Data from: Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies

Gobioidei is one of the largest suborders of teleost fishes, with nearly
2000 extant species currently recognized. They have a worldwide
distribution and show a spectacular variety in morphology, ecology, and
behavior. Despite their importance, phylogenetic relationships among many
groups of gobioids (including some of the major lineages) still remain
poorly understood. In this study, we analyze sequence data of five
molecular markers (two mitochondrial and three nuclear) averaging 6000 bp
for 222 species of gobioids. Our study is the first to include both
multiple nuclear and mitochondrial genes to reconstruct a comprehensive
multilocus phylogeny of gobioids encompassing most major lineages
representing the overall diversity of one of the most speciose vertebrate
lineages. Two separate datasets are produced and used to specifically
address the phylogenetic placement of Rhyacichthyidae and Odontobutidae,
and the phylogenetic relationships among the lineages of Gobioidei. Our
results strongly support that the initial split in the gobioid tree
separated a clade containing Rhyacichthyidae + Odontobutidae as the sister
group of all other lineages. The family Eleotrididae branches off the
gobioid tree after the Rhyacichthyidae + Odontobutidae clade, followed by
the Butidae as sister to the Gobiidae. Additionally, several major
monophyletic groups are confidently identified within the two major
Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like
gobiids. Robustness of the phylogenetic trees inferred here is
significantly higher than that of previous studies, hence our results
provide the most compelling molecular phylogenetic hypothesis of Gobioidei
thus far. For the first time, we provide a comprehensive sampling of
European gobies that traditionally have been divided into “transverse” and
“sand gobies”. We show that the European gobies cluster in three distinct
lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former
resolved within the gobionelline-like gobiids and the latter two within
the gobiine-like gobiids. These findings have significant implications for
our understanding of the phylogeographic origin of European gobies in the
light of the closure of the Paratethys. A rogue taxon analysis identified
Kraemeria as an unstable taxon decreasing support at the base of the
gobiine-like gobiids. Removal of this rogue taxon significantly increased
phylogenetic resolution in that part of the tree and revealed additional
insights into early bursts of cladogenesis of the gobiine-like gobiids.