A comprehensive test for negative frequency-dependent selection

Female preference counteracts negative frequency dependent selection for a stable polymorphism in a livebearing fish

The maintenance of variation within natural populations is key for natural selection to operate. Polymorphism is an intriguing form of variation that involves the persistence of multiple discrete phenotypes called morphs. Polymorphism is often explained by negative frequency dependent selection (NFDS), under which rare morphs have an advantage, such that no one morph takes over. We tested whether mating polymorphism is maintained by NFDS generated by female choice, in the livebearing poeciliid fish, Girardinus metallicus, whose males are either common, plain morphs or rare, black morphs. Females were treated with one morph for several weeks and tested with both, in mate choice and direct competition assays. Contrary to NFDS via female choice, females preferred the morph with which they were treated. This may disrupt the polymorphism given the rarity of black morphs in the wild, unless black morphs have other advantages: we found that black morphs tended to exhibit higher mating activity, and other studies have demonstrated that they are more aggressive. Interestingly, only black morphs display to females prior to copulation; however, there is little evidence for female preference for this morph or the mating display. These results suggest functions for the mating display of black morphs beyond courtship, including aggressive mate guarding, and prompt a discussion of what constitutes courtship behavior.

The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living kākāpō to understand the evolution of its feather color polymorphism. The kākāpō is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species' color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the kākāpō a "ghost of selection past."

Spatial structure could explain the maintenance of alternative reproductive tactics in tree cricket males

Trait polymorphisms are widespread in nature, and explaining their stable co-existence is a central problem in ecology and evolution. Alternative reproductive tactics, in which individuals of one or more sex exhibit discrete, discontinuous traits in response to reproductive competition, represent a special case of trait polymorphism in which the traits are often complex, behavioural, and dynamic. Thus, studying how alternative reproductive tactics are maintained may provide general insights into how complex trait polymorphisms are maintained in populations. We construct a spatially explicit individual-based model inspired from extensively collected empirical data to address the mechanisms behind the co-existence of three behavioural alternative reproductive tactics in males of a tree cricket (Oecanthus henryi). Our results show that the co-existence of these tactics over ecological time scales is facilitated by the spatial structure of the landscape they inhabit, which serves to equalise the otherwise unequal mating benefits of the three tactics. We also show that this co-existence is unlikely if spatial aspects of the system are not considered. Our findings highlight the importance of spatial dynamics in understanding ecological and evolutionary processes and underscore the power of integrative approaches that combine models with empirical data.

Balancing selection on genomic deletion polymorphisms in humans

A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains an imperative exercise. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS (genome-wide association studies) associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.

Different stress from parasites and mate choice in two female morphs of the blue-tailed damselfly

In Odonates, female colour polymorphism is common and implies the presence of two or more female types with different colours and behaviours. To explain this phenomenon, several hypotheses have been proposed that consider morph frequency, population density, the presence of parasites, and mating behaviour. We studied the blue-tailed damselfly Ischnura elegans, a species with a blue androchrome morph and two gynochrome morphs (the common green infuscans, and the rare orange rufescens-obsoleta). The size of adult males and females, the presence of parasites, and pairing behaviour between males and the three female morphs was assessed in field conditions throughout the reproductive season in NW Italy. Moreover, growth and emergence success of larvae produced by the different morphs was analyzed in standardized conditions. In the field, males showed a preference for the gynochrome infuscans females, despite a similar frequency of androchrome females. In test conditions, male preference for the infuscans females was also observed. Paired males and paired androchrome females were larger than unpaired individuals, while there were no differences in size between paired and unpaired infuscans females. Males and androchrome females were more parasitized than infuscans females. The survival and emergence success of larvae produced by androchrome females was higher than those of offspring produced by the infuscans females. Our results suggest that a higher survival of progeny at the larval stage could counterbalance the higher parasitism and the lower pairing success of andromorph adult females and highlight the importance of considering the whole life-cycle in polymorphism studies.

Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution

The geographic mosaic theory of coevolution (GMC) posits that coevolutionary dynamics go beyond local coevolution and are comprised of the following three components: geographic selection mosaics, coevolutionary hot spots, and trait remixing. It is unclear whether the GMC applies to bacteria, as horizontal gene transfer and cosmopolitan dispersal may violate theoretical assumptions. Here, we test key GMC predictions in an antibiotic-producing bacterial symbiont (genus Pseudonocardia) that protects the crops of neotropical fungus-farming ants (Apterostigma dentigerum) from a specialized pathogen (genus Escovopsis). We found that Pseudonocardia antibiotic inhibition of common Escovopsis pathogens was elevated in A. dentigerum colonies from Panama compared to those from Costa Rica. Furthermore, a Panama Canal Zone population of Pseudonocardia on Barro Colorado Island (BCI) was locally adapted, whereas two neighboring populations were not, consistent with a GMC-predicted selection mosaic and a hot spot of adaptation surrounded by areas of maladaptation. Maladaptation was shaped by incongruent Pseudonocardia-Escovopsis population genetic structure, whereas local adaptation was facilitated by geographic isolation on BCI after the flooding of the Panama Canal. Genomic assessments of antibiotic potential of 29 Pseudonocardia strains identified diverse and unique biosynthetic gene clusters in BCI strains despite low genetic diversity in the core genome. The strength of antibiotic inhibition was not correlated with the presence/absence of individual biosynthetic gene clusters or with parasite location. Rather, biosynthetic gene clusters have undergone selective sweeps, suggesting that the trait remixing dynamics conferring the long-term maintenance of antibiotic potency rely on evolutionary genetic changes within already-present biosynthetic gene clusters and not simply on the horizontal acquisition of novel genetic elements or pathways.IMPORTANCE Recently, coevolutionary theory in macroorganisms has been advanced by the geographic mosaic theory of coevolution (GMC), which considers how geography and local adaptation shape coevolutionary dynamics. Here, we test GMC in an ancient symbiosis in which the ant Apterostigma dentigerum cultivates fungi in an agricultural system analogous to human farming. The cultivars are parasitized by the fungus Escovopsis The ants maintain symbiotic actinobacteria with antibiotic properties that help combat Escovopsis infection. This antibiotic symbiosis has persisted for tens of millions of years, raising the question of how antibiotic potency is maintained over these time scales. Our study tests the GMC in a bacterial defensive symbiosis and in a multipartite symbiosis framework. Our results show that this multipartite symbiotic system conforms to the GMC and demonstrate that this theory is applicable in both microbes and indirect symbiont-symbiont interactions.

Intergenerational fluctuations in colour morph frequencies may maintain elytral polymorphisms in the ladybird beetle Cheilomenes sexmaculata (Coleoptera: Coccinellidae)

Phenotypic polymorphisms are found in a wide array of taxa, and unravelling the mechanisms that maintain them is of great interest to evolutionary and ecological biologists. Temporal environmental heterogeneity may play a role in the maintenance of polymorphisms but is poorly understood. In the present study, we analysed trends in intergenerational elytral colour morph frequencies in relation to changes in fitness and life history traits (i.e. body size, mortality, fecundity, hatching rate and mate preference) in the ladybird beetle Cheilomenes sexmaculata (Coleoptera: Coccinellidae). A long-term field survey spanning nine years showed that the frequency of dark morphs increases over winter and then decreases in spring. Dark morphs may have an advantage in winter due to their higher tolerance of low temperatures compared with light morphs. Light-morph females were heavier in winter than dark-morph females. They also mated more frequently and had higher hatching rates, potentially causing an increase in light morphs in spring. These results suggest that fluctuations in morph frequencies resulting from the conflicting directions of selection pressures between overwintering and spring generations may help to maintain genetic polymorphism.

Nonlinear frequency-dependent selection promotes long-term coexistence between bacteria species

Negative frequency-dependent selection (NFDS) is an important mechanism for species coexistence and for the maintenance of genetic polymorphism. Long-term coexistence nevertheless requires NFDS interactions to be resilient to further evolution of the interacting species or genotypes. For closely related genotypes, NFDS interactions have been shown to be preserved through successive rounds of evolution in coexisting lineages. On the contrary, the evolution of NFDS interactions between distantly related species has received less attention. Here, we tracked the co-evolution of Escherichia coli and Citrobacter freundii that initially differ in their ecological characteristics. We showed that these two bacterial species engaged in an NFDS interaction particularly resilient to further evolution: despite a very strong asymmetric rate of adaptation, their coexistence was maintained owing to an NFDS pattern where fitness increases steeply as the frequency decreases towards zero. Using a model, we showed how and why such NFDS pattern can emerge. These findings provide a robust explanation for the long-term maintenance of species at very low frequencies.

No selection for change in polyandry under experimental evolution

What drives mating system variation is a major question in evolutionary biology. Female multiple mating (polyandry) has diverse evolutionary consequences, and there are many potential benefits and costs of polyandry. However, our understanding of its evolution is biased towards studies enforcing monandry in polyandrous species. What drives and maintains variation in polyandry between individuals, genotypes, populations and species remains poorly understood. Genetic variation in polyandry may be actively maintained by selection, or arise by chance if polyandry is selectively neutral. In Drosophila pseudoobscura, there is genetic variation in polyandry between and within populations. We used isofemale lines to found replicate populations with high or low initial levels of polyandry and tracked polyandry under experimental evolution over seven generations. Polyandry remained relatively stable, reflecting the starting frequencies of the experimental populations. There were no clear fitness differences between high versus low polyandry genotypes, and there was no signature of balancing selection. We confirmed these patterns in direct comparisons between evolved and ancestral females and found no consequences of polyandry for female fecundity. The absence of differential selection even when initiating populations with major differences in polyandry casts some doubt on the importance of polyandry for female fitness.

Genetic structure of Hepatica nobilis var. japonica, focusing on within population flower color polymorphism

How phenotypic or genetic diversity is maintained in a natural habitat is a fundamental question in evolutionary biology. Flower color polymorphism in plants is a common polymorphism. Hepatica nobilis var. japonica on the Sea of Japan (SJ) side of the Japanese mainland exhibits within population flower color polymorphism (e.g., white, pink, and purple), while only white flowers are observed on the Pacific Ocean (PO) side. To determine the relationships between flower color polymorphism, within and among populations, and the genetic structure of H. nobilis var. japonica, we estimated the genetic variation using simple sequence repeat (SSR) markers. First, we examined whether cryptic lineages corresponding to distinct flower colors contribute to the flower color polymorphisms in H. nobilis var. japonica. In our field observations, no bias in color frequency was observed among populations on Sado Island, a region with high variation in flower color. Simple sequence repeat (SSR) analyses revealed that 18% of the genetic variance was explained by differences among populations, whereas no genetic variation was explained by flower color hue or intensity (0% for both components). These results indicate that the flower color polymorphism is likely not explained by cryptic lineages that have different flower colors. In contrast, populations in the SJ and PO regions were genetically distinguishable. As with the other plant species in these regions, refugial isolation and subsequent migration history may have caused the genetic structure as well as the spatially heterogeneous patterns of flower color polymorphisms in H. nobilis var. japonica.

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes

Positively frequency-dependent selection is predicted from theory to promote diversity in patchily structured populations and communities, but empirical support for this prediction has been lacking. Here, we investigate frequency-dependent selection among isolates from a local natural population of the highly social bacterium Myxococcus xanthus. Upon starvation, closely related cells of M. xanthus cooperate to construct multicellular fruiting bodies, yet recently diverged genotypes co-residing in a local soil population often antagonize one another during fruiting-body development in mixed groups. In the experiments reported here, both fitness per se and strong forms of interference competition exhibit pervasive and strong positive frequency dependence (PFD) among many isolates from a centimeter-scale soil population of M. xanthus. All strains that compete poorly at intermediate frequency are shown to be competitively dominant at high frequency in most genotype pairings during both growth and development, and strongly so. Interference competition is often lethal and appears to be contact dependent rather than mediated by diffusible compounds. Finally, we experimentally demonstrate that positively frequency-dependent selection maintains diversity when genotype frequencies vary patchily in structured populations. These results suggest that PFD contributes to the high levels of local diversity found among M. xanthus social groups in natural soil populations by reinforcing social barriers to cross-territory invasion and thereby also promotes high within-group relatedness. More broadly, our results suggest that potential roles of PFD in maintaining patchily distributed diversity should be investigated more extensively in other species.