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

Abstract

19Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 20 species with high popularity and commercial value, such as porgies and seabreams. Although 21 the phylogeny of this family has been investigated multiple times, its position among other 22 teleost groups remains ambiguous. Most studies have used a single or few genes to decipher 23 the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to 24 resolve the position of the family using five recently available Sparidae gene-sets and 26 25 available fish proteomes from species with a sequenced genome, to ensure higher quality of 26 the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes 27 (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding 28 that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the 29 european seabass as closest taxa of sparids. By analytically comparing the methodologies 30 applied in both cases, we show that this discordance is not due to different orthology 31 assignment algorithms; on the contrary, we prove that it is caused by the increased taxon 32 sampling of the present study, outlining the great importance of this aspect in phylogenomic 33 analyses in general. 34 35 Keywords: Sparidae; fish phylogenomics; orthology assignment; jackknife phylogeny test; 36 taxon sampling; 37Teleostei represent the dominant group within ray-finned fish (Actinopterygii), with 39 more than 26,000 extant species. Their evolution has been extensively studied through past 40 decades, using a variety of data including fossil records, morphological characters and 41 molecular data, leading to a gradual resolution of teleost phylogeny (Betancur-R. et al., 2013(Betancur-R. et al., 42 & 2017. 43 With the continuous emergence of new whole-genome sequences, phylogenomic 44 techniques are applied to characterise the evolutionary relationships among species. Whole-45 genome information can help in resolving uncertain nodes, as well as provide stronger evidence 46 on already established relationships. Regarding fish phylogeny, several genome-wide 47 approaches have been implemented so far. One of the first efforts to study ray-finned fish 48 phylogenomics was conducted by (Li et al., 2007). Since then, several studies have been 49 published using not only gene markers, but also noncoding elements such as the work of 50 (Faircloth et al., 2013) who used UCE (ultra-conserved elements) to investigate the 51 diversification of basal clades in ray-finned fish. Most genome papers include a phylogenomic 52 analysis albeit with limited taxon sampling (e.g. Vij et al., 2016 and Xu et al., 2017), while the 53 use of whole-transcriptome data is being employed to uncover phylogenetic relationships of 54 specific taxonomic groups as well (Dai et al., 2018; Rodgers et al., 2018). With the emergence 55 of new genomes and the possibilities of modern sequencing technologies, bigger datasets are ...

Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

“…Particularly, the high degree of synteny observed between the medaka and meagre, agreed with the same comparison between the yellow croaker (which is also a Sciaenid), and medaka 31 . The evolutionary proximity between Sciaenids and European seabass, which was shown 44 using the yellow croaker genome, was also reflected in this study, showing the same pattern with European seabass being phylogenetically closer to meagre than gilthead seabream. Moreover, the same 1:2 chromosomal homologies between stickleback-meagre, and stickleback-European seabass were shown.…”

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Figure 3 Meagre’s LG17 intricate homologies. ( A )–( D ) refers to the putative order of divergence from the last common ancestor 44 , 45 , showing a series of rearrangements 46 , ENSEMBL comparative genomics database, and the findings of this study.

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Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L.

“…The CN of Scyphostegia and Dianyuea are 2 n = 18 and 38 (perhaps 36 + 2B), respectively. They are possibly based on the same basic chromosome number, and a polyploid event probably happened in Dianyuea , which is fairly common in Malpighiales [ 56 ]. Therefore, our results provide additional evidence for the sister relationship between Dianyuea and Scyphostegia , which indicate by molecular phylogenetic study [ 46 ].…”

“…In the second proposed phylogeny, they sampled 22 genera (3 subfamilies). More and more studies show that even if the same gene marker set is used, the difference of taxon sampling density will lead to the contradiction of phylogenetic trees [ 56 ]. And the increasing importance of taxon sampling for phylogenetic inference has been proposed and high-lightened [ 56 – 58 ].…”

“…More and more studies show that even if the same gene marker set is used, the difference of taxon sampling density will lead to the contradiction of phylogenetic trees [ 56 ]. And the increasing importance of taxon sampling for phylogenetic inference has been proposed and high-lightened [ 56 – 58 ]. Our results in the chromosome number and genome size also provide some hints.…”