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      Trophic niche overlap between round sardinella ( Sardinella aurita) and sympatric pelagic fish species in the Western Mediterranean

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          Abstract

          The northward expansion of round sardinella ( Sardinella aurita) in the Mediterranean Sea, together with declines and fluctuations in biomass and landings of European sardine ( Sardina pilchardus) and anchovy ( Engraulis encrasicolus) observed in recent decades, may suggest potential inter‐specific competition in the pelagic domain. The coexistence of sympatric zooplanktivorous fish species might therefore be exposed in part to trophic niche overlap and competition for food. Combining visual diet characterization under the microscope with DNA metabarcoding from stomach contents of fish collected in spring results show that predation on relatively large krill is equally important for sardinella than for the other two niche overlapping species. Furthermore, an important overlap is found in their isotopic niche, especially with anchovy, using nitrogen (δ 15N) and carbon (δ 13C) stable isotopes in muscle tissue. In fact, the three fish species are able to feed effectively in the whole prey size spectrum available during the sampled season, from the smallest diatoms and copepods to the larger prey (i.e., decapods and euphausiids), including fish larvae. Moreover, effective predation upon other large prey like siphonophores, which is observed only when multi‐proxy analyses in stomach contents are applied, might also be relevant in the diet of sardinella. The overlapping diet composition in spring, together with the effective use of food resource by sardinella, can be of special interest in potential future scenarios with warmer water temperature leading to lower zooplankton and/or higher jellyfish availability, where sardinella may take advantage over other species due to its feeding plasticity.

          Abstract

          The present study studies the trophic ecology of sardinella, anchovy, and sardine in the NW Mediterranean Sea, combining microscope visual analysis with DNA metabarcoding in gut contents as well as stable isotope analysis in muscle. Results with high taxonomic resolution determined an important degree of trophic niche overlap between the three species, which adapt their feeding to a wide range of available plankton, from the phytoplankton as well as the smallest copepods to larger krill or jelly organisms. Therefore, in the Mediterranean pelagic fish community, the diet plasticity of the recently incorporated (and expanding) sardinella might increase the inter‐specific competition if the food availability changes in the future.

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          Cutadapt removes adapter sequences from high-throughput sequencing reads

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            QIIME allows analysis of high-throughput community sequencing data.

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              FLASH: fast length adjustment of short reads to improve genome assemblies.

              Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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                Author and article information

                Contributors
                ebachiller@mail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                10 November 2021
                November 2021
                : 11
                : 22 ( doiID: 10.1002/ece3.v11.22 )
                : 16126-16142
                Affiliations
                [ 1 ] Marine Renewable Resources Department Institute of Marine Science (ICM‐CSIC) Barcelona Spain
                [ 2 ] MaREI Centre Environmental Research Institute University College Cork Cork Ireland
                [ 3 ] School of Biological, Earth, and Environmental Sciences University College Cork Cork Ireland
                [ 4 ] Centro de Ciências do Mar Universidade do Algarve (CCMAR‐UAlg) Faro Portugal
                [ 5 ] Centro Oceanográfico de Vigo Instituto Español de Oceanografía Vigo Spain
                [ 6 ] AllGenetics & Biology SL. Oleiros A Coruña Spain
                [ 7 ] Centro Oceanográfico de Murcia Instituto Español de Oceanografía San Pedro del Pinatar Spain
                Author notes
                [*] [* ] Correspondence

                Eneko Bachiller, AZTI, Sustainable Fisheries Management (Data), Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia (Basque Country), Spain.

                Email: ebachiller@ 123456mail.com

                Author information
                https://orcid.org/0000-0002-6189-6176
                https://orcid.org/0000-0001-9207-4792
                https://orcid.org/0000-0002-0477-5984
                https://orcid.org/0000-0002-7577-2617
                https://orcid.org/0000-0002-6887-4391
                https://orcid.org/0000-0001-6235-5868
                Article
                ECE38293
                10.1002/ece3.8293
                8601905
                34824816
                74051cd7-947a-461c-b497-fa0b9e0b03c9
                © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 October 2021
                : 17 May 2021
                : 15 October 2021
                Page count
                Figures: 8, Tables: 3, Pages: 17, Words: 11785
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                November 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.0.9 mode:remove_FC converted:18.11.2021

                Evolutionary Biology
                diet dissimilarity,multi‐proxy diet analysis,prey preference,small pelagic fish,trophic interactions,trophic niche width

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