Jonathan W. Armbruster

Balancing hydropower and biodiversity in the Amazon, Congo, and Mekong

Basin-scale planning is needed to minimize impacts in mega-diverse rivers The worlds most biodiverse river basins—the Amazon, Congo, and Mekong—are experiencing an unprecedented boom in construction of hydropower dams. These projects address important energy needs, but advocates often overestimate economic benefits and underestimate far-reaching effects on biodiversity and critically important fisheries. Powerful new analytical tools and high-resolution environmental data can clarify trade-offs between engineering and environmental goals and can enable governments and funding institutions to compare alternative sites for dam building. Current site-specific assessment protocols largely ignore cumulative impacts on hydrology and ecosystem services as ever more dams are constructed within a watershed (1). To achieve true sustainability, assessments of new projects must go beyond local impacts by accounting for synergies with existing dams, as well as land cover changes and likely climatic shifts (2, 3). We call for more sophisticated and holistic hydropower planning, including validation of technologies intended to mitigate environmental impacts. Should anything less be required when tampering with the worlds great river ecosystems?

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.

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.

Modifications of the Digestive Tract for Holding Air in Loricariid and Scoloplacid Catfishes

Loricariid catfishes have evolved several modifications of the digestive tract that appear to function as accessory respiratory organs or hydrostatic organs. Adaptations include an enlarged stomach in Pterygoplichthys, Liposarcus, Glyptoperichthys, Hemiancistrus annectens, Hemiancistrus maracaiboensis, Hypostomus panamensis, and Lithoxus, a U-shaped diverticulum in Rhinelepis, Pseudorinelepis, Pogonopoma, and Pogonopomoides; and a ringlike diverticulum in Otocinclus. Scoloplacids, closely related to loricariids, have enlarged, clear, air-filled stomachs similar to that of Lithoxus. The ability to breathe air in Otocinclus was confirmed; the ability of Lithoxus and Scoloplax to breathe air is inferred from morphology. The diverticula of Pogonopomoides and Pogonopoma are similar to swim bladders and may be used as hydrostatic organs. The various modifications of the stomach probably represent characters that define monophyletic clades. The ovaries of Lithoxus were also examined and were shown to have very few (15-17) mature eggs that were large (1.6-2.2 mm) for the small

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

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.

Convergence of a cryptic saddle pattern in benthic freshwater fishes

SynopsisMany North American stream fishes have a similar color pattern of four dark saddles against a light background. An interesting feature of the pattern, in addition to its widespread taxonomic distribution, is its consistent configuration. The interval between the first and second saddle is usually the largest, and the last (third) interval is the smallest. All saddled North American freshwater fishes live on uneven, rocky substrates, and nearly all live in flowing water. It is hypothesized that these fishes achieve crypsis through disruptive coloration; the light spaces between the saddles mimic rocks and the dark saddles appear as shadows or gaps between rocks. Saddles are spaced unevenly because rocks in streams are a mixture of sizes; a fish that mimics a series of rocks of similar sizes is more conspicuous than one that mimics rocks of different sizes. The placement of saddles was measured on five North American species. In four of five North American species measured (a sculpin and three darters), the longest spaces are towards the head where the body is also the widest, this is thought to enhance crypsis because pieces of gravel tend to be round or square. In the madtom, the saddle pattern tends more towards even spacing. The madtom may not rely on camouflage to the same extent as other species examined because of decreased predation pressure associated with being nocturnal and possessing sharp spines and venom glands.

Redescription of Pterygoplichthys punctatus and description of a new species of Pterygoplichthys (Siluriformes: Loricariidae)

Pterygoplichthys punctatus and P. weberi, new species, are unique among hypostomines in having a medially divided buccal papilla. The two species can be separated from one another by color (small spots in P. punctatus, large in P. weberi), condition of the buccal papilla (deeply divided at all ages in P. punctatus vs. shallowly divided in adults of P. weberi), condition of the lateral keel odontodes (fairly short and directed posteriorly in P. punctatus vs. large and directed almost laterally in P. weberi), and body width (SL/cleithral width 3.6-4.0 in P. punctatus vs. 3.3-3.4 in P. weberi). Pterygoplichthys punctatus is known from the rio Madeira drainage and the rio Urubu of Brazil and has published, but unconfirmed localities in the rio Purus and rio Tocantins basin, and P. weberi is known from the Rio Maranon, Rio Ucayali, and upper Rio Amazonas drainages of Colombia, Ecuador, and Peru.

Morphological and functional diversity of the mandible in suckermouth armored catfishes (Siluriformes: Loricariidae)

We examined the mandibles of 377 individuals representing 25 species, 12 genera, 5 tribes, and 2 subfamilies of the Loricariidae, a species‐rich radiation of detritivorous–herbivorous neotropical freshwater fishes distinguished by having a ventral oral disk and jaws specialized for surface attachment and benthic feeding. Loricariid mandibles are transversely oriented and bilaterally independent, each rotating predominantly around its long axis, although rotational axes likely vary with mandibular geometry. On each mandible, we measured three traditional and three novel morphological parameters chosen primarily for their functional relevance. Five parameters were linear distances and three of these were analogous to traditional teleost in‐ and out‐levers for mandibular adduction. The sixth parameter was insertion area of the combined adductor mandibulae muscle (AMarea), which correlated with adductor mandibulae volume across a subset of taxa and is interpreted as being proportional to maximum force deliverable to the mandible. Multivariate analysis revealed distributions of phylogenetically diagnosed taxonomic groupings in mandibular morphospace that are consistent with an evolutionary pattern of basal niche conservatism giving rise to multiple adaptive radiations within nested clades. Correspondence between mandibular geometry and function was explored using a 3D model of spatial relationships among measured parameters, potential forces, and axes of rotation. By combining the model with known loricariid jaw kinematics, we developed explicit hypotheses for how individual parameters might relate to each other during kinesis. We hypothesize that the ratio [AMarea/tooth row length2] predicts interspecific variation in the magnitude of force entering the mandible per unit of substrate contacted during feeding. Other newly proposed metrics are hypothesized to predict variation in aspects of mandibular mechanical advantage that may be specific to Loricariidae and perhaps shared with other herbivorous and detritivorous fishes. 2011.

Trophic diversity in the evolution and community assembly of loricariid catfishes

BackgroundThe Neotropical catfish family Loricariidae contains over 830 species that display extraordinary variation in jaw morphologies but nonetheless reveal little interspecific variation from a generalized diet of detritus and algae. To investigate this paradox, we collected δ13C and δ15N stable isotope signatures from 649 specimens representing 32 loricariid genera and 82 species from 19 local assemblages distributed across South America. We calculated vectors representing the distance and direction of each specimen relative to the δ15N/δ13C centroid for its local assemblage, and then examined the evolutionary diversification of loricariids across assemblage isotope niche space by regressing the mean vector for each genus in each assemblage onto a phylogeny reconstructed from osteological characters.ResultsLoricariids displayed a total range of δ15N assemblage centroid deviation spanning 4.9‰, which is within the tissue–diet discrimination range known for Loricariidae, indicating that they feed at a similar trophic level and that δ15N largely reflects differences in their dietary protein content. Total range of δ13C deviation spanned 7.4‰, which is less than the minimum range reported for neotropical river fish communities, suggesting that loricariids selectively assimilate a restricted subset of the full basal resource spectrum available to fishes. Phylogenetic regression of assemblage centroid-standardized vectors for δ15N and δ13C revealed that loricariid genera with allopatric distributions in disjunct river basins partition basal resources in an evolutionarily conserved manner concordant with patterns of jaw morphological specialization and with evolutionary diversification via ecological radiation.ConclusionsTrophic partitioning along elemental/nutritional gradients may provide an important mechanism of dietary segregation and evolutionary diversification among loricariids and perhaps other taxonomic groups of apparently generalist detritivores and herbivores. Evolutionary patterns among the Loricariidae show a high degree of trophic niche conservatism, indicating that evolutionary lineage affiliation can be a strong predictor of how basal consumers segregate trophic niche space.

Phylogenetic Relationships of the Suckermouth Armored Catfishes of the Rhinelepis Group (Loricariidae: Hypostominae)

The loricariid catfish genera Pogonopoma, Pogonopomoides, Pseudorinelepis, and Rhinelepis form a monophyletic clade within the subfamily Hypostominae. Phylogenetic analysis of morphological characters reveals the following relationships: (Pseudorinelepis + (Rhinelepis + (Pogonopoma + Pogonopomoides))). These nodes are strongly supported with several synapomorphies, and each genus is redescribed and diagnosed. Phylogenetic analysis revealed a split between the Amazonian genus (Pseudorinelepis) and the remainder of the genera which occur in southeastern Brazil.

The loricariid catfish genus Lasiancistrus (Siluriformes) with descriptions of two new species

Lasiancistrus (Loricariidae: Hypostominae: Ancistrini) is diagnosed by the unique presence of a ventral strut of the pterotic and the presence of whiskerlike odontodes on the snout. Lasiancistrus has about 16 species assigned to it; however, only four are valid (L. schomburgkii, L. caucanus, L. guacharote, and L. heteracanthus), L. nationi is an Ancistrus, and L. trinitatus is incertae sedis in the Loricariidae. Lasiancistrus maracaiboensis and L. mystacinus are synonyms of L. guacharote; L. pictus, L. castelnaui, L. caquetae, L. guapore, L. multispinis, and L. scolymus are synonyms of L. schomburgkii; and L. planiceps, L. mayoloi, and L. volcanensis are synonyms of L. caucanus. Two new species are described: L. tentaculatus from the rio Orinoco basin and L. saetiger from the rio Guama. The species can largely be told apart via color (L. schomburgkii has no or white spots on the fins, L. saetiger has entirely gray fins, and the rest have black spots in the fins), the presence of abdominal plates (L. caucanus, L. saetiger, and L. tentaculatus have naked abdomens, L. guacharote has a few small plates near the insertion of the pectoral fin, L. heteracanthus has a large patch of small plates, and L. schomburgkii is variable), and nuptial male condition (L. tentaculatus has small tentacles along the edge of the snout and the other species have a patch of whiskerlike odontodes at the corners of the snout). Most species are widespread in piedmont regions of South America with L. schomburgkii occurring in the Amazon, Orinoco, and Essequibo basins. Lasiancistrus (Loricariidae: Hypostominae: Ancistrini) e diagnosticado pela presenca do suporte ventral do pterotico e pelos odontodeos em forma de vibrissas no focinho. Lasiancistrus possui cerca de 16 especies nominais, sendo que apenas quarto sao reconhecidas como validas (L. schomburgkii, L. caucanus, L. guacharote e L. heteracanthus), L. nationi e um Ancistrus, e L. trinitatus, incertae sedis dentro de Loricariidae. Lasiancistrus maracaiboensis e L. mystacinus sao sinonimos de L. guacharote; L. pictus, L. castelnaui, L. caquetae, L. guapore, L. multispinis e L. scolymus sao sinonimos de L. schomburgkii; e L. planiceps, L. mayoloi e L. volcanensis sao sinonimos de L. caucanus. Duas novas especies sao descritas: L. tentaculatus da bacia do rio Orinoco e L. saetiger do rio Guama. As especies podem ser claramente distinguidas pelo padrao de colorido (L. schomburgkii nao possui maculas brancas nas nadadeiras, L. saetiger possui nadadeiras completamente acinzentadas, enquanto as demais especies possuem maculas negras nas nadadeiras), pelo padrao de placas abdominais (L. caucanus, L. saetiger e L. tentaculatus possuem abdomen nu, L. guacharote possui poucas placas proximas a insercao da nadadeira peitoral, L. heteracanthus possui um grande grupo de pequenas placas e L. schomburgkii e variavel), e pela condicao nupcial dos machos (L. tentaculatus possui pequenos tentaculos ao longo da borda do focinho e as demais especies possuem um grupo de odontodeos semelhantes a vibrissas na margem do focinho). A maior parte das especies encontra-se distribuida em regioes proximas a base da cordilheira na America do Sul, sendo que L. schomburgkii ocorre nas bacias Amazonica, do Orinoco e Essequibo.