Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection on Local Markets and Fish Gathering Centers
2.2. DNA Extraction and PCR Amplification
2.3. Sequence Analysis
2.4. Species and Genetic Diversity in Panama Pacific Fisheries
2.4.1. Species and Family Diversity
2.4.2. Genetic Diversity
2.4.3. Genetic Connectivity and Demographic History
2.4.4. Developing Tools for Molecular Taxonomy and Traceability
3. Results
3.1. Sequence Analysis
3.2. Species, Family and Genetic Diversity in Panama Pacific Fisheries
3.3. Genetic Diversity
3.3.1. Genetic Connectivity and Demographic History
3.3.2. Developing Tools for Molecular Taxonomy and Traceability
4. Discussion
4.1. Species Diversity
4.2. Genetic Connectivity and Demographic History
4.3. Developing Tools for Molecular Taxonomy and Traceability
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Site | Family | Species | Common Name | GenBank Accession Number |
---|---|---|---|---|
GP _1_SFelipe | Scombridae | Scomberomorus sierra | Pacific Sierra | OQ790166–OQ790174 |
Euthynnus affinis | Tuna | OQ844071 | ||
Carangidae | Caranx vinctus | Cocinero | OQ790077 | |
Caranx caninus | Pacific Crevalle Jack | OQ801572 | ||
Centropomus unionensis | Bigeye trevally | OQ850133 | ||
Caranx caballus | Green Jack | OQ789895 | ||
Selene peruviana | Peruvian moonfish | OQ843845 | ||
Haemulidae | Pomadasys panamensis | Panama grunt | OQ789718 | |
Lobotidae | Lobotes surinamensis * | Atlantic Triple Tail | OQ844072 | |
Lobotes pacificus | Pacific Triple Tail | OQ844073 | ||
Serranidae | Mycteroperca xenarcha * | Caribbean grouper | OQ844067 | |
Hyporthodus acanthistius | Pacific grouper | OQ844070 | ||
Sphyraenidae | Sphryraena ensis | Pacific barracuda | OQ850073 | |
Scianidae | Nebris occidentalis | Guabina | OQ843562 | |
Cynoscion phoxocephalus | Cachema weakfish | OQ843904 | ||
Lutjanidae | Lutjanus guttatus | Rose spotted snapper | OQ850300 | |
Lutjanus argentiventris | Yellow snapper | OQ790134–OQ790136 | ||
Melacanthidae | Caulolatilus affinis | Bighead tilefish | OQ844074 | |
GP_2_Anton | Scombridae | Scomberomorus sierra | Sierra fish | OQ790166–OQ790174 |
Carangidae | Caranx caballus | Green Jack | OQ789895 | |
Caranx caninus | Pacific Crevalle Jack | OQ801572 | ||
Selene peruviana | Peruvian Moonfish | OQ843845 | ||
Centropomidae | Centropomus robalito | Yellowfin Snook | OQ844075 | |
Lutjanidae | Lutjanus guttatus | Spotted rose snapper | OQ850300 | |
Scianidae | Cynoscion othonopterus | Gulf weakfish | OQ850144 | |
Ophioscion scierus | Tuza croaker | OQ848437 | ||
Paralonchurus dumerilii | Banded croacker | OQ848738 | ||
Stromateidae | Peprilus medius | Pacific Harvest Fish | OQ848659 | |
GP_3Coquira | ||||
Carangidae | Caranx caninus | Pacific crevalle Jack | OQ801572 | |
Caranx caballus | Green Jack | OQ789895 | ||
Centropomidae | Centropomus viridis * | Common Snook | ||
Centropomus medius | Blackfin snook | OQ848755 | ||
Lutjanidae | Lutjannus gutattus | Rose spotted snapper | OQ850300 | |
Haemulidae | Haemulopsis leuciscus | Raucous grunt | OQ849145 | |
Orthopristis chalceus | Brassy grunt | OQ849164 | ||
Scianidae | Nebris occidentalis | Pacific smalleye croaker | OQ843562 | |
Cynoscion phoxocephalus | Cachema weakfish | OQ843904 | ||
Cynoscion leiarchus * | Smooth weak fish | |||
Larimus pacificus | Pacific drum | OQ849155 | ||
Guerridae | Gerres simillimus | Yellow fin mojarra | OQ872776 | |
Lobotidae | Lobotus pacificus | Pacific Triple Tail | OQ844073 | |
Ariidae | Bagre marinus * | Gafftopsail catfish | ||
Mugilidade | Mugil curema * | White mullet | ||
GCH_1-Pedregal | ||||
Carangidae | Caranx caballus | Green Jack | OQ789895 | |
Lutjanidae | Lutjanus argentiventris | Yellow snapper | OQ790134–OQ790136 | |
Lutjanus guttatus | Rose spotted snapper | OQ850300 | ||
Lutjanus peru | Red Snapper | OQ791284 | ||
Scombridae | Scomberomorus sierra | Pacific sierra | OQ790166–OQ790174 | |
GMon_1-Mutis | ||||
Scombridae | Scomberomorus sierra | Pacific sierra | OQ790166–OQ790174 | |
Scianidae | Cynoscion phoxocephalus | Cachema weakfish | OQ843904 | |
Stromatidae | Peprilus medius | Pacific Harvest fish | OQ848659 | |
Lutjanidae | Lutjanus argentiventris | Yellow snapper | OQ790134–OQ790136 | |
Lutjanus guttatus | Rose spotted snapper | OQ850300 | ||
GMon_2-Santiago | ||||
Carangidae | Caranx vinctus | Jack | OQ790077 | |
Caranx caninus | Pacific Crevalle Jack | OQ801572 | ||
Caranx caballus | Green Jack | OQ789895 | ||
Lutjanidae | Lutjanus Colorado | Colorado snapper | OQ801537–OQ801540 | |
GCH_PixCOIBA | Lutjanidae | Lutjanus guttatus | Rose spotted snapper | OQ850300 |
Lutjanus peru | Red Snapper | OQ791284 |
Common Name | Species | Familia | Total de Secuencias | Haplotype Diversity (Hd) | Nucleotide Diversity (π) | Tajima’s D |
---|---|---|---|---|---|---|
Spotted rose snapper | Lutjanus guttatus | Lutjanidae | 36 | 0.775 | 0.020 | −0.155 |
Yellow snapper | Lutjanus argentiventris | Lutjanidae | 12 | 0.63 | 0.031 | −2.25 ** |
Red snapper | Lutjanus peru | Lutjanidae | 17 | 0.86 | 0.010 | −2.17 ** |
Pacific Sierra | Scomberomorus sierra | Scombridae | 16 | 0.90 | 0.0045 | −1.09 |
Green jack | Caranx caballus | Caranjidae | 13 | 0.91 | 0.0039 | −1.26 |
Pacific crevalle jack | Caranx caninus | Caranjidae | 10 | 0.93 | 0.0038 | −0.86 |
Lutjanus guttatus | Panama | Montijo | Chiriqui | Overall by Sp. Hudson 2000 Snn p < 0.0001 |
---|---|---|---|---|
Gulf of Panama | 0.00 | |||
Gulf of Montijo | 0.087 | 0.00 | ||
Gulf of Chiriqui | 0.41 | 0.45 | 0.00 | L. guttatus ** |
Coiba-Pixvae | 0.052 | 0.00 | 0.44 | |
Caranx caballus | ||||
Gulf of Panama | 0.00 | |||
Gulf of Montijo | 0.424 | 0.00 | C. caballus (p > 0.05 ns) | |
Gulf of Chiriqui | 0.500 | 0.00 | 0.00 | |
Scomberomorus sierra | ||||
Gulf of Panama | 0.00 | |||
Gulf of Montijo | 0.0694 | 0.00 | S. sierra (p > 0.05 ns) | |
Gulf of Chiriqui | 0.0614 | −0.058 | 0.00 |
Species | Primers Sequences | Probe Name and Sequence | Amplicon Size |
---|---|---|---|
L. guttatus | L-GATCGGAGGATTCGGGAACT R-GGGTAGACTGTTCACCCAGT | 5′FAM-TCCAGCACCGGCTTCTACTCCA-3′TAMRA | 168 bp |
L. argentiventris | L-TACTACTCGCCTCCTCTGGA R-TGGTTAGGTCAACAGACGCT | 5′FAM-TCCTGTTCCGGCACCGGCTT-3′TAMRA | 108 bp |
C. caballus | L-TGGGACTGGCTGAACTGTTT R-CCCTGCTAGGTGAAGGGAAA | 5′FAM-TGCCCACGCGGGAGCATCAGT-TAMRA | 97 bp |
C. caninus | L-GCTTCTGACTTCTCCCTCCT R-GGCATGGGCAAGATTACCAG | 5′FAM-AGCCTGTTCCAGCTCCGGCT-TAMRA | 116 bp |
S. sierra | L-AGCCCTTCTTGGAGATGACC R-TCAGTTTCCAAACCCTCCGA | 5′FAM-ACAATGTAATCGTTACGGCCCATGCC-TAMRA | 109 bp |
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Díaz-Ferguson, E.; Chial, M.; Gonzalez, M.; Muñoz, E.; Chen, O.; Durán, O.; Vega, A.J.; Delgado, C.R. Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets. Animals 2023, 13, 2272. https://doi.org/10.3390/ani13142272
Díaz-Ferguson E, Chial M, Gonzalez M, Muñoz E, Chen O, Durán O, Vega AJ, Delgado CR. Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets. Animals. 2023; 13(14):2272. https://doi.org/10.3390/ani13142272
Chicago/Turabian StyleDíaz-Ferguson, Edgardo, Magaly Chial, Maribel Gonzalez, Edgardo Muñoz, Olga Chen, Ovidio Durán, Angel Javier Vega, and Carlos Ramos Delgado. 2023. "Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets" Animals 13, no. 14: 2272. https://doi.org/10.3390/ani13142272