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DNA metabarcoding reveals prey diversity overlap among tunas and seabirds of Eastern Tropical Atlantic: implications for an ecosystem-based management

ABSTRACT: Overfishing has been drastically changing food webs in marine ecosystems, and it is pivotal to quantify these changes at the ecosystem level. This is especially important for ecosystems with a high diversity of top predators such as the Eastern Atlantic marine region. In this work we used high-throughput sequencing methods to describe the diet of the two most abundant tuna species, the Skipjack tuna (Katsuwonus pelamis) and the Yellowfin tuna (Thunnus albacares), highly targeted by fisheries off west Africa. We also explored prey diversity overlap between these tuna species and the seabird species breeding in Cabo Verde that are most likely to share prey preferences and suffer from bycatch, the Brown booby (Sula leucogaster) and Cape Verde shearwater (Calonectris edwardsii). Overall, the diet of both tuna species was more diverse than that of seabirds. Skipjack tuna diet was dominated by prey from lower trophic levels, such as krill, anchovies, and siphonophores, while the Yellowfin tuna diet was mainly based on epipelagic fish such as flying and halfbeak fishes. Some of the most abundant prey families detected in the Yellowfin tuna diet were shared with both seabird species, resulting in a high diet overlap between this tuna and seabirds These results have implications for the management of tuna fisheries in the Eastern Tropical Atlantic, because a large decrease of both tuna species might have cascading effects on both primary and secondary consumer levels, and the decrease of these underwater predators may have implications on the viability of tropical seabird populations.

ORGANISM(S): Thunnus albacares Sula leucogaster Katsuwonus pelamis Calonectris edwardsii

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PROVIDER: S-BSST918 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

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DNA metabarcoding reveals prey diversity overlap among tunas and seabirds of Eastern Tropical Atlantic: implications for an ecosystem-based management

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