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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. [ABSTRACT FROM AUTHOR]

This study presents an inventory of the ichthyofauna of Cuniã Lake, situated in the floodplain of the Madeira River in Rondônia State, Brazil. A total of 11,949 specimens representing eight orders, 34 families, and 189 species were sampled with gill, seine, and hand nets during the dry and wet seasons between 2008 and 2012. Most of the species recorded in Cuniã Lake are commonly found in other locations in the central Amazonian floodplains, although some are rare in collections (e.g. Acestrorhynchus minimus, Triportheus culter, Oxybrycon parvulus, Tyttocharax madeirae, Trachycorystes trachycorystes and Scorpiodoras lyophisus) or represent new distributional records. [ABSTRACT FROM AUTHOR]

- Habitat connectivity is considered a central factor shaping ecological communities, and the effects of waterway barriers such as natural waterfalls on fish movements are expected to produce differing assemblage structures in riverine ecosystems. Here, we evaluate the influence of a sequence of waterfalls on the compositional dissimilarity of fish assemblages along the Madeira River, the largest tributary of the Amazon River. We found significant differences in species composition between rivers stretches located upstream and downstream of Teotônio waterfall and, to a less extent, Jirau waterfall, independently of the hydrological period. After accounting for the relative roles of local and regional factors in explaining fish compositional dissimilarity, we still observe a significant effect of the waterfalls. We conclude that these waterfalls act as natural ecological barriers limiting fish dispersal processes and discuss aspects of these ecological filters and the potential effects of two dams currently under construction in the Madeira River. [ABSTRACT FROM AUTHOR]

In the last ten years Araipama gigas, commonly known as pirarucu, expanded its distribution upstream into the Madeira River rapids where it is not a native species. The invasion was favored by escapes from Peruvian fish farms upstream in the Madeira River Basin, where they have been raising pirarucu since the 1970s. Although the Madeira River rapids had formerly represented a geographical barrier to this invasion by limiting floodplain habitats, the construction of the Santo Antônio and Jirau dams in 2011 flooded the two most important falls, replacing the rapids stretch with a lentic or semi-lentic habitat favoring the invasion of A. gigas. Since construction of the dams, fisheries reports have been marked by the decrease of traditional commercial species, coupled with the presence of invasive populations of A. gigas. This example highlights a major emergent threat to artisanal fishing in the Amazonian freshwater system: government policies favoring dam construction and the consequent spread of native fish species used in aquaculture to new regions upstream of waterfalls where they are not native. [ABSTRACT FROM AUTHOR]

Aim: Phylogenetic relatedness among species can provide useful information on the diversification history and past dispersal events that may have shaped contemporary assemblages. Here, using of the most comprehensive fish occurrence database currently available and a global molecular phylogeny of ray‐finned fishes, we evaluate the respective roles of historical and contemporary processes in generating and maintaining fish assemblage phylodiversity patterns among 97 sub‐drainages covering the Amazon River basin. Location: Amazon River basin. Taxon: Freshwater fishes. Methods: Using a large comprehensive database of freshwater fish species distributions, and a global molecular phylogeny of ray‐finned (actinopterygian) fishes, we estimated historical and contemporary environmental effects on sub‐drainage fish phylodiversity patterns using three phylogenetic metrics standardized for richness effect: Phylogenetic Diversity (ses.PD), Mean pairwise Phylogenetic Distance between species capturing patterns at older evolutionary timescales (ses.MPD), and Mean Nearest Taxon Distance capturing patterns at younger evolutionary timescales (ses.MNTD). Results: We found significant effects of elevation gradients, contemporary climate, and water types on assemblage phylodiversity patterns. Furthermore, we found significant relationships among the three phylogenetic metrics used, and between these metrics and the distance of sub‐drainages to the Amazon River mouth, representing the Amazon basin West‐East longitudinal gradient. Main conclusions: Phylogenetic diversity showed a highly non‐random spatial distribution across the Amazon basin. Beyond significant regional effects of several contemporary and historical drivers, there was a significant West‐East decline in sub‐drainage assemblages phylogenetic clustering, along with an increase in phylogenetic diversity. These latter patterns suggest deeper evolutionary divergences among taxa located to the East, and more recent radiations in the Western sub‐drainages. Based on these findings and given that assemblages are, on average more species‐rich in sub‐basins of the Western part of the basin than in their Eastern relatives, we conclude that Western Amazon can be seen as an evolutionary "cradle" of biodiversity for freshwater fishes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. Article Impact Statement: Alternative scenarios of diversity hotspots for freshwater fish can be used to define conservation priorities in the Amazon Basin. [ABSTRACT FROM AUTHOR]

Amazonian goliath catfishes are widespread in the Amazon Basin. Recently, otolith 87Sr:86Sr analyses using laser ablation–multi‐collector–inductively coupled plasma mass spectrometry (LA‐MC‐ICPMS) revealed a >8,000 km trans‐Amazonian natal homing in Brachyplatystoma rousseauxii among fish caught and hatched in the largest Amazon River tributary, the upper Madeira basin. Although also suspected for fish in the upper Amazon, homing could not be demonstrated owing to less distinct environmental 87Sr:86Sr gradients along the Amazon mainstem. Using scanning X‐ray fluorescence microscopy (SXFM), a separate study provided evidence that Se:Ca and Sr:Ca are useful markers for identifying migration into Andean headwaters and the estuarine environment.We analysed otoliths of known 87Sr:86Sr profiles using SXFM mapping to test if Sr:Ca and Se:Ca patterns could demonstrate natal homing for three fish caught in the upper Amazon, using as reference two individuals that were natal homers and two forced residents (hatched after the construction of hydroelectric dams on the Madeira River) from the upper Madeira River.As hypothesised, although the Sr isotope profiles of the upper Amazon individuals were uninformative, two of them presented similar alternating mirror patterns of Sr:Ca and Se:Ca to those of the upper Madeira natal homers, indicating migrations out of the Andean region and into the estuary area. Both were therefore natal homers from the upper Amazon.The third individual from the upper Amazon presented similar Sr:Ca and Se:Ca patterns to those of the upper Madeira residents, suggesting it was a natural resident from the upper Amazon.By combining the results of 87Sr:86Sr analyses (LA‐MC‐ICPMS) and Sr:Ca and Se:Ca mappings (SXFM) that are completely independent of one another, we demonstrated that B. rousseauxii also performs natal homing in the upper Amazon. Our results indicate that the life cycle of B. rousseauxii is more complex than previous literature hypothesised, with the existence of partial migration, even in absence of physical barriers. Quantifying the relative importance of these different life‐history strategies will have important implications for fisheries management. Our results also lay the groundwork for conservation efforts in the context of hydropower development in the Amazon Basin and set testable hypotheses of the potential impacts of the Madeira River dams. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

• We inferred a comprehensive phylogeny of the species-rich and widespread catfish genus Hypostomus. • Morphology together with multispecies coalescent analyses unraveled 108 species and 118 clusters. • We present the Cluster Credibility index that allows testing alternative cluster delimitations. • To delimit species, the COI pairwise divergence threshold of 2% is not applicable in Hypostomus. • Our phylogeny reveals four Hypostomus super-groups for which we give diagnostic characters. 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. [ABSTRACT FROM AUTHOR]