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Din Dipita A, Missoup AD, Aguillon S, Lecompte E, Momboua BR, Chaber AL, Abernethy K, Njiokou F, Tindo M, Ntie S, Gaubert P. Genetic tracing of the illegal trade of the white-bellied pangolin (Phataginus tricuspis) in western Central Africa. Sci Rep 2024; 14:13131. [PMID: 38849460 PMCID: PMC11161582 DOI: 10.1038/s41598-024-63666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1-82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins' domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.
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Affiliation(s)
- Alain Din Dipita
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
| | - Samantha Aguillon
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Emilie Lecompte
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Brice Roxan Momboua
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anne-Lise Chaber
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide SA, Australia
| | - Katharine Abernethy
- African Forest Ecology Group, Biological and Environmental Sciences, University of Stirling, Stirling, UK
- Institut de Recherche en Ecologie Tropicale, Libreville, Gabon
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Universite de Yaoundé I, Yaoundé, 812, Cameroon
| | - Maurice Tindo
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon
| | - Stephan Ntie
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC), Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Philippe Gaubert
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
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2
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Engleman A, Cox K, Brooke S. Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral. PeerJ 2023; 11:e16101. [PMID: 37842045 PMCID: PMC10576496 DOI: 10.7717/peerj.16101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals' complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.
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Affiliation(s)
- Abigail Engleman
- Department of Biological Science, Florida State University, Tallahassee, United States of America
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
- Marine Station, Smithsonian, Fort Pierce, FL, United States of America
| | - Kieran Cox
- Marine Station, Smithsonian, Fort Pierce, FL, United States of America
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
- Hakai Institute, Calvert Island, British Columbia, Canada
| | - Sandra Brooke
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
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3
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Baker CS, Claridge D, Dunn C, Fetherston T, Baker DN, Klinck H, Steel D. Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville's beaked whales, with assisted localization from an acoustic array. PLoS One 2023; 18:e0291187. [PMID: 37703242 PMCID: PMC10499200 DOI: 10.1371/journal.pone.0291187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy's Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville's beaked whales (Mesoplodon densirostris). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville's beaked whales, suggested the potential for further resolution of differences between oceanic populations.
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Affiliation(s)
- Charles Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - Diane Claridge
- Bahamas Marine Mammal Research Organisation, Sandy Point, Abaco, The Bahamas
| | - Charlotte Dunn
- Bahamas Marine Mammal Research Organisation, Sandy Point, Abaco, The Bahamas
| | - Thomas Fetherston
- Naval Undersea Warfare Center, Newport, RI, United States of America
| | - Dorothy Nevé Baker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of America
| | - Holger Klinck
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
- Center for Conservation Bioacoustics Cornell Lab of Ornithology, Cornell University, Ithaca, NY, United States of America
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
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4
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Gossé KJ, Gonedelé-Bi S, Justy F, Chaber AL, Kramoko B, Gaubert P. DNA-typing surveillance of the bushmeat in Côte d'Ivoire: a multi-faceted tool for wildlife trade management in West Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01474-2] [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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5
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Richards JL, Sheng V, Chung HWY, Liu M, Tsang RHH, McIlroy SE, Baker D. Development of an eDNA‐based survey method for urban fish markets. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John L. Richards
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Victoria Sheng
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Haze Wing Yi Chung
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Min Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences Xiamen University Xiamen Fujian China
| | - Rainbow Hin Hung Tsang
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - David Baker
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
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6
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Kraft D, Meyer L, Webb M, Scidmore-Rossing K, Huveneers C, Clua E, Meyer C. Development and successful real-world use of a transfer DNA technique to identify species involved in shark bite incidents. J Forensic Sci 2021; 66:2438-2443. [PMID: 34286850 DOI: 10.1111/1556-4029.14808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022]
Abstract
Identifying the species involved in shark bite incidents is an ongoing challenge but is important to mitigate risk. We developed a sampling protocol to identify shark species from DNA transferred to inanimate objects during bite incidents. To develop and refine the technique, we swabbed shark bite impressions on surfboards and wetsuit neoprene collected under semicontrolled conditions. Methods were tested experimentally and then successfully used to identify the species involved in a real-world shark bite incident. Thirty-two of 33 bite impressions yielded sufficient DNA sequences for species identification, producing barcodes from five test species, including dusky, Galapagos, bull, tiger, and white shark. The latter three species collectively account for a majority of shark bites worldwide. Our method successfully identified the species (Galeocerdo cuvier) responsible for a fatal shark bite on December 8th, 2020 on the island of Maui, from swab samples collected from the victim's surfboard 49 h after the bite incident. Our experimental results demonstrate that shark species can be accurately identified from transfer DNA recovered from bite impressions on surfboards and wetsuit neoprene. The successful use of our method in the real-world incident shows great potential for the practicality of this tool. We recommend DNA swabbing as a routine part of the forensic analysis of shark bites to help identify the species involved in human-shark interactions.
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Affiliation(s)
- Derek Kraft
- Hawaii Institute of Marine Biology, Kaneohe, Hawaii, USA
| | - Lauren Meyer
- Southern Shark Ecology Group, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.,The Georgia Aquarium, Atlanta, Georgia, USA
| | - Maryann Webb
- Hawaii Institute of Marine Biology, Kaneohe, Hawaii, USA
| | | | - Charlie Huveneers
- Southern Shark Ecology Group, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Eric Clua
- Laboratoire d'excellence CORAIL, CRIOBE USR3278 EPHE-CNRS-UPVD, EPHE, PSL Research University, Perpignan, France
| | - Carl Meyer
- Hawaii Institute of Marine Biology, Kaneohe, Hawaii, USA
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7
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Tapkir SD, Kumkar P, Gosavi SM, Kharat SS, Patoka J, Kalous L. Far from home: Tracking the global ornamental fish trade in endangered zebra loach, Botia striata, from freshwater ecoregion and biodiversity hotspot in India. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Cazelles K, Zemlak TS, Gutgesell M, Myles-Gonzalez E, Hanner R, Shear McCann K. Spatial Fingerprinting: Horizontal Fusion of Multi-Dimensional Bio-Tracers as Solution to Global Food Provenance Problems. Foods 2021; 10:foods10040717. [PMID: 33800611 PMCID: PMC8066529 DOI: 10.3390/foods10040717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
Building the capacity of efficiently determining the provenance of food products represents a crucial step towards the sustainability of the global food system. Despite species specific empirical examples of multi-tracer approaches to provenance, the precise benefit and efficacy of multi-tracers remains poorly understood. Here we show why, and when, data fusion of bio-tracers is an extremely powerful technique for geographical provenance discrimination. Specifically, we show using extensive simulations how, and under what conditions, geographical relationships between bio-tracers (e.g., spatial covariance) can act like a spatial fingerprint, in many naturally occurring applications likely allowing rapid identification with limited data. To highlight the theory, we outline several statistic methodologies, including artificial intelligence, and apply these methodologies as a proof of concept to a limited data set of 90 individuals of highly mobile Sockeye salmon that originate from 3 different areas. Using 17 measured bio-tracers, we demonstrate that increasing combined bio-tracers results in stronger discriminatory power. We argue such applications likely even work for such highly mobile and critical fisheries as tuna.
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9
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Naseem A, Batool S, Abbas FI. Utility of mitochondrial COI gene for identification of wild ungulate species of conservational importance from Pakistan. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Asif Naseem
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Sargodha, Pakistan
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - Sajida Batool
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - Fakhar- i- Abbas
- Zoology, Centre for Bioresource Research (CBR), Islamabad, Pakistan
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10
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Juan Guo
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaomei Jiang
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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11
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Baeza JA, Behringer DC. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 2017; 5:e3786. [PMID: 28948100 PMCID: PMC5607919 DOI: 10.7717/peerj.3786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, United States of America.,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
| | - Donald C Behringer
- Program in Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, United States of America.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
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12
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Gaubert P, Njiokou F, Ngua G, Afiademanyo K, Dufour S, Malekani J, Bi SG, Tougard C, Olayemi A, Danquah E, Djagoun CAMS, Kaleme P, Mololo CN, Stanley W, Luo SJ, Antunes A. Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification. Mol Ecol 2016; 25:5975-5993. [PMID: 27862533 DOI: 10.1111/mec.13886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 01/03/2023]
Abstract
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, BP 812, Yaoundé, Cameroon
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE), Barrio Ukomba, S/N, Bata, Equatorial Guinea
| | - Komlan Afiademanyo
- Département de Zoologie et de Biologie Animale, Université de Lomé, BP 1515, Lomé, Togo
| | | | - Jean Malekani
- Department of Biology, University of Kinshasa, PO Box 218, Kinshasa XI, Democratic Republic of Congo
| | - Sery Gonedelé Bi
- Laboratoire de Génétique, Université Félix Houphouët Boigny d'Abidjan-Cocody, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005, Ile-Ife, Nigeria
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 LEA-FSA, Cotonou, Benin
| | - Prince Kaleme
- Laboratoire de Mammalogie, Département de Biologie, Centre de Recherches en Sciences Naturelles (CRSN) - Lwiro, DS (Dépêche Spéciale) Bukavu, Democratic Republic of Congo.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Casimir Nebesse Mololo
- Université de Kisangani, Faculté des Sciences, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - William Stanley
- Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
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13
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Carroll EL, Fewster RM, Childerhouse SJ, Patenaude NJ, Boren L, Baker CS. First Direct Evidence for Natal Wintering Ground Fidelity and Estimate of Juvenile Survival in the New Zealand Southern Right Whale Eubalaena australis. PLoS One 2016; 11:e0146590. [PMID: 26751689 PMCID: PMC4709107 DOI: 10.1371/journal.pone.0146590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 12/18/2015] [Indexed: 11/25/2022] Open
Abstract
Juvenile survival and recruitment can be more sensitive to environmental, ecological and anthropogenic factors than adult survival, influencing population-level processes like recruitment and growth rate in long-lived, iteroparous species such as southern right whales. Conventionally, Southern right whales are individually identified using callosity patterns, which do not stabilise until 6–12 months, by which time the whale has left its natal wintering grounds. Here we use DNA profiling of skin biopsy samples to identify individual Southern right whales from year of birth and document their return to the species’ primary wintering ground in New Zealand waters, the Subantarctic Auckland Islands. We find evidence of natal fidelity to the New Zealand wintering ground by the recapture of 15 of 57 whales, first sampled in year of birth and available for subsequent recapture, during winter surveys to the Auckland Islands in 1995–1998 and 2006–2009. Four individuals were recaptured at the ages of 9 to 11, including two females first sampled as calves in 1998 and subsequently resampled as cows with calves in 2007. Using these capture-recapture records of known-age individuals, we estimate changes in survival with age using Cormack-Jolly-Seber models. Survival is modelled using discrete age classes and as a continuous function of age. Using a bootstrap method to account for uncertainty in model selection and fitting, we provide the first direct estimate of juvenile survival for this population. Our analyses indicate a high annual apparent survival for juveniles at between 0.87 (standard error (SE) 0.17, to age 1) and 0.95 (SE 0.05: ages 2–8). Individual identification by DNA profiling is an effective method for long-term demographic and genetic monitoring, particularly in animals that change identifiable features as they develop or experience tag loss over time.
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Affiliation(s)
- E. L. Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Scotland
- * E-mail:
| | - R. M. Fewster
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | | | - N. J. Patenaude
- Collégial International Sainte-Anne, Montréal, Québec, Canada
| | - L. Boren
- New Zealand Department of Conservation, Wellington, New Zealand
| | - C. S. Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, United States of America
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Li Y, Tong Y, Xing F. DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China. FRONTIERS IN PLANT SCIENCE 2016; 7:1791. [PMID: 27994608 PMCID: PMC5136562 DOI: 10.3389/fpls.2016.01791] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.
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Affiliation(s)
- Yuling Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yi Tong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
| | - Fuwu Xing
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Fuwu Xing
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15
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Damasceno JS, Siccha-Ramirez R, Oliveira C, Mendonça FF, Lima AC, Machado LF, Tosta VC, Farro APC, Hostim-Silva M. Molecular identification of Atlantic goliath grouper Epinephelus itajara (Lichtenstein, 1822) (Perciformes: Epinephelidae) and related commercial species applying multiplex PCR. NEOTROPICAL ICHTHYOLOGY 2016. [DOI: 10.1590/1982-0224-20150128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT The Atlantic goliath grouper, Epinephelus itajara , is a critically endangered species, threatened by illegal fishing and the destruction of its habitats. A number of other closely related grouper species found in the western Atlantic are also fished intensively. While some countries apply rigorous legislation, illegal harvesting followed by the falsification of fish products, which impedes the correct identification of the species, is a common practice, allowing the catch to be marketed as a different grouper species. In this case, molecular techniques represent an important tool for the monitoring and regulation of fishery practices, and are essential for the forensic identification of a number of different species. In the present study, species-specific primers were developed for the Cytochrome Oxidase subunit I gene, which were applied in a multiplex PCR for the simultaneous identification of nine different species of Epinephelidae: Epinephelus itajara , E. quinquefasciatus , E. morio , Hyporthodus flavolimbatus , H. niveatus , Mycteroperca acutirostris , M. bonaci , M. marginata , and M. microlepis . Multiplex PCR is a rapid, reliable and cost-effective procedure for the identification of commercially-valuable endangered fish species, and may represent a valuable tool for the regulation and sustainable management of fishery resources.
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Affiliation(s)
- Júnio S. Damasceno
- Universidade Federal do Espírito Santo, Brazil; Pontifícia Universidade Católica de Minas Gerais, Brazil
| | | | | | | | | | - Leonardo F. Machado
- Universidade Estadual Paulista, Brazil; Universidade Federal do Espírito Santo, Brazil
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16
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Garcia DA, Lasso CA, Morales M, Caballero SJ. Molecular systematics of the freshwater stingrays (myliobatiformes: potamotrygonidae) of the Amazon, Orinoco, Magdalena, Esequibo, Caribbean, and Maracaibo basins (Colombia - Venezuela): evidence from three mitochondrial genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4479-4491. [PMID: 26702899 DOI: 10.3109/19401736.2015.1101536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lack of adequate information about the taxonomic and evolutionary relationships, ecology, biology, and distribution of several species belonging to the family Potamotrygonidae makes these species vulnerable to anthropic activities, including commercial overexploitation for the ornamental fish market. The aim of this study was to investigate the systematic relationships among genera and species belonging to this family by analyses of three mitochondrial gene regions. Samples were collected from the main river basins in Colombia and Venezuela for four genera and seven species of the family, as well as for what appear to be unidentified species. Three mitochondrial molecular markers COI, Cytb, and ATP6 were amplified and sequenced. Maximum likelihood and Bayesian inference analysis were performed to obtain topologies for each marker and for a concatenated dataset including the three genes. Small dataset may compromise some methods estimations of sequence divergence in the ATP6 marker. Monophyly of the four genera in Potamotrygonidae was confirmed and phylogenetic relationships among members of the Potamotrygon genus were not clearly resolved. However, results obtained with the molecular marker Cytb appear to offer a good starting point to differentiate among genera and species as a tool that could be used for barcoding. The application of this gene as a barcode could be applied for management and regulation of extraction practices for these genera. Sequencing complete mitochondrial genomes would be the next step for testing evolutionary hypothesis among these genera. Population structure analyses should be undertaken for Paratrygon, Potamotrygon magdalenae and motoro.
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Affiliation(s)
- David Alejandro Garcia
- a Laboratorio De Ecología Molecular De Vertebrados Acuáticos , Universidad De Los Andes , Bogota , Colombia and
| | - Carlos Andres Lasso
- b Instituto De Investigación De Recursos Biológicos Alexander Von Humboldt , Bogota , Colombia
| | - Monica Morales
- b Instituto De Investigación De Recursos Biológicos Alexander Von Humboldt , Bogota , Colombia
| | - Susana Josefina Caballero
- a Laboratorio De Ecología Molecular De Vertebrados Acuáticos , Universidad De Los Andes , Bogota , Colombia and
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17
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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18
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Yan LJ, Liu J, Möller M, Zhang L, Zhang XM, Li DZ, Gao LM. DNA barcoding ofRhododendron(Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains. Mol Ecol Resour 2014; 15:932-44. [DOI: 10.1111/1755-0998.12353] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/22/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- 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
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Michael Möller
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Lin Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xue-Mei Zhang
- Landscape and Horticultural College; Yunnan Agricultural University; Kunming 650201 Yunnan China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
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19
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Ovenden JR, Macbeth GM, Pope L, Thuesen P, Street R, Broderick D. Translocation between freshwater catchments has facilitated the spread of tilapia in eastern Australia. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0754-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor MEK, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A. Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. Mol Ecol Resour 2014; 15:633-51. [DOI: 10.1111/1755-0998.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier Cedex 05 France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et d'Ecologie; Faculté des Sciences; Université de Yaoundé I; BP 812 Yaoundé Cameroon
| | - Ayodeji Olayemi
- Natural History Museum; Obafemi Awolowo University; Ho 220005 Ile-Ife Osun State Nigeria
| | - Paolo Pagani
- Dutch Wildlife Health Centre; Faculty of Veterinary Medicine; Yalelaan 1 3584 CL Utrecht The Netherlands
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Mac Elikem K. Nutsuakor
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE); Barrió Ukomba, S/N Bata Equatorial Guinea
| | - Alain-Didier Missoup
- Biologie de l'Evolution - Mammalogie; Département de Biologie des Organismes Animaux; Faculté des Sciences; Université de Douala; BP 24157 Douala Cameroon
| | - Pablo A. Tedesco
- Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; UMR Biologie des ORganismes et des Ecosystèmes Aquatiques (UMR BOREA IRD 207-CNRS 7208-UPMC-MNHN); 43 rue Cuvier FR-75231 Paris Cedex France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution - CNRS UMR 5554; Plateforme Bioinformatique LabEx; Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 177 4050-123 Porto Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre 4169-007 Porto Portugal
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21
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Salinas C, Cubillos JC, Gómez R, Trujillo F, Caballero S. "Pig in a poke (gato por liebre)": the "mota" (Calophysus macropterus) fishery, molecular evidence of commercialization in Colombia and toxicological analyses. ECOHEALTH 2014; 11:197-206. [PMID: 24419666 DOI: 10.1007/s10393-013-0893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 11/27/2013] [Accepted: 12/04/2013] [Indexed: 06/03/2023]
Abstract
Overfishing has affected the population abundance trends of many commercial fish species. In the Amazon, the fishery of a catfish commonly known as "mota" or "piracatinga" (Calophysus macropterus) has become an important economic activity in the region as this species has replaced a number of other overexploited great catfish species in the markets. Due to this high exploitation, ways in which to increase captures have been identified. One strategy is to use decomposing animal carcasses as bait. Such strategy has increased the hunting pressure on endangered species such as caimans and river dolphins. We investigated which catfish species are currently commercialized in Colombian fish markets using DNA barcoding, and measured mercury concentration in the tissues of fish molecularly identified as C. macropterus. We collected 86 fish samples in markets of four Colombian cities. Sixty-eight of these were identified molecularly as C.macropterus. The mercury concentration of 29 such samples was analyzed. Samples presented total Hg concentrations higher than the limit for human consumption established by the WHO (0.5 μg/g). These results are worrisome and suggest that (1) C. macropterus is a widely used fish species for human consumption in Colombia and (2) C. macropterus has high concentrations of total Hg, making its consumption a public health risk. Results presented here suggest that C. macropterus has replaced capaz in most Colombian markets. This fishery threatens wild species of river dolphins and caimans, and is also a public health risk given the high mercury levels we found in a subsample of these fishes.
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Affiliation(s)
- Cristian Salinas
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Biological Sciences Department, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá, Colombia
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22
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Hart KM, Hunter ME, King TL. Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0563-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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The Role of Genomics in Conservation and Reproductive Sciences. REPRODUCTIVE SCIENCES IN ANIMAL CONSERVATION 2014; 753:71-96. [DOI: 10.1007/978-1-4939-0820-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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24
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Baker CS, Hutt A, Thompson K, Dalebout ML, Robins J, Brownell RL, Stone GS. Species identity and human consumption of beaked whales in the Gilbert Islands, Republic of Kiribati. Anim Conserv 2013. [DOI: 10.1111/acv.12039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. S. Baker
- Marine Mammal Institute; Oregon State University; Newport OR USA
- School of Biological Sciences; University of Auckland; Auckland New Zealand
| | - A. Hutt
- Department of Conservation; Akaroa New Zealand
| | - K. Thompson
- School of Biological Sciences; University of Auckland; Auckland New Zealand
| | - M. L. Dalebout
- School of Biological, Earth, and Environmental Sciences; University of New South Wales; Sydney NSW Australia
| | - J. Robins
- Department of Anthropology; University of Auckland; Auckland New Zealand
| | - R. L. Brownell
- NOAA Fisheries; Southwest Fisheries Science Center; Pacific Grove CA USA
| | - G. S. Stone
- Conservation International; Arlington VA USA
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Ishida Y, Georgiadis NJ, Hondo T, Roca AL. Triangulating the provenance of African elephants using mitochondrial DNA. Evol Appl 2013; 6:253-65. [PMID: 23798975 PMCID: PMC3689351 DOI: 10.1111/j.1752-4571.2012.00286.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 06/25/2012] [Indexed: 12/01/2022] Open
Abstract
African elephant mitochondrial (mt) DNA follows a distinctive evolutionary trajectory. As females do not migrate between elephant herds, mtDNA exhibits low geographic dispersal. We therefore examined the effectiveness of mtDNA for assigning the provenance of African elephants (or their ivory). For 653 savanna and forest elephants from 22 localities in 13 countries, 4258 bp of mtDNA was sequenced. We detected eight mtDNA subclades, of which seven had regionally restricted distributions. Among 108 unique haplotypes identified, 72% were found at only one locality and 84% were country specific, while 44% of individuals carried a haplotype detected only at their sampling locality. We combined 316 bp of our control region sequences with those generated by previous trans-national surveys of African elephants. Among 101 unique control region haplotypes detected in African elephants across 81 locations in 22 countries, 62% were present in only a single country. Applying our mtDNA results to a previous microsatellite-based assignment study would improve estimates of the provenance of elephants in 115 of 122 mis-assigned cases. Nuclear partitioning followed species boundaries and not mtDNA subclade boundaries. For taxa such as elephants in which nuclear and mtDNA markers differ in phylogeography, combining the two markers can triangulate the origins of confiscated wildlife products.
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Affiliation(s)
- Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA
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26
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Sonricker Hansen AL, Li A, Joly D, Mekaru S, Brownstein JS. Digital surveillance: a novel approach to monitoring the illegal wildlife trade. PLoS One 2012; 7:e51156. [PMID: 23236444 PMCID: PMC3517447 DOI: 10.1371/journal.pone.0051156] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/29/2012] [Indexed: 11/18/2022] Open
Abstract
A dearth of information obscures the true scale of the global illegal trade in wildlife. Herein, we introduce an automated web crawling surveillance system developed to monitor reports on illegally traded wildlife. A resource for enforcement officials as well as the general public, the freely available website, http://www.healthmap.org/wildlifetrade, provides a customizable visualization of worldwide reports on interceptions of illegally traded wildlife and wildlife products. From August 1, 2010 to July 31, 2011, publicly available English language illegal wildlife trade reports from official and unofficial sources were collected and categorized by location and species involved. During this interval, 858 illegal wildlife trade reports were collected from 89 countries. Countries with the highest number of reports included India (n = 146, 15.6%), the United States (n = 143, 15.3%), South Africa (n = 75, 8.0%), China (n = 41, 4.4%), and Vietnam (n = 37, 4.0%). Species reported as traded or poached included elephants (n = 107, 12.5%), rhinoceros (n = 103, 12.0%), tigers (n = 68, 7.9%), leopards (n = 54, 6.3%), and pangolins (n = 45, 5.2%). The use of unofficial data sources, such as online news sites and social networks, to collect information on international wildlife trade augments traditional approaches drawing on official reporting and presents a novel source of intelligence with which to monitor and collect news in support of enforcement against this threat to wildlife conservation worldwide.
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Affiliation(s)
- Amy L. Sonricker Hansen
- HealthMap, Children’s Hospital Informatics Program, Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
- Division of Emergency Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- State University of New York at Albany, School of Public Health, Department of Epidemiology and Biostatistics, Rensselaer, New York, United States of America
- * E-mail:
| | - Annie Li
- HealthMap, Children’s Hospital Informatics Program, Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
- City University of Hong Kong, Department of Biology and Chemistry, Kowloon, Hong Kong
| | - Damien Joly
- Wildlife Health Program, Wildlife Conservation Society, Nanaimo, British Columbia, Canada
| | - Sumiko Mekaru
- HealthMap, Children’s Hospital Informatics Program, Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
- Division of Emergency Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Boston University, School of Public Health, Department of Epidemiology, Boston, Massachusetts, United States of America
| | - John S. Brownstein
- HealthMap, Children’s Hospital Informatics Program, Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
- Division of Emergency Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Departments of Medicine and Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
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27
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Ribeiro ADO, Caires RA, Mariguela TC, Pereira LHG, Hanner R, Oliveira C. DNA barcodes identify marine fishes of São Paulo State, Brazil. Mol Ecol Resour 2012; 12:1012-20. [PMID: 22958713 DOI: 10.1111/1755-0998.12007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/15/2012] [Accepted: 08/02/2012] [Indexed: 11/28/2022]
Abstract
Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp 'barcode' fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour-joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43-fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species-pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna - extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation.
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Affiliation(s)
- Amanda de Oliveira Ribeiro
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.
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Doukakis P, Pikitch EK, Rothschild A, DeSalle R, Amato G, Kolokotronis SO. Testing the effectiveness of an international conservation agreement: marketplace forensics and CITES caviar trade regulation. PLoS One 2012; 7:e40907. [PMID: 22848410 PMCID: PMC3405056 DOI: 10.1371/journal.pone.0040907] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The international wildlife trade is a key threat to biodiversity. Temporal genetic marketplace monitoring can determine if wildlife trade regulation efforts such as the Convention on International Trade in Endangered Species (CITES) are succeeding. Protected under CITES effective 1997, sturgeons and paddlefishes, the producers of black caviar, are flagship CITES species. METHODOLOGY/PRINCIPAL FINDINGS We test whether CITES has limited the amount of fraudulent black caviar reaching the marketplace. Using mitochondrial DNA-based methods, we compare mislabeling in caviar and meat purchased in the New York City area pre and post CITES listing. Our recent sampling of this market reveals a decrease in mislabeled caviar (2006-2008; 10%; n = 90) compared to pre-CITES implementation (1995-1996; 19%; n = 95). Mislabeled caviar was found only in online purchase (n = 49 online/41 retail). CONCLUSIONS/SIGNIFICANCE Stricter controls on importing and exporting as per CITES policies may be having a positive conservation effect by limiting the amount of fraudulent caviar reaching the marketplace. Sturgeons and paddlefishes remain a conservation priority, however, due to continued overfishing and habitat degradation. Other marine and aquatic species stand to benefit from the international trade regulation that can result from CITES listing.
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Affiliation(s)
- Phaedra Doukakis
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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Caballero S, Cardeñosa D, Soler G, Hyde J. Application of multiplex PCR approaches for shark molecular identification: feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific. Mol Ecol Resour 2011; 12:233-7. [PMID: 22067369 DOI: 10.1111/j.1755-0998.2011.03089.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we describe the application of new and existing multiplex PCR methodologies for shark species molecular identification. Four multiplex systems (group ID, thresher sharks, hammerhead sharks and miscellaneous shark) were employed with primers previously described and some designed in this study, which allow for species identification after running PCR products through an agarose gel. This system was implemented for samples (bodies and fins) collected from unidentified sharks landed in the port of Buenaventura and from confiscated tissues obtained from illegal fishing around the Malpelo Island Marine Protected Area, Pacific Coast of Colombia. This method has allowed reliable identification, to date, of 407 samples to the genus and/or species levels, most of them (380) identified as the pelagic thresher shark (Alopias pelagicus). Another seven samples were identified as scalloped hammerhead sharks (Sphyrna lewini). This is an easy-to-implement and reliable identification method that could even be used locally to monitor shark captures in the main fishing ports of developed and developing countries.
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Affiliation(s)
- S Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá, Colombia.
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Jackson JA, Laikre L, Baker CS, Kendall KC. Guidelines for collecting and maintaining archives for genetic monitoring. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9545-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Lee SJ, Jung G, Min MS, Kim CK, Lee H, Kim CB, Lee MY. Genetic origin identification of Siberian chipmunks (Tamias sibiricus) in pet shops of South Korea. Anim Cells Syst (Seoul) 2011. [DOI: 10.1080/19768354.2011.577586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling. PLoS One 2011; 6:e17319. [PMID: 21364886 PMCID: PMC3045434 DOI: 10.1371/journal.pone.0017319] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 01/29/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. METHODOLOGY/PRINCIPAL FINDINGS We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279-modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively. CONCLUSIONS/SIGNIFICANCE Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.
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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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Olayemi A, Oyeyiola A, Antunes A, Bonillo C, Cruaud C, Gaubert P. Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria. WILDLIFE RESEARCH 2011. [DOI: 10.1071/wr11015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Following recent socioeconomic transformations in western and central Africa, the volume of bushmeat hunting, a traditional source of proteins and revenue for rural populations, has reached unsustainable levels. The morphological identification of species sold on bushmeat market stalls may be challenging because of the presence of cryptic taxa and smoked or processed carcasses.
Aims
To assess the contribution of DNA-typing to traditional bushmeat surveys. We conducted a case study at a roadside bushmeat market in Asejire, south-western Nigeria, to characterise the mammalian diversity and sketch out the dynamics of the bushmeat trade.
Methods
We generated a 402-bp Cytochrome b fragment using a ‘universal’ mitochondrial primer pair that successfully amplified across five mammalian orders, and used assignment procedures to assess the taxonomic identification of the traded species. We combined DNA-typing with morphological-based market surveys and questionnaires to half (n = 20) of the market stakeholders.
Key results
Our combined morphological–DNA-based survey revealed a total of 17 species, representing seven mammalian orders (Rodentia, Lagomorpha, Primates, Hyracoidea, Carnivora, Pholidota and Artiodactyla). DNA-typing allowed identifying the Walter’s duiker, a cryptic, newly described species from the Dahomey Gap, and diagnosing an unidentified primate as the white-throated monkey, Cercopithecus erythrogaster, a species of high conservation concern in Nigeria. K2P pairwise genetic distances among all species exceeded the 11% threshold, indicative of species-level distinction. The most hunted species were the Walter’s duiker and, to a lesser extent, the greater cane rat, Thryonomys swinderianus. Questionnaires to traders revealed that the Asejire roadside market was a straightforward trader–hunter system centralising off-takes from distant hunting sites.
Conclusions
We showed how mitochondrial DNA-typing combined with assignment procedures improved the characterisation of the mammalian diversity sold on bushmeat markets. The hunted mammalian community consisted of versatile, small- to medium-sized secondary forest species characteristic of the Dahomey Gap assemblage; their sustainable management is in doubt because of the lack of conservation and health awareness within the traders’ community.
Implications
Given the utility of mitochondrial DNA-typing in identifying species sold in bushmeat markets, we argue in favour of multi-entry investigations to reach a comprehensive characterisation of the bushmeat trade. The building of a web-accessible mtDNA database covering the spectrum of the species hunted for bushmeat would appear to be a valuable diagnostic tool that may help Nigeria and neighbouring countries to set up a rigorous monitoring of wildlife extirpation.
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Teletchea F. After 7 years and 1000 citations: Comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists. ACTA ACUST UNITED AC 2010; 21:206-26. [DOI: 10.3109/19401736.2010.532212] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Barber-Meyer SM. Dealing with the clandestine nature of wildlife-trade market surveys. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2010; 24:918-923. [PMID: 20408867 DOI: 10.1111/j.1523-1739.2010.01500.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Illegal international trade in wildlife (excluding fisheries and timber) has been valued at more than US$20 billion. A more precise figure has not been determined in part because of the clandestine nature of the trade, and for this same reason even regional and local levels of wildlife trade are difficult to assess. The application of recent developments in wildlife field-survey methods (e.g., occupancy) now allows for a more-accurate estimation of wildlife trade occurrence, including its hidden components at a variety of scales (e.g., regional, local) and periods (e.g., single season, 1 year, multiple years). Occupancy models have been applied in wildlife field studies to address the problem of false absences when conducting presence-absence surveys. Occupancy surveys differ from traditional presence-absence surveys because they incorporate repeat surveys, allowing for the likelihood of detecting a species (the probability of detection) to be estimated explicitly (in contrast to traditional surveys that often incorrectly treat this probability as close to one to allow for estimation of presence). Occupancy methods can be applied to a variety of wildlife-trade surveys, including, for example, single-species availability, links between two illegally traded species (i.e., co-occurrence), and disease occurrence in live trade. In addition, free user-friendly software (i.e., PRESENCE) allows even nonstatisticians to adequately address this issue. I simulated a hypothetical wildlife-trade market survey that resulted in an apparent 20% decline in naïve occupancy (proportion of surveyed towns engaged in the trade) over 2 years, but when I accounted for change in probability of detection over the years the difference in occupancy was not statistically significant. As more sophisticated methods, such as occupancy, are applied to wildlife-trade market surveys, results will be more robust and defensible and therefore, theoretically, more powerful when presented to conservation policy and decision makers.
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Affiliation(s)
- Shannon M Barber-Meyer
- World Wildlife Fund/TRAFFIC North America, 1250 24th Street N.W., Washington, DC 20037-1193, USA.
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Baker CS, Steel D, Choi Y, Lee H, Kim KS, Choi SK, Ma YU, Hambleton C, Psihoyos L, Brownell RL, Funahashi N. Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea. Biol Lett 2010; 6:647-50. [PMID: 20392716 PMCID: PMC2936163 DOI: 10.1098/rsbl.2010.0239] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report on genetic identification of 'whale meat' purchased in sushi restaurants in Los Angeles, CA (USA) in October 2009 and in Seoul, South Korea in June and September 2009. Phylogenetic analyses of mtDNA cytochrome b sequences confirmed that the products included three species of whale currently killed in the controversial scientific whaling programme of Japan, but which are protected from international trade: the fin, sei and Antarctic minke. The DNA profile of the fin whale sold in Seoul established a match to products purchased previously in Japan in September 2007, confirming unauthorized trade between these two countries. Following species identification, these products were handed over to the appropriate national or local authorities for further investigation. The illegal trade of products from protected species of whales, presumably taken under a national permit for scientific research, is a timely reminder of the need for independent, transparent and robust monitoring of any future whaling.
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Affiliation(s)
- C Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Oregon State University, Newport, OR 97365, USA.
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Meganathan PR, Dubey B, Jogayya KN, Whitaker N, Haque I. A novel multiplex PCR assay for the identification of Indian crocodiles. Mol Ecol Resour 2010; 10:744-7. [PMID: 21565084 DOI: 10.1111/j.1755-0998.2010.02834.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.
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Affiliation(s)
- P R Meganathan
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30-Gorachand Road, Kolkata 700 014, West Bengal, India Madras Crocodile Bank Trust, Centre for Herpetology, Mamallapuram 603 104, Tamil Nadu, India
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Genetic tools to support the conservation of the endangered smalltooth sawfish, Pristis pectinata. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9175-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Lowenstein JH, Amato G, Kolokotronis SO. The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances. PLoS One 2009; 4:e7866. [PMID: 19924239 PMCID: PMC2773415 DOI: 10.1371/journal.pone.0007866] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 10/13/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. METHODOLOGY/PRINCIPAL FINDINGS Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. CONCLUSIONS/SIGNIFICANCE The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.
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Affiliation(s)
- Jacob H. Lowenstein
- Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, United States of America
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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Lukoschek V, Funahashi N, Lavery S, Dalebout ML, Cipriano F, Baker CS. High proportion of protected minke whales sold on Japanese markets is due to illegal, unreported or unregulated exploitation. Anim Conserv 2009. [DOI: 10.1111/j.1469-1795.2009.00302.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Read AJ. Lessons from Japanese markets for the conservation of whale populations. Anim Conserv 2009. [DOI: 10.1111/j.1469-1795.2009.00314.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Eaton MJ, Meyers GL, Kolokotronis SO, Leslie MS, Martin AP, Amato G. Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9967-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Doukakis P, Parsons ECM, Burns WCG, Salomon AK, Hines E, Cigliano JA. Gaining traction: retreading the wheels of marine conservation. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2009; 23:841-846. [PMID: 19627316 DOI: 10.1111/j.1523-1739.2009.01281.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A number of international treaties address the conservation of marine resources. The declining state of the world's oceans suggests that these treaties are not succeeding and could use improvement. The Convention on International Trade in Endangered Species (CITES) is increasingly embracing the conservation of marine species. We examine the evolution of marine species protection under CITES and illuminate some of the mechanisms used and challenges faced in implementing CITES protection. We found that clarification is needed on when and where CITES applies and how CITES should work with other treaties and institutions. The Society for Conservation Biology (SCB) can contribute to increased effectiveness of CITES for marine conservation. Foremost, the SCB community could foster dialogue on creating a broad vision of how CITES should apply to marine species and how it can synergistically interact with other important marine-conservation treaties and institutions. More specific contributions could focus on defining listing criteria for marine species, improving the science behind the nondetriment finding, and offering technical guidance on species proposals. A future role for SCB could be to contribute to the enhanced effectiveness of other marine conservation agreements such as the Convention on the Conservation of Migratory Species of Wild Animals, the International Whaling Commission, and the United Nations Convention on the Law of the Sea.
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Affiliation(s)
- Phaedra Doukakis
- Institute for Ocean Conservation Science, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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Rasmussen RS, Morrissey MT. Application of DNA-Based Methods to Identify Fish and Seafood Substitution on the Commercial Market. Compr Rev Food Sci Food Saf 2009. [DOI: 10.1111/j.1541-4337.2009.00073.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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