Data from: Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)

The Gonorynchiformes are the sister lineage of the species-rich Otophysi
and provide important insights into the diversification of ostariophysan
fishes. Phylogenies of gonorynchiforms inferred using morphological
characters and mtDNA gene sequences provide differing resolutions with
regard to the sister lineage of all other gonorynchiforms (Chanos vs.
Gonorynchus) and support for monophyly of the two miniaturized lineages
Cromeria and Grasseichthys. In this study the phylogeny and divergence
times of gonorynchiforms are investigated with DNA sequences sampled from
nine nuclear genes and a published morphological character matrix.
Bayesian phylogenetic analyses reveal substantial congruence among
individual gene trees with inferences from eight genes placing Gonorynchus
as the sister lineage to all other gonorynchiforms. Seven gene trees
resolve Cromeria and Grasseichthys as a clade, supporting previous
inferences using morphological characters. Phylogenies resulting from
either concatenating the nuclear genes, performing a multispecies
coalescent species tree analysis, or combining the morphological and
nuclear gene DNA sequences resolve Gonorynchus as the living sister
lineage of all other gonorynchiforms, strongly support the monophyly of
Cromeria and Grasseichthys, and resolve a clade containing Parakneria,
Cromeria, and Grasseichthys. The morphological dataset, which includes 13
gonorynchiform fossil taxa that range in age from Early Cretaceous to
Eocene, was analyzed in combination with DNA sequences from the nine
nuclear genes and a relaxed molecular clock to estimate times of
evolutionary divergence. This “tip dating” strategy accommodates
uncertainty in the phylogenetic resolution of fossil taxa that provide
calibration information in the relaxed molecular clock analysis. The
estimated age of the most recent common ancestor (MRCA) of living
gonorynchiforms is slightly older than estimates from previous node dating
efforts, but the molecular tip dating estimated ages of Kneriinae (Kneria,
Parakneria, Cromeria, and Grasseichthys) and the two paedomorphic
lineages, Cromeria and Grasseichthys, are considerably younger.