What big lips are good for: on the adaptive function of repeatedly evolved hypertrophied lips of cichlid fishes

Linking phenotypic traits to an adaptive ecological function is a major goal of evolutionary biology. However, this task is challenging and has been accomplished in only a handful of species and ecological model systems. The repeatedly evolved adaptive radiations of cichlid fishes are composed of an enormously diverse set of species that differ in trophic morphology, body shape, coloration, and behaviour. Ecological guilds of species with conspicuously hypertrophied lips have evolved in parallel in all major cichlid radiations and are characterized by large lips and pointed and narrow heads. In the present study, we experimentally tested the adaptive significance of this set of conspicuous traits by comparing the success of hypertrophied‐lipped and closely‐related thin‐lipped endemic Lake Victoria cichlids in a novel foraging assay. The hypertrophied‐lipped species (Haplochromis chilotes) was clearly more successful in exploiting food resources from narrow crevices and the observed difference in foraging success increased more at narrower angles. Furthermore, pronounced differences in exploratory behaviour between the species suggest that the evolution of hypertrophied‐lipped species involved the co‐evolution of a suite of traits that include foraging behaviour. The repeated evolution of hypertrophied‐lip morphology in conjunction with a narrow and pointed head shape in cichlids represents an evolutionary innovation that facilitates foraging in rocky crevices, thus allowing access to a novel niche. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 448–455.     

Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes

Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick‐lipped) and Pundamilia nyererei (thin‐lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small‐to‐moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive‐effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick‐lipped ecomorph is the result of selection on numerous loci distributed throughout the genome.     

Incipient speciation driven by hypertrophied lips in Midas cichlid fishes?

Sympatric speciation has been debated in evolutionary biology for decades. Although it has gained in acceptance recently, still only a handful of empirical examples are seen as valid (e.g. crater lake cichlids). In this study, we disentangle the role of hypertrophied lips in the repeated adaptive radiations of Nicaraguan crater lake cichlid fish. We assessed the role of disruptive selection and assortative mating during the early stages of divergence and found a functional trade‐off in feeding behaviour between thick‐ and thin‐lipped ecotypes, suggesting that this trait is a target of disruptive selection. Thick‐lipped fish perform better on nonevasive prey at the cost of a poorer performance on evasive prey. Using enclosures in the wild, we found that thick‐lipped fish perform significantly better in rocky than in sandy habitats. We found almost no mixed pairs during two breeding seasons and hence significant assortative mating. Genetic differentiation between ecotypes seems to be related to the time since colonization, being subtle in L. Masaya (1600 generations ago) and absent in the younger L. Apoyeque (<600 generations ago). Genome‐wide differentiation between ecotypes was higher in the old source lakes than in the young crater lakes. Our results suggest that hypertrophied lips might be promoting incipient sympatric speciation through divergent selection (ecological divergence in feeding performance) and nonrandom mating (assortative mating) in the young Nicaraguan crater lakes. Nonetheless, further manipulative experiments are needed in order to confirm the role of hypertrophied lips as the main cue for assortative mating.     

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits — including body shape, colour, lips and jaws — is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high‐bodied benthic species (Amphilophus astorquii). A total of 453 genome‐wide informative SNPs were identified in 240 F₂ hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy‐two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL‐linked genomic regions, genes that might contribute to divergence in body shape along the benthic–limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.     

PHENOTYPIC PLASTICITY AND HETEROCHRONY IN CICHLASOMA MANAGUENSE (PISCES,CICHLIDAE) AND THEIR IMPLICATIONS FOR SPECIATION IN CICHLID FISHES

Cichlid fishes in African rift lakes have undergone rapid speciation, resulting in “species flocks” with more than 300 endemic species in some of the lakes. Most researchers assume that there is little phenotypic variation in cichlid fishes. I report here extensive phenotypic plasticity in a Neotropical cichlid species. I examined the influence of diet on trophic morphology during ontogeny in Cichlasoma managuense. Two groups of full siblings were fed two different diets for eight months after the onset of feeding; thereafter both groups were fed a common diet. Phenotypes that differed significantly at 8.5 months converged almost completely at 16.5 months. If feeding on two different diets is continued after 8.5 months, the phenotypes remain distinct. Differences in diet and possibly in feeding mode are believed to have caused these phenotypic changes. Phenotypic plasticity is described in terms of a qualitative model of heterochrony in which phenotypic change in morphology is explained as retardation of the normal developmental rate. If phenotypic expression of morphology is equally plastic in African cichlid species as it may be in the American cichlids, as exemplified by C. managuense, then taxonomic, ecological, and evolutionary analyses of “species flocks” may be in need of revision. However, Old World cichlids may be less phenotypically plastic than New World cichlids, and this may contribute to the observed differences in speciation rate and degree of endemism.     

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.     

One cost of being gold: selective predation and implications for the maintenance of the Midas cichlid colour polymorphism (Perciformes: Cichlidae)

In the colour‐polymorphic Midas cichlid fish species complex (Amphilophus citrinellus spp.), gold morphs occur at much lower frequencies (< 10%) than dark individuals. This might be surprising because gold coloration is dominant and coded for by a single Mendelian locus. Furthermore, gold individuals are considered to be competitively advantaged over dark ones because they grow faster and win aggressive encounters more often compared to dark individuals of equal size. However, one might expect a cost of being gold in terms of natural selection as a result of predation. We tested whether the Jaguar cichlid (Parachromis managuensis), a major fish predator of Midas cichlids, preys differentially on colour variants of goldfish (Carassius auratus auratus), which were used as a proxy for Midas cichlids because of their similarity in colour. Size‐matched pairs of prey fish (gold and dark) were offered to the predator and the time until the fish were attacked was recorded. The gold morph was attacked first more often (approximately 70%) but not faster than the dark morph. This suggests that the predator perceives the gold individual first, and/or that the predator exhibits a preference or higher motivation to attack the gold prey fish. The increased risk of predation of gold prey fish suggests for the Midas cichlid system that being gold may carry significant costs in terms of natural selection as a result of its major piscivorous predator. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 350–358.     

Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes

Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.     

ADAPTIVE GENETIC VARIATION IN GROWTH AND DEVELOPMENT OF TADPOLES OF THE HYBRIDOGENETIC RANA ESCULENTA COMPLEX

The distribution and proportion of the sexual species Rana lessonae to the hemiclonal hybrid R. esculenta among natural habitats suggests that these anurans may differ in adaptive abilities. I used a half-sib design to partition phenotypic and quantitative genetic variation in tadpole responses at two food levels into causal variance components. Rana lessonae displays strong phenotypic variation across food levels. Growth rate is strictly determined by environmental factors and includes weak maternal effects. Larval period and body size at metamorphosis both contain moderate levels of additive genetic variance. The sire x food interactions and the lack of environmental correlations indicate that adaptive phenotypic plasticity is present in both of these traits. In contrast, R. esculenta displays less phenotypic variation across food levels, especially for larval period. Variation in body size at metamorphosis is underlain by genetic variation as shown by high levels of additive genetic variance, yet growth rate and larval period are not. Significant environmental correlations between larval period at high food level and growth, larval period, and body size at low food, indicate phenotypic plasticity is absent. A positive phenotypic correlation between body size at metamorphosis and larval period for R. lessonae at both food levels suggests a trade-off between growing large and metamorphosing quickly to escape predation or pond drying. The lack of a similar correlation for R. esculenta at the high food level suggests it may be less constrained. Different levels of adaptive genetic variation among larval traits suggest that the sexual species and the hybridogenetic hemiclone differ in their abilities to cope with temporally and spatially heterogeneous environments.     

What Ecological and Anthropogenic Factors Affect Group Size in White‐lipped Peccaries (Tayassu pecari)?

Group living among ungulates has evolved mainly in species living in open habitats, such as grasslands and savannas, whereas in the forest, few ungulate species form groups and these tend to be small. Therefore, the white‐lipped peccary (Tayassu pecari), a Neotropical ungulate listed as Vulnerable by the IUCN, represents an almost unique social occurrence as it lives in large and cohesive groups, yet it inhabits dense tropical forests. Large variations in group sizes have been observed throughout the species range, with reports of herds with less than 10 to around 300 individuals. We examined factors that might cause variation in group size in white‐lipped peccary, including ecological and anthropogenic variables. We conducted an extensive literature review and used our original data to compile information on white‐lipped peccary's group size across its range. We built models to quantitate generalizations for group sizes distinguishing data from areas with high human influence, and areas that have not been significantly disturbed by humans for at least the last 20 years. We found that white‐lipped peccary's group size for all sites was most strongly predicted by a combination of the distances to the nearest human settlement and rainfall and its seasonality. Results from the undisturbed sites indicated that group size is positively influenced by rainfall. Our results contribute to understand why group size varies in different environments that are subjected to different ecological and human conditions. Information on these relationships is a key to advance our understanding of the socio‐ecological strategies of animal species living in groups.     

Adult plasticity in African cichlids: Rapid changes in opsin expression in response to environmental light differences

Phenotypic plasticity allows organisms to adapt quickly to local environmental conditions and could facilitate adaptive radiations. Cichlids have recently undergone an adaptive radiation in Lake Malawi where they inhabit diverse light environments and tune their visual sensitivity through differences in cone opsin expression. While cichlid opsin expression is known to be plastic over development, whether adults remain plastic is unknown. Adult plasticity in visual tuning could play a role in cichlid radiations by enabling survival in changing environments and facilitating invasion into novel environments. Here we examine the existence of and temporal changes in adult visual plasticity of two closely related species. In complementary experiments, wild adult Metriaclima mbenji from Lake Malawi were moved to the lab under UV‐deficient fluorescent lighting; while lab raised M. benetos were placed under UV‐rich lighting designed to mimic light conditions in the wild. Surprisingly, adult cichlids in both experiments showed significant changes in the expression of the UV‐sensitive single cone opsin, SWS1, in only 3 days. Modeling quantum catches in the light environments revealed a possible link between the light available to the SWS1 visual pigment and SWS1 expression. We conclude that adult cichlids can undergo rapid and significant changes in opsin expression in response to environmental light shifts that are relevant to their habitat and evolutionary history in Lake Malawi. This could have contributed to the rapid divergence characteristic of these fantastic fishes.     

Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification.

The growing body of empirical evidence for sympatric speciation has been complemented by recent theoretical treatments that have identified evolutionary conditions conducive to speciation in sympatry. The Neotropical Midas cichlid (Amphilophus citrinellum) fits both of the key characteristics of these models, with strong assortative mating on the basis of a colour polymorphism coupled with trophic and ecological differentiation derived from a polymorphism in their pharyngeal jaws. We used microsatellite markers and a 480 bp fragment of the mitochondrial DNA control region to study four polymorphic populations of the Midas cichlid from three crater lakes and one large lake in Nicaragua in an investigation of incipient sympatric speciation. All populations were strongly genetically differentiated on the basis of geography. We identified strong genetic separation based on colour polymorphism for populations from Lake Nicaragua and one crater lake (Lake Apoyo), but failed to find significant genetic structuring based on trophic differences and ecological niche separation in any of the four populations studied. These data support the idea that sexual selection through assortative mating contributes more strongly or earlier during speciation in sympatry than ecological separation in these cichlids. The long-term persistence of divergent cichlid ecotypes (as measured by the percentage sequence divergence between populations) in Central American crater lakes, despite a lack of fixed genetic differentiation, differs strikingly from the patterns of extremely rapid speciation in the cichlids in Africa, including its crater lakes. It is unclear whether extrinsic environmental factors or intrinsic biological differences, e.g. in the degree of phenotypic plasticity, promote different mechanisms and thereby rates of speciation of cichlid fishes from the Old and New Worlds.     

Experimental evidence for adaptive phenotypic plasticity in a rock-dwelling cichlid fish from Lake Victoria

We demonstrate adaptive phenotypic plasticity (PP) in Neochromis greenwoodi , a rock-dwelling haplochromine cichlid from Lake Victoria. Adaptive phenotypic plasticity will enhance the chance of survival and reproduction in changing or novel environments. For rock-dwelling cichlids it may contribute to the success of settlement after migration between rocky outcrops or islands, since newly colonized patches of rock may offer different food regimes and different competitors. In our experiments, we simulated such situations by raising fry on different diets and with different competitors. We chose diet treatments in such a way that we could predict the direction of anatomical changes from functional demands. We expected an indirect effect of interspecific competition: selectively removing one prey-type by the competing species would leave N. greenwoodi with the other. We found the predicted phenotypic responses to food in trophic traits of N. greenwoodi . However, in the current experimental set-up we did not find a differentiating effect of species of competitor. We discuss the possible role of PP in allopatric and sympatric speciation.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 185−192.     

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model‐based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species‐level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors.     

TESTING FOR ANCIENT ADAPTIVE RADIATIONS IN NEOTROPICAL CICHLID FISHES

Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether patterns of lineage and morphological diversification are congruent with hypothesized adaptive radiations in South and Central America. We found that diversification in the Neotropical cichlid clade and the highly diverse tribe Geophagini was consistent with diversity‐dependent, early bursts of divergence followed by decreased rates of lineage accumulation. South American Geophagini underwent early rapid differentiation in body shape, expanding into novel morphological space characterized by elongate‐bodied predators. Divergence in head shape attributes associated with trophic specialization evolved under strong adaptive constraints in all Neotropical cichlid clades. The South American Cichlasomatini followed patterns consistent with constant rates of morphological divergence. Although morphological diversification in South American Heroini was limited, Eocene invasion of Central American habitats was followed by convergent diversification mirroring variation observed in Geophagini. Diversification in Neotropical cichlids was influenced by the early adaptive radiation of Geophagini, which potentially limited differentiation in other cichlid clades.     

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high‐throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing‐by‐synthesis: restriction‐site‐associated DNA sequencing (RADSeq). We developed a new, more time‐ and cost‐efficient double‐digest RAD paired‐end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large‐scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small‐scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A. centrarchus open new research avenues providing an ideal system to investigate genome‐level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.     

Adaptive plasticity and genetic divergence in feeding efficiency during parallel adaptive radiation of whitefish (Coregonus spp.)

Parallel phenotypic divergence in replicated adaptive radiations could either result from parallel genetic divergence in response to similar divergent selection regimes or from equivalent phenotypically plastic response to the repeated occurrence of contrasting environments. In post‐glacial fish, replicated divergence in phenotypes along the benthic‐limnetic habitat axis is commonly observed. Here, we use two benthic‐limnetic species pairs of whitefish from two Swiss lakes, raised in a common garden design, with reciprocal food treatments in one species pair, to experimentally measure whether feeding efficiency on benthic prey has a genetic basis or whether it underlies phenotypic plasticity (or both). To do so, we offered experimental fish mosquito larvae, partially burried in sand, and measured multiple feeding efficiency variables. Our results reveal both, genetic divergence as well as phenotypically plastic divergence in feeding efficiency, with the phenotypically benthic species raised on benthic food being the most efficient forager on benthic prey. This indicates that both, divergent natural selection on genetically heritable traits and adaptive phenotypic plasticity, are likely important mechanisms driving phenotypic divergence in adaptive radiation.     

Getting into Shape: An Empirical Comparison of Traditional Truss-Based Morphometric Methods with a Newer Geometric Method Applied to New World Cichlids

Body shape is a difficult, but important, trait to quantify. Researchers have traditionally used multivariate analysis of several linear measures ('trusses') across the body form to quantify shape. Newer geometric morphometric methods claim to better estimate shape because they analyze the geometry among the locations of all landmarks simultaneously rather than the linear distances between pairs of landmarks. We tested this claim by comparing the results of several traditional morphometric analyses against a newer geometric analysis involving thin-plate splines (TPS), all applied to a common data set of morphologically variable new world cichlids Amphilophus citrinellus and A. zaliosus. The TPS method yielded slightly stronger evidence of morphological differences among forms, although traditional methods also distinguished the two species. Perhaps our most important result was the idiosyncratic interpretation of shape variation among the traditional truss-based methods, whereas the generation of deformation grids using the TPS approach yielded clear and visually interpretable figures. Our results indicate that geometric morphometrics can be a more effective way to analyze and interpret body form, but also that traditional methods can be relied upon to provide statistical evidence of shape differences, although not necessarily accurate information about the nature of variation in shape.