Fabrice Duponchelle

Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna.

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.

Towards a universal scale to assess sexual maturation and related life history traits in oviparous teleost fishes

The literature presents a confusing number of macroscopic maturation scales for fish gonads, varying from over-simplified scales comprising three to four stages to highly specific and relatively complicated nine-stage scales. The estimation of some important life history traits are dependent on a correct assessment and use of the gonadal maturation scales, and frequent mistakes have been made in many studies. The goal of this report is to provide a synthetic, relatively simple, yet precise maturation scale that works for most oviparous teleost fishes. The synthetic scale proposed here is based on the correspondence between key physiological and cytological processes of gamete development and corresponding modifications observed at the macroscopic level. It is based on previous and ongoing studies of several fish species pertaining to some of the most important African and Neotropical taxa, including Characiformes, Siluriformes, Osteoglossiformes and Perciformes. This scale should allow for standardized protocols of field studies and improve intra- and inter-specific comparisons of life history traits. Guidelines on the correct use of this scale to estimate these life history traits are provided.

Evidence of environmental effects on reproductive characteristics of Nile tilapia (Oreochromis niloticus) populations from man-made lakes of Ivory Coast

Abstract Large differences in reproductive traits were observed between populations of Oreochromis niloticus sampled in 9 manmade lakes of Ivory Coast. In order to assess whether these variations in reproductive characteristics resulted from short term adaptation or from a longer evolutionary process, living specimens were caught in the two most differentiated populations in term of life history traits, and placed in a common environment in culture conditions. Genetic analysis of fish from these two populations were performed using four microsatellite markers and revealed that both descended originally from the same strain (Bouake station) which was constituted from broodfish initially caught in the Nile and Volta basins. Fish from the two populations were subjected to a common environment (pond and aquariums) for five months. Then, their reproductive characteristics were analysed and no significant differences were found in fecundity, egg size and spawning frequency. These results indicate that reproductive differences between the two populations, originally observed in the two reservoirs, mostly reflect the phenotypic plasticity of the species in facing different environmental conditions.

Isolation by distance and Pleistocene expansion of the lowland populations of the white piranha Serrasalmus rhombeus

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.

Breeding, growth and exploitation of Brachyplatystoma rousseauxii Castelnau, 1855 in the Caqueta River, Colombia

The main life history traits of the large Amazonian migratory catfish Brachyplatystoma rousseauxii were determined in the Caqueta River, Colombia. The breeding season occurred during the rising and falling water periods. The size at first sexual maturity was significantly larger for females (88.5 cm Ls) than males (81.7 cm). Both males and females reproduce for the first time between their third and fourth year. The growth characteristics were estimated using length frequency analyses. Females grew systematically larger than males, the difference being about 9% after the first year and increasing to 12% for ten years old individuals. Mortality estimates, calculated from different models, some taking into account the effect of body size, ranged from 0.32 to 0.42 year-1 for natural mortality and from 0.72 to 0.82 year-1 for fishing mortality, indicating high fishing pressure in the Caqueta River, higher than in the Peruvian Amazon. Resulting exploitation rates (0.63 to 0.72) pointed towards overexploitation of the species in the Caqueta. The situation calls for a concerted management between the countries sharing this resource (Brazil, Colombia, and Peru) and potential solutions are proposed.

Rapid phenotypic changes of reproductive traits in response to experimental modifications of spatial structure in Nile tilapia, Oreochromis niloticus

Abstract The reproductive characteristics of Oreochromis niloticus, a multiple spawner, have been compared between populations submitted experimentally to three types of spatial structure. Fish from a same original stock were divided and reared for 2 months in: 1) concrete tanks with a bare bottom, 2) concrete tanks with a sandy bottom, or 3) concrete tanks equipped with an artificial reef. The females were then killed and their gonads examined for sexual stage and fecundity determination. Fecundity was inversely correlated to the spatial complexity of the environment whereas oocyte size tented to increase together with spatial complexity. Females placed in tanks with artificial reefs presented a lower fecundity and reproductive investment and bigger oocytes than those maintained in the bare bottom tanks. Fish reared in tanks with a sandy bottom had intermediate reproductive traits. The response of females to changes in the spatial structure of their environment was observed after only one or two reproductive cycles, providing the first experimental evidence of such rapid phenotypic adaptation to environmental complexity. The results also indicate that the perception of living space, arising from the availability of refuges and spawning sites, is more likely to influence the reproduction of tilapias than substrate quality.

Molecular identification of a cryptic species in the Amazonian predatory catfish genus Pseudoplatystoma (Bleeker, 1962) from Peru

AbstractPseudoplatystoma species are highly prized South American Pimelodid migratory catfishes. Until recently, their taxonomy was not clearly established, with discrepancies between morphological and molecular analyses. Here, Pseudoplatystoma species from the Peruvian Amazon were characterized at the molecular level from a sample representing the observed range of their color pattern variations in the study area. Analyses were performed using seven microsatellite loci for 103 specimens and, for part of them (52), using sequences of two regions of their mitochondrial genome [Cytochrome Oxidase subunit I (COI) and Control Region (CR)]. Factorial correspondence analysis and assignment tests based on microsatellite polymorphism showed that the specimens originally identified as P. punctifer belonged to two different gene pools highly differentiated from P. tigrinum. Morphological examination identified two different morphotypes (with and without black stripes), suggesting the existence of two distinct taxa within P. punctifer. This result was corroborated by the ML tree based on CR sequences, where all individuals but four clustered in a similar way as in the FCA and Bayesian assignment tests. For these four individuals, mitochondrial introgression or retention of ancestral polymorphism was likely. In contrast, the ML tree based on COI sequences showed that reciprocal monophyly was not yet achieved for this marker for the two P. punctifer taxa. The existence of three sympatric species of Pseudoplatystoma in the Peruvian Amazon is discussed in relation to their molecular characteristics, color patterns and ecology. Evolutionary scenarios regarding their divergence are hypothesized.

Rapid phenotypic changes of reproductive traits in response to experimental modifications of spatial structure in Nile tilapia, Oreochromis niloticusAdaptation phénotypique rapide des caractéristiques de reproduction des tilapias, Oreochromis niloticus, en réponse à des modifications expérimentales de lˈenvironnement.

Abstract The reproductive characteristics of Oreochromis niloticus, a multiple spawner, have been compared between populations submitted experimentally to three types of spatial structure. Fish from a same original stock were divided and reared for 2 months in: 1) concrete tanks with a bare bottom, 2) concrete tanks with a sandy bottom, or 3) concrete tanks equipped with an artificial reef. The females were then killed and their gonads examined for sexual stage and fecundity determination. Fecundity was inversely correlated to the spatial complexity of the environment whereas oocyte size tented to increase together with spatial complexity. Females placed in tanks with artificial reefs presented a lower fecundity and reproductive investment and bigger oocytes than those maintained in the bare bottom tanks. Fish reared in tanks with a sandy bottom had intermediate reproductive traits. The response of females to changes in the spatial structure of their environment was observed after only one or two reproductive cycles, providing the first experimental evidence of such rapid phenotypic adaptation to environmental complexity. The results also indicate that the perception of living space, arising from the availability of refuges and spawning sites, is more likely to influence the reproduction of tilapias than substrate quality.

Population genetic structure of Cichla pleiozona (Perciformes: Cichlidae) in the Upper Madera basin (Bolivian Amazon): Sex-biased dispersal?

This study investigates the population structure of the Tucunaré (Cichla pleiozona) in the Bolivian Amazon (Upper Madera) by using nuclear (EPIC-PCR, 67 individuals) and mitochondrial (Control Region, 41 published and 76 new sequences) DNA analyses, in relation with ecological (water quality: muddy, clear and mix) and geographic factors. Our analyses of both markers showed the highest diversity in clear waters (Yata, Middle and Upper Iténez), and the existence of two populations in muddy waters (Sécure and Ichilo) and one in mix waters (Manuripi). On the other hand, mitochondrial analyses identified three populations in clear waters where nuclear analyses identified a panmictic population. The highest diversity observed in the Yata-Iténez system suggests that an aquatic refuge occurred during the past in this area. The possible explanations for the observed discrepancy between nuclear and mitochondrial markers are discussed, and a sex-biased dispersal seems to be the most plausible hypothesis in the light of the available information and field observations.

DNA Metabarcoding of Amazonian Ichthyoplankton Swarms

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 Ucayalí 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.