scholarly journals Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Kevin León García-Castro ◽  
José David Rangel-Medrano ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
South American ◽  
Important Species ◽  
Large Size ◽  
Genetic Diversity And Structure ◽  
Commercially Important ◽  
Species Specific ◽  
Generation Sequencing

ABSTRACT The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.

scholarly journals Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5959 ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Marquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Molecular Tools ◽  
Migratory Species ◽  
Lower Section ◽  
Neotropical Fish ◽  
International Union ◽  
Commercially Important ◽  
Species Specific ◽  
Near Threatened

The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.

scholarly journals Population genetics of the fish Brycon henni (Characiformes: Bryconidae) using species-specific polymorphic microsatellite loci

2020 ◽  
Vol 68 (3) ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Márquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
International Union ◽  
Genetic Population ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Species Specific ◽  
Low Coverage ◽  
Risk Categorization

Introduction: The freshwater fish Brycon henni (Characiformes: Bryconidae) is endemic to Colombia and currently considered as “least concern” according to the International Union for Conservation of Nature (IUCN). Objective: To develop microsatellite markers to examine population genetics in Brycon henni. Methods: Using a low-coverage sequenced genomic library, this study developed the first set of microsatellite loci to study the population genetics of this Neotropical species. These loci were used to evaluate the genetic diversity and structure of B. henni from three sites of the Magdalena-Cauca Basin (Colombia). Results: A set of twenty-one polymorphic microsatellite loci was highly informative and revealed that B. henni is evenly genetically structured between two tributaries of the Cauca River separated by only 30 km, a finding that indicates it conforms to reproductively isolated groups. Conclusions: We reported a set of twenty-one polymorphic microsatellite loci that was highly informative and allowed the detection of genetic structure at local and regional scales. This genetic population structure, concordant with that found in eight congeners, is relevant to estimate the B. henni risk categorization as well as for management, conservation, and restocking programs.

scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

Rapid Seafood Species Identification Using Chip-Based Capillary Electrophoresis and Protein Pattern Matching

2017 ◽  
Vol 100 (5) ◽  
pp. 1500-1510 ◽  
Author(s):  
Calvin C Walker ◽  
Cheryl L Lassitter ◽  
Shannara N Lynn ◽  
Courtney B Ford ◽  
Kevin R Rademacher ◽  
...  
Keyword(s):  
Protein Extraction ◽  
Protein Pattern ◽  
Screening Method ◽  
Fish Muscle ◽  
Protein Profiling ◽  
Rapid Screening ◽  
Important Species ◽  
Commercially Important ◽  
Species Specific ◽  
High Level

Abstract Authenticity is crucial to the seafood industry, as substitution and mislabeling have important economic, environmental, and food safety consequences. Toaddress this problem, protein profiling and softwarealgorithm techniques were developed to classify fishmuscle samples by species. The method uses water-based protein extraction, chip-based microfluidic electrophoresis (Agilent 2100 Bioanalyzer) for the analysis of high abundance fish muscle proteins, and a novel data analysis method for species-specific proteinpattern recognition. The method's performance in distinguishing commercially important fish from commonly reported substitutions was evaluated using sensitivity, specificity, and accuracy determinations with all three performance measures at >98% for commonsubstitutions. This study demonstrates that uncookedseafood products of commercially important species of catfish, snapper, and grouper can be rapidly distinguished from commonly substituted species with a high level of confidence. A tiered testing approach toseafood species verification by sequentially applying a rapid screening method and DNA testing is proposed to more effectively ensure accurate product labeling.

scholarly journals Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10327
Author(s):  
Ricardo M. Landínez-García ◽  
Juan Carlos Narváez ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Freshwater Fish ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Stocks ◽  
Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

scholarly journals Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus)

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1253 ◽  
Author(s):  
Alicia C. Bertolotti ◽  
Sarah M. Griffiths ◽  
Nathan K. Truelove ◽  
Stephen J. Box ◽  
Richard F. Preziosi ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Marine Reserve ◽  
Iucn Red List ◽  
Closely Related Species ◽  
Important Species ◽  
Isolation And Characterization ◽  
Commercially Important ◽  
Paired End Sequencing ◽  
Galapagos Marine Reserve

The white-spotted sandbass (Paralabrax albomaculatus)is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11–49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata : Holothuriidae)

2012 ◽  
Vol 60 (6) ◽  
pp. 368 ◽  
Author(s):  
Alison J. Fitch ◽  
Grant Leeworthy ◽  
Xiaoxu Li ◽  
Will Bowman ◽  
Luke Turner ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Sea Cucumber ◽  
Asia Pacific ◽  
Asia Pacific Region ◽  
Single Population ◽  
Important Species ◽  
Holothuria Scabra ◽  
Commercially Important ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

We isolated 18 new, polymorphic, microsatellite markers from Holothuria scabra, a commercially important species of sea cucumber found throughout the Asia-Pacific region. Next-generation sequencing was used to identify 206 unique loci for which primers were designed. Of these unique loci, we trialled 65 primer pairs in the target species, and 48 (74%) amplified a product of the expected size. Eighteen loci were found to be polymorphic and reliable, and were screened for variation in 50 individuals, from a single population from Croker Island, Northern Territory, Australia. Observed heterozygosity ranged from 0.00 to 0.96 (mean = 0.46) and the number of alleles per locus from 2 to 28 (mean = 9.61). These loci will be useful for the investigation of population structure and mating systems in H. scabra and may also be of use in other holothurian species.

Spatiotemporal variation among demersal ichthyofauna in a subtropical estuary bordering World Heritage-listed and marine protected areas: implications for resource management

2017 ◽  
Vol 68 (4) ◽  
pp. 703 ◽  
Author(s):  
Fernanda E. Possatto ◽  
Matt K. Broadhurst ◽  
Charles A. Gray ◽  
Henry L. Spach ◽  
Marcelo R. Lamour
Keyword(s):  
Marine Protected Areas ◽  
Fishing Effort ◽  
Spatiotemporal Variation ◽  
South American ◽  
Important Species ◽  
Prey Preferences ◽  
Subtropical Estuary ◽  
Species Specific ◽  
Total Species ◽  
Trawl Surveys

Benthic trawl surveys were performed to quantify the spatiotemporal distributions of teleosts and key abiotic associations throughout an ecologically important estuary within Brazil’s Atlantic Forest biosphere. Approximately 52000 fish (51% juveniles) representing 75 species were sampled, with residents accounting for 36 and 61% of total species and individuals respectively. Five artisanally important species comprised 77 and 81% of individuals and biomass respectively. Cathorops spixii was most abundant (>40% of total), whereas Stellifer rastrifer, Aspistor luniscutis, Sphoeroides greeleyi and S. testudineus collectively contributed towards 37 and 34% of individuals and biomass respectively. The abundance of A. luniscutis, C. spixii and S. rastrifer was negatively associated with salinity, whereas the presence of the latter two species was also positively associated with temperature, and S. greeleyi and S. testudineus (mostly adults) were more abundant in deeper areas. These relationships seemed to be affected by species-specific reproductive (S. rastrifer, C. spixii and A. luniscutis), habitat (S. greeleyi and S. testudineus) and prey preferences (juvenile C. spixii and A. luniscutis). Protection for these various species may be achieved via immediate fishing effort regulations, but more research is required to manage other anthropogenic effects. Such work should be a priority to ultimately preserve what is one of the most important South American biodiversity areas.

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