Exploring a Local Genetic Interaction Network Using Evolutionary Replay Experiments

Understanding how genes interact is a central challenge in biology. Experimental evolution provides a useful, but underutilized, tool for identifying genetic interactions, particularly those that involve non-loss-of-function mutations or mutations in essential genes. We previously identified a strong positive genetic interaction between specific mutations in KEL1 (P344T) and HSL7 (A695fs) that arose in an experimentally evolved Saccharomyces cerevisiae population. Because this genetic interaction is not phenocopied by gene deletion, it was previously unknown. Using “evolutionary replay” experiments, we identified additional mutations that have positive genetic interactions with the kel1-P344T mutation. We replayed the evolution of this population 672 times from six timepoints. We identified 30 populations where the kel1-P344T mutation reached high frequency. We performed whole-genome sequencing on these populations to identify genes in which mutations arose specifically in the kel1-P344T background. We reconstructed mutations in the ancestral and kel1-P344T backgrounds to validate positive genetic interactions. We identify several genetic interactors with KEL1, we validate these interactions by reconstruction experiments, and we show these interactions are not recapitulated by loss-of-function mutations. Our results demonstrate the power of experimental evolution to identify genetic interactions that are positive, allele specific, and not readily detected by other methods, shedding light on an underexplored region of the yeast genetic interaction network.     

Ecological and Evolutionary Processes Drive the Origin and Maintenance of Imperfect Mimicry

Although the forces behind the evolution of imperfect mimicry remain poorly studied, recent hypotheses suggest that relaxed selection on small-bodied individuals leads to imperfect mimicry. While evolutionary history undoubtedly affects the development of imperfect mimicry, ecological community context has largely been ignored and may be an important driver of imperfect mimicry. Here we investigate how evolutionary and ecological contexts might influence mimetic fidelity in Müllerian and Batesian mimicry systems. In Batesian hoverfly systems we find that body size is not a strong predictor of mimetic fidelity. However, in Müllerian velvet ants we find a weak positive relationship between body size and mimetic fidelity when evolutionary context is controlled for and a much stronger relationship between community diversity and mimetic fidelity. These results suggest that reduced selection on small-bodied individuals may not be a major driver of the evolution of imperfect mimicry and that other factors, such as ecological community context, should be considered when studying the evolution of imperfect mimicry.     

Evolutionary Biosemiotics and Multilevel Construction Networks

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism (in a broad sense) to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components (i.e., agents, scaffolds, signs, and resources) that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents.     

Clonality and Evolutionary History of Rhabdomyosarcoma

To infer the subclonality of rhabdomyosarcoma (RMS) and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS) subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP) subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS.     

Ecological and Evolutionary Implications of Bird Pollination

This paper addresses the question of how, and under what ecologicalcircumstances, bird pollination will be optimal for a plant,and which or how many of the available nectar-feeding bird specieswill be optimal pollen vectors. Pollination by birds is energetically expensive for the plants,and should accur only when birds can mediate optimal patternsof pollen flow and seed set. Each nectar-feeding bird has potentialadvantages and disadvantages as a pollen vector, related toits size, morphology, and foraging behavior. Which availablebird is the optimal pollinator depends on the plant's growthhabit, spatial distribution, and breeding system. The variousadaptations shown by plants favoring one pollinator over anotherall revolve around the secretion of nectar and the manner ofpresenting it to the birds. However, other aspects of plantmorphology, physiology, ecology, or life cycle may affect theproduction and presentation of nectar, and influence plant-pollinatorcoevolution. Many question remain regarding the interrelationsbetween pollination and the total biology of the plant; birdpollination systems may prove fruitful in yielding meaningfulanswers.     

Evolutionary History and Functional Diversification of Phosphomannomutase Genes

Phosphomannomutases (PMMs) catalyze the interconversion of mannose-6-phosphate to mannose-1-phosphate. In humans, two PMM enzymes exist—PMM1 and PMM2; yet, they have different functional specificities. PMM2 presents PMM activity, and its deficiency causes a Congenital Disorder of Glycosylation (PMM2-CDG). On the other hand, PMM1 can also act as glucose-1,6-bisphosphatase in the brain after stimulation with inosine monophosphate and thus far has not been implicated in any human disease. This study aims to refine the evolutionary time frame at which gene duplication gave rise to PMM1 and PMM2, and to identify the most likely amino acid positions underlying the proteins’ different functions. The phylogenetic analysis using available protein sequences, allowed us to establish that duplication occurred early in vertebrate evolution. In order to understand the molecular basis underlying the functional divergence, conserved and most likely functional divergence-related sites were identified, through the analysis of site-specific evolutionary rates. This analysis indicates that most of the sites known to be important in the homodimer formation and in the catalytic activity are conserved in both proteins. Among those potentially related to functional divergence, two positions (183 and 186 in human PMM1) emerge as the most interesting ones. The residues at these positions have different side-chain conformations in the protein structure in the unbound and bound states, and are highly but differently conserved in PMM1 and in PMM2 proteins. Altogether, these results provide new data into the evolutionary history of PMM1 and PMM2 duplicates and highlight the most probable sites that evolved to distinct functional specificities.     

Solar Ultraviolet and the Evolutionary History of Cyanobacteria

On the basis of photobiological, evolutionary, paleontological, paleoenvironmental and physiological arguments, a time course for the role of solar ultraviolet radiation (UVR, wavelengths below 400 nm) in the ecology and evolution of cyanobacteria is proposed in which three main periods can be distinguished. An initial stage, before the advent of oxygenic photosynthesis, when high environmental fluxes of UVC (wavelengths below 280 nm) and UVB (280–320 nm) may have depressed the ability of protocyanobacteria to develop large populations or restricted them to UVR refuges. A second stage lasting between 500 and 1500 Ma (million years), started with the appearance of true oxygen-evolving cyanobacteria and the concomitant formation of oxygenated (micro)environments under an oxygen free-atmosphere. In this second stage, the age of UV, the overall importance of UVR must have increased substantially, since the incident fluxes of UVC and UVB remained virtually unchanged, but additionally the UVA portion of the spectrum (320–400 nm) suddenly became biologically injurious and extremely reactive oxygen species must have formed wherever oxygen and UVR spatially coincided. The last period began with the gradual oxygenation of the atmosphere and the formation of the stratospheric ozone shield. The physiological stress due to UVC all but disappeared and the effects of UVB were reduced to a large extent. Evidence in support of this dynamics is drawn from the phylogenetic distribution of biochemical UV-defense mechanisms among cyanobacteria and other microorganisms. The specific physical characteristics of UVR and oxygen exposure in planktonic, sedimentary and terrestrial habitats are used to explore the plausible impact of UVR in each of the periods on the ecological distribution of cyanobacteria.     

Local and Regional Processes in Community Assembly

Controversy on whether local (deterministic) or regional (stochastic) factors control the structure of communities persists after decades of research. The main reason for why it has not been resolved may lie in the nature of evidence which largely comes from realized natural communities. In such communities assembly history leaves a mark that may support either set of factors. To avoid the confounding effects of assembly history we controlled for these effects experimentally. We created a null community by mixing 17 rock pool communities. We then divided the null community into replicates and distributed among treatments representing a gradient of factors from local to regional. We hypothesized that if deterministic factors dominate the assembly of communities, community structures should show a corresponding gradient from being very similar and convergent to dissimilar and divergent. In contrast, if local processes are predominantly stochastic in nature, such a gradient of community configurations should emerge even in the homogeneous setting. Our results appear to partially support both hypotheses and thus suggest that both deterministic and stochastic processes contribute to the assembly of communities. Furthermore, we found that to satisfactorily explain patterns observed in natural communities environmental heterogeneity and regional processes must also be considered. In conclusion, although deterministic mechanisms seem to be important in the assembly of communities, in natural systems their signal may be diluted and masked whenever other factors exert meaningful influence. Such factors increase the number of possible paths to the point that the number of paths equals the number of communities in a metacommunity.     

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae

During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.     

Plant-soil Interactions: Ecological Aspects and Evolutionary Implications

Building on the concept of plants as ecosystem engineers, and on published information on effects of particular plant species on soils, we review the evidence that such effects can provide a positive feedback to such plants. Based on case studies involving dune formation by Marram grass, N supply by N2-fixing plants, depression of N availability by ericaceous plants, islands of fertility in deserts, mull- and mor-forming temperate forest trees, and formation of peatbogs, as well as similar other cases, we conclude that there is strong evidence for plant-soil feedbacks in a variety of ecosystems. We argue, moreover, that these feedbacks could have played a role in the evolution of the plant species in question. These ideas are based mainly on correlative observations, and need further testing.