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

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 thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, 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

Biological and trophic consequences of genetic introgression between endemic and invasive Barbus fishes.

Genetic introgression with native species is recognized as a detrimental impact resulting from biological invasions involving taxonomically similar invaders. Whilst the underlying genetic mechanisms are increasingly understood, the ecological consequences of introgression are relatively less studied, despite their utility for increasing knowledge on how invasion impacts can manifest. Here, the ecological consequences of genetic introgression from an invasive congener were tested using the endemic barbel populations of central Italy, where the invader was the European barbel Barbus barbus. Four populations of native Barbus species (B. plebejus and B. tyberinus) were studied: two purebred and two completely introgressed with alien B. barbus. Across the four populations, differences in their biological traits (growth, body condition and population demographic structure) and trophic ecology (gut content analysis and stable isotope analysis) were tested. While all populations had similar body condition and were dominated by fish up to 2 years of age, the introgressed fish had substantially greater lengths at the same age, with maximum lengths 410-460 mm in hybrids versus 340-360 mm in native purebred barbel. The population characterized by the highest number of introgressed B. barbus alleles (81 %) had the largest trophic niche and a substantially lower trophic position than the other populations through its exploitation of a wider range of resources (e.g. small fishes and plants). These results attest that the genetic introgression of an invasive congener with native species can result in substantial ecological consequences, including the potential for cascading effects. Supplementary Information: The online version contains supplementary material available at 10.1007/s10530-021-02577-6

Prevalence and survival of escaped European seabass Dicentrarchus labrax in Cyprus identified using genetic markers

The escape of European seabass Dicentrarchus labrax (L.) from fish farms is considered to be a widespread problem in the Mediterranean area, where this species is produced in large quantities in offshore cages. Whilst estimates of the number of escaped seabass in the wild have been made previously, the actual distribution, long-term survival and the potential effects on native populations remain largely unknown. This study characterises the genetic profiles of all contemporary and some historic aquaculture sources of European seabass in Cyprus and uses these profiles to identify escaped fish in seabass collected from the wild around the island. Significant differences in the microsatellite and mitochondrial DNA marker profiles were found between farmed and wild fish. The number of escapees identified was 15% of the total number of wild-caught fish sampled. However, escapees were not equally distributed; at one location ~70% of wild-caught fish were escapees while in other areas escapees only accounted for up to 4%. Escapees were present in all size classes of fish, but the majority were of commercial size (300-500 g) typical of seabass farmed in seacages. This indicates that they may have escaped recently and during normal aquaculture operations as no escape event was reported in the course of the study. Two large, egg-bearing females and some juvenile fish were also classified as escapees, which suggests that long-term survival and interbreeding with wild fish is possible in Cypriot waters

Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA -: Evolutionary significance of this region (vol 22, pg 91, 2002)

[Abstract Not Available

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

ABSTRACTSparidae (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.</jats:p

A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L

European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback.status: publishe

Evidence for 'escape through spawning' in large gilthead sea bream Sparus aurata reared in commercial sea-cages

During the last decade, farming of species that may reproduce within marine fish farms has become more common. However, knowledge of the extent and ecological effects of reproduction of farmed fish within commercial farms is sparse. We examined whether large gilthead sea bream Sparus aurata reared in farms in Greece produced fertilized eggs that survived and dispersed into surrounding waters. Extensive histological investigation of gonads sampled from 5 different farms revealed that female sea bream cultivated beyond the size of sex reversal matured, ovulated and released eggs during the normal spawning period of the species. Annual fecundities (108 000 ± 60 081 eggs kg-1 of female in farms) were low relative to commercial broodstock and decreased considerably with sex ratio (i.e. with fish size in the cage). An egg-collector experiment and site-intensive ichthyoplankton study with genetic identification of sparid eggs demonstrated that sea bream eggs were spawned in farms and released to the environment. If 5-10% of the 130 000 tons yr-1 production is fish of larger size, we estimate that 3.5 × 1011 to 7.0 × 1011 eggs yr-1 are released into the Mediterranean Sea. Whilst we documented low daily survival rates of fertilized eggs in the vicinity of sea-cages, our findings imply that the escape of eggs from sea bream farms may have ecological consequences, which likely depend on the sex ratio and intensity of farming within specific regions. To avoid potentially negative ecological and genetic con sequences of escape through spawning, farms with large fish should not be placed close to the nursery grounds of wild sea bream, such as in coastal lagoons. © Inter-Research 2013