Digest: Resolving phylogenomic conflicts in characiform fishes†

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

Phylogenomics and evolutionary history of Oreobates (Anura: Craugastoridae) Neotropical frogs along elevational gradients

Mountain ranges offer opportunities for understanding how species evolved and diversified across different environmental conditions. Neotropical frogs of the genus Oreobates (Anura: Craugastoridae) are adapted to highland and lowland habitats along the Andes, but many aspects of their evolution remain unknown. We studied their evolutionary history using ~18,000 exons enriched by targeted sequence-capture. Since capture success was very variable across samples, we evaluated to what degree differing data filtering produced robust inferences. The inferred evolutionary framework evidenced phylogenetic discordances among lowland species that can be explained by taxonomic misidentification or admixture of ancestral lineages. Highland species showed smaller effective populations than lowland frogs, probably due to greater habitat fragmentation in montane environments. Stronger genetic drift likely decreased the power of purifying selection and led to an increased proportion of nonsynonymous mutations in highland populations that could play an important role in their adaptation. Overall, our work sheds light on the evolutionary history and diversification of this group of Neotropical frogs along elevational gradients in the Andes as well as on their patterns of intraspecific diversity.

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T--/TA-. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.