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Boehm JT, Bovee E, Harris SE, Eddins K, Akahoho I, Foster M, Pell SK, Hickerson MJ, Amato G, DeSalle R, Waldman J. The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification. PLoS One 2023; 18:e0291874. [PMID: 37788253 PMCID: PMC10547177 DOI: 10.1371/journal.pone.0291874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
Tens of millions of dried seahorses (genus Hippocampus) are traded annually, and the pressure from this trade along with their life history traits (involved parental care and small migration distances and home ranges) has led to near global population declines. This and other forms of overexploitation have led to all seahorse species being listed in Appendix II under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The signatory nations of CITES recommended a 10-cm size limit of seahorses to ensure harvested individuals have reached reproductive maturity, and have thus had the chance to produce offspring, to maintain a more sustainable global seahorse fishery. We assessed adherence to CITES recommendations using DNA barcoding and size measurements to compare two prominent U.S. dried seahorse markets: (1) traditional Chinese medicine (TCM), and (2) non-medicinal ecommerce and coastal curio (ECC). We also estimated U.S. import abundance from CITES records. Of the nine species identified among all samples (n = 532), eight were found in the TCM trade (n = 168); composed mostly (75%) of the Indo-Pacific species Hippocampus trimaculatus, and Hippocampus spinosissimus, and the Latin American Hippocampus ingens. In contrast, ECC samples (n = 344) included 5 species, primarily juvenile Indo-Pacific Hippocampus kuda (51.5%) and the western Atlantic Hippocampus zosterae (40.7). The majority of TCM samples (85.7%) met the CITES size recommendation, in contrast to 4.8% of ECC samples. These results suggest non-size discriminatory bycatch is the most likely source of imported ECC specimens. In addition, CITES records indicate that approximately 602,275 dried specimens were imported into the U.S. from 2004-2020, but the exact species composition remains unknown as many U.S. imports records list one species or Hippocampus spp. from confiscated shipments due to difficulties in morphological identification and large numbers of individuals per shipment. Molecular identification was used to identify the species composition of confiscated shipment imports containing undesignated species, and similar to TCM, found H. trimaculatus and H. spinosissimus the most abundant. By combining DNA barcoding, size comparisons, and CITES database records, these results provide an important glimpse into the two primary dried U.S. seahorse end-markets, and may further inform the conservation status of several Hippocampus species.
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Affiliation(s)
- J T Boehm
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
| | - Eric Bovee
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Stephen E Harris
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- School of Natural and Social Science, SUNY Purchase College, Purchase, New York, United States of America
| | - Kathryn Eddins
- The New School, New York, New York, United States of America
| | - Ishmael Akahoho
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Marcia Foster
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Susan K Pell
- Brooklyn Botanic Garden, Brooklyn, New York, United States of America
| | - Michael J Hickerson
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, 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
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - John Waldman
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Biology Department, Queens College, City University of New York, New York, United States of America
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Miga M, Jahari PNS, Vei Siang C, Kamarudin KR, Shamsir MS, Tokiman L, Parimannan S, Rajandas H, Mohamed F, Salleh FM. The complete mitochondrial genome data of the Common Rose butterfly, Pachliopta aristolochiae (Lepidoptera, Papilionoidea, Papilionidae) from Malaysia. Data Brief 2022; 40:107740. [PMID: 35141362 PMCID: PMC8813591 DOI: 10.1016/j.dib.2021.107740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Here, we present the complete mitochondrial genome of Pachliopta aristolochiae, a Common Rose butterfly from Malaysia. The sequence was generated using Illumina NovaSeq 6000 sequencing platform. The mitogenome is 15,235bp long, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two D-loop regions. The total base composition was (81.6%), with A (39.3%), T (42.3%), C (11.0%) and G (7.3%). The gene order of the three tRNAs was trnM-trnI-trnQ, which differs from the ancestral insect gene order trnI-trnQ-trnM. Phylogenetic tree analysis revealed that the sequenced Pachliopta aristolochiae in this data is closely related to Losaria neptunus (NC 037868), with highly supported ML and BI analysis. The data presented in this work can provide useful resources for other researchers to study deeper into the phylogenetic relationships of Lepidoptera and the diversification of the Pachliopta species. Also, as one of the bioindicator species, this data can be used to assess environmental changes in the terrestrial and aquatic ecosystem via enviromental DNA approahes. The mitogenome of Pachliopta aristolochiae is available in GenBank under the accession number MZ781228.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Chan Vei Siang
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Kamarul Rahim Kamarudin
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Mohd Shahir Shamsir
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, Iskandar Puteri, Johor 79575, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Farhan Mohamed
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
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Teske PR. Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species’ native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored.
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, Mohd Salleh F. Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:502-504. [PMID: 33628904 PMCID: PMC7889269 DOI: 10.1080/23802359.2021.1872433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru, Malaysia
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Jahari PNS, Mohd Azman S, Munian K, Zakaria NA, Omar MSS, Richter SR, Mohd Salleh F. The first mitochondrial genome data of an old world fruit bat, Cynopterus sphinx from Malaysia. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:53-55. [PMID: 33521264 PMCID: PMC7808394 DOI: 10.1080/23802359.2020.1846472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We assembled the complete mitogenome of Cynopterus sphinx (Vahl, 1797) of the family Pteropodidae originating from Malaysia. The total mitogenome size was 16,710bp which consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region). A phylogenetic and BLASTn result showed the mitogenome sequence in this study varies by nearly 7% (93.48% similarity) from the same species in Cambodia. The next closest match of BLASTn was at 92% similarity to the C. brachyotis. This suggests the species-complex in Cynopterus sp. has given rise to the genetic variability.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Nur Alwani Zakaria
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Mohd Shahir Shamsir Omar
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Jahari PNS, Mohd Azman S, Munian K, M Fauzi NF, Shamsir MS, Richter SR, Mohd Salleh F. The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3262-3264. [PMID: 33458132 PMCID: PMC7781998 DOI: 10.1080/23802359.2020.1812449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy’s rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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