New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

Distribución espacio-temporal de la edad 1 de anchoa del golfo de Bizkaia (Engraulis encrasicolus) en el momento de puesta

To efficiently manage and maintain fish stock abundance and age structure, it is necessary to understand variability in its spatial distribution. The main objective of this study was to describe the demographic structure of the Bay of Biscay anchovy during the main spawning period based on adult samples from 15 daily egg production method surveys. The proportion of age-1 individuals was modelled using generalized additive models with a binomial distribution and a logit link in relation to geographical and environmental covariates. The possibility of obtaining different models depending on the average age-1 proportion (low or high) was also explored. In general, age-1 individuals were found in shallow waters close to the coast, especially associated with the Gironde and Adour river plumes, whereas older individuals were prevalent on the shelf break and in oceanic waters. However, in years with a high age-1 proportion the younger individuals were also dominant in oceanic waters. These results could be used for management purposes, such as defining protected areas for particular age groups.Con el fin de gestionar eficientemente la abundancia y la estructura espacial de un stock es necesario entender su distribución espacial. El objetivo principal de este trabajo es describir la estructura demográfica de la anchoa del golfo de Bizkaia durante el periodo de desove a partir de las muestras de adultos recogidas en 15 campañas del método de producción diaria de huevos. La proporción de individuos de edad 1 se modeló en función de variables geográficas y ambientales por medio de un modelo aditivo generalizado con distribución binomial y función enlace logit. Además se estudió la posibilidad de obtener diferentes modelos dependiendo de si la proporción de edad 1 promedio es baja o alta. En general, los individuos de edad 1 se encontraron en aguas poco profundas cerca de la costa, especialmente en las plumas de los ríos Garona y Adur, mientras que los individuos de mayor edad prevalecieron en el cantil y en aguas oceánicas. Sin embargo, los años con una alta proporción de edad 1, los individuos jóvenes fueron también predominantes en aguas oceánicas. Estos resultados podrían utilizarse para fines relacionados con la gestión, tales como la definición de áreas protegidas para determinados grupos de edad

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure.

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.This work was supported by ATM2010Hegaluze (351BI20090047), ATM2009Hegalabur (351BI20090034) and ATM2008Bonorte (ACM2008BONORTE) projects funded by the Basque Government, and the ACEITUNA (CTM2011-27505) project funded by the Spanish Ministerio de Economía y Competitividad

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts

Estudio genético de la estructura poblacional del atún blanco (Thunnus alalunga) y filogenia del género Thunnus

El contenido del capítulo V está sujeto a confidencialidad. 164 p. (eusk) . 172 p. (cast)Para comprender mejor la estructura genética del atún blanco (Thunnus alalunga), en este trabajo se han llevado a cabo estrategias de búsqueda y aplicación de nucleótidos de polimorfismo únicos (SNPs). Definiendo cuatro poblaciones genéticas: Mediterráneo, Atlántico, Índico y Pacífico. Además, mediante secuencias mitocondriales se ha estudiado la filogenia del género Thunnus. Para finalizar, se ha diseñado una herramienta en base a SNPs nucleares y mitocondriales para asignar el origen geográfico del atún blanco

Estudio genético de la estructura poblacional del atún blanco (Thunnus alalunga) y filogenia del género Thunnus

El contenido del capítulo V está sujeto a confidencialidad. 164 p. (eusk) . 172 p. (cast)Para comprender mejor la estructura genética del atún blanco (Thunnus alalunga), en este trabajo se han llevado a cabo estrategias de búsqueda y aplicación de nucleótidos de polimorfismo únicos (SNPs). Definiendo cuatro poblaciones genéticas: Mediterráneo, Atlántico, Índico y Pacífico. Además, mediante secuencias mitocondriales se ha estudiado la filogenia del género Thunnus. Para finalizar, se ha diseñado una herramienta en base a SNPs nucleares y mitocondriales para asignar el origen geográfico del atún blanco

New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

New SNP markers in european anchovy and albacore: useful genetic tools for stock delimitation

Peer Reviewe

Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management

There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore (“Bonito del Norte con Eusko Label”) and Bay of Biscay anchovy (“Anchoa del Cantábrico”) are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling