Trophic specialization on unique resources despite limited niche divergence in a celebrated example of sympatric speciation.

Trophic niche partitioning is observed in many adaptive radiations and is hypothesized to be a central process underlying species divergence. However, patterns of dietary niche partitioning are inconsistent across radiations and there are few studies of niche partitioning in putative examples of sympatric speciation. Here, we conducted the first quantitative study of dietary niche partitioning using stomach contents and stable isotope analyses in one of the most celebrated examples of sympatric speciation: the cichlid radiation from crater lake Barombi Mbo, Cameroon. We found little evidence for trophic niche partitioning among cichlids, including the nine species coexisting in the narrow littoral zone. Stable isotope analyses supported these conclusions of substantial dietary overlap. Our data, however, did reveal that five of eleven species consume rare dietary items, including freshwater sponge, terrestrial ants, and nocturnal foraging on shrimp. Stomach contents of the spongivore (Pungu maclareni) were 20% freshwater sponge, notable considering that only 0.04% of all fishes consume sponges. Overall, we conclude that cichlid species in lake Barombi Mbo overlap considerably in broad dietary niches-in part due to the large proportion of detritus in the stomach contents of all species-but there is evidence for divergence among species in their diet specializations on unique resources. We speculate that these species may utilize these additional specialized resources during periods of low resource abundance in support of Liem's paradox.

A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape.

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.

Asymmetric reinforcement in Lucania killifish: assessing reproductive isolation when both sexes choose.

Reinforcement can occur when maladaptive hybridization in sympatry favors the evolution of conspecific preferences and target traits that promote behavioral isolation (BI). In many systems, enhanced BI is due to increased female preference for conspecifics. In others, BI is driven by male preference, and in other systems both sexes exert preferences. Some of these patterns can be attributed to classic sex-specific costs and benefits of preference. Alternatively, sex differences in conspecific preference can emerge due to asymmetric postzygotic isolation (e.g., hybrid offspring from female A × male B have lower fitness than hybrid offspring from female B × male A), which can lead to asymmetric BI (e.g., female A and male B are less likely to mate than female B and male A). Understanding reinforcement requires understanding how conspecific preferences evolve in sympatry. Yet, estimating conspecific preferences can be difficult when both sexes are choosy. In this study, we use Lucania killifish to test the hypothesis that patterns of reinforcement are driven by asymmetric postzygotic isolation between species. If true, we predicted that sympatric female Lucania goodei and sympatric male L. parva should have lower levels of BI compared with their sympatric counterparts, as they produce hybrid offspring with the highest fitness. To address the problem of measuring BI when both sexes are choosy, we inferred the contribution to BI of each partner using assays where one sex in the mating pair comes from an allopatric population with potentially low preference, whereas the other comes from a sympatric population with high preference. For one hybrid cross direction, we found that both female L. parva and male L. goodei have high contributions to BI in sympatry. In the other hybrid cross direction, we found that only female L. goodei contribute to BI. Sympatric male L. parva readily engaged in hybrid spawnings with allopatric L. goodei females. These results indicate that both asymmetric postzygotic isolation and the traditional sex-specific costs to preference likely affect the nature of selection on conspecific preferences and target traits.

Oral shelling within an adaptive radiation of pupfishes: Testing the adaptive function of a novel nasal protrusion and behavioural preference.

Dietary specialization on hard prey items, such as mollusks and crustaceans, is commonly observed in a diverse array of fish species. Many fish consume these types of prey by crushing the shell to consume the soft tissue within, but a few fishes extricate the soft tissue without breaking the shell using a method known as oral shelling. Oral shelling involves pulling a mollusc from its shell and it may be a way to subvert an otherwise insurmountable shell defence. However, the biomechanical requirements and potential adaptations for oral shelling are unknown. Here, we test the hypothesis that a novel nasal protrusion is an adaptation for oral shelling in the durophagous pupfish (Cyprinodon brontotheroides). We first demonstrate oral shelling in this species and then predict that a larger nasal protrusion would allow pupfish to consume larger snails. Durophagous pupfish are found within an endemic radiation of pupfish on San Salvador Island, Bahamas. We took advantage of closely related sympatric species and outgroups to test: (a) whether durophagous pupfish shell and consume more snails than other species, (b) if F1 and F2 durophagous hybrids consume similar amounts of snails as purebred durophagous pupfish, and (c) if nasal protrusion size in parental and hybrid populations increases the maximum size of consumed snails. We found that durophagous pupfish and their hybrids consumed the most snails, but did not find a strong association between nasal protrusion size and maximum snail size consumed within the parental or F2 hybrid population, suggesting that the size of their novel nasal protrusion does not provide a major benefit in oral shelling. Instead, we suggest that the nasal protrusion may increase feeding efficiency, act as a sensory organ, or is a sexually selected trait, and that a strong feeding preference may be most important for oral shelling.

Rapid adaptive evolution of scale-eating kinematics to a novel ecological niche.

The origins of novel trophic specialization, in which organisms begin to exploit resources for the first time, may be explained by shifts in behavior such as foraging preferences or feeding kinematics. One way to investigate behavioral mechanisms underlying ecological novelty is by comparing prey capture kinematics among species. We investigated the contribution of kinematics to the origins of a novel ecological niche for scale-eating within a microendemic adaptive radiation of pupfishes on San Salvador Island, Bahamas. We compared prey capture kinematics across three species of pupfish while they consumed shrimp and scales in the lab, and found that scale-eating pupfish exhibited peak gape sizes twice as large as in other species, but also attacked prey with a more obtuse angle between their lower jaw and suspensorium. We then investigated how this variation in feeding kinematics could explain scale-biting performance by measuring bite size (surface area removed) from standardized gelatin cubes. We found that a combination of larger peak gape and more obtuse lower jaw and suspensorium angles resulted in approximately 40% more surface area removed per strike, indicating that scale-eaters may reside on a performance optimum for scale biting. To test whether feeding performance could contribute to reproductive isolation between species, we also measured F1 hybrids and found that their kinematics and performance more closely resembled generalists, suggesting that F1 hybrids may have low fitness in the scale-eating niche. Ultimately, our results suggest that the evolution of strike kinematics in this radiation is an adaptation to the novel niche of scale eating.

The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes?

Behavioral changes in a new environment are often assumed to precede the origins of evolutionary novelties. Here, we examined whether an increase in aggression is associated with a novel scale-eating trophic niche within a recent radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. We measured aggression using multiple behavioral assays and used transcriptomic analyses to identify differentially expressed genes in aggression and other behavioral pathways across 3 sympatric species in the San Salvador radiation (generalist, snail-eating specialist, and scale-eating specialist) and 2 generalist outgroups. Surprisingly, we found increased behavioral aggression and differential expression of aggression-related pathways in both the scale-eating and snail-eating specialists, despite their independent evolutionary origins. Increased behavioral aggression varied across both sex and stimulus context in both species. Our results indicate that aggression is not unique to scale-eating specialists. Instead, selection may increase aggression in other contexts such as niche specialization in general or mate competition. Alternatively, increased aggression may result from indirect selection on craniofacial traits, pigmentation, or metabolism-all traits which are highly divergent, exhibit signs of selective sweeps, and are affected by aggression-related genetic pathways which are differentially expressed in this system. In conclusion, the evolution of a novel predatory trophic niche within a recent adaptive radiation does not have clear-cut behavioral origins as previously assumed, highlighting the multivariate nature of adaptation and the complex integration of behavior with other phenotypic traits.