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.

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BackgroundCypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp).ResultsConcatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae.ConclusionsMost major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0819-5) contains supplementary material, which is available to authorized users.

The Hypostomus cochliodon group consists of eight species that were formerly recognized as Cochliodon Kner: H. cochliodon Kner, H. hondae (Regan), H. levis (Pearson), H. oculeus (Fowler), H. plecostomoides (Eigenmann), H. pospisili (Schultz; a synonym of H. hondae), H. pyrineusi (Miranda-Ribeiro), and H. taphorni (Lilyestrom) and four additional species described herein: H. ericius, H. hemicochliodon, H. pagei, and H. sculpodon. The species occur in four phenetic groups: the intermediate group of H. hemicochliodon and H. sculpodon that appear to be transitional species between other Hypostomus and the H. cochliodon group in terms of diet and tooth shape, a monotypic group containing H. cochliodon, a group characterized by an odontodeless opercle that contains H. ericius, H. levis, H. oculeus, H. pyrineusi, and H. taphorni, and an undifferentiated northern group that contains H. hondae, H. pagei, and H. plecostomoides.

Peckoltia contains 12 described species, eight of which are considered valid. Peckoltia arenaria, P. filicaudata, and P. ucayalensis are recognized as synonyms of P. bachi and P. kuhlmanni is recognized as a synonym of P. vittata. In addition, two new species are described. The type species of Peckoltichthys and Sophiancistrus are synonyms of P. bachi and both genera are recognized as junior synonyms of Peckoltia. The species of Peckoltia range throughout much of the Amazon basin, the upper Orinoco, the upper Essequibo, and perhaps the Maroni, and can be identified from most other ancistrins by having dentaries that form angle of 90° or less and from others with angled dentaries by lacking the synapomorphies of those genera. The species of Peckoltia vary from one another mostly in coloration. Peckoltia braueri, P. caenosa n. sp., P. cavatica and P. vittata lack spots on the head while the other species have them. Peckoltia braueri and P. cavatica have orange bands in the dorsal and caudal fins and have the bones and plates of the head and nape outlined in black (vs. no orange bands and head plates and bones not outlined in black in P. caenosa and P. vittata). Peckoltia caenosa has a color pattern consisting of dark vermiculations on the head and abdomen (vs. saddles or blotches on the head and faint dark spots on the abdomen in P. vittata). Among the species with spots on the head, P. lineola n. sp. and P. vermiculata have some of the spots combining to form vermiculations (vs. spots free in P. bachi, P. brevis, P. furcata, and P.oligospila) with the vermiculations larger than the pupil in P. lineola and narrower in P. vermiculata and the vermiculations radiating from a central point in P. vermiculata vs. no such pattern in P. lineola. Peckoltia bachi can be identified from the other species by having widened pelvic-fin spines that can be pulled ventrally such that they are completely ventral and parallel to the body (vs. pelvic-fin spines narrow and cannot be adducted ventral to body) and by having the eye low on the head (vs. high). Peckoltia brevis can be identified from P. furcata and P. oligospila by having well-developed dorsal saddles (vs. saddles faint), no spots on the body behind the nape (vs. spots generally present behind the nape); from P. oligospila by having bands in the caudal fin (vs. spots); and from P. furcata by having the lower caudal-fin spine longer than the upper (vs. upper spine longer). Peckoltia furcata can be identified from P. oligospila by having the upper caudal-fin spine longer than the lower (vs. lower spine longer) and by having bands in the caudal fin (vs. spots). Ancistrus yaravi had been recognized as a species of Peckoltia. The type of A. yaravi is lost, but the original description suggests that the species is the senior synonym of Neblinichthys roraima. A revised morphological phylogeny demonstrates the lack of support for Peckoltia and Hemiancistrus as monophyletic, and phenetic definitions are provided for the two genera. The phylogeny also demonstrates a lack of support of the genus Watawata.