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

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.

Population genetics of the fish Brycon henni (Characiformes: Bryconidae) using species-specific polymorphic microsatellite loci / Genética de poblaciones del pez Brycon henni (Characiformes: Bryconidae) utilizando loci microsatélites polimórficos especie-específicos

Introduction: The freshwater fish Brycon henni (Characiformes: Bryconidae) is endemic to Colombia and currently considered as a "least concern" species according to the International Union for Conservation of Nature (IUCN). Objective: To develop microsatellite markers to examine population genetics in B. henni. Methods: Using a low-coverage sequencing 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 21 polymorphic microsatellite loci was highly informative and revealed that B. henni exhibits genetic diversity (5.143-5.619 alleles/locus, observed and expected heterozygosity = 0.461-0.645 and 0.604-0.662, respectively) and is evenly genetically structured between two tributaries of the Cauca River separated by only 30 km (F'ST = 0.093, Jost's DEST = 0.311, P < 0.001) a finding that indicates these may be reproductively isolated groups. Conclusions: We reported a set of 21 polymorphic microsatellite loci that allowed the detection of genetic structure at local and regional scales. This population genetic structure, concordant with that found in eight congeners, is relevant when determining the risk categorization of B. henni, as well as management, conservation, and restocking programs for this species.

Introducción: El pez de agua dulce Brycon henni (Characiformes: Bryconidae) es una especie endémica de Colombia que actualmente está catalogada como de "menor preocupación" por la Unión Internacional para la Conservación de la Naturaleza (UICN). Objetivo: Desarrollar marcadores microsatélites para estudiar la genética poblacional de Brycon henni. Métodos: Usando una biblioteca genómica de secuenciación de baja cobertura, este estudio desarrolló el primer grupo de loci microsatélites para el estudio de la genética poblacional de esta especie neotropical. Estos loci fueron usados para evaluar la diversidad genética y estructura de B. henni en tres sitios de la cuenca Magdalena-Cauca (Colombia). Resultados: Un grupo de 21 loci polimórficos tipo microsatélite fueron altamente informativos y revelaron que B. henni exhibe diversidad genética (5.143-5.619 alelos/locus, heterocigosidad observada y esperada = 0.461-0.645 y 0.604-0.662, respectivamente) y se encuentra genéticamente estructurado entre dos tributarios del río Cauca separados únicamente por 30 km (F'ST = 0.093, Jost's DEST = 0.311, P < 0.001), un resultado que indica que puede existir aislamiento reproductivo entre dichos grupos. Conclusiones: Reportamos un grupo de 21 loci polimórficos tipo microsatélite que permitieron la detección de la estructura genética a escala local y regional. Esta estructura genética poblacional, concordante con lo que se reporta para otros ocho congéneres, es relevante al determinar la categorización de riesgo de B. henni, así como los programas de manejo, conservación y repoblamiento para esta especie.

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

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.

Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae).

The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.

Complete mitogenome of the Neotropical fish Brycon henni, Eigenmann 1913 (Characiformes, Bryconidae).

Brycon henni (Characiformes, Bryconidae) is a trans-Andean omnivorous fish considered as promising species in aquaculture of temperate zones. In this work we report for first time the complete mitochondrial genome of B. henni. This mitogenome spans 16,885 bp and encodes 13 proteins, 22 tRNAs and 2 ribosomal RNAs. Additionally, the synteny is conserved with others species of the order Characiformes.

Mitochondrial genome of the Neotropical trans-Andean fish Ichthyoelephas longirostris, Steindachner 1879 (Characiformes, Prochilodontidae).

Ichthyoelephas longirostris is a trans-Andean migratory species belonging to Prochilodontidae family. In this work, the mitochondrial genome of I. longirostris was sequenced by Illumina technology. The 16,840 bp mitogenome encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and present a conserved synteny with others species of the Order Characiformes.

Mitochondrial genome of the Neotropical detritivore fish Curimata mivartii Steindachner 1878 (Characiformes, Curimatidae).

Curimata mivartii is a detritivorous species Neotropical, which is of great importance to local fisheries and riverine ecosystems. In this work, the mitochondrial genome of C. mivartii was completely sequenced using a combination of 454 FLX(+) platform and Sanger/capillary sequencing. The mitogenome is 16,705 bp in length, encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and exhibit perfect synteny with others Characiformes.