Biodiversity underpins fisheries resilience to exploitation in the Amazon river basin.

Inland fisheries feed greater than 150 million people globally, yet their status is rarely assessed due to their socio-ecological complexity and pervasive lack of data. Here, we leverage an unprecedented landings time series from the Amazon, Earth's largest river basin, together with theoretical food web models to examine (i) taxonomic and trait-based signatures of exploitation in inland fish landings and (ii) implications of changing biodiversity for fisheries resilience. In both landings time series and theory, we find that multi-species exploitation of diverse inland fisheries results in a hump-shaped landings evenness curve. Along this trajectory, abundant and large species are sequentially replaced with faster growing and smaller species. Further theoretical analysis indicates that harvests can be maintained for a period of time but that continued biodiversity depletion reduces the pool of compensating species and consequently diminishes fisheries resilience. Critically, higher fisheries biodiversity can delay fishery collapse. Although existing landings data provide an incomplete snapshot of long-term dynamics, our results suggest that multi-species exploitation is affecting freshwater biodiversity and eroding fisheries resilience in the Amazon. More broadly, we conclude that trends in landings evenness could characterize multi-species fisheries development and aid in assessing their sustainability.

Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding.

The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Marañón and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Marañón was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for ~80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovía Amazónica, and should serve as a pre-impact baseline.

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

Pseudoplatystoma 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.

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA.

To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.

Parallel life history evolution in mouthbrooding cichlids from the African Great Lakes.

The existence of ancient deep-water lakes provides an opportunity to study the independent adaptation of aquatic organisms to pelagic, benthic, and rocky shore habitats. With improving resolution of their phylogenetic relationships, the many cichlid fish species endemic to the African Great Lakes Malawi, Tanganyika, and Victoria provide a significant resource for the comparative study of such evolutionary processes. Here, we show that cichlid lineages colonizing rocky shores and pelagic habitats in the different lakes have independently evolved larger eggs and lower fecundities than benthic lineages, suggesting parallel adaptive life-history evolution. By contrast, other pelagic teleost fishes in both marine and freshwater habitats, including African lakes, typically produce large numbers of very small eggs. Our results also suggest that decreased fecundity and increased egg size not only occurred independently in each lake but occurred independently in the colonization of rocky and pelagic habitats.

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.

Patterns of commercial fish landings in the Loreto region (Peruvian Amazon) between 1984 and 2006.

Patterns of commercial fish catches over the period from 1984 to 2006 were studied in the Loreto region and in Iquitos, which is the most important town of the region and the principal fish marketplace of the Peruvian Amazon. Despite important inter-annual variations, the overall fish landings have significantly increased in the region during this period. The same three species dominated the catches during the whole period (Prochilodus nigricans, Potamorhina altamazonica and Psectrogaster amazonica), making up about 62% of the catches. However, the number of species exploited by commercial fisheries increased considerably during the 22 years of this study (from about 21 species in 1984 to over 65 in 2006), although part of the difference may be accounted for by a better identification of individual species nowadays. At the same time, the large high-valued species, such as Arapaima gigas, Colossoma macropomum and Brachyplatystoma rousseauxii, declined significantly and were replaced by smaller, short-lived and lower-valued species. Catches of the silver Arahuana (Osteoglossum bicirrhosum) also declined significantly during the studied period, strengthening recent warnings about the species' conservation status (Moreau and Coomes, Oryx 40:152-160, 2006). The relative proportions of the trophic groups (detritivores, omnivores and piscivores) remained relatively constant over the study period, but there were significant changes in the relative abundances of the species groups. The proportion of the dominant group, the Characiformes, which averaged about 81% of the catches, increased between 1984 and 2006, whereas the proportion of the Siluriformes and Perciformes remained constant. On the other hand, the proportion of Osteoglossiformes, represented only by two well known species (Arapaima gigas and Osteoglossum bicirrhosum), declined sharply during the same period. Important differences were observed between the landings of Iquitos and the landing of the whole Loreto region, indicating that conclusions drawn from the study of the Iquitos landings cannot be extrapolated to the whole landings of the Loreto region. The most important difference was the decreasing fish landings in Iquitos, whereas the total landings increased in the Loreto region at the same time. Potential causes of this phenomenon are discussed. Decreasing fish abundance around Iquitos (because of a higher fishing pressure) and a behavioural adaptation of fishermen to better law enforcement in Iquitos are likely explanations to be further investigated.

Life history trait variations and population dynamics of Calophysus macropterus (Siluriformes: Pimelodidae) in two river systems of the Colombian and Peruvian Amazon

The catfish Calophysus macropterus is heavily exploited in the Amazon basin, yet its life history characteristics are poorly documented, hampering proper fisheries management. In order to fill this gap, monthly sampling in the upper Putumayo River and in the Amazonas, lower Marañón and Ucayali (AMU) rivers were carried out over several years (2013-2015 in the AMU, 2013-2017 in the Putumayo) to provide detailed information about its reproduction, growth and mortality patterns (using length frequency data). Reproduction, which occurs during the dry and early flooding season, was only observed in the upper Putumayo River and not in the sampled portion of the AMU system, suggesting that the species reproduces closer to the Andes than other pimelodid catfishes. Size at first sexual maturity did not differ significantly among sex or among river systems, ranging from 25-28 cm SL. In both river systems, females had a faster growth than males and both genders also tended to have a better growth in the AMU than in the upper Putumayo. Mortality and exploitation estimate all indicated overexploitation of the species in both river systems. The implications of these results for fisheries management and conservation are discussed.(AU)

El bagre Calophysus macropterus está fuertemente explotado en la cuenca Amazónica. Sin embargo, su ciclo de vida está poco documentado, lo que dificulta su gestión pesquera. Para llenar este vacío, se realizaron muestreos mensuales en el alto río Putumayo alrededor de Puerto Leguízamo y en el Amazonas y los ríos bajo Marañón y Ucayali (AMU) cerca de Iquitos durante varios años (2013-2015 en AMU, 2013-2017 en Putumayo) para generar información sobre su reproducción, crecimiento y mortalidad. La reproducción, que se produce durante la estación seca y el inicio de la inundación, sólo se observó en el curso superior del río Putumayo y no en la parte muestreada del sistema de la AMU, lo que sugiere que la especie se reproduce más cerca de los Andes que otros pimelodidos. El tamaño de primera madurez sexual no difirió entre sexos o entre sistemas fluviales, oscilando entre 25-28 cm. En ambos sistemas fluviales, las hembras tuvieron un crecimiento más rápido que los machos y ambos géneros también tendieron a tener un mejor crecimiento en el AMU que en el alto Putumayo. Estimaciones de mortalidad y explotación indicaron una sobreexplotación en ambos sistemas. Se discuten las implicaciones de estos resultados para la gestión y conservación de las pesquerías.(AU)

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae).

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary.

Age validation and contrasted growth performances of Pseudoplatystoma punctifer (Siluriformes: Pimelodidae) in two river systems of the Western Amazon

The doncella Pseudoplatystoma punctifer is an economically and ecologically important catfish in the Amazon basin. However, little is known about its age, growth and population dynamics parameters. This study aims to validate the formation of growth marks in vertebrae of individuals collected from two rivers systems of the Peruvian Amazon (Amazon-Marañón-Ucayali and Putumayo) and compare growth parameters using the von Bertalanffy growth function between sexes and systems. A total of 372 individuals from the Amazon-Marañón-Ucayali (AMU) system and 93 from the Putumayo River were analyzed. The formation of one growth ring per year was validated and the individual ages ranged from zero to nine years old. Females grew significantly larger than males in both systems. Both females and males grew significantly better in the AMU system than in the Putumayo River. Maximum observed length and size at maturity in the AMU system were lower than those reported in previous studies in the area, and together with an important proportion of juveniles in the catches, suggest that the species is heavily exploited. Further studies on the reproductive biology and population dynamics of the doncella are needed in order to implement management measures more in line with the current situation.(AU)

La doncella Pseudoplatystoma punctifer es un bagre de importancia económica y ecológica en la cuenca Amazonica. Pese a ello, poco se conoce acerca de parámetros de edad, crecimiento y dinámica poblacional. Este estudio tuvo como objetivo validar la formación de marcas de crecimiento en vértebras de individuos colectados en dos sistemas fluviales de la Amazonia Peruana (Amazonas-Marañón-Ucayali y Putumayo) y comparar los parámetros de crecimiento usando la función de von Bertalanffy entre sexos y sistemas. Fueron analizados 372 individuos del sistema Amazonas-Marañón-Ucayali (AMU) y 93 del Putumayo. Se validó la formación de un anillo de crecimiento por año, la edad osciló entre cero y nueve años. Las hembras fueron significativamente más grandes que los machos en ambos sistemas. Para ambos sexos el crecimiento fue significativamente mayor en el sistema AMU que en el Putumayo. Las máximas tallas y edades de primera madurez observadas en el sistema AMU fueron menores a las reportadas en estudios previos en el área, y junto con un considerable porcentaje de juveniles presentes en las capturas, se sugiere que la especie está siendo fuertemente explotada. Son necesarios estudios de biología reproductiva y dinámica poblacional de doncella para implementar medidas de manejo acordes a la situación actual.(AU)

Upstream dam impacts on gilded catfish Brachyplatystoma rousseauxii (Siluriformes: Pimelodidae) in the Bolivian Amazon

This paper explores the effects of two run-of-river dams (Jirau and Santo Antônio) built in cascade in the middle Madeira River (Brazil) on the interruption of long-distance migration routes of the gilded catfish (Brachyplatystoma rousseauxii). A participative monitoring system was set up to compare capture by commercial fishers approximately 1500 km upstream of the dams in Bolivia, before (1998-2007) and after (2015-2017) dam closure. A significant decrease in gilded catfish catches and in catch per unit effort was observed after dam closure, whereas no significant difference in mean weight was found. Back-estimation of age suggests that the few individuals remaining after dam closure in 2009 are a mixture of old homers that returned upstream before dam closure, and residents hatched after dam closure and trapped in the upper Madeira. Unless fishways in the Madeira River dams improve their efficiency, the gilded catfish might become rare and in danger of regional extinction in the upper Madeira basin in the next few years, negatively affecting river fisheries.(AU)

Este estudio explora el impacto de las represas en cascada Jirau y Santo Antônio en el curso medio del río Madeira (Brasil) sobre la interrupción de la ruta de migración del bagre dorado (Brachyplatystoma rousseauxii). Se estableció un sistema de monitoreo participativo para comparar la captura de dorado por pescadores comerciales en Bolivia, aproximadamente 1 500 km río arriba de las represas, antes (1998-2007) y después (2015-2017) de su cierre. Se observó una disminución significativa en las capturas y en la captura por unidad de esfuerzo de dorado después del cierre de ambas represas. No hubo diferencias significativas en el peso promedio antes y después del cierre. La estimación de la edad de los pocos individuos capturados arriba de las represas sugiere que se trata de una mezcla de individuos adultos que han podido pasar las represas antes de su cierre en 2009, y residentes nacidos después del cierre de las represas, atrapados en el alto Madeira. Si los sistemas de traspaso de peces implementados en las represas del rio Madeira no mejoran su eficiencia, el dorado podría volverse escaso y en peligro de extinción regional en la cuenca alta del Madeira en los próximos años, afectando negativamente la pesca de esta especie.(AU)

Population dynamics of Prochilodus nigricans (Characiformes: Prochilodontidae) in the Putumayo River

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 Leguízamo 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.(AU)

El bocachico (Prochilodus nigricans) es uno de los peces de escama más comercializados en la cuenca media y alta del río Putumayo en la zona tri-nacional entre Colombia, Ecuador y Perú. Sin embargo, a pesar de su importancia, existe muy poca información biológica sobre esta especie que permita guiar el manejo pesquero para este sector de la Amazonia colombiana. Para ello, fueron analizados 10884 ejemplares colectados en puntos de expendio de pescado y zonas de pesca aledaños a la ciudad de Puerto Leguízamo entre los años 2009 a 2017. Se determinaron los parámetros de reproducción, así como de crecimiento y de mortalidad en base a análisis de distribución de frecuencia de tallas. Se recomienda establecer la talla mínima de captura a 22 cm Le, talla a la cual todos los peces son maduros y han tenido la posibilidad de reproducirse por lo menos una vez ante su captura. Los parámetros de crecimiento y mortalidad indicaron un crecimiento más lento en el Putumayo que en otras cuencas de la Amazonia y una tasa de explotación relativamente elevada.(AU)

Age and growth of the Amazonian migratory catfish Brachyplatystoma rousseauxii in the Madeira River basin before the construction of dams

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' 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.(AU)

Brachyplatystoma rousseauxii é um bagre de importante papel econômico e ecológico na bacia amazônica. Embora existam estudos acerca de sua história de vida na Amazônia, há pouca informação para a bacia do rio Madeira, onde existem populações geneticamente distintas e recentemente foram construídas duas usinas hidrelétricas. Este estudo validou a deposição das marcas de crescimento e detalhou os padrões de desenvolvimento dessa espécie no rio Madeira, antes da construção das barragens. As coletas abrangeram os territórios brasileiro, boliviano e peruano, com estrutura etária e parâmetros de crescimento determinados a partir de 497 otólitos. Foram observadas duas marcas de crescimento por ano e indivíduos entre 0 e 16 anos. Na porção brasileira foram encontrados principalmente jovens menores de 5 anos, enquanto que os peixes mais velhos (> 5 anos) foram capturados apenas na Bolívia e Peru, indicando que após a migração reprodutiva, os adultos permanecem nas cabeceiras do rio Madeira. Comparando com estudos prévios realizados na calha principal do rio Amazonas, B. rousseauxii apresentou crescimento mais lento e comprimento padrão máximo inferior de 20 cm no rio Madeira. Este estudo fornece uma base para a avaliação futura das mudanças na dinâmica populacional desse espécie após o implementação das barragens.(AU)

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.

Se determinaron las principales características del ciclo biológico de dorado Brachyplatystoma rousseauxii en el río Caquetá, Colombia. La época reproductiva ocurre durante la transición del período de aguas altas a aguas en descenso. La talla de primera madurez sexual fue significativamente mayor en hembras (88,5 cm Ls) que en machos (81,7 cm). Tanto hembras como machos se reproducen por primera vez entre su tercer y cuarto año de vida. Los parámetros de crecimiento fueron estimados mediante el análisis de frecuencia de tallas. Las hembras alcanzan un mayor tamaño que los machos, con una diferencia de cerca del 9% en el primer año que luego aumenta hasta un 12% en el décimo año de edad. La estimación de mortalidad, calculada a partir de diferentes modelos, variaron entre 0,32 a 0,42 años-1 para la mortalidad natural y 0,72 a 0,82 años-1 para la mortalidad por pesca, lo que indica una alta presión de la pesca en el río Caquetá, mucho más elevada que en la Amazonía peruana. Las tasas de explotación resultantes (0,63 a 0,72) para el río Caquetá, señalan una sobre-utilización del recurso. La situación exige una gestión concertada entre los países que comparten y utilizan con elevada frecuencia este recurso amazónico (Brasil, Colombia y Perú), por lo que se proponen posibles estrategias de solución.

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.

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.