Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes

Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of LakeVictoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the EastAfrican radiations that started 8-12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.Peer reviewe

Contrasting signatures of genomic divergence during sympatric speciation

Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures. The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin(1,2). Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process(3). Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs(4), but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories(5). Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.Peer reviewe

Sympatric and Allopatric Diversification in the Adaptive Radiations of Midas Cichlids in Nicaraguan Lakes

The Nicaraguan Midas cichlid species complex is a natural experiment where fish from a large source population from turbid and shallow great lakes very recently (<20,000 years ago) colonized eight small crater lakes. The colonizers experienced completely novel environments in the clear and deep calderas. So far, 13 Midas cichlid species have been described, but more genetic clusters were identified. Although some of these species arose in allopatry, many more evolved in the absence of barriers to gene flow within two crater lakes. They contain small radiations of four and six endemics, respectively. These radiations constitute one of the few generally accepted empirical examples for sympatric speciation making them an ideal system for studying repeated evolution of adaptations and speciation at different levels of biological organization, including the genome level. Diversification occurred repeatedly in parallel including body morphology, coloration, color perception, and trophic structures such as pharyngeal jaws and hypertrophied lips. Additionally, parallel speciation happened in the two small crater lake radiations, where ecomorphologically similar species evolved repeatedly. Genomic differentiation associated with oligogenic traits (e.g., hypertrophic lips and coloration) is shallow, remaining polymorphisms, but much higher for polygenic traits (e.g., body shape and pharyngeal jaw morphology) that distinguish new species.publishe

Rapid adaptation to a novel light environment : The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.)

Colonization of novel habitats is typically challenging to organisms. In the initial stage after colonization, approximation to fitness optima in the new environment can occur by selection acting on standing genetic variation, modification of developmental patterns or phenotypic plasticity. Midas cichlids have recently colonized crater Lake Apoyo from great Lake Nicaragua. The photic environment of crater Lake Apoyo is shifted towards shorter wavelengths compared to great Lake Nicaragua and Midas cichlids from both lakes differ in visual sensitivity. We investigated the contribution of ontogeny and phenotypic plasticity in shaping the visual system of Midas cichlids after colonizing this novel photic environment. To this end, we measured cone opsin expression both during development and after experimental exposure to different light treatments. Midas cichlids from both lakes undergo ontogenetic changes in cone opsin expression, but visual sensitivity is consistently shifted towards shorter wavelengths in crater lake fish, which leads to a paedomorphic retention of their visual phenotype. This shift might be mediated by lower levels of thyroid hormone in crater lake Midas cichlids (measured indirectly as dio2 and dio3 gene expression). Exposing fish to different light treatments revealed that cone opsin expression is phenotypically plastic in both species during early development, with short and long wavelength light slowing or accelerating ontogenetic changes, respectively. Notably, this plastic response was maintained into adulthood only in the derived crater lake Midas cichlids. We conclude that the rapid evolution of Midas cichlids’ visual system after colonizing crater Lake Apoyo was mediated by a shift in visual sensitivity during ontogeny and was further aided by phenotypic plasticity during development.publishe

The imperiled fish fauna in the Nicaragua Canal zone

Large-scale infrastructure projects commonly have strong effects on the environment. Thus, it is of highest importance to evaluate possible impacts on biodiversity and take measures to reduce these. The planned construction of the Nicaragua Canal will irreversibly alter the aquatic environment of Nicaragua in many ways. Two distinct drainage basins (San Juan and Punta Gorda) will be connected, fostering biotic homogenization due to establishment of non-native species, extirpation of local species and alteration of numerous ecosystems. Considering the far-reaching impact of this project on Nicaragua's environment, too few studies on biodiversity have been performed in affected areas. This limits the ability to make solid environmental impact assessments. Here, we explore the geographic distribution of taxonomic and genetic diversity from representative freshwater fish species across the Nicaragua Canal Zone. We show that freshwater fish faunas likely differ substantially between drainage basins (Jaccard similarity = 0.33). Further, most populations from distinct drainage basins are highly differentiated based on mitochondrial cytb. Removing the geographic barrier between these basins will promote genetic homogenization and the loss of unique diversity. Moreover, we found species in areas where they were not known to exist and provide insights into the distribution of an undescribed, highly distinct clade of livebearing fish (Poecilia). Our results indicate that the Nicaragua Canal likely will have strong impacts on Nicaragua's freshwater biodiversity. However, knowledge about the extent of these impacts remains scarce, highlighting the need for more thorough investigations to inform more cogently on the status quo before the environment is altered irreversibly.publishe

Reverting ontogeny : rapid phenotypic plasticity of colour vision in cichlid fish

Phenotypic plasticity, particularly during development, allows organisms to rapidly adjust to different environmental conditions. Yet, it is often unclear whether the extent and direction of plastic changes are restricted by an individual's ontogeny. Many species of cichlid fishes go through ontogenetic changes in visual sensitivity, from short to long wavelengths, by switching expression of cone opsin genes crucial for colour vision. During this progression, individuals often exhibit phenotypic plasticity to the ambient light conditions. However, it is commonly assumed that once an adult visual phenotype is reached, reverting to an earlier ontogenetic state with higher sensitivity at shorter wavelengths is not common. In this study, we experimentally demonstrate that four-month-old Midas cichlid fish (Amphilophus astorquii) show plasticity in single cone opsin expression after experiencing drastic changes in light conditions. Resulting shifts of visual sensitivity occurred presumably in an adaptive direction—towards shorter or longer wavelengths when exposed to short- or long-wavelength light, respectively. Single cone opsin expression changed within only a few days and went through a transitional phase of co-expression. When the environment was experimentally enriched in long-wavelength light, the corresponding change occurred gradually along a dorsoventral gradient within the retina. This plasticity allowed individuals to revert earlier ontogenetic changes and return to a more juvenile visual phenotype demonstrating previously unrecognized insights into temporal and spatial dynamics of phenotypic plasticity of the visual system in response to ambient light.publishe

Heterochronic opsin expression due to early light deprivation results in drastically shifted visual sensitivity in a cichlid fish : Possible role of thyroid hormone signaling

During early ontogeny, visual opsin gene expression in cichlids is influenced by prevailing light regimen. Red light, for example, leads to an early switch from the expression of short‐wavelength sensitive to long‐wavelength sensitive opsins. Here, we address the influence of light deprivation on opsin expression. Individuals reared in constant darkness during the first 14 days post‐hatching (dph) showed a general developmental delay compared with fish reared under a 12:12 hr light–dark cycle (control group). Several characters including pigmentation patterns and eye development, appeared later in dark‐reared individuals. Quantitative real‐time PCR and fluorescent in situ hybridization at six time points during the 14 days period revealed that fish from the control group expressed opsin genes from 5 dph on and maintained a short‐wavelength sensitive phenotype (sws1, rh2b, and rh2a). Onset of opsin expression in dark‐reared Midas cichlids was delayed by 4 days and visual sensitivity rapidly progressed toward a long‐wavelength sensitive phenotype (sws2b, rh2a, and lws). Shifts in visual sensitivities toward longer wavelengths are mediated by thyroid hormone (TH) in many vertebrates. Compared to control fish, dark‐reared individuals showed elevated dio3 expression levels ‐ a validated proxy for TH concentration ‐ suggesting higher circulating TH levels. Despite decelerated overall development, ontogeny of opsin gene expression was accelerated, resulting in retinae with long‐wavelength shifted predicted sensitivities compared to light‐reared individuals. Indirect evidence suggests that this was due to altered TH metabolism.publishe

Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish

Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth and the inherent optical properties of the water. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than 4,000 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing two-week-old Midas cichlids to exogenous TH or a TH-inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Whereas exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter-wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments.publishe

Heterogeneity across Neotropical aquatic environments affects prokaryotic and eukaryotic biodiversity based on environmental DNA

Characterizing biological communities and knowledge on the distribution of biodiversity allows the assessment of ecological quality. This provides valuable information for conservation biology and monitoring purposes. While obtaining such data has been challenging in the past, environmental DNA (eDNA) sampling represents a promising tool to describe biodiversity on a broad taxonomic scale. In this study, we provide the first broad-scale biodiversity assessment for ten Neotropical water bodies in Nicaragua (a major river, two great lakes, and seven relatively young and small crater lakes) using eDNA sampling to determine how abiotic factors structure the distribution of prokaryotic and eukaryotic biodiversity across these environments. Further, we explored to what extent levels of biodiversity are associated across different taxonomic groups and environments. We found that prokaryotic and eukaryotic α-diversity was consistently higher in the great lakes (i.e., Lakes Nicaragua and Managua) as well as in Río San Juan compared with the young and small crater lakes. Differences of prokaryotic and eukaryotic communities (β-diversity) were significantly correlated, indicating that biological communities are similarly structured across environments. Accordingly, differences in salinity were correlated with prokaryotic and eukaryotic communities, whereas differences in dissolved oxygen were only correlated with prokaryotic communities (β-diversity). Yet, salinity and dissolved oxygen only affected prokaryotic α-diversity, suggesting different effects of these two abiotic factors on biodiversity within aquatic environments. Moreover, α-diversity of different phyla was positively correlated, although more strongly in prokaryotes, showing that biodiversity patterns are congruent across a broad range of lineages, particularly in prokaryotes.publishe

The role of rare morph advantage and conspicuousness in the stable gold-dark colour polymorphism of a crater lake Midas cichlid fish

1. Genetically based stable colour polymorphisms provide a unique opportunity to study the evolutionary processes that preserve genetic variability in the wild. Different mechanisms are proposed to promote the stability of polymorphisms, but only few empirical examples have been documented, resulting in an incomplete understanding of these mechanisms.2. A remarkable genetically determined stable colour polymorphism is found in the Nicaraguan Midas cichlid species complex (Amphilophus cf. citrinellus). All Midas cichlids start their life with a dark-grey coloration (dark morph), but individuals carrying the dominant “gold” allele (c. 10%) lose their melanophores later in life, revealing the underlying orange coloration (gold morph). How this polymorphism is maintained remains unclear. Two main hypotheses have been proposed, both suggesting differential predation upon colour morphs as the proximate mechanism. One predicts that the conspicuous gold morph is more likely to be preyed upon, but this disadvantage is balanced by their competitive dominance over the dark morph. The second hypothesis suggests a rare morph advantage where the rarer gold morph experiences less predation. Empirical evidence for either of these mechanisms is still circumstantial and inconclusive.3. We conducted two field experiments in a Nicaraguan crater lake using wax models simulating both morphs to determine predation pressure upon Midas cichlid colour morphs. First, we tested the interaction of coloration and depth on attack rate. Second, we tested the interaction of fish size and coloration. We contrasted the pattern of attacks from these experiments to the predicted predation patterns from the hypotheses proposed to explain the colour polymorphism's stability.4. Large models imitating colour morphs were attacked at similar rates irrespectively of their position in the water column. Yet, attacks upon small models resembling juveniles were directed mainly towards dark models. This resulted in a significant size-by-colour interaction.5. We suggest that gold Midas cichlids experience a rare morph advantage as juveniles when individuals of this morph are extremely uncommon. But this effect is reduced or disappears among adults, where gold individuals are relatively more common. Thus, the interaction of rare morph advantage and conspicuousness, rather than either of those factors alone, is a likely mechanism resulting in the stability of the colour polymorphism in Midas cichlids.publishe