 11/09/2012] [Indexed: 11/18/2022] Open
Abstract
Background The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis. Methodology/Principal Findings In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization. Conclusions/Significance This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species identification. The suspected tilapia hybrids that consist of O. niloticus are present in captive and wild populations in Hawaii.
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Affiliation(s)
- Liang Wu
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Wozney KM, Wilson PJ. Real-time PCR detection and quantification of elephantid DNA: Species identification for highly processed samples associated with the ivory trade. Forensic Sci Int 2012; 219:106-12. [DOI: 10.1016/j.forsciint.2011.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 12/12/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
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12
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Chiu TH, Su YC, Pai JY, Chang HC. Molecular markers for detection and diagnosis of the giant grouper (Epinephelus lanceolatus). Food Control 2012. [DOI: 10.1016/j.foodcont.2011.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lucentini L, Puletti ME, Ricciolini C, Gigliarelli L, Fontaneto D, Lanfaloni L, Bilò F, Natali M, Panara F. Molecular and phenotypic evidence of a new species of genus Esox (Esocidae, Esociformes, Actinopterygii): the southern pike, Esox flaviae. PLoS One 2011; 6:e25218. [PMID: 22164201 PMCID: PMC3229480 DOI: 10.1371/journal.pone.0025218] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 08/29/2011] [Indexed: 11/18/2022] Open
Abstract
We address the taxonomic position of the southern European individuals of pike, performing a series of tests and comparisons from morphology, DNA taxonomy and population genetics parameters, in order to support the hypothesis that two species of pike, and not only one, exist in Europe. A strong relationship emerged between a northern genotype supported by COI, Cytb, AFLP and specific fragments, and a phenotype with round spot skin colour pattern and a large number of scales in the lateral line, clearly separated from a southern genotype with other skin colour pattern and a low number of scales in the lateral line. DNA taxonomy, based on a coalescent approach (GMYC) from phylogenetic reconstructions on COI and Cytb together with AFLP admixture analysis, supported the existence of two independently evolving entities. Such differences are not simply due to geographic distances, as northern European samples are more similar to Canadian and Chinese samples than the southern Europe ones. Thus, given that the differences between the two groups of European pike are significant at the phenotypic, genotypic and geographical levels, we propose the identification of two pike species: the already known northern pike (Esox lucius) and the southern pike (E. flaviae n.sp.). The correct identification of these two lineages as independent species should give rise to a ban on the introduction of northern pikes in southern Europe for recreational fishing, due to potential problems of hybridisation.
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Affiliation(s)
- Livia Lucentini
- Dipartimento di Biologia Cellulare e Ambientale, Università degli Studi di Perugia, Perugia, Italy.
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Carvalho DC, Neto DAP, Brasil BSAF, Oliveira DAA. DNA barcoding unveils a high rate of mislabeling in a commercial freshwater catfish from Brazil. ACTA ACUST UNITED AC 2011; 22 Suppl 1:97-105. [DOI: 10.3109/19401736.2011.588219] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Rojas M, González I, Pavón MÁ, Pegels N, Hernández PE, García T, Martín R. Development of a real-time PCR assay to control the illegal trade of meat from protected capercaillie species (Tetrao urogallus). Forensic Sci Int 2011; 210:133-8. [PMID: 21414736 DOI: 10.1016/j.forsciint.2011.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 01/05/2011] [Accepted: 02/20/2011] [Indexed: 11/26/2022]
Abstract
A rapid and highly species-specific real-time polymerase chain reaction (PCR) assay has been developed for the detection of capercaillie DNA (Tetrao urogallus) in meat and meat mixtures. The method combines the use of capercaillie-specific primers, that amplify a 142bp fragment of the mitochondrial 12S rRNA gene, and a positive control primer pair that amplifies a 141bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. SYBR(®) Green dye or TaqMan(®) fluorogenic probes were used to monitor the amplification of the target genes. Results obtained with the use of TaqMan(®) probes as detection platform increased the specificity of the real-time PCR assay in comparison with the results obtained using SYBR(®) Green. The proposed real-time PCR assay represents a rapid and straightforward method for the accurate identification of capercaillie that could be used by law enforcement agencies as a tool for the control of poaching and illegal trade of meat from this protected species.
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Affiliation(s)
- María Rojas
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Avenida Puerta de Hierro, S/N, 28040 Madrid, Spain
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Asgharian H, Sahafi HH, Ardalan AA, Shekarriz S, Elahi E. Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Mol Ecol Resour 2011; 11:461-72. [PMID: 21481204 DOI: 10.1111/j.1755-0998.2011.02989.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter- to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2-parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour-joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta-data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available.
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Affiliation(s)
- Hosseinali Asgharian
- Department Biotechnology, College of Science, University of Tehran, No 13, Shafiie Alley, Qods St., Enghelab St., 14155-6455, Tehran, Iran
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Bitanyi S, Bjørnstad G, Ernest EM, Nesje M, Kusiluka LJ, Keyyu JD, Mdegela RH, Røed KH. Species identification of Tanzanian antelopes using DNA barcoding. Mol Ecol Resour 2011; 11:442-9. [PMID: 21481202 DOI: 10.1111/j.1755-0998.2011.02980.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Efficient tools for consistent species identification are important in wildlife conservation as it can provide information on the levels of species exploitation and assist in solving forensic-related problems. In this study, we evaluated the effectiveness of the mitochondrial cytochrome c oxidase subunit I (COI) barcode in species identification of Tanzanian antelope species. A 470 base-pair region of the COI gene was examined in 95 specimens representing 20 species of antelopes, buffalo and domestic Bovidae. All the Tanzanian species showed unique clades, and sequence divergence within species was <1%, whereas divergence between species ranged from 6.3% to 22%. Lowest interspecific divergence was noted within the Tragelaphus genus. Neighbour-joining phylogenetic analyses demonstrated that the examined COI region provided correct and highly supported species clustering using short fragments down to 100 base-pair lengths. This study demonstrates that even short COI fragments can efficiently identify antelope species, thus demonstrating its high potential for use in wildlife conservation activities.
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Affiliation(s)
- Stella Bitanyi
- Ministry of Livestock Development and Fisheries, Veterinary Investigation Centre, Temeke, Dar es Salaam, Tanzania
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Pardiñas AF, Campo D, Pola IG, Miralles L, Juanes F, Garcia-Vazquez E. Climate change and oceanic barriers: genetic differentiation in Pomatomus saltatrix (Pisces: Pomatomidae) in the North Atlantic Ocean and the Mediterranean Sea. JOURNAL OF FISH BIOLOGY 2010; 77:1993-1998. [PMID: 21078102 DOI: 10.1111/j.1095-8649.2010.02774.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Nucleotide variation of partial cytochrome b sequences was analysed in the bluefish Pomatomus saltatrix to investigate the population-structuring roles of climate change and oceanic barriers. Western and eastern North Atlantic Ocean populations appeared to be totally isolated, with the latter connected to the Mediterranean Sea within which further structuring occurred.
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Affiliation(s)
- A F Pardiñas
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Julian Claveria s/n, 33006 Oviedo, Asturias, Spain
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Rasmussen Hellberg RS, Morrissey MT, Hanner RH. A Multiplex PCR Method for the Identification of Commercially Important Salmon and Trout Species (Oncorhynchus and Salmo) in North America. J Food Sci 2010; 75:C595-606. [DOI: 10.1111/j.1750-3841.2010.01752.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Marín JC, Saucedo CE, Corti P, González BA. Application of DNA forensic techniques for identifying poached guanacos (Lama guanicoe) in Chilean Patagonia*. J Forensic Sci 2009; 54:1073-6. [PMID: 19549029 DOI: 10.1111/j.1556-4029.2009.01087.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanaco (Lama guanicoe) is a protected and widely distributed ungulate in South America. A poacher, after killing guanacos in Valle Chacabuco, Chilean Patagonia, transported and stored the meat. Samples were retrieved by local police but the suspect argued that the meat was from a horse. Mitochondrial cytochrome b gene (774 pb), 15 loci microsatellites, and SRY gene were used to identify the species, number of animals and their population origin, and the sex of the animals, respectively. Analysis revealed that the samples came from a female (absence of SRY gene) Patagonian guanaco (assignment probability between 0.0075 and 0.0282), and clearly distinguishing it from sympatric ungulates (E-value = 0). Based on the evidence obtained in the field in addition to forensic data, the suspect was convicted of poaching and illegally carrying fire arms. This is the first report of molecular tools being used in forensic investigations of Chilean wildlife indicating its promising future application in guanaco management and conservation.
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Affiliation(s)
- Juan C Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Laboratorio de Genómica y Biodiversidad, Universidad del Bío-Bío, Casilla 447, Chillán, Chile.
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Rea S, Storani G, Mascaro N, Stocchi R, Loschi A. Species identification in anchovy pastes from the market by PCR-RFLP technique. Food Control 2009. [DOI: 10.1016/j.foodcont.2008.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Weese DA, Santos SR. Genetic identification of source populations for an aquarium-traded invertebrate. Anim Conserv 2009. [DOI: 10.1111/j.1469-1795.2008.00215.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rasmussen RS, Morrissey MT. DNA-Based Methods for the Identification of Commercial Fish and Seafood Species. Compr Rev Food Sci Food Saf 2008; 7:280-295. [PMID: 33467804 DOI: 10.1111/j.1541-4337.2008.00046.x] [Citation(s) in RCA: 230] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The detection of species substitution has become an important topic within the food industry and there is a growing need for rapid, reliable, and reproducible tests to verify species in commercial fish and seafood products. Increases in international trade and global seafood consumption, along with fluctuations in the supply and demand of different fish and seafood species, have resulted in intentional product mislabeling. The effects of species substitution are far-reaching and include economic fraud, health hazards, and illegal trade of protected species. To improve detection of commercial seafood fraud, a variety of DNA-based techniques have been developed, including Multiplex PCR, FINS, PCR-RFLP, PCR-RAPD, PCR-AFLP, and PCR-SSCP, which are all based on polymorphisms in the genetic codes of different species. These techniques have been applied in the differentiation of many types of fish and seafood species, such as gadoids, salmonids, scombroids, and bivalves. Some emerging technologies in this field include the use of real-time PCR, lab-on-a-chip, and DNA microarray chips. In this review article, the major DNA-based methods currently employed in the authentication of commercial fish and seafood species are discussed and future trends are highlighted. Examples of commercial applications and the use of online database resources are also considered.
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Affiliation(s)
- Rosalee S Rasmussen
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
| | - Michael T Morrissey
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
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