The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes.

Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

Damming in the Madeira River modifies the food spectrum of piscivorous and affects their resource partitioning

Phylogenetic proximity suggests some degree of diet similarity among species. Usually, studies of diet show that species coexistence is allowed by partitioning food resources. We evaluate how visually oriented piscivorous fishes (Characiformes) share prey before and after building the Santo Antônio Hydroelectric Power Plant (HPP) in the Madeira River (Brazil), the largest muddy-water tributary of the Amazon River. Piscivorous species (Acestrorhynchus falcirostris, Acestrorhynchus heterolepis, Hydrolycus scomberoides, and Rhaphiodon vulpinus) were sampled under pristine (pre-HPP) and disturbed (post-HPP) environmental conditions. We analyzed species abundance and stomach contents for stomach fullness and prey composition to check variations between congeneric and non-congeneric species. The percent volume of prey taxa was normalized by stomach fullness and grouped into the taxonomic family level to determine diet, niche breadth, and overlap. Only R. vulpinus abundance increased in post-HPP. There was no significant variation in niche breadth between the periods, while niche overlap decreased in congeneric and non-congeneric species. Our results indicate that river impoundment affected piscivorous fishes in distinct ways and modified their resource partitioning. Therefore, evaluate interspecific interactions is a required tool to understand how fishes respond to river damming.(AU)

A proximidade filogenética pode indicar similaridade da dieta entre espécies e a partilha de recursos alimentares é um mecanismo que possibilita a coexistência. Neste trabalho, avaliamos como peixes piscívoros compartilham presas antes e depois da construção da Usina Hidrelétrica (UHE) Santo Antônio no rio Madeira (Brasil), o maior afluente de águas brancas do rio Amazonas. Espécies piscívoras (Acestrorhynchus falcirostris, Acestrorhynchus heterolepis, Hydrolycus scomberoides e Rhaphiodon vulpinus) foram coletadas em condições ambientais pristinas (pré-HPP) e impactadas (pós-HPP). Nós avaliamos as abundâncias e as dietas para identificar variações entre as espécies congenéricas e não-congenéricas. O percentual de volume de cada presa foi corrigido pelo grau de repleção estomacal e os itens agrupados ao nível taxonômico de família para determinar dieta, amplitude e sobreposição alimentar. Apenas a abundância de R. vulpinus aumentou no pós-HPP. Não houve diferença na amplitude alimentar das espécies após o represamento, contudo a sobreposição de nicho diminuiu para as espécies congenéricas e não congenéricas. Nossos resultados indicam que o represamento do rio afetou os peixes piscívoros modificando sua partilha de recursos. Avaliar as interações interespecíficas, portanto, é uma ferramenta necessária para entender como os peixes respondem ao represamento de rios.(AU)

The combined effects of climate change and river fragmentation on the distribution of Andean Amazon fishes.

Upstream range shifts of freshwater fishes have been documented in recent years due to ongoing climate change. River fragmentation by dams, presenting physical barriers, can limit the climatically induced spatial redistribution of fishes. Andean freshwater ecosystems in the Neotropical region are expected to be highly affected by these future disturbances. However, proper evaluations are still missing. Combining species distribution models and functional traits of Andean Amazon fishes, coupled with dam locations and climatic projections (2070s), we (a) evaluated the potential impacts of future climate on species ranges, (b) investigated the combined impact of river fragmentation and climate change and (c) tested the relationships between these impacts and species functional traits. Results show that climate change will induce range contraction for most of the Andean Amazon fish species, particularly those inhabiting highlands. Dams are not predicted to greatly limit future range shifts for most species (i.e., the Barrier effect). However, some of these barriers should prevent upstream shifts for a considerable number of species, reducing future potential diversity in some basins. River fragmentation is predicted to act jointly with climate change in promoting a considerable decrease in the probability of species to persist in the long-term because of splitting species ranges in smaller fragments (i.e., the Isolation effect). Benthic and fast-flowing water adapted species with hydrodynamic bodies are significantly associated with severe range contractions from climate change.

A database of freshwater fish species of the Amazon Basin.

The Amazon Basin is an unquestionable biodiversity hotspot, containing the highest freshwater biodiversity on earth and facing off a recent increase in anthropogenic threats. The current knowledge on the spatial distribution of the freshwater fish species is greatly deficient in this basin, preventing a comprehensive understanding of this hyper-diverse ecosystem as a whole. Filling this gap was the priority of a transnational collaborative project, i.e. the AmazonFish project - https://www.amazon-fish.com/. Relying on the outputs of this project, we provide the most complete fish species distribution records covering the whole Amazon drainage. The database, including 2,406 validated freshwater native fish species, 232,936 georeferenced records, results from an extensive survey of species distribution including 590 different sources (e.g. published articles, grey literature, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions conducted during the project. This database, delivered at both georeferenced localities (21,500 localities) and sub-drainages grains (144 units), represents a highly valuable source of information for further studies on freshwater fish biodiversity, biogeography and conservation.

Freshwater fish diversity hotspots for conservation priorities in the Amazon Basin.

Conserving freshwater habitats and their biodiversity in the Amazon Basin is a growing challenge in the face of rapid anthropogenic changes. We used the most comprehensive fish-occurrence database available (2355 valid species; 21,248 sampling points) and 3 ecological criteria (irreplaceability, representativeness, and vulnerability) to identify biodiversity hotspots based on 6 conservation templates (3 proactive, 1 reactive, 1 representative, and 1 balanced) to provide a set of alternative planning solutions for freshwater fish protection in the Amazon Basin. We identified empirically for each template the 17% of sub-basins that should be conserved and performed a prioritization analysis by identifying current and future (2050) threats (i.e., degree of deforestation and habitat fragmentation by dams). Two of our 3 proactive templates had around 65% of their surface covered by protected areas; high levels of irreplaceability (60% of endemics) and representativeness (71% of the Amazonian fish fauna); and low current and future vulnerability. These 2 templates, then, seemed more robust for conservation prioritization. The future of the selected sub-basins in these 2 proactive templates is not immediately threatened by human activities, and these sub-basins host the largest part of Amazonian biodiversity. They could easily be conserved if no additional threats occur between now and 2050.

Puntos Calientes de Diversidad de Peces de Agua Dulce para las Prioridades de Conservación en la Cuenca del Amazonas Resumen Cada día, la conservación de los hábitats de agua dulce y su biodiversidad en la cuenca del Amazonas es un reto creciente de cara a los rápidos cambios antropogénicos. Usamos la base de datos de presencia de peces más completa que existe (2,355 especies válidas; 21,248 puntos de muestreo) y tres criterios ecológicos (carácter irremplazable, representatividad y vulnerabilidad) para identificar los puntos calientes de biodiversidad con base en seis patrones de conservación (tres proactivos, uno reactivo, uno representativo y uno balanceado) y así proporcionar un conjunto de soluciones alternativas para la planeación de la protección de peces de agua dulce en la cuenca del Amazonas. Identificamos para cada patrón de manera empírica el 17% de las subcuencas que deberían conservarse y realizamos un análisis de priorización identificando amenazas actuales y a futuro (2050) (es decir, grado de deforestación y fragmentación del hábitat causado por presas). Dos de nuestros tres patrones proactivos tuvieron alrededor del 65% de su superficie cubierta por áreas protegidas; niveles altos de carácter irremplazable (60% de especies endémicas) y de representatividad (71% de la fauna ictiológica del Amazonas); y una vulnerabilidad baja actual y a futuro. Entonces, estos dos patrones parecen estar más completos para la priorización de la conservación. El futuro de las subcuencas en estos dos patrones proactivos no está amenazado por las actividades humanas a corto plazo. Además, estas subcuencas albergan la mayor parte de la biodiversidad amazónica. Se podrían conservar fácilmente si ninguna amenaza adicional sucede entre ahora y el 2050.

Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.

With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

Unexpected fish diversity gradients in the Amazon basin.

Using the most comprehensive fish occurrence database, we evaluated the importance of ecological and historical drivers in diversity patterns of subdrainage basins across the Amazon system. Linear models reveal the influence of climatic conditions, habitat size and sub-basin isolation on species diversity. Unexpectedly, the species richness model also highlighted a negative upriver-downriver gradient, contrary to predictions of increasing richness at more downriver locations along fluvial gradients. This reverse gradient may be linked to the history of the Amazon drainage network, which, after isolation as western and eastern basins throughout the Miocene, only began flowing eastward 1-9 million years (Ma) ago. Our results suggest that the main center of fish diversity was located westward, with fish dispersal progressing eastward after the basins were united and the Amazon River assumed its modern course toward the Atlantic. This dispersal process seems not yet achieved, suggesting a recent formation of the current Amazon system.

Multielemental composition and consumption risk characterization of three commercial marine fish species.

Marine fish are considered a source of high quality proteins and fatty acids. However, the consumption of fish may pose a health risk as it may have potentially toxic elements in high concentrations. In this study we quantify the multielemental composition of muscle and fins for three species of commercial marine fish from Brazil: Sphyraena guachancho (Barracuda), Priacantus arenatus (Common bigeye) and Genidens genidens (Guri sea catfish). We then assessed the potential risk of fish consumption by means of a Provisional Hazard Indices. Amongst the elements detected in fish tissue were potentially toxic elements such as Ag, Ba, Cd, Cr and Hg. Concentration differences were species-specific, and affected by the species trophic level, morphological characteristics and feeding habits. Results suggest the higher the trophic level of the fish, the higher the risk of consumption. Caution is recommended for the frequent ingestion of high trophic level fish species in Brazil.

Spatial segregation between Chalceus guaporensis and Chalceus epakros (Osteichthyes: Characiformes) in the Madeira River, Amazon Basin / Segregação espacial entre Chalceus guaporensis e Chalceus epakros (Osteichthyes: Characiformes) no rio Madeira, Bacia Amazônica

Chalceus guaporensis is an endemic fish to the upper Madeira River whereas C. epakros is widespread in many rivers of the central and lower portions of the Amazon Basin, middle and upper Orinoco River Basin, the Essequibo River in Guyana and in the Nanay River in northern Peru. According to literature, both species do not occur in syntopy. We carried out ichthyological surveys along the Madeira River Basin and its rapids, and data on abundance, diet and habitat use were obtained for both species. Chalceus guaporensis and C. epakros are morphologically similar, occupying floodplain habitats and exploiting similar food resources. The former predominated upstream from the Jirau Fall, whereas the latter had most of its abundance bellow the last fall of the Madeira River; both species co-occurred along part of the rapids stretch and in the Machado River, but with strongly uneven abundances. This pattern may have developed in the past by speciation regarding the presence of the falls, while co-occurrence of the two species seems to be regulated by competitive interactions or maintained by slight differences in environmental requirements nowadays. The recent disruption of the Madeira River by two run-of-river dams built in cascade submerged a large portion of the rapids stretch and substituted it by semi-lenthic habitats created by the dam reservoirs, together with the construction of a fish passage. These environmental changes may allow the invasion of the upper reaches of the Madeira River by C. epakros, and disturb the population of endemic C. guaporensis.

Chalceus guaporensis é descrita como uma espécie endêmica do alto rio Madeira, enquanto C. epakros está amplamente distribuída em rios das porções central e inferior da bacia Amazônica, no médio e alto rio Orinoco, e nos rios Essequibo, na Guiana, e Nanay, no norte do Peru. A literatura não registra essas espécies como sintópicas. Expedições ictiológicas realizadas ao longo do rio Madeira e suas corredeiras nos deram a oportunidade de registrar a presença, abundância, habitat e dieta utilizadas por essas espécies. Chalceus guaporensis e C. epakros são muito similares morfologicamente, ocupam habitats inundáveis e apresentam espectro alimentar semelhante. A primeira espécie predominou a montante da cachoeira Jirau, enquanto que a segunda teve a maior parte de sua abundância registrada à jusante das cachoeiras do rio Madeira. Ambas espécies coocorreram ao longo de parte do trecho de corredeiras e no rio Machado, mas com abundâncias muito desiguais. Esse padrão pode ter se desenvolvido no passado, por especiação, em função da presença das corredeiras, enquanto a coocorrência das duas espécies parece ser regulada por interações competitivas ou mantida por diferenças sutis em requisitos ecológicos no tempo atual. O recente barramento do rio Madeira por duas hidrelétricas construídas em cascata submergiu uma grande porção do trecho de corredeiras e o substituiu por habitats semilênticos, criados pelos reservatórios das hidrelétricas a fio dágua, juntamente com a construção de uma passagem para peixes. Essas alterações ambientais podem permitir que C. epakros invada o trecho superior da bacia do rio Madeira, com possíveis impactos negativos sobre a população da espécie endêmica C. guaporensis.

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)

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish.

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin.

Fish collection of the Universidade Federal de Rondônia: its importance to the knowledge of Amazonian fish diversity / A coleção ictiológica da Universidade Federal de Rondônia: sua importância para o conhecimento da diversidade de peixes da Amazônia

Biological collections preserve the biodiversity of a nation. The fish collection of the Universidade Federal de Rondônia, recently established, contains about 41% of freshwater fish species known to occur in Brazil, and 24% of South America. The biological material is distributed into 1,067 species, 21,963 lots and 149,192 specimens, gathered during five years of work. From this collection, 99% of the lots have georeferenced location, and 94% of the species were sampled in the Madeira River basin, the largest tributary in flow, drainage area and sediment discharge of the Amazonas River basin. Among the 1,008 species collected in the Madeira River basin, 80% were reviewed by Brazilian, North American and French experts, and represents the highest richness among tributaries of the Amazonas River and other rivers worldwide. Fish collection from the Madeira River basin deposited in the ichthyological collection of the Universidade Federal de Rondônia accounts for about 75% of the lots and specimens of fish from that basin available for study in collections worldwide.

Coleções biológicas preservam a biodiversidade de uma nação. A coleção ictiológica da Universidade Federal de Rondônia, recentemente estabelecida, contém cerca de 41% das espécies de peixes de água doce conhecidas para o Brasil e 24% da América do Sul. O material biológico encontra-se distribuído em 1.067 espécies, 21.963 lotes e 149.192 exemplares, organizados durante 5 anos de trabalho. Desse acervo, 99% dos lotes possuem localidade georreferenciada e 94% das espécies foram coletadas na bacia do rio Madeira, o maior afluente em vazão, área de drenagem e descarga de sedimentos da bacia Amazônica. Do total de 1.008 espécies coletadas na bacia do rio Madeira, 80% foram revisadas por especialistas brasileiros, norte-americanos e franceses, e constitui a maior riqueza de espécies conhecida para um afluente do rio Amazonas e entre outros rios do mundo. O acervo de peixes da bacia do rio Madeira depositado na Coleção de peixes da Universidade Federal de Rondônia representa cerca de 75% dos lotes e de exemplares de peixes dessa bacia disponíveis para estudos em coleções ictiológicas do mundo.

Composition and trophic structure of the ichthyofauna from a stream downriver from Santo Antonio Falls in the Madeira River, Porto Velho, RO / Composição e estrutura trófica da ictiofauna de um igarapé a jusante da cachoeira de Santo Antônio no Rio Madeira, Porto Velho, RO

Belmont Stream is the main tributary of the Madeira River in the area immediately downriver from the Santo Antonio Fall. Samplings were carried out using gill nets in the mouth of this stream between May 2005 and April 2006 and resulted in a list of 74 species. The analyses included values of composition, constancy of occurrence, species richness, abundance, Catch Per Unit of Effort and trophic structure about the ten most abundant species. Characiformes and Siluriformes were dominant order in the samples and Curimatidae (popularly known as "branquinhas") was the most abundant family, represented by Psectrogaster rutiloides (32.57 percent of the collected specimens), Potamorhina altamazonica (10.72 percent), and Potamorhina latior (7.79 percent). The most of species were considered accessory and accidental and richness suggests high values in the rising and high water. Belmont maybe considered as a moderate richness when compared to those found for others Amazon rivers. Detritivorous fishes composed 60 percent of the assemblage and the constancy of the most abundant species of this family suggests Belmont as an important area to these migratory fishes.

O igarapé Belmont localiza-se a cerca de 30 km de Porto Velho e é o principal afluente do rio Madeira na área imediatamente a jusante da cachoeira de Santo Antonio. No período compreendido entre maio de 2005 a abril de 2006, dez coletas realizadas na foz deste igarapé geraram uma lista com 74 espécies coletadas por malhadeiras. As análises incluem características físico-químicas do igarapé estudado, valores de riqueza, composição, constância, estrutura trófica da assembléia de peixes e valores de CPUE. O predomínio das ordens Characiformes e Siluriformes confirma o esperado para a Amazônia. A família Curimatidae foi a mais abundante, representada por Psectrogaster rutiloides (32,57 por cento), Potamorhina altamazonica (10,72 por cento) e Potamorhina latior (7,79 por cento), popularmente conhecidas como branquinhas. A riqueza e constância de algumas espécies sugerem um papel especial da área no que diz respeito à transposição das corredeiras pelas espécies. Conclui-se que a estrutura e a composição da ictiofauna na área estudada do igarapé Belmont é marcada por espécies migradoras detritívoras, possivelmente em função do papel do rio Madeira nas rotas migratórias.