Sympatric ecological divergence associated with a color polymorphism

Background selection for camouflage shifts in accordance with color change in an intertidal prawn

To maximize camouflage across visually heterogeneous habitats, animals have evolved a variety of strategies, including polyphenism, color change, and behavioral background matching. Despite the expected importance of behavioral processes for mediating camouflage, such as selection for matching substrates, behavior has received less attention than color traits themselves, and interactions between color change and behavior are largely unexplored. Here, we investigated behavioral background matching in green and red chameleon prawns (Hippolyte varians) over the course of a color change experiment. Prawns were housed on mismatching green and red seaweeds for 30 days and periodically given a choice test between the same seaweeds in y-choice trials over the experiment. We found that, as prawns change color and improve camouflage (to the perspective of a fish predator), there is a reinforcing shift in behavior. That is, as prawns shift from red to green color, or vice versa, their seaweed color preference follows this. We provide key empirical evidence that plasticity of appearance (color) is accompanied by a plastic shift in behavior (color preference) that reinforces camouflage in a color changing species on its natural substrate. Overall, our research highlights how short-term plasticity of behavior and longer-term color change act in tandem to maintain crypsis over time.

Ecophenotypic Variation of Midas Cichlid, Amphilophus citrinellus (Gunther, 1864), in Lake Batur, Bali, Indonesia

Cichlid fishes exhibit rapid adaptive radiations with significant diversification rates in response to ecological variability, i.e., ecological opportunity or geographical isolation. The discovery of a Midas cichlid species in Lake Batur, Indonesia's largest volcanic lake, first reported in 2013, could represent such adaptations. Midas cichlids can now be found in a range of habitats in Lake Batur and dominate the lake's fish population by up to 60%. This study aimed to identify the interaction between habitat, water quality, and Midas cichlid in Lake Batur, facilitating morphometric variances in the fish populations. The fish were captured at five locations in Lake Batur using fishing rods, community nets with mesh sizes of 2-3 inches, experimental gillnets with mesh sizes of 1 inch, and fish scoops in floating net cages during August and November 2022. There were 46 fish samples caught from the five stations, all photographed using a digital camera and later measured using the ZEN 2012 software. The fish measurement employed a truss morphometric method using 21 distinct morphometric body features. Canonical analysis was used to determine the distribution of characteristics, while discriminant analysis was used to examine the closeness of association. The measured water quality parameters included pH, DO, temperature, conductivity, and TDS for in-situ and TSS, TP, TN, and chlorophyll A for ex-situ. The findings revealed morphometric changes among Midas cichlid species in Lake Batur caused by habitat and water quality differences. The distinction can be detected in the anterior and posterior bodies (C1, B1, C3, C6, C5, B3 and B4). Temperature and aquatic plants, Azolla pinnata, may detect the station and shape of fish in Lake Batur. Body shape cannot be identified by chlorophyll A, TN, DO, and TDS. Future genetic research could answer why fish groups with varied body types coexist in the same location.

Ecological disruptive selection acting on quantitative loci can drive sympatric speciation

The process of speciation generates biodiversity. According to the null model of speciation, barriers between populations arise in allopatry, where, prior to biology, geography imposes barriers to gene flow. On the other hand, sympatric speciation requires that the process of speciation happen in the absence of a geographical barrier, where the members of the population have no spatial, temporal barriers. Several attempts have been made to theoretically identify the conditions in which speciation can occur in sympatry. However, these efforts suffer from several limitations. We propose a model for sympatric speciation based on adaptation for resource utilization. We use a genetics-based model to investigate the relative roles of prezygotic and postzygotic barriers, from the context of ecological disruptive selection, sexual selection, and genetic architecture, in causing and maintaining sympatric speciation. Our results show that sexual selection that acts on secondary sexual traits does not play any role in the process of speciation in sympatry and that assortative mating based on an ecologically relevant trait forces the population to show an adaptive response. We also demonstrate that understanding the genetic architecture of the trait under ecological selection is very important and that it is not required for the strength of ecological disruptive selection to be very high in order for speciation to occur in sympatry. Our results provide an insight into the kind of scenarios in which sympatric speciation can be demonstrated in the lab.

Contrasting patterns of genetic and phenotypic divergence of two sympatric congeners, Phragmites australis and P. hirsuta, in heterogeneous habitats

Habitat heterogeneity leads to genome-wide differentiation and morphological and ecological differentiation, which will progress along the speciation continuum, eventually leading to speciation. Phragmites hirsuta and Phragmites australis are sympatric congeners that coexist in saline-alkaline meadow soil (SAS) and sandy soil (SS) habitats of the Songnen Meadow. The results provided genetic evidence for two separate species of reeds. Genetic diversity and spatial genetic structure supported the specialist-generalist variation hypothesis (SGVH) in these two sympatric reed species, suggesting that P. australis is a generalist and P. hirsuta is a habitat specialist. When we compared these different species with respect to phenotypic and genetic variation patterns in different habitats, we found that the phenotypic differentiation of P. australis between the two habitats was higher than that of P. hirsuta. Multiple subtle differences in morphology, genetic background, and habitat use collectively contribute to ecological success for similar congeners. This study provided evidence of the two reed congeners, which should contribute to their success in harsh environments.

Climate mediates color morph turnover in a species exhibiting alternative reproductive strategies

Sexual selection is considered the primary driver of morph turnover in many color polymorphic taxa, yet the potential for other factors (like climate) to contribute to polymorphism maintenance and evolution remains unclear. Appreciation for a role of environmental conditions in the maintenance and evolution of color polymorphisms has grown in recent years, generating evidence suggesting that color morphs linked to sexual selection may also diverge in climate sensitivity. Focusing on the three color components contributing to the male tree lizard (Urosaurus ornatus) color morphs, I reveal a marked concordance between patterns of turnover over space and time, with a general affinity of orange- and yellow-colored males to hotter, more variable conditions, and blue colored males to wetter, cooler conditions. An assessment of long-term turnover in the blue color component in response to recent climate change over the past 60 years reinforces these findings. Overall, behavioral asymmetries attributed to sexual selection likely expose competing morphs to divergent environmental conditions in heterogeneous habitats, creating opportunity for natural selection to shape climate sensitivities that also drive turnover in morph color composition. Ultimately, these processes may favor stark asymmetries in morph persistence over the coming decades.

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remain elusive. Here, we aim to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic "dark morph", about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous "gold morph". Using a new haplotype-resolved long-read assembly we discover an 8.2 kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term goldentouch in reference to the Greek myth of King Midas. The gene goldentouch is differentially expressed between morphs, presumably due to structural implications of inverted repeats in both DNA and/or RNA (cruciform and hairpin formation). The near-perfect association of the insertion with the phenotype across independent populations suggests that it likely underlies this trans-specific, stable polymorphism.

Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio

The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.

EcoQBNs: First Application of Ecological Modeling with Quantum Bayesian Networks

A recent advancement in modeling was the development of quantum Bayesian networks (QBNs). QBNs generally differ from BNs by substituting traditional Bayes calculus in probability tables with the quantum amplification wave functions. QBNs can solve a variety of problems which are unsolvable by, or are too complex for, traditional BNs. These include problems with feedback loops and temporal expansions; problems with non-commutative dependencies in which the order of the specification of priors affects the posterior outcomes; problems with intransitive dependencies constituting the circular dominance of the outcomes; problems in which the input variables can affect each other, even if they are not causally linked (entanglement); problems in which there may be >1 dominant probability outcome dependent on small variations in inputs (superpositioning); and problems in which the outcomes are nonintuitive and defy traditional probability calculus (Parrondo’s paradox and the violation of the Sure Thing Principle). I present simple examples of these situations illustrating problems in prediction and diagnosis, and I demonstrate how BN solutions are infeasible, or at best require overly-complex latent variable structures. I then argue that many problems in ecology and evolution can be better depicted with ecological QBN (EcoQBN) modeling. The situations that fit these kinds of problems include noncommutative and intransitive ecosystems responding to suites of disturbance regimes with no specific or single climax condition, or that respond differently depending on the specific sequence of the disturbances (priors). Case examples are presented on the evaluation of habitat conditions for a bat species, representing state-transition models of a boreal forest under disturbance, and the entrainment of auditory signals among organisms. I argue that many current ecological analysis structures—such as state-and-transition models, predator–prey dynamics, the evolution of symbiotic relationships, ecological disturbance models, and much more—could greatly benefit from a QBN approach. I conclude by presenting EcoQBNs as a nascent field needing the further development of the quantum mathematical structures and, eventually, adjuncts to existing BN modeling shells or entirely new software programs to facilitate model development and application.

Genomic landscape of geographically structured colour polymorphism in a temperate marine fish

The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.

Contrasting signatures of genomic divergence during sympatric speciation

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 Darwin1,2. 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 process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, 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 histories5. 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.

Functional colour genes and signals of selection in colour-polymorphic salamanders

Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs-ancestral black-yellow striped, fully yellow and fully brown-differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype-phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and 'omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.

Colour change and behavioural choice facilitate chameleon prawn camouflage against different seaweed backgrounds

Camouflage is driven by matching the visual environment, yet natural habitats are rarely uniform and comprise many backgrounds. Therefore, species often exhibit adaptive traits to maintain crypsis, including colour change and behavioural choice of substrates. However, previous work largely considered these solutions in isolation, whereas many species may use a combination of behaviour and appearance to facilitate concealment. Here we show that green and red chameleon prawns (Hippolyte varians) closely resemble their associated seaweed substrates to the vision of predatory fish, and that they can change colour to effectively match new backgrounds. Prawns also select colour-matching substrates when offered a choice. However, colour change occurs over weeks, consistent with seasonal changes in algal cover, whereas behavioural choice of matching substrates occurs in the short-term, facilitating matches within heterogeneous environments. We demonstrate how colour change and behaviour combine to facilitate camouflage against different substrates in environments varying spatially and temporally.

Shape, colour plasticity, and habitat use indicate morph-specific camouflage strategies in a marine shrimp

Background

Colour and shape polymorphisms are important features of many species and may allow individuals to exploit a wider array of habitats, including through behavioural differences among morphs. In addition, differences among individuals in behaviour and morphology may reflect different strategies, for example utilising different approaches to camouflage. Hippolyte obliquimanus is a small shrimp species inhabiting different shallow-water vegetated habitats. Populations comprise two main morphs: homogeneous shrimp of variable colour (H) and transparent individuals with coloured stripes (ST). These morphs follow different distribution patterns between their main algal habitats; the brown weed Sargassum furcatum and the pink-red weed Galaxaura marginata. In this study, we first investigated morph-specific colour change and habitat selection, as mechanisms underlying camouflage and spatial distribution patterns in nature. Then, we examined habitat fidelity, mobility, and morphological traits, further indicating patterns of habitat use.

Results

H shrimp are capable of changing colour in just a few days towards their algal background, achieving better concealment in the more marginal, and less preferred, red weed habitat. Furthermore, laboratory trials showed that habitat fidelity is higher for H shrimp, whereas swimming activity is higher for the ST morph, aligned to morphological evidence indicating these two morphs comprise a more benthic (H) and a more pelagic (ST) life-style, respectively.

Conclusions

Results suggest that H shrimp utilise a camouflage strategy specialised to a limited number of backgrounds at any one time, whereas ST individuals comprise a phenotype with more generalist camouflage (transparency) linked to a more generalist background utilisation. The coexistence within a population of distinct morphotypes with apparently alternative strategies of habitat use and camouflage may reflect differential responses to substantial seasonal changes in macroalgal cover. Our findings also demonstrate how colour change, behaviour, morphology, and background use all interact in achieving camouflage.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0796-8) contains supplementary material, which is available to authorized users.

High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis

Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water.

Sympatric speciation in structureless environments

BACKGROUND

Darwin and the architects of the Modern Synthesis found sympatric speciation difficult to explain and suggested it is unlikely to occur. Increasingly, evidence over the past few decades suggest that sympatric speciation can occur under ecological conditions that require at most intraspecific competition for a structured resource. Here we used an individual-based population model with variable foraging strategies to study the evolution of mating behavior among foraging strategy types. Initially, individuals were placed at random on a structureless resource landscape, with subsequent spatial variation induced through foraging activity itself. The fitness of individuals was determined by their biomass at the end of each generational cycle. The model incorporates three diallelic, codominant foraging strategy genes, and one mate-choice or m-trait (i.e. incipient magic trait) gene, where the latter is inactive when random mating is assumed.

RESULTS

Under non-random mating, the m-trait gene promotes increasing levels of either disassortative or assortative mating when the frequency of m respectively increases or decreases from 0.5. Our evolutionary simulations demonstrate that, under initial random mating conditions, an activated m-trait gene evolves to promote assortative mating because the system, in trying to fit a multipeak adaptive landscape, causes heterozygous individuals to be less fit than homozygous individuals.

CONCLUSION

Our results extend our theoretical understanding that sympatric speciation can evolve under nicheless or gradientless resource conditions: i.e. the underlying resource is monomorphic and initially spatially homogeneous. Further the simplicity and generality of our model suggests that sympatric speciation may be more likely than previously thought to occur in mobile, sexually-reproducing organisms.