@article {5630, title = {Age and growth of the Amazonian migratory catfish Brachyplatystoma rousseauxii in the Madeira River basin before the construction of dams}, journal = {Neotropical Ichthyology}, volume = {16}, year = {2018}, pages = {e170130, 2018}, abstract = {

The goliath catfish Brachyplatystoma rousseauxii has crucial economical and ecological functions in the Amazon basin. Although its life history characteristics have been studied in the Amazon, there is little information in the Madeira River basin, which holds genetically distinct populations and where dams were recently built. Using fish collected in Bolivia, Brazil and Peru, this study provides a validation of growth rings deposition and details the growth patterns of B. rousseauxii in the Madeira before the dams{\textquoteright} construction. Age structure and growth parameters were determined from 497 otolith readings. The species exhibits two growth rings per year and sampled fish were between 0 and 16 years old. In the Brazilian portion of the basin, mainly young individuals below 5 years old were found, whereas older fish (\> 5 years) were caught only in the Bolivian and Peruvian stretches, indicating that after migrating upstream to reproduce, adults remain in the headwaters of the Madeira River. Comparing with previous publications, B. rousseauxii had a slower growth and 20 cm lower maximum standard length in the Madeira River than in the Amazon River. This study provides a baseline for future evaluation of changes in population dynamics of the species following dams closure.

Palabras clave:\ Amazon; Biannual rings; Goliath catfish; Life cycle; Otolith

}, doi = {10.1590/1982-0224-20170130}, author = {Hauser, Marilia and Doria, C R C and Melo, L and Santos, A and Ayala, D and Nogueira, L and Amadio, S. A. and Fabr{\'e}, N and Torrente-Vilara, Gislene and Garc{\'\i}a V{\'a}squez, A and Renno, Jean-Francois and Carvajal-Vallejos, F M and Alonso, J-C and N{\'u}{\~n}ez-Rodr{\'\i}guez, Jes{\'u}s and Fabrice Duponchelle} } @article {5632, title = {Metabarcoding by Capture using a Single COI Probe (MCSP) to identify and quantify fish species in plankton swarms}, journal = {PLoS ONE }, volume = {13}, year = {2018}, pages = {e0202976}, abstract = {

The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.

}, doi = {https://doi.org/10.1371/journal.pone.0202976}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202976}, author = {Mariac, C{\'e}dric and Vigouroux, Y. and Fabrice Duponchelle and Garc{\'\i}a-D{\'a}vila, C and Nu{\~n}ez L. and Desmarais, E and Renno, Jean-Francois} } @book {5650, title = {Peces de consumo de la Amazon{\'\i}a Peruana}, year = {2018}, pages = {218}, edition = {Instituto de Investigaciones de la Amazon{\'\i}a Peruana (IIAP), Iquitos, Per{\'u}}, author = {Garc{\'\i}a-D{\'a}vila, C and Sanchez, H. and Flores, M and Mejia, J. and Angulo, C. and Castro-Ruiz, D. and Estivals, G. and Garcia, Aurea and Vargas, G. and Nolorbe, C. and Jesus Nu{\~n}ez-Rodriguez and Mariac, C{\'e}dric and Fabrice Duponchelle and Renno, Jean-Francois} } @article {5631, title = {Population dynamics of Prochilodus nigricans (Characiformes: Prochilodontidae) in the Putumayo River}, journal = {Neotropical Ichthyology}, volume = {16}, year = {2018}, pages = {e170139}, abstract = {

The black prochilodus (Prochilodus nigricans) is one of the most landed scaled fish species of the middle and upper parts of the Putumayo River, in the tri-national area between Colombia, Ecuador and Peru. Despite its importance, biological information about this species is too scant to guide fisheries management in this portion of the Colombian Amazon. In this study, 10884 individuals were sampled in the fish markets of Puerto Legu{\'\i}zamo between 2009 and 2017. This sampling was used to document reproductive patterns, but also growth and mortality parameters from length frequency distributions. The size at which all fish were mature was 22 cm Ls, which should be the established as the minimum size of capture to ensure that all fish have had a chance to reproduce before being caught. Growth and mortality parameters indicated a slower growth in the Putumayo than in other Amazonian rivers and a relatively high exploitation rate.

Keywords:\ Black prochilodus; Colombia; Growth; Mortality; Reproduction

}, doi = {http://dx.doi.org/10.1590/1982-0224-20170139}, author = {Bonilla-Castillo, C S and Agudelo C{\'o}rdoba, E and G{\'o}mez, G and Fabrice Duponchelle} } @article {5629, title = {Review of fisheries resource use and status in the Madeira River basin (Brazil, Bolivia and Peru) before the hydroelectric dam{\textquoteright}s completion}, journal = {Reviews in Fisheries Science \& Aquaculture }, volume = {26}, year = {2018}, pages = {494-514}, abstract = {

The Madeira River, which drains one of the major tributary river basins of the upper Amazon, contributes to small-scale fisheries in Peru, Bolivia, and Brazil. This paper provides a base-line of fisheries resources and their status in six sub-basins of the Madeira River: upper Madre de Dios River basin (Peru), Beni and Mamor{\'e} River basins (Bolivia), It{\'e}nez or Guapor{\'e} River basin (Bolivia and Brazil), middle Madeira, and (two sections of the) lower Madeira River (Brazil). Data were collected between 2009 and 2011, before the completion of two hydroelectric dams in the Brazilian portion of the basin. Biophysical, social, and biological indicators were used to characterize the fisheries. The results show an overall small-scale multispecies fisheries pattern but with notorious differences between the Madeira sub-basins. The Beni and Mamor{\'e} sub-basin shows the largest flooded area, with associated higher total fisheries yields. Trophic level of the catch, diversity, and mean weight of fish caught were shown to be very sensitive to exploitation level, river water type (white or clear water), flooded area, and the introduction of\ Arapaima gigas in Bolivia. The Bolivian fisheries are characterized by less exploited stocks, whereas stocks in Peru and Brazil show signs of intensive exploitation, resulting in fisheries of smaller bodied, lower trophic-level species. Landing data in the upper basin show a predominant reliance on migrating fish resources, which might be vulnerable to the construction of dams. These data serve as a baseline to evaluate anthropogenic impacts on the Madeira River basin fisheries in the future.

KEYWORDS:\ Amazon,\ freshwater ecosystem,\ trophic level,\ diversity,\ fish catch

}, doi = {The goliath catfish Brachyplatystoma rousseauxii has crucial economical and ecological functions in the Amazon basin. Although its life history characteristics have been studied in the Amazon, there is little information in the Madeira River basin, which }, author = {Doria, C R C and Fabrice Duponchelle and Lima, M A L and Garc{\'\i}a V{\'a}squez, A and Carvajal-Vallejos, F and Coca M{\'e}ndez, C and Catarino, M F and Carlos E.C. Freitas and Vega, B and Van Damme, P A} } @article {5005, title = {Description of a new maternal larvophilic mouth-brooding cichlid species, Apistogramma megastoma sp. n. (Teleostei: Perciformes: Geophaginae), from Loreto, Peru}, journal = {Vertebrate Zoology }, volume = {67}, year = {2017}, author = {R{\"o}mer, CI and Estivals, G and Vela Diaz, A and Fabrice Duponchelle and Garcia Davila, C and Hahn, I and Renno, J-F}, editor = {R{\"o}mer, U} } @article {5033, title = {Description of a new maternal larvophilic mouth-brooding cichlid species, Apistogramma megastoma sp. n. (Teleostei: Perciformes: Geophaginae), from Loreto, Peru}, journal = {Vertebrate Zoology }, volume = {67}, year = {2017}, author = {R{\"o}mer, Uwe and R{\"o}mer, CI and Estivals, G and Vela Diaz, A. and Fabrice Duponchelle and Garcia Davila, C and Hahn, I and Renno, Jean-Francois} } @article {4796, title = {DNA Metabarcoding of Amazonian Ichthyoplankton Swarms}, journal = {PLoSOne}, volume = {Jan 17;12}, year = {2017}, month = {01/2017}, pages = {:e0170009}, abstract = {

Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30\% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very promising tools for the identification of larvae at the species level. However, one of their limits is obtaining individual sequences with large samples of larvae. To facilitate this task, we developed a new method based on the massive parallel sequencing capability of next generation sequencing (NGS) coupled with hybridization capture. We focused on the mitochondrial marker cytochrome oxidase I (COI). The results obtained using the new method were compared with individual larval sequencing. We validated the ability of the method to identify Amazonian catfish larvae at the species level and to estimate the relative abundance of species in batches of larvae. Finally, we applied the method and provided evidence for strong temporal variation in reproductive activity of catfish species in the Ucayal{\'\i} River in the Peruvian Amazon. This new time and cost effective method enables the acquisition of large datasets, paving the way for a finer understanding of reproductive dynamics and recruitment patterns of tropical fish species, with major implications for fisheries management and conservation.

}, author = {Maggia, M. E. and Vigouroux, Y. and Renno, Jean-Francois and Fabrice Duponchelle and Desmarais, E and Jesus Nu{\~n}ez-Rodriguez and Garc{\'\i}a-D{\'a}vila, C and Carvajal-Vallejos, F M and Paradis, Emmanuel and Martin, Jean-Fran{\c c}ois and Mariac, C{\'e}dric} } @article {5034, title = {Tempo and Rates of diversification in the South American Cichlid Genus Apistogramma (Teleostei: Perciformes: Cichlidae)}, journal = {PLoS ONE }, volume = {in press}, year = {2017}, author = {Tougard, C and Garcia Davila, C and R{\"o}mer, U and Fabrice Duponchelle and Cerqueira, F and Guinand, B and Angulo Ch{\'a}vez, C and Salas, V and Sophie Qu{\'e}rouil and Sirvas Cornero, S and Renno, Jean-Francois} } @article {4280, title = {Trans-Amazonian natal homing in giant catfish}, journal = {Journal of Applied Ecology}, volume = {53}, year = {2016}, pages = {1511-1520}, abstract = {

1.Knowledge of fish migration is a prerequisite to sustainable fisheries management and preservation, especially in large international river basins. In particular, understanding whether a migratory lifestyle is compulsory or facultative, and whether adults home to their natal geographic area is paramount to fully appraise disruptions of longitudinal connectivity resulting from damming.2.In the Amazon, the large migratory catfishes of the Brachyplatystoma genus are apex predators of considerable interest for fisheries. They are believed to use the entire length of the basin to perform their life cycle, with hypothesized homing behaviours. Here we tested these hypotheses, using the emblematic B. rousseauxii as a model species.3.We sampled adults close to major breeding areas in the Amazon basin (upper Madeira and upper Amazonas) and assessed their lifetime movements by measuring variations in 87Sr/86Sr along transverse sections of their otoliths (ear stones) using laser ablation multicollector mass spectrometry (LA-MC-ICPMS).4.We demonstrate that larvae migrate downstream from the Andean piedmont to the lower Amazon, where they grow over a protracted period before migrating upstream as adults. Contrary to prevailing inferences, not all fish spend their nursery stages in the Amazon estuary. By contrast, the passage in the lower or central Amazon seems an obligate part of the life cycle. We further evidence that most adults home to their natal geographic area within the Madeira sub-basin. Such long-distance natal homing is exceptional in purely freshwater fishes.5.Synthesis and applications. By using otolith microchemistry, we were able to demonstrate a seemingly compulsory basin-wide migratory life cycle of large Amazonian catfishes. This makes them the organisms performing the longest migrations (\>8000 km) in fresh waters. This exceptional life history is already jeopardized by two dams recently built in the Madeira River, which block a major migration route and access to a substantial part of their spawning grounds. Major impacts can be anticipated from the current and forthcoming hydroelectric development in the Amazon basin, not only on the populations and fisheries of this apex predator, but also on Amazonian food webs through trophic cascades.This article is protected by copyright. All rights reserved.

}, keywords = {87Sr/86Sr ratios, Amazon, anthropogenic activities, Brachyplatystoma spp, freshwater fish, giant catfish, hydroelectric dams, Migration, otoliths}, issn = {1365-2664}, doi = {10.1111/1365-2664.12665}, url = {http://dx.doi.org/10.1111/1365-2664.12665}, author = {Fabrice Duponchelle and Marc Pouilly and Pecheyran, Christophe and Hauser, Marilia and Renno, Jean-Francois and Panfili, Jacques and Darnaude, Audrey M. and Garc{\'\i}a-Vasquez, Aurea and Carvajal-Vallejos, Fernando and Carmen Garc{\'\i}a-D{\'a}vila and Doria, Carolina and B{\'e}rail, Sylvain and Donard, Ariane and Sondag, Francis and Santos, Roberto V. and Jesus Nu{\~n}ez-Rodriguez and Point, David and Labonne, Maylis and Baras, Etienne} } @article {4398, title = {Movement patterns and home range of wild and re-stocked Arapaima gigas (Schinz, 1822) monitored by radio-telemetry in Lake Imiria, Peru}, journal = {Journal of Applied Ichthyology}, volume = {31}, year = {2015}, pages = {10{\textendash}18}, issn = {1439-0426}, doi = {10.1111/jai.12972}, url = {http://dx.doi.org/10.1111/jai.12972}, author = {Jesus Nu{\~n}ez-Rodriguez and Fabrice Duponchelle and Cotrina-Doria, M. and Renno, Jean-Francois and Ch{\'a}vez Veintemilla, C and Rebaza, C. and Deza, S. and Garc{\'\i}a-D{\'a}vila, C and Chu-Koo, F and Salvador Tello and Baras, Etienne} } @article {4234, title = {Opinion Paper: how vulnerable are Amazonian freshwater fishes to ongoing climate change?}, journal = {Journal of Applied Ichthyology}, volume = {31}, year = {2015}, pages = {4-9}, abstract = {

With around 15\% of all described freshwater fish species in the world, the Amazon Basin is by far the most fish species- rich freshwater ecosystem on the planet. In this opinion paper, a rough evaluation is given on just how vulnerable Amazonian freshwater fishes are to ongoing climate change. And to argue that current anthropogenic threats through rapid expansion of human infrastructure and economic activ- ities in the basin could be a far greater threat to fish commu- nities than those anticipated by any future climate change. Conservation actions in the Amazon Basin should focus preferentially on reducing the impacts of present-day anthro- pogenic threats.

}, doi = {doi: 10.1111/jai.12971}, author = {Thierry Oberdorff and C. J{\'e}z{\'e}quel and M. Campero and F. Carvajal-Vallejos and J.F. Cornu and M.S. Dias and Fabrice Duponchelle and J.A. Maldonado-Ocampo and H. Ortega and J.F. Renno and Pablo Tedesco} } @article {4552, title = {Opinion Paper: how vulnerable are Amazonian freshwater fishes to ongoing climate change?}, journal = {Journal of Applied Ichthytology}, volume = {31}, year = {2015}, pages = {4-9}, author = {Thierry Oberdorff and J{\'e}z{\'e}quel, C{\'e}line and Campero, Melina and Carvajal-Vallejos, Fernando and Cornu, Jean-Fran{\c c}ois and Dias, Murilo S and Fabrice Duponchelle and Maldonado, Mabel and H. Ortega and Renno, Jean-Francois and Pablo Tedesco} } @article {4397, title = {Periodic life history strategy of Psectrogaster rutiloides, Kner 1858, in the Iquitos~region, Peruvian Amazon}, journal = {Journal of Applied Ichthyology}, volume = {31}, year = {2015}, pages = {31{\textendash}39}, issn = {1439-0426}, doi = {10.1111/jai.12974}, url = {http://dx.doi.org/10.1111/jai.12974}, author = {Garc{\'\i}a-Vasquez, Aurea and Vargas, Gladys and S{\'a}nchez, H and Salvador Tello and Fabrice Duponchelle} } @article {4400, title = {Re-description of Apistogramma payaminonis Kullander, 1986, with descriptions of two new cichlid species of the genus Apistogramma (Teleostei, Perciformes, Geophaginae) from northern Peru}, journal = {Vertebrate Zoology}, volume = {65}, year = {2015}, pages = {287-314}, author = {R{\"o}mer, Uwe and Soares, D. P. and Garc{\'\i}a-D{\'a}vila, C. and Fabrice Duponchelle and Renno, Jean-Francois and Hanh, I.} } @article {3778, title = {Temporal and spatial distribution of young Brachyplatystoma spp. (Siluriformes: Pimelodidae) along the rapids stretch of the Madeira River (Brazil) before the construction of two hydroelectric dams}, journal = {Journal of Fish Biology}, volume = {86}, year = {2015}, pages = {1429-1437}, author = {Cella-Ribeiro, Ariana and Assakawa, L. F. and Torrente-Vilara, Gislene and Zuanon, Jansen and Leite, R. G. and Doria, C. and Fabrice Duponchelle} } @article {3586, title = {Temporal and spatial distribution of young Brachyplatystoma spp. (Siluriformes: Pimelodidae) along the rapids stretch of the Madeira River (Brazil) before the construction of two hydroelectric dams}, journal = {Journal of Fish Biology}, volume = {86}, year = {2015}, month = {04/2015}, pages = {1429-37}, author = {Cella Ribeiro, A. and Fugimoto Assakawa, L. and Torrente-Vilara, Gislene and Zuanon, Jansen and Leite, R.G. and Doria, C. and Fabrice Duponchelle} } @article {4399, title = {Using barcoding of larvae for investigating the breeding seasons of pimelodid catfishes from the Mara{\~n}on, Napo and Ucayali rivers in the Peruvian Amazon}, journal = {Journal of Applied Ichthyology}, volume = {31}, year = {2015}, pages = {40{\textendash}51}, issn = {1439-0426}, doi = {10.1111/jai.12987}, url = {http://dx.doi.org/10.1111/jai.12987}, author = {Garc{\'\i}a-D{\'a}vila, C. and Castro-Ruiz, Diana and Renno, Jean-Francois and Chota-Macuyama, Werner and Carvajal-Vallejos, Fernando and Sanchez, H. and Angulo, C. and Nolorbe, C. and Alvarado, J. and Estivals, G and Jesus Nu{\~n}ez-Rodriguez and Fabrice Duponchelle} } @article {4392, title = {Variations in reproductive strategy of the silver Arowana, Osteoglossum bicirrhosum Cuvier, 1829 from four sub-basins of the Peruvian Amazon}, journal = {Journal of Applied Ichthyology }, volume = {31}, year = {2015}, pages = {19-30}, author = {Fabrice Duponchelle and Ruiz-Arce Adela and Waty, A. and Garc{\'\i}a-Vasquez, Aurea and Renno, J-F and Chu-Koo, F and Garc{\'\i}a-D{\'a}vila, C. and Vargas, Gladys and Salvador Tello and Ortiz, A. and Pinedo, R. and Manzanares V{\'a}squez, R. and Jesus Nu{\~n}ez-Rodriguez} } @article {3445, title = {Genetic structure in the Amazonian catfish Brachyplatystoma rousseauxii: influence of life history strategies.}, journal = {Genetica}, volume = {142}, year = {2014}, month = {2014 Aug}, pages = {323-36}, abstract = {

The Dorado or Plateado (Gilded catfish) Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) is a commercially valuable migratory catfish performing the largest migration in freshwaters: from the Amazonian headwaters in the Andean foothills (breeding area) to the Amazon estuary (nursery area). In spite of its importance to inform management and conservation efforts, the genetic variability of this species has only recently begun to be studied. The aim of the present work was to determine the population genetic structure of B. rousseauxii in two regions: the Upper Madera Basin (five locations in the Bolivian Amazon) and the Western Amazon Basin (one regional sample from the Uyucal{\'\i}-Napo-Mara{\~n}on-Amazon basin, Peru). Length polymorphism at nine microsatellite loci (284 individuals) was used to determine genetic variability and to identify the most probable panmictic units (using a Bayesian approach), after a significant departure from Hardy-Weinberg equilibrium was observed in the overall dataset (Western Amazon\ +\ Upper Madera). Bayesian analyses revealed at least three clusters in admixture in the five locations sampled in the Bolivian Amazon, whereas only two of these clusters were observed in the Western Amazon. Considering the migratory behaviour of B. rousseauxii, different life history strategies, including homing, are proposed to explain the cluster distribution. Our results are discussed in the light of the numerous threats to the species survival in the Madera basin, in particular dam and reservoir construction.

}, issn = {1573-6857}, doi = {10.1007/s10709-014-9777-2}, author = {Carvajal-Vallejos, F M and Fabrice Duponchelle and Desmarais, E and Cerqueira, F and Sophie Qu{\'e}rouil and Jesus Nu{\~n}ez-Rodriguez and Garc{\'\i}a, C and Renno, J-F} } @article {3250, title = {Histological development of the digestive system of the Amazonian pimelodid catfish Pseudoplatystoma punctifer.}, journal = {Animal}, volume = {8}, year = {2014}, month = {2014 Nov}, pages = {1765-76}, abstract = {

The organogenesis of the digestive system was described in the Amazonian pimelodid catfish species Pseudoplatystoma punctifer from hatching (3.5 mm total length, TL) to 41 days post-fertilization (dpf) (58.1 mm TL) reared at 28{\textdegree}C. Newly hatched larvae showed a simple digestive tract, which appeared as a straight undifferentiated and unfolded tube lined by a single layer of columnar epithelial cells (future enterocytes). During the endogenous feeding period, comprised between 20 and 96 h post-fertilization (3.5 to 6.1 mm TL), the larval digestive system experienced a fast transformation with the almost complete development and differentiation of most of digestive organs (buccopahrynx, oesophagus, intestine, liver and exocrine pancreas). Yolk reserves were not completely depleted at the onset of exogenous feeding (4 dpf, 6.1 mm TL), and a period of mixed nutrition was observed up to 6 to 7 dpf (6.8 to 7.3 mm TL) when yolk was definitively exhausted. The stomach was the organ that latest achieved its complete differentiation, characterized by the development of abundant gastric glands in the fundic stomach between 10 and 15 dpf (10.9 to 15.8 mm TL) and the formation of the pyloric sphincter at the junction of the pyloric stomach and the anterior intestine at 15 dpf (15.8 mm TL). The above-mentioned morphological and histological features observed suggested the achievement of a digestive system characteristic of P. punctifer juveniles and adults. The ontogeny of the digestive system in P. punctifer followed the same general pattern as in most Siluriform species so far, although some species-specific differences in the timing of differentiation of several digestive structures were noted, which might be related to different reproductive guilds, egg and larval size or even different larval rearing practices. According to present findings on the histological development of the digestive system in P. punctifer, some recommendations regarding the rearing practices of this species are also provided in order to improve the actual larval rearing techniques of this fast-growing Neotropical catfish species.

}, issn = {1751-732X}, doi = {10.1017/S1751731114001797}, author = {Gisbert, E and Moreira, C and Castro-Ruiz, D and Ozt{\"u}rk, S and Fern{\'a}ndez, C and Gilles, S and Jesus Nu{\~n}ez-Rodriguez and Fabrice Duponchelle and Salvador Tello and Renno, J F and Garc{\'\i}a-D{\'a}vila, C and Darias, Maria} }