Browsing by Autor "Nicolas Hubert"

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Early Biogeography of Otophysi Points to the Neotropics as the Cradle of Characiphysan Fishes
(Wiley, 2025) Achille Lenglin; Max Hidalgo; Guido Miranda; A. Sota; Pierre Caminade; Khalid Belkhir; Olga Otero; Pierre‐Olivier Antoine; Carmen Rosa GARCÍA-DÁVILA; Nicolas Hubert
Freshwaters represent less than 1% of Earth's surface and only 0.02% of the available aquatic habitable volume, yet they host nearly half of the 35,500 known species of bony fishes. Ostariophysan fishes account for 70% of all freshwater fish diversity, comprising approximately 12,000 species across five highly speciose orders. They represent a major evolutionary radiation, the internal phylogenetic relationships of which remain the subject of intense debate. To better understand their early evolutionary history and origin, we reconstructed their phylogeny using dense taxonomic sampling and a combined dataset of complete mitochondrial genomes and sequences from four nuclear genes. Phylogenetic relationships and divergence times were inferred using Bayesian and Maximum Likelihood approaches and molecular dating analyses on a dataset of 687 ostariophysan species, comprising 21,701 aligned positions, including 15,707 variable sites. We also applied model-based Maximum Likelihood ancestral area reconstruction to investigate the early evolutionary history of Otophysi. Our analyses yielded a highly supported phylogenetic hypothesis for Otophysi, highlighting the role of plate tectonics in driving multiple divergence events, along with subsequent range shifts. These findings are further supported by the contraction of the tropical belt, which began at the end of the Cretaceous and continued throughout the Paleogene. Our results support the divergence of Cypriniformes and Characiphysi as a consequence of the breakup of Laurasia and Gondwana. The origin of Characiphysi is traced to West Gondwana, and the subsequent expansion of the group cannot be explained without invoking transcontinental dispersal during the Upper Cretaceous-Paleocene.
Environment‐related life‐history trait variations of the red‐bellied piranha Pygocentrus nattereri in two river basins of the Bolivian Amazon
(Wiley, 2007) Fabrice Duponchelle; Faviany Lino; Nicolas Hubert; Jacques Panfili; Jean‐François Renno; Etienne Baras; J.P. Torrico; Remi Dugué; J. N. Rodrìguez
Life‐history traits of Pygocentrus nattereri were compared in two populations inhabiting connected tributaries of the upper Madera River: the white water Mamoré River and the clear water Iténez River. As white waters provide better trophic conditions than clear waters, the size at maturity, fecundity, reproductive effort, condition and growth of P. nattereri should be greater in the more productive white water river (Mamoré) than in the less‐productive clear water river (Iténez). Breeding periods were highly seasonal and similar in both rivers and under strong influence of photoperiod. Oocyte size‐frequency distributions, together with the frequent occurrence of recovering females indicated that an individual female spawns at least twice during the breeding season. As predicted, fish of the Mamoré were significantly larger at maturity and had higher fecundity and condition factor values than those of the Iténez. Fish from both rivers matured as yearlings. The higher growth potential of females was better expressed in the Mamoré than in the Iténez, where growth differences between sexes were weak. Females had a significantly better growth in the Mamoré than in the Iténez. The observed life‐history traits associations were consistent with the hypothesis of better trophic conditions in the Mamoré. In addition, previous genetic analyses evidenced that the colonization of the two basins is recent and that extant populations have very similar genetic backgrounds. This suggests that the observed variations in life‐history traits of P. nattereri are not related to historical factors (genetic drift) between two phylogeographically distinct lineages, but rather due to the contrasting environmental conditions in the white and clear waters.
Evidence of reproductive isolation among closely related sympatric species of Serrasalmus (Ostariophysii, Characidae) from the Upper Madeira River, Amazon, Bolivia
(Wiley, 2006) Nicolas Hubert; Fabrice Duponchelle; J. N. Rodrìguez; Rosario Rivera; Jean‐François Renno
The delimitation of the Serrasalmus species (Characiformes, Serrasalminae) from the Bolivian Amazon (Amazonas, Madeira) was examined using intron length polymorphism assessed by EPIC‐PCR. The six pairs of primers provided 16 polymorphic loci across the species of the region and the allelic diversity ranged between two and 10 alleles per locus. For each locus, the lack of departure from Hardy‐Weinberg expectations in a large number of the populations analysed and the homogenous distribution of linkage disequilibrium between paralogous loci and loci belonging to different intronic systems provided strong lines of evidence that the 16 amplified loci constituted independent neutral markers. Furthermore, allelic diversity was size‐dependent, thereby indicating that insertion‐deletions occurred frequently but randomly in introns, and that intron length polymorphism was a valid marker for investigating the systematics of piranhas. EPIC‐PCR demonstrated that eight of the nine nominal species of piranha of the Upper Madeira were reproductively isolated and identified a new species that differed from its closest morphological and genetic relatives by seven diagnostic or semi‐diagnostic loci. By contrast, no diagnostic or semi‐diagnostic locus was found between S. spilopleura and S. eigenmanni , nor were their allelic frequencies different, thereby questioning the validity of their biological species status, at least in the Upper Madeira. This study, which was one of the first applications of EPIC‐PCR to a large‐scale molecular systematic purpose, demonstrates that it is a rapid, reliable and cost‐effective tool for elucidating issues pertaining to fish systematics.
Induced breeding and larval rearing of Surubí, Pseudoplatystoma fasciatum (Linnaeus, 1766), from the Bolivian Amazon
(Wiley, 2008) J. N. Rodrìguez; Remi Dugué; Navil Corcuy Arana; Fabrice Duponchelle; Jean‐François Renno; Thomas Raynaud; Nicolas Hubert; Marc Legendre
Brooders of Surubí (Pseudoplatystoma fasciatum) were caught in the Ichillo River (Bolivian Amazon) and adapted to captivity conditions for 1 year in the facilities of the experimental aquaculture station of ‘El Prado’ (Santa Cruz de la Sierra) under natural temperature and photoperiod conditions. Induced reproduction was obtained by means of Ovaprim® (Syndel, Canada) injections and artificial fertilization. Sperm and ova were obtained by gentle stripping of male and female brooders. Fertilized eggs were incubated in 60 L Zug jars. A mean hatching rate of 73.7±19.0% was obtained after 24 h at 26.5 °C. For larval rearing, several protocols were tested with different settings of photoperiod, light intensity, food type and period of distribution, and stocking density. The best survival rates were obtained with Artemia nauplii feeding in total darkness. A high level of aggressiveness between larvae and precocious appearance of jumpers was observed, but these can be controlled with appropriate rearing conditions.
Isolation by distance and Pleistocene expansion of the lowland populations of the white piranha Serrasalmus rhombeus
(Wiley, 2007) Nicolas Hubert; Fabrice Duponchelle; J. N. Rodrìguez; Rosario Rivera; François Bonhomme; Jean‐François Renno
The genetic variability and distribution of Amazonian fish species have likely been influenced by major disturbance events in recent geological times. Alternatively, the great diversity of aquatic habitat in the Amazon is likely to shape ongoing gene flow and genetic diversity. In this context, complex patterns of genetic structure originating from a joint influence of historical and contemporary gene flow are to be expected. We explored the relative influence of Pleistocene climatic fluctuations and current water chemistry on the genetic structure of a piranha, Serrasalmus rhombeus, in the Upper Amazon by the simultaneous analysis of intron length polymorphism and mitochondrial DNA sequences. The Madeira river is well suited for that purpose as it is characterized by a great diversity of water types, the presence of one of the largest floodplain of the Amazon and the potential occurrence of two Pleistocene refuges. We found evidence of genetic structure even at a small geographical scale (less than 10 km), indicating that the floodplain is not a homogenizing factor promoting interdrainage dispersal in S. rhombeus. Likewise, the hierarchical genetic structure inferred was correlated to geographical distance instead of habitat characteristic. Our results also support the hypothesis that the area underwent population expansion during the last 800,000 years. In addition, a higher level of genetic diversity was found in the samples from the putative Aripuanã refuge. The present findings suggest that Pleistocene refuges contributed significantly to the colonization of the lowlands in the Upper Amazon valley during the Pleistocene.
Molecular phylogeny of the genus Pseudoplatystoma (Bleeker, 1862): Biogeographic and evolutionary implications
(Elsevier BV, 2008) J.P. Torrico; Nicolas Hubert; Érick Desmarais; Fabrice Duponchelle; J. N. Rodrìguez; Juan I. Montoya‐Burgos; Carmen Rosa GARCÍA-DÁVILA; Fernando M. Carvajal‐Vallejos; Alejandro Grajales; François Bonhomme
Morphology–diet relationships in four killifishes (Teleostei, Cyprinodontidae,Orestias) from Lake Titicaca
(Wiley, 2009) Elizabeth Maldonado; Nicolas Hubert; Pierre Sagnes; Bernard de Mérona
This study explores the relationship between morphology and diet in four Andean killifishes (Orestias) from Lake Titicaca that are known to differ in habitat use. Species that fed preferentially on amphipods (Orestias albus) or molluscs (Orestias luteus) separated in multivariate space from other species that feed on cladocera and algae (Orestias agassii and Orestias jussiei). Generally, specimens feeding on cladocera were characterized by a short, blunt nose with a small mouth; whereas, specimens feeding on amphipods exhibited a long snout with a large mouth. Specimens including molluscs in their diet tended to have a larger posterior part of the head and the larger opercles than others; while the occurrence of substratum in gut content was generally related to a short but deep head. The present analysis suggests that the littoral O. jussiei has an intermediate phenotype and diet between the pelagic (O. agassii) and benthic (O. albus and O. luteus) species. Results suggest that resource partitioning was occurring and that several morphological traits relate to characteristics of the diet, and it is inferred that the benthic, the pelagic and the littoral zones in the lake host different prey communities constituting distinct adaptive landscapes.
Phylogeography of Cichla (Cichlidae) in the upper Madera basin (Bolivian Amazon)
(Elsevier BV, 2006) Jean‐François Renno; Nicolas Hubert; J.P. Torrico; Fabrice Duponchelle; J. N. Rodrìguez; Carmen Rosa GARCÍA-DÁVILA; Stuart C. Willis; Érick Desmarais
Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna
(Wiley, 2007) Nicolas Hubert; Fabrice Duponchelle; J. N. Rodrìguez; Carmen Rosa GARCÍA-DÁVILA; Didier Paugy; Jean‐François Renno
The phylogenetic relationships within the piranhas were assessed using mitochondrial sequences with the aim of testing several hypotheses proposed to explain the origin of Neotropical diversity (palaeogeography, hydrogeology and museum hypotheses). Sequences of the ribosomal 16S gene (510 bp) and control region (980 bp) were obtained from 15 localities throughout the main South American rivers for 21 of the 28 extant piranha species. The results indicate that the genus Serrasalmus is monophyletic and comprises three major clades. The phylogeographical analyses of these clades allowed the identification of five vicariant events, extensive dispersal and four lineage duplications suggesting the occurrence of sympatric speciation. Biogeographical patterns are consistent with the prediction made by the museum hypothesis that lineages from the Precambrian shields are older than those from the lowlands of the Amazon. The vicariant events inferred here match the distribution of the palaeoarches and several postdispersal speciation events are identified, thereby matching the predictions of the palaeogeography and hydrogeology hypotheses, respectively. Molecular clock calibration of the control region sequences indicates that the main lineages differentiated from their most recent common ancestor at 9 million years ago in the proto Amazon-Orinoco and the present rate of diversification is the highest reported to date for large carnivorous Characiformes. The present results emphasize that an interaction among geology, sea-level changes, and hydrography created opportunities for cladogenesis in the piranhas at different temporal and geographical scales.
Population genetic structure of Cichla pleiozona (Perciformes: Cichlidae) in the Upper Madera basin (Bolivian Amazon): Sex-biased dispersal?
(Elsevier BV, 2010) Fernando M. Carvajal‐Vallejos; Fabrice Duponchelle; J.P. Torrico Ballivian; Nicolas Hubert; J. N. Rodrìguez; Patrick Berrebi; S. Sirvas Cornejo; Jean‐François Renno
Species polyphyly and mtDNA introgression among three Serrasalmus sister-species
(Elsevier BV, 2007) Nicolas Hubert; J.P. Torrico; François Bonhomme; Jean‐François Renno