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Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

By P Natsidis, A Tsakogiannis, P. Pavlidis, CS Tsigenopoulos, T Manousaki

Posted 24 Aug 2019
bioRxiv DOI: 10.1101/746115 (published DOI: 10.1038/s42003-019-0654-5)

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to resolve the position of the family using five recently available Sparidae gene-sets and 26 available fish proteomes from species with a sequenced genome, to ensure higher quality of the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the european seabass as closest taxa of sparids. By analytically comparing the methodologies applied in both cases, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

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