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

  title={Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling},
  author={Paschalis Natsidis and A Tsakogiannis and Pavlos Pavlidis and Costas S. Tsigenopoulos and Tereza Manousaki},
  journal={Communications Biology},
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… 


Phylogenomic analysis of Fundulidae (Teleostei: Cyprinodotiformes) using RNA-sequencing data.
Novel RNA-sequencing data is utilized for phylogenetic inference among16 members of Fundulidae to better refine the basal nodes of the family and confront long-standing questions regarding the monophyletic status of genus Fundulus and validity of the Lucania and recently synonymized Adinia genera.
Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses.
The results suggested high evolutionary plasticity of the characters in sparids, indicating that it causes species-diversity and taxonomic confusion at various taxonomic levels, and that such convergent evolution may occur more frequently also in other coastal fishes.
First multi-locus timetree of seabreams and porgies (Percomorpha: Sparidae)
This study corroborates the non-monophyly of the traditional sparids without the inclusion of the family Centracanthidae, as well as that of many sparid genera, and finds robust support for a scenario of multiple radiations.
A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data.
The porgies (Sparidae) comprise a diverse group of neritic fishes with a broad geographic distribution. We used mitochondrial DNA sequences from partial 16S ribosomal RNA and cytochrome b genes to
Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages
It is estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major o tocephalan lineages were hypothesized.
Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae).
The authors' analyses suggest a close affinity between the orders Spariformes and Lobotiformes (including the tripletails or Lobotidae, the barbeled grunters, and tigerperches or Datnioididae), albeit support for this group is low.
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
A practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny is presented and is an improvement over traditional approaches because it uses genomic information and automates the process to identify large numbers of candidate makers.
Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences.
Mitogenomic data strongly supported the monophyly of tetraodontiform fishes, placing them as a sister-group of either Lophiiformes plus Caproidei or Caproidi only, and the sister- group relationship between Acanthuroidei and Tetraodentiformes was statistically rejected using Bayes factors.
The molecular phylogeny of the Sparidae (Pisces, Perciformes) based on two satellite DNA families
It is concluded that the Sparidae family is composed by two major lineages: one comprising the species of the genera Sparus, Diplodus, Lithognathus, Boops, Sarpa and Spondyliosoma, and one species of Pagellus (P. erythrinus).
Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts.
The resultant phylogenies indicated explicitly that previously recognized members of Gasterosteiformes had diverged basally within the Percomorpha into three different clades with the following subgroups: Syngnathoidei, Gasterosomidae, and Indostomidae.