Untangling lineages: population genetics and phylogenomics of Auxis Rochei and Euthynnus Alletteratus

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ENG- The Little Tunny (Euthynnus alletteratus) and the Bullet Tuna (Auxis rochei) are two fish species within the tuna family that are closely related to larger tunas. Although they have a lower market value, thousands of tonnes of these species are captured each year, making the study of their populations essential for ensuring sustainable exploitation. Genetic tools play a vital role in this research by allowing us to examine genetic diversity, assess its distribution across their geographic ranges and trough time, and identify distinct populations. Additionally, molecular methods can validate the correct identification of captured species. This thesis investigates these aspects for both species, focusing on population differentiation, the levels of genetic diversity, and the accuracy of visual species identification through genetic assignment. Given their evolutionary relationship and similar ecological behaviours, this thesis also aimed to compare the dynamics between species. This study both classical genetic markers and high-throughput sequencing techniques have been analysed. For the Little Tunny, results revealed significant genetic differences between individuals in the North Atlantic and those in the tropical Atlantic, indicating that they may represent two distinct species. Within each species, we observed shallower genetic differences among localities, suggesting the presence of multiple populations. Regarding the Bullet Tuna, we identified two populations in the Mediterranean Sea: one around the Iberian Peninsula and another in North Africa. Notably, our study revealed that some captures of Mediterranean Bullet Tuna were actually Frigate Tuna, a closely related species previously believed to be absent from the region. The results of this thesis should guide the implementation of fishery management policies that ensure sustainable fisheries. These practices include accurate capture and stock identification. Recognizing the two Little Tunny species as separate fishery stocks is the most urgent policy that should be implemented by the relevant agency ​
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