Basin-scale planning is needed to minimize impacts in mega-diverse rivers

A phylogenetic analysis of nearly all genera of the Hypostominae and the Ancistrinae is provided based on osteology, external anatomy, and digestive tract anatomy. The results suggest that the Hypostominae is a paraphyletic assemblage. Delturus and Upsilodus form a monophyletic group sister to all other loricariids. Hemipsilichthys, Isbrueckerichthys, Kronichthys, and Pareiorhina form a monophyletic group with Neoplecostomus and the Hypoptopomatinae and are transferred to the Neoplecostominae. The remainder of the Hypostominae is made paraphyletic by the continuing recognition of the Ancistrinae. Ancistrinae is returned to the Hypostominae and recognized as a tribe, Ancistrini. In addition, four new tribes (Corymbophanini, Hypostomini, Pterygoplichthini, and Rhinelepini) are described. Hypostomus is also paraphyletic, the bulk of it forming a monophyletic clade with Aphanotorulus, Cochliodon, and Isorineloricaria. All of the potential monophyletic groups within Hypostomus grade into one another; therefore, Aphanotorulus, Cochliodon, and Isorineloricaria are placed in the synonymy of Hypostomus. Pterygoplichthys and Glyptoperichthys are also polyphyletic, and Liposarcus and Glyptoperichthys are recognized as synonyms of Pterygoplichthys. Sister to Pterygoplichthys is the Hemiancistrus annectens group (including Hypostomus panamensis) which represents an undescribed genus. The phylogeny presented is compared with previous hypotheses.

Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.

Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.

No abstract