Mercury in aquatic ecosystems of two indigenous communities in the Piedmont Ecuadorian Amazon: evidence from fish, water, and sediments.

Mercury is a highly toxic element present in water, soil, air, and biota. Anthropogenic activities, such as burning fossil fuels, mining, and deforestation, contribute to the presence and mobilization of mercury between environmental compartments. Although current research on mercury pathways has advanced our understanding of the risks associated with human exposure, limited information exists for remote areas with high diversity of fauna, flora, and indigenous communities. This study aims to deepen our understanding of the presence of total mercury in water, sediments, and fish, within aquatic ecosystems of two indigenous territories: Gomataon (Waorani Nationality) and Sinangoé (Ai´Cofán Nationality) in the Ecuadorian Amazon. Our findings indicate that, for most fish (91.5%), sediment (100%) and water (95.3%) samples, mercury levels fall under international limits. For fish, no significant differences in mercury levels were detected between the two communities. However, eight species exceeded recommended global limits, and one surpassed the threshold according to Ecuadorian legislation. Piscivore and omnivore fish exhibited the highest concentrations of total mercury among trophic guilds. Only one water sample from each community's territory exceeded these limits. Total mercury in sediments exhibited greater concentrations in Gomataon than Sinangoé. Greater levels of mercury in sediments were associated with the occurrence of total organic carbon. Considering that members of the communities consume the analyzed fish, an interdisciplinary approach, including isotopic analysis, methylmercury sampling in humans, and mercury monitoring over time, is imperative for a detailed risk assessment of mercury exposure in Amazonian communities.

New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding.

DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.

Validating the occurrence of the giant mottled eel (Anguilla marmorata) in the Galápagos Islands.

The giant mottled eel (Anguilla marmorata) is distributed mostly in the Indo-West Pacific. However, a few records indicate the presence of this eel in the Tropical Central and East Pacific. In April 2019, an eel specimen was caught in a small stream in San Cristobal Island, Galápagos. Morphological and molecular characters (16S and Cytb mtDNA sequences) confirmed the species as A. marmorata Quoy & Gaimard, 1824. The re-discovery of A. marmorata in Galápagos supports the hypothesis of an eastward range expansion from the west, probably through the North Equatorial Counter-Current.

Climate and sea surface trends in the Galapagos Islands.

The Galapagos Islands are a global hotspot of environmental change. However, despite their potentially major repercussions, little is known about current and expected changes in regional terrestrial climate variables and sea surface temperatures (SST). Here, by analysing existing meteorological observations and secondary datasets, we find that the Islands have warmed by about 0.6 °C since the early 1980s, while at the same time becoming drier. In fact, the onset of the wet season is currently delayed 20 days. This drying trend may reverse, however, given that future climate projections for the region suggest mean annual precipitation may increase between 20 and 70%. This would also be accompanied by more extreme wet and hot conditions. Further, we find that regional SST has increased by 1.2 °C over the last two decades. These changes will, in turn, translate into deterioration of marine ecosystems and coral, proliferation of invasive species, and damages to human water, food, and infrastructure systems. Future projections, however, may be overestimated due to the poor capacity of climatic models to capture Eastern-Pacific ENSO dynamics. Our findings emphasize the need to design resilient climate adaptation policies that will remain robust in the face of a wide range of uncertain and changing climatic futures.

Conservation threats and future prospects for the freshwater fishes of Ecuador: A hotspot of Neotropical fish diversity.

Freshwater fish communities in Ecuador exhibit some of the highest levels of diversity and endemism in the Neotropics. Unfortunately, aquatic ecosystems in the country are under serious threat and conditions are deteriorating. In 2018-19, the government of Ecuador sponsored a series of workshops to examine the conservation status of Ecuador's freshwater fishes. Concerns were identified for 35 species, most of which are native to the Amazon region, and overfishing of Amazonian pimelodid catfishes emerged as a major issue. However, much of the information needed to make decisions across fish groups and regions was not available, hindering the process and highlighting the need for a review of the conservation threats to Ecuador's freshwater fishes. Here, we review how the physical alteration of rivers, deforestation, wetland and floodplain degradation, agricultural and urban water pollution, mining, oil extraction, dams, overfishing, introduced species and climate change are affecting freshwater fishes in Ecuador. Although many of these factors affect fishes throughout the Neotropics, the lack of data on Ecuadorian fish communities is staggering and highlights the urgent need for more research. We also make recommendations, including the need for proper enforcement of existing environmental laws, restoration of degraded aquatic ecosystems, establishment of a national monitoring system for freshwater ecosystems, investment in research to fill gaps in knowledge, and encouragement of public engagement in citizen science and conservation efforts. Freshwater fishes are an important component of the cultural and biological legacy of the Ecuadorian people. Conserving them for future generations is critical.

Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning.

Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.

Seeing the rainbow: mechanisms underlying spectral sensitivity in teleost fishes.

Among vertebrates, teleost eye diversity exceeds that found in all other groups. Their spectral sensitivities range from ultraviolet to red, and the number of visual pigments varies from 1 to over 40. This variation is correlated with the different ecologies and life histories of fish species, including their variable aquatic habitats: murky lakes, clear oceans, deep seas and turbulent rivers. These ecotopes often change with the season, but fish may also migrate between ecotopes diurnally, seasonally or ontogenetically. To survive in these variable light habitats, fish visual systems have evolved a suite of mechanisms that modulate spectral sensitivities on a range of timescales. These mechanisms include: (1) optical media that filter light, (2) variations in photoreceptor type and size to vary absorbance and sensitivity, and (3) changes in photoreceptor visual pigments to optimize peak sensitivity. The visual pigment changes can result from changes in chromophore or changes to the opsin. Opsin variation results from changes in opsin sequence, opsin expression or co-expression, and opsin gene duplications and losses. Here, we review visual diversity in a number of teleost groups where the structural and molecular mechanisms underlying their spectral sensitivities have been relatively well determined. Although we document considerable variability, this alone does not imply functional difference per se. We therefore highlight the need for more studies that examine species with known sensitivity differences, emphasizing behavioral experiments to test whether such differences actually matter in the execution of visual tasks that are relevant to the fish.

Visual adaptation could aid sympatric speciation in a deep crater lake.

Allopatric speciation was originally suggested to be the primary mechanism of animal speciation (Mayr, 1942; Figure 1). During allopatric speciation, populations diverge when gene flow is reduced across significant biogeographic barriers. Sympatric speciation, where species diverge while inhabiting the same location, was thought to be essentially impossible. However, the advent of theoretical models followed by new experimental evidence made sympatric speciation more plausible (Via, 2001). The cichlid fishes of Barombi Mbo, a small crater lake in western Cameroon, became one of the most widely accepted examples of sympatric speciation (Schliewen, Tautz, & Paabo, 1994). Although the phylogenetic history of this clade is not quite as simple as originally thought, it remains one of the best examples of sympatric speciation (Richards, Poelstra, & Martin, 2018). However, little is known about the molecular mechanisms contributing to the splitting of these species in situ. In a From the Cover article in this issue of Molecular Ecology, Musilova et al. (2019) focus on the diversity of visual systems among these fishes. They identify genetic changes associated with several aspects of visual adaptation that may have contributed to the ecological specialization and sympatric speciation of cichlids in this lake.

Color discrimination thresholds in a cichlid fish: Metriaclima benetos.

Color vision is essential for animals as it allows them to detect, recognize and discriminate between colored objects. Studies analyzing color vision require an integrative approach, combining behavioral experiments, physiological models and quantitative analyses of photoreceptor stimulation. Here, we demonstrate, for the first time, the limits of chromatic discrimination in Metriaclima benetos, a rock-dwelling cichlid from Lake Malawi, using behavioral experiments and visual modeling. Fish were trained to discriminate between colored stimuli. Color discrimination thresholds were quantified by testing fish chromatic discrimination between the rewarded stimulus and distracter stimuli that varied in chromatic distance (ΔS). This was done under fluorescent lights alone and with additional violet lights. Our results provide two main outcomes. First, cichlid color discrimination thresholds correspond with predictions from the receptor noise limited (RNL) model but only if we assume a Weber fraction higher than the typical value of 5%. Second, cichlids may exhibit limited color constancy under certain lighting conditions as most individuals failed to discriminate colors when violet light was added. We further used the color discrimination thresholds obtained from these experiments to model color discrimination of actual fish colors and backgrounds under natural lighting for Lake Malawi. We found that, for M. benetos, blue is most chromatically contrasting against yellows and space-light, which might be important for discriminating male nuptial colorations and detecting males against the background. This study highlights the importance of lab-based behavioral experiments in understanding color vision and in parameterizing the assumptions of the RNL vision model for different species.

Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses.

To determine the visual sensitivities of an organism of interest, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is often used to quantify expression of the light-sensitive opsins in the retina. While qRT-PCR is an affordable, high-throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1-hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT-PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1-α and ß-actin), (b) total RNA concentration, (c) GNAT2, (the cone-specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time-of-day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.

Variable vision in variable environments: the visual system of an invasive cichlid (Cichla monoculus) in Lake Gatun, Panama.

An adaptive visual system is essential for organisms inhabiting new or changing light environments. The Panama Canal exhibits such variable environments owing to its anthropogenic origin and current human activities. Within the Panama Canal, Lake Gatun harbors several exotic fish species including the invasive peacock bass (Cichla monoculus), a predatory Amazonian cichlid. In this research, through spectral measurements and molecular and physiological experiments, we studied the visual system of C. monoculus and its adaptive capabilities. Our results suggest that (1) Lake Gatun is a highly variable environment, where light transmission changes throughout the canal waterway, and that (2) C. monoculus has several visual adaptations suited for this red-shifted light environment. Cichla monoculus filters short wavelengths (∼400 nm) from the environment through its ocular media and tunes its visual sensitivities to the available light through opsin gene expression. More importantly, based on shifts in spectral sensitivities of photoreceptors alone, and on transcriptome analysis, C. monoculus exhibits extreme intraspecific variation in the use of vitamin A1/A2 chromophore in their photoreceptors. Fish living in turbid water had higher proportions of vitamin A2, shifting sensitivities to longer wavelengths, than fish living in clear water. Furthermore, we also found variation in retinal transcriptomes, where fish from turbid and clear waters exhibited differentially expressed genes that vary greatly in their function. We suggest that this phenotypic plasticity has been key in the invasion success of C. monoculus.

Behavioral color vision in a cichlid fish: Metriaclima benetos.

Color vision is the capacity to discriminate color regardless of brightness. It is essential for many fish species as they rely on color discrimination for numerous ecological tasks. The study of color vision is important because it can unveil the mechanisms that shape coloration patterns, visual system sensitivities and, hence, visual signals. In order to better understand the mechanisms underlying color vision, an integrative approach is necessary. This usually requires combining behavioral, physiological and genetic experiments with quantitative modeling, resulting in a distinctive characterization of the visual system. Here, we provide new data on the color vision of a rock-dwelling cichlid from Lake Malawi: Metriaclima benetos. For this study we used a behavioral approach to demonstrate color vision through classical conditioning, complemented with modeling of color vision to estimate color contrast. For our experiments we took into account opsin coexpression and considered whether cichlids exhibit a dichromatic or a trichromatic visual system. Behavioral experiments confirmed color vision in M. benetos; most fish were significantly more likely to choose the trained over the distracter stimuli, irrespective of brightness. Our results are supported by visual modeling that suggests that cichlids are trichromats and achieve color vision through color opponency mechanisms, which are a result of three different photoreceptor channels. Our analyses also suggest that opsin coexpression can negatively affect perceived color contrast. This study is particularly relevant for research on the cichlid lineage because cichlid visual capabilities and coloration patterns are implicated in their adaptive radiation.

The opsin genes of amazonian cichlids.

Vision is a critical sense for organismal survival with visual sensitivities strongly shaped by the environment. Some freshwater fishes with a Gondwanan origin are distributed in both South American rivers including the Amazon and African rivers and lakes. These different habitats likely required adaptations to murky and clear environments. In this study, we compare the molecular basis of Amazonian and African cichlid fishes' visual systems. We used next-generation sequencing of genomes and retinal transcriptomes to examine three Amazonian cichlid species. Genome assemblies revealed six cone opsin classes (SWS1, SWS2B, SWS2A, RH2B, RH2A and LWS) and rod opsin (RH1). However, the functionality of these genes varies across species with different pseudogenes found in different species. Our results support evidence of an RH2A gene duplication event that is shared across both cichlid groups, but which was probably followed by gene conversion. Transcriptome analyses show that Amazonian species mainly express three opsin classes (SWS2A, RH2A and LWS), which likely are a good match to the long-wavelength-oriented light environment of the Amazon basin. Furthermore, analysis of amino acid sequences suggests that the short-wavelength-sensitive genes (SWS2B, SWS2A) may be under selective pressures to shift their spectral properties to a longer-wavelength visual palette. Our results agree with the 'sensitivity hypothesis' where the light environment causes visual adaptation. Amazonian cichlid visual systems are likely adapting through gene expression, gene loss and possibly spectral tuning of opsin sequences. Such mechanisms may be shared across the Amazonian fish fauna.

Proximate and ultimate causes of variable visual sensitivities: Insights from cichlid fish radiations.

Animals vary in their sensitivities to different wavelengths of light. Sensitivity differences can have fitness implications in terms of animals' ability to forage, find mates, and avoid predators. As a result, visual systems are likely selected to operate in particular lighting environments and for specific visual tasks. This review focuses on cichlid vision, as cichlids have diverse visual sensitivities, and considerable progress has been made in determining the genetic basis for this variation. We describe both the proximate and ultimate mechanisms shaping cichlid visual diversity using the structure of Tinbergen's four questions. We describe (1) the molecular mechanisms that tune visual sensitivities including changes in opsin sequence and expression; (2) the evolutionary history of visual sensitivity across the African cichlid flocks; (3) the ontological changes in visual sensitivity and how modifying this developmental program alters sensitivities among species; and (4) the fitness benefits of spectral tuning mechanisms with respect to survival and mating success. We further discuss progress to unravel the gene regulatory networks controlling opsin expression and suggest that a simple genetic architecture contributes to the lability of opsin gene expression. Finally, we identify unanswered questions including whether visual sensitivities are experiencing selection, and whether similar spectral tuning mechanisms shape visual sensitivities of other fishes. genesis 54:299-325, 2016. © 2016 Wiley Periodicals, Inc.

Sensory modalities in cichlid fish behavior.

Among teleosts, cichlids are a great model for studies of evolution, behavior, diversity and speciation. Studies of cichlid sensory systems have revealed diverse sensory capabilities that vary among species. Hence, sensory systems are important for understanding cichlid behavior from proximate and ultimate points of view. Cichlids primarily rely on five sensory channels: hearing, mechanosensation, taste, vision, and olfaction, to receive information from the environment and respond accordingly. Within these sensory channels, cichlid species exhibit different adaptations to their surrounding environment, which differ in abiotic and biotic stimuli. Research on cichlid sensory capabilities and behaviors incorporates integrative approaches and relies on diverse scientific disciplines from physics to chemistry to neurobiology to understand the evolution of the cichlid sensory systems.

Discovering Hidden Diversity of Characins (Teleostei: Characiformes) in Ecuador's Yasuní National Park.

BACKGROUND: Management and conservation of biodiversity requires adequate species inventories. The Yasuní National Park is one of the most diverse regions on Earth and recent studies of terrestrial vertebrates, based on genetic evidence, have shown high levels of cryptic and undescribed diversity. Few genetic studies have been carried out in freshwater fishes from western Amazonia. Thus, in contrast with terrestrial vertebrates, their content of cryptic diversity remains unknown. In this study, we carried out genetic and morphological analyses on characin fishes at Yasuní National Park, in eastern Ecuador. Our goal was to identify cryptic diversity among one of the most speciose fish families in the Amazon region. This is the first time that genetic evidence has been used to assess the species content of the Napo Basin, one of the richest regions in vertebrate diversity. RESULTS: Phylogenetic analyses of partial mitochondrial 16S ribosomal RNA gene (∼600 pb) DNA sequences from 232 specimens of the family Characidae and its closest groups revealed eight candidate new species among 33 species sampled, representing a 24% increase in species number. Analyses of external morphology allowed us to confirm the species status of six of the candidate species. CONCLUSIONS: Our results show high levels of cryptic diversity in Amazonian characins. If this group is representative of other Amazonian fish, our results would imply that the species richness of the Amazonian ichthyofauna is highly underestimated. Molecular methods are a necessary tool to obtain more realistic inventories of Neotropical freshwater fishes.