Mark H. Sabaj

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.

Taxonomic assessment of Leptodoras (Siluriformes: Doradidae) with descriptions of three new species

O genero Leptodoras Boulenger e um agrupamento monofiletico com pelo menos dez especies, distribuidas em rios grandes e predominantemente de terras baixas na metade norte da regiao cis-Andina da America do Sul. Leptodoras e diagnosticado em Doradidae pelas morfologias unicas da regiao bucal (extensoes labiais superiores distintas com superficie ventral comparativamente lisa, margens laterais destas extensoes inteiras, fracamente franjadas ou fimbriadas e sem papilas marginais, e membranas interlabiais estreitas a moderadamente largas), do primeiro arco branquial (lamellas acessorias aumentadas, extendendo-se pela face medial dos filamentos branquiais), e da bexiga natatoria (tamanho reduzido e formato cordiforme modificado, dois diverticulos em forma de guampas projetando-se das paredes posteriores das câmaras posteriores, e um par de diverticulos bulbosos projetando-se das paredes laterais da câmara anterior). O exame de exeplares de Leptodoras em sua area de distribuicao permitiu a distincao de sete especies nominais (L. acipenserinus, L. copei, L. hasemani, L. juruensis, L. linnelli, L. myersi e L. praelongus) e revelou tres especies novas, descritas aqui (Leptodoras nelsoni, L. rogersae, e L. cataniai). E designado um lectotipo para L. hasemani.

Catfish Genus Corymbophanes (Loricariidae: Hypostominae) with Description of One New Species: Corymbophanes kaiei

Abstract The genus Corymbophanes and its type, Corymbophanes andersoni, are redescribed, and one new species, Corymbophanes kaiei is described. Among loricariids, Corymbophanes is diagnosed by a unique combination of characteristics: absence of dorsal flap of iris; absence of adipose fin; and presence of an elongate postdorsal ridge of 13–17 raised median unpaired plates. Corymbophanes kaiei differs from C. andersoni by the presence of vermiculations on the abdomen (vs abdomen lightly colored in C. andersoni), presence of distinct alternating light and dark bands on the caudal fin (vs light bands largely absent), anal fin I,5 (vs I,4), caudal peduncle moderately (vs strongly) compressed, and three to four (vs five) plates below the adpressed pectoral fin spine. Corymbophanes is known only from the Potaro River Drainage above Kaieteur Falls in west-central Guyana. Corymbophanes bahianus is transferred to Hemipsilichthys.

Two New Species of Thicklip Thornycats, Genus Rhinodoras (Teleostei: Siluriformes: Doradidae)

Abstract Rhinodoras is newly diagnosed within Doradidae by its unique combination of coloration (sides darkly mottled, usually with wide dark bars, light midlateral stripe absent) and lip morphology (labial tissue thick, fleshy, considerably expanded at corners of mouth forming rounded flap-like extensions with entire margins, all surfaces rugose with low, rounded, and tightly spaced papillae, and distal margin of lower lip draped over bases of outer and inner jaw barbels, at times nearly encircling the latter). Three previously described species are considered valid, R. thomersoni (Lake Maracaibo basin), R. boehlkei (Amazonas), and R. dorbignyi (Paraguay–Paraná), and two new species are described. Rhinodoras armbrusteri from the Branco/Essequibo basins is diagnosed by having ventral surfaces with dark pigment, anterior midlateral plates moderately deep with dorsal and ventral wings subequal in depth, sum of midlateral plates 57–60, midlateral plates anterior to vertical through pelvic-fin origin usually five, tympanal portion of lateral-line canal moderately ossified with three distinct plates, postcleithral process moderately short and broad, adipose eyelid moderate to large, pectoral-fin rays usually eight, and one-part gas bladder. Rhinodoras gallagheri from the Orinoco basin is diagnosed by having ventral surfaces pale, anterior midlateral plates shallow to moderately deep with dorsal and ventral wings about equal in depth, midlateral plates anterior to vertical through pelvic-fin origin usually five, tympanal portion of lateral-line canal weakly ossified with two to three emergent plates, postcleithral process moderately long and narrow, adipose eyelid moderate to large, pectoral-fin rays usually eight, and one-part gas bladder. Rhinodoras is the only doradid genus with extant species in both trans- and cis-Andean drainages. Se actualiza el diagnosis del género Rhinodoras dentro de la familia Doradidae en base a su patrón de coloración; éste que consiste en lo siguiente: costados oscuramente moteados, carencia de una franja media lateral clara, y generalmente posee tres franjas verticales oscuras; estos caracteres en combinación con una morfología labial especial que en tener el tejido labial grueso, carnoso, y expandido considerablemente en las esquinas de la boca para formar una solapa redondeada sin borde aserrados; la superficie de este tejido es rugosa, con papilas bajas, redondas y casi tocándose entre si; el margen distal del labio inferior pasa por encima de las bases de las barbillas mentonianas externas e internas, a veces casi encierran a éstas últimas. Se consideran válidas tres especies previamente descritas: R. thomersoni (cuenca del Lago de Maracaibo), R. boehlkei (Amazonas), and R. dorbignyi (Paraguay–Paraná), y se describen dos especies como nuevas. Rhinodoras armbrusteri del cuencas del Branco/Essequibo se distingue en poseer las superficies ventrales con pigmento oscuro, las placas laterales medias anteriores son moderadamente profundas y con las alas dorsales y ventrales desiguales en altura; la suma de los conteos de las placas medias laterales de ambos lados oscila entre 57 y 60; presenta cinco placas medias laterales anteriores hasta llegar al nivel del origen de las aletas pélvicas; la porción encima del tímpano del canal de la línea lateral está bien osificada y consiste de tres placas distintas; el proceso postcleitral es moderadamente corto y ancho; el ojo es de moderado a grande, los radios pectorales generalmente son ocho, y la vejiga natatoria presenta una sola cámara. Rhinodoras gallagheri del cuenca del Orinoco se distingue de las otras especies del género porque tiene las superficies ventrales claras, las placas medias laterales anteriores son de poca profundidad o de profundidad moderada y con las alas dorsales y ventrales más o menos iguales en altura, cinco placas medias laterales anteriores hasta el nivel de las aletas pélvicas, la porción encima del tímpano del canal de la línea lateral es pobremente osificada, con dos o tres placas emergentes; el proceso postcleitral es moderadamente largo y estrecho, el ojo es de moderado a grande, los radios pectorales usualmente son ocho, y la vejiga natatoria y tiene una sola cámara. Rhinodoras es el único género de doradidos existente que habita cuencas en ambos lados de los Andes.

New Species of Rhynchodoras from the Río Orinoco, Venezuela, with Comments on the Genus (Siluriformes: Doradidae)

Abstract A new species of proboscoid thornycat, Rhynchodoras castilloi, is described from the Río Apure, Orinoco basin, Venezuela. The new species is distinguished from R. woodsi (Essequibo and Amazon basins minus Xingu and Tocantins basins) by having a simple gas bladder (vs. each posterior chamber of gas bladder expanded into elongate horn-like diverticulum) and tubercles punctate and abundant (vs. tubercles elongate, dash-like, and sparse). The new species is distinguished from R. xingui (Xingu and Tocantins basins) by having all three tympanal scutes weakly developed (vs. second and particularly third well developed, latter with medial carina), midlateral scutes modally 35 per side, range 34–36 (vs. 34, range 33–34), and anterior midlateral scutes relatively shallow, depth about one-fifth (vs. about one-third to one-quarter) of corresponding body depth, with weakly developed dorsal and ventral laminae lacking distinct serrations along posterior margins (vs. dorsal and ventral laminae of midlateral scutes well developed with conspicuously serrated posterior margins). The type species, R. xingui, is distinguished from R. woodsi by having a simple gas bladder (vs. with two posterior horn-like diverticula), midlateral scutes modally 34 per side, range 33–34 (vs. 35, range 34–37), and anterior midlateral scutes with conspicuous medial thorns (vs. thorns absent or weak, procumbent). Notable features of the genus are discussed, including jaw and gas bladder morphology, development of anterior nuchal plate, presence of multiple pores in skin beneath postcleithral process, and tubercle morphology and distribution. Shared derived characters suggest a sister-group relationship between Rhynchodoras and Rhinodoras plus Orinocodoras.

Baryancistrus demantoides and Hemiancistrus subviridis, two new uniquely colored species of catfishes from Venezuela (Siluriformes: Loricariidae)

Baryancistrus demantoides and Hemiancistrus subviridis are two new species of loricariids from southern Venezuela with an olive ground coloration and white to cream-colored or golden-yellow spots. Baryancistrus demantoides is known only from the upper rio Orinoco drainage while H. subviridis is also known from the rio Casiquiare drainage. In addition to its coloration, B. demantoides can be distinguished from all other ancistrins by having the dorsal and adipose fins connected by an expanded posterior section of the dorsal-fin membrane, golden-yellow spots confined to the anterior portion of the body, and greater than 30 teeth per jaw ramus. Hemiancistrus subviridis can be separated from all other ancistrins by coloration, lacking a connection between the dorsal and adipose fins and having less than 30 teeth per jaw ramus. Baryancistrus demantoides e Hemiancistrus subviridis sao duas especies novas de loricariideos do sul da Venezuela, de cor de fundo verde-oliva e manchas brancas a creme ou amarelo-douradas. Baryancistrus demantoides e conhecida somente da bacia do rio Orinoco superior, enquanto H. subviridis e tambem conhecida da bacia do rio Casiquiare. Alem da coloracao, B. demantoides pode ser distinguido de todos os outros ancistrineos por ter as nadadeiras dorsal e adiposa conectadas por uma seccao posterior expandida da membrana da nadadeira dorsal, manchas amarelo-douradas restritas a porcao anterior do corpo, e mais de 30 dentes por ramo mandibular. Hemiancistrus subviridis pode ser separado de todos os outros ancistrineos pela falta de uma coneccao entre as nadadeiras dorsal e adiposa e por possuir menos de 30 dentes por ramo mandibular.

Description of a New Blind and Rare Species of Xyliphius (Siluriformes: Aspredinidae) from the Amazon Basin Using High-Resolution Computed Tomography

Xyliphius sofiae, new species, is described based on a unique specimen exhibiting four autapomorphies: eyes absent vs. present (though reduced); color pale, lacking pigment vs. head and body darkly pigmented; branchiostegal rays five vs. four; and unculiferous tubercles on posterior body distributed evenly vs. enlarged unculiferous tubercles typically arranged in five distinct rows above pelvic-fin base to posterior end of caudal peduncle. In addition, the pectoral fin of X. sofiae, new species, has one ossified proximal radial vs. two in congeners (except X. magdalenae, not examined). Xyliphius sofiae, new species, differs from all congeners except X. lepturus by snout tip elongated and narrowly rounded vs. short and broadly rounded, often with small median notch; fifth ceratobranchial relatively narrow with elongate acicular teeth vs. broadly expanded, leaf-shaped, with shorter and broader, conical teeth; anterior limits of branchial apertures separated by distance less than length of aperture vs. greater than length of aperture; anal-fin rays modally nine vs. seven; and lateral line extending onto base of caudal-fin rays vs. finishing in hypural region. Based on the single specimen collected in the main channel of the Río Amazonas near Iquitos, Peru, we describe the osteology of X. sofiae, new species, using a non-invasive technique: high-resolution X-ray computed tomography (HRXCT). We consider Xyliphius lombarderoi Risso and Risso, 1964, a species based on a unique holotype that is now lost, to be a subjective junior synonym of X. barbatus Alonso de Arámburu and Arámburu, 1962. Variable characteristics are summarized for the seven species of Xyliphius treated here as valid, and their distributions are plotted based on a comprehensive review of museum specimens.

A new subspecies, Polynemus melanochir dulcis, from Tonle Sap Lake, Cambodia, and redescription of P. m. melanochir Valenciennes in Cuvier and Valenciennes, 1831 with designation of a neotype

Abstract A poorly known threadfin, Polynemus melanochir Valenciennes in Cuvier and Valenciennes, 1831, is redescribed (as P. melanochir melanochir) on the basis of a newly designated neotype and a large number of specimens. Polynemus melanopus Sauvage, 1881 and 3 species commonly regarded as valid, Galeoides microps Steindachner, 1869, P. borneensis Bleeker, 1857, and Trichidion hilleri Fowler, 1905, are all considered junior synonyms of P. m. melanochir. In addition, a new subspecies, P. melanochir dulcis, is described on the basis of 3 specimens. Polynemus m. dulcis differs from P. m. melanochir in having a greater snout length [7% of SL vs. mean 6% (range 5–6%) of SL in the latter] and shorter upper caudal-fin lobe length [35% (34–35%) of SL vs. 39% (35–44%) of SL]. The former is currently known only from Tonle Sap Lake, Cambodia, whereas the latter is known from the Mekong River (Cambodia and southern Vietnam) and Kalimantan (=Borneo; Malaysia and Indonesia).

Molecular phylogeny of Banjo catfishes (Ostaryophisi: Siluriformes: Aspredinidae): A continental radiation in South American freshwaters

The family Aspredinidae is a moderately diverse and broadly distributed group of freshwater fishes endemic to South America. Commonly known as Banjo Catfishes, Aspredinidae currently includes 44 valid species divided among 13 genera. The first species-comprehensive hypothesis on phylogenetic relationships among aspredinids is presented. The phylogeny is based on DNA sequence data for five gene fragments (mitochondrial 16S and COI; nuclear RAG1, MYH6 and SH3PX3) from 114 individuals representing 31 species in 12 aspredinid genera. Analyses of molecular data support the monophyly of most genera (Bunocephalus excepted) and several higher-level relationships previously proposed by morphological studies. Based on the molecular phylogeny, a new suprageneric classification for Aspredinidae is proposed with the new monotypic subfamily Pseudobunocephalinae as the sister taxon to all other aspredinids.

Multilocus phylogeny of the zebra mussel family Dreissenidae (Mollusca: Bivalvia) reveals a fourth Neotropical genus sister to all other genera

Dreissenidae is one of the most economically and ecologically important families of freshwater and estuarine mollusks. Fourteen extant species and three genera are currently recognized: Congeria contains three species from karst caves along the eastern Adriatic coast and one from the Orinoco River of Venezuela, Dreissena contains six species native to Eastern European rivers and estuaries, and Mytilopsis contains three species from the Gulf of Mexico, Caribbean, and northwestern coast of South America and one from the Tocantins River of Brazil. Previous molecular phylogenetic studies have examined all species except those from South American rivers, and found each genus to be monophyletic with Congeria and Mytilopsis forming a clade sister to Dreissena. We present the first multilocus phylogeny of Dreissenidae inclusive of South American riverine species. Bayesian and maximum likelihood analyses of a 3085 bp alignment consisting of mitochondrial (COI and 16S) and nuclear (18S and 28S) gene regions found Neotropical species to be consistently and strongly supported as sister to all other dreissenids, although incomplete sequencing of the single Orinoco specimen obscured Neotropical monophyly. Our intergeneric relationships are inconsistent with an extensive fossil record suggesting that dreissenids originated in Europe approximately 30 My before dispersing to the Western Hemisphere. Fossil-calibrated analyses indicated that Neotropical dreissenids diverged from European lineages in the mid to late Eocene (∼39.3 Ma), and Brazilian and Guiana shield populations diversified during the Oligocene to Miocene. We erect the new genus Rheodreissena for all Neotropical freshwater dreissenids and present haplotype data indicative of at least three species. Widespread anthropogenic alteration of the middle Xingu River and lower Amazon threatens the persistence of these endemic, poorly studied mussels and may facilitate introduction beyond their native range.