The phylogenetic placement of sinipercid fishes (“Perciformes”) revealed by 11 nuclear loci

Sinipercids are freshwater fishes from East Asia assigned to the genera Siniperca (8–9 species) and Coreoperca (3 species). Although supported as a monophyletic group, the phylogenetic placement of sinipercids among percomorph fishes and the identification of their closest relatives have perplexed generations of taxonomists. Here, we collect and analyze new molecular evidence from 11 nuclear genes – six of them novel markers developed for this study – sampled from seven sinipercid species and several closely-related species that have been proposed as their putative sister taxa in the past. The concatenated alignment of the 11 loci included 10,560 bp that were split into 18 blocks for a partitioned analysis using Bayesian and Maximum Likelihood methods. Both approaches resulted in nearly identical topologies, in which the monophyly of the sinipercids was strongly supported (Bootstrap Support = 99; Posterior Probability = 1.0) with Centrarchidae as their sister taxon (BS = 87; PP = 1.0). Percichthyidae formed a sister group to the sinipercid–centrarchid clade (BS = 100; PP = 1.0). Tests for alternative hypotheses of relationships significantly rejected the placement of sinipercids within the Serranidae, Moronidae, or Centropomidae, or as sister taxon to Lateolabrax japonicus, Perca flavescens, or Pristigenys alta (SH test, p < 0.001,). The contribution of individual gene genealogies to support this result was explored further using a multispecies coalescent approach (BEST) to infer the species phylogeny. The sister-group relationship with Centrarchidae also is supported by this approach but relationships among species within the genus Siniperca showed a different pattern than the results obtained with the concatenated data set. Our study supports the designation of a distinct family, Sinipercidae, for this group of fishes (Siniperca and Coreoperca).