Two new species of Varicus from Caribbean deep reefs, with comments on the related genus Pinnichthys (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup)

Tropical deep reefs (~40–300 m) are diverse ecosystems that serve as habitats for diverse communities of reef-associated fishes. Deep-reef fish communities are taxonomically and ecologically distinct from those on shallow reefs, but like those on shallow reefs, they are home to a species-rich assemblage of small, cryptobenthic reef fishes, including many species from the family Gobiidae (gobies). Here we describe two new species of deep-reef gobies, Varicus prometheus sp. nov. and V. roatanensis sp. nov., that were collected using the submersible Idabel from rariphotic reefs off the island of Roatan (Honduras) in the Caribbean. The new species are the 11th and 12th species of the genus Varicus, and their placement in the genus is supported by morphological data and molecular phylogenetic analyses. Additionally, we also collected new specimens of the closely-related genus and species Pinnichthys aimoriensis during submersible collections off the islands of Bonaire and St. Eustatius (Netherland Antilles) and included them in this study to expand the current description of that species and document its range extension from Brazil into the Caribbean. Collectively, the two new species of Varicus and new records of P. aimoriensis add to our growing knowledge of cryptobenthic fish diversity on deep reefs of the Caribbean

Discovery of a Distinctive Spotted Color Pattern in the Cuskeel Neobythites unicolor (Teleostei, Ophidiidae) Based on Underwater-Vehicle Dives, with New Records from the Southern and Eastern Caribbean

In situ images and/or collection of seven specimens by underwater-vehicle dives at 269–609 m depth off Curaçao, Dominica, and Puerto Rico (S, E, and NE Caribbean) revealed new records and a previously unknown, distinctive color pattern for the cuskeel Neobythites unicolor (Ophidiidae). Species identification was based on detailed comparisons with earlier studied type and non-type material using morphometric, meristic, and otolith-form characters. A revised color description is provided based on images of live specimens in situ in their habitat, shortly after capture, and after preservation. Live and fresh specimens of Neobythites unicolor show a large number of distinctive, dark, rounded or irregularly shaped spots distributed dorsally on head, dorsal portion of body, and on the dorsal fin. This color pattern fades when fish are frozen, and it is completely lost during preservation over several years. The available images of fresh color patterns indicate an increase in spot size with fish size. In addition, some of the quantitatively examined morphometric and otolith characters of museum specimens show positive allometry. No geographic variation in color patterns could be detected. Although the Curaçao population is separated from all other known populations of N. unicolor by at least 650 km, the only population difference found was a slightly lower pectoral-fin ray count for the four specimens collected off Curaçao. An updated distribution map is provided correcting for an erroneous record in the inner Gulf of Mexico from which N. unicolor appears to be completely absent. While the spotted color pattern described here is unique among the 54 species of Neobythites, a similar pattern occurs in two other genera of the subfamily Neobythitinae, Sirembo and Spottobrotula. Further requirements to more fully understand the color diversity and related biology, ecology, and evolution in the species-rich genus Neobythites are emphasized.publishedVersio

A new species of Leptoderma Vaillant, 1886 (Osmeriformes: Alepocephalidae) from the Pacific coast of Central America

A new species of Leptoderma Vaillant, 1886 is described from a single specimen trawled at 1368–1406 m depth off El Salvador, Central America, tropical eastern Pacific. Leptoderma ospesca n. sp. can be readily distinguished from its congeners by the following combination of characters: dermal papillae absent along the lateral line, pectoral-fin rays 6, pelvic-fin rays 5, pre-dorsal length 54.9% of SL, both dorsal and anal fins separated from the caudal fin, dorsal- and anal-fin rays long, procurrent caudal-fin rays numerous and extending far forward on caudal peduncle, caudal-fin rays 16, and total pre-ural vertebrae 60. A key to the species of the genus is presented.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias del Mar y Limnología (CIMAR

Peces marinos de los órdenes Stomiiformes, Aulopiformes y Myctophiformes en aguas colombianas del Pacífico oriental tropical

These expeditions have explored portions of the ocean below 200 m, making knowledge accessible about deepsea life that has not been recorded by any national agency until date. Only a few studies of Colombian ichthyologists have reported on species belonging to these orders (Sterling 1976, Rubio 1987, Beltrán-León & Rubio 1994). Rubio (1987), for example, compiled information about the distribution of many of the deep-sea fish species of the Colombian Pacific, many of them without a collection register in Colombian waters. Beltrán-León & Rios (2000) documented the early stages of many groups of deep-sea fishes in the Pacific, including several of the three orders examined in this paper.Estas expediciones han explorado porciones del océano por debajo de los 200 m, haciendo accesible el conocimiento de la vida en estas zonas que no ha sido obtenido por ninguna agencia nacional hasta la fecha. Solo algunos estudios a cargo de ictiólogos nacionales han reportado ocasionalmente especies pertenecientes a estos ordenes (Sterling 1976, Rubio1987, Beltrán-León & Rubio 1994). Por ejemplo, Rubio (1987) recopiló información sobre la distribución de muchas especies de peces de profundidad del Pacífico colombiano, muchas de ellas sin un registro de colección en aguas colombianas. Beltrán-León & Ríos (2000) documentaron los estadios larvales de una gran cantidad de grupos de zonas profundas, incluyendo muchas de las especies examinadas en el presente documento

A new species of western Atlantic lizardfish (Teleostei: Synodontidae: Synodus) and resurrection of Synodus bondi Fowler, 1939, as a valid species from the Caribbean with redescriptions of S. bondi, S. foetens (Linnaeus, 1766), and S. intermedius (Agassiz, 1829)

Western Atlantic synodontid species were studied as part of an ongoing effort to reanalyze Caribbean shorefish diversity. A neighbor-joining tree constructed from cytochrome c oxidase I (COI) data revealed 2 highly divergent genetic lineages within both Synodus intermedius (Agassiz, 1829) (Sand Diver) and S. foetens (Linnaeus, 1766) (Inshore Lizardfish). A new species, Synodus macrostigmus, is described for one of the S. intermedius lineages. Synodus macrostigmus and S. intermedius differ in number of lateral-line scales, caudal pigmentation, size of the scapular blotch, and shape of the anterior-nostril flap. Synodus macrostigmus and S. intermedius have overlapping geographic and depth distributions, but S. macrostigmus generally inhabits deeper water (>28 m) than does S. intermedius and is known only from coastal waters of the southeastern United States and the Gulf of Mexico, in contrast to those areas and the Caribbean for S. intermedius. Synodus bondi Fowler, 1939, is resurrected from the synonymy of S. foetens for one of the S. foetens genetic lineages. The 2 species differ in length and shape of the snout, number of anal-fin rays, and shape of the anterior-nostril flap. Synodus bondi and S. foetens co-occur in the central Caribbean, but S. bondi otherwise has a more southerly distribution than does S. foetens. Redescriptions are provided for S. intermedius, S. foetens, and S. bondi. Neotypes are designated for S. intermedius and S. foetens. A revised key to Synodus species in the western Atlantic is presented

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-Scale Transcriptome Data for Fish Evolution Studies

Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in ‘omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the “Transcriptomes of 1,000 Fishes” (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; República de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; República de Chin

Evolutionary determinism and convergence associated with water-column transitions in marine fishes

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic–pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution. This is a postprint of the published article.This research was supported by NSF grants DEB-1932759 and DEB-1929248 to R.B.-R., DEB-1457426 and DEB-1541554 to G.O., DEB-1541552 to C.C.B., and DEB-2015404 to D.A. M.R.-S. was supported by a postdoctoral fellowship from Colciencias (Grant 848-2019). Financial support was provided from the Office of the Vice President for Research and Partnerships and the Office of the Provost, University of Oklahoma.Ye

Impact of the HIV-1 env Genetic Context outside HR1–HR2 on Resistance to the Fusion Inhibitor Enfuvirtide and Viral Infectivity in Clinical Isolates

Resistance mutations to the HIV-1 fusion inhibitor enfuvirtide emerge mainly within the drug's target region, HR1, and compensatory mutations have been described within HR2. The surrounding envelope (env) genetic context might also contribute to resistance, although to what extent and through which determinants remains elusive. To quantify the direct role of the env context in resistance to enfuvirtide and in viral infectivity, we compared enfuvirtide susceptibility and infectivity of recombinant viral pairs harboring the HR1–HR2 region or the full Env ectodomain of longitudinal env clones from 5 heavily treated patients failing enfuvirtide therapy. Prior to enfuvirtide treatment onset, no env carried known resistance mutations and full Env viruses were on average less susceptible than HR1–HR2 recombinants. All escape clones carried at least one of G36D, V38A, N42D and/or N43D/S in HR1, and accordingly, resistance increased 11- to 2800-fold relative to baseline. Resistance of full Env recombinant viruses was similar to resistance of their HR1–HR2 counterpart, indicating that HR1 and HR2 are the main contributors to resistance. Strictly X4 viruses were more resistant than strictly R5 viruses, while dual-tropic Envs featured similar resistance levels irrespective of the coreceptor expressed by the cell line used. Full Env recombinants from all patients gained infectivity under prolonged drug pressure; for HR1–HR2 viruses, infectivity remained steady for 3/5 patients, while for 2/5 patients, gains in infectivity paralleled those of the corresponding full Env recombinants, indicating that the env genetic context accounts mainly for infectivity adjustments. Phylogenetic analyses revealed that quasispecies selection is a step-wise process where selection of enfuvirtide resistance is a dominant factor early during therapy, while increased infectivity is the prominent driver under prolonged therapy