The dynamics of genome size and GC contents evolution in genus Nicotiana

Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one’s (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.

The Organization of the Pig T-cell Receptor Gamma (TRG) Locus Provides Insights Into the Evolutionary Patterns of the TRG Genes Across Cetartiodactyla

The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC &ldquo;cassettes&rdquo;, each containing the basic V-J-J-C unit. Eighteen genes arranged in four TRGC cassettes, form the pig TRG locus. All the functional TRG genes were expressed, and the TRGV genes preferentially rearrange with the TRGJ genes within their own cassette, which correlates the diversity of the gamma-chain repertoire with the number of cassettes. Among them, the TRGC5, located at the 5&rsquo; end of the locus, is the only cassette that retains a marked homology with the corresponding TRGC cassettes of all the analyzed species. The preservation of the TRGC5 cassette for such a long evolutionary time presumes a highly specialized function of its genes, which could be essential for the survival of species. Therefore, the maintenance of this cassette in pigs confirms that it is the most evolutionarily ancient within Cetartiodactyla, and it has undergone a process of duplication to give rise to the other TRGC cassettes in the different artiodactyl species in a lineage-specific manner.

Dynamic collateral sensitivity profiles highlight challenges and opportunities for optimizing antibiotic sequences

As traditional antimicrobial therapies fail at escalating rates, recent focus has shifted to evolution-based therapies to slow resistance. Collateral sensitivity-the increased susceptibility to one drug associated with evolved resistance to a different drug-offers a potentially exploitable evolutionary constraint, but the manner in which collateral effects emerge over time is not well understood. Here, we use laboratory evolution in the opportunistic pathogen E. faecalis to phenotypically characterize collateral profiles through evolutionary time. Specifically, we measure collateral profiles for 400 strain-antibiotic combinations over the course of 4 evolutionary time points as strains are selected in increasing concentrations of antibiotic. We find that collateral resistance dominates during early phases of adaptation, whereas a diverse set of collateral profiles are accessible with further selection. Using simple numerical simulations, we illustrate how these temporally dynamic profiles potentially impact sequential drug therapies. Finally, we show experimentally how dynamic collateral sensitivity relationships can create optimal dosing windows that depend on finely timed switching between drugs.

The genomics of exceptional longevity in rockfishes refine genetic foundations of human lifespan variation

Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, ranging in longevity from 11 to over 205 years. Shifts in rockfish longevity occurred multiple times independently, and in a short evolutionary time frame, thus empowering convergence analyses. Our analyses reveal a common network of genes under convergent restricted evolution in long-lived lineages, encompassing established aging regulators such as insulin-signaling, yet also identify flavonoid (aryl-hydrocarbon) metabolism as a novel pathway modulating longevity. Further, these genes were used to refine human longevity GWAS, identifying the aryl-hydrocarbon metabolism pathway to be significantly associated with the 99th percentile of human longevity, independently validating its importance and conservation. This evolutionary intersection highlights a novel, conserved genetic architecture that associates with the evolution of longevity across vertebrates and provides actionable targets for research into lifespan and healthspan modulation.

The predator-dependent replicator dynamics

Ecological interactions are central to understanding evolution. For example, Darwin noticed that the beautiful colours of the male peacock increase the chance of successful mating. However, the colours can be a threat because of the increased probability of being caught by predators. Eco-evolutionary dynamics takes into account environmental interactions to model the process of evolution. The selection of prey types in the presence of predators may be subjected to pressure on both reproduction and survival. Here, we analyze the evolutionary game dynamics of two types of prey in the presence of predators. We call this model \textit{the predator-dependent replicator dynamics}. If the evolutionary time scales are different, the number of predators can be assumed constant, and the traditional replicator dynamics is recovered. However, if the time scales are the same, we end up with sixteen possible dynamics: the combinations of four reproduction’s games with four predation’s games. We analyze the dynamics and calculate conditions for the coexistence of prey and predator. The main result is that predators can change the equilibrium of the traditional replicator dynamics. For example, the presence of predators can induce polymorphism in prey if one type of prey is more attractive than the other, with the prey ending with a lower capture rate in this new equilibrium. Lastly, we provide two illustrations of the dynamics, which can be seen as rapid feedback responses in a predator-prey evolutionary arm’s race.

Wave Functional of the Universe and Time

A version of the quantum theory of gravity based on the concept of the wave functional of the universe is proposed. To determine the physical wave functional, the quantum principle of least action is formulated as a secular equation for the corresponding action operator. Its solution, the wave functional, is an invariant of general covariant transformations of spacetime. In the new formulation, the history of the evolution of the universe is described in terms of coordinate time together with arbitrary lapse and shift functions, which makes this description close to the formulation of the principle of general covariance in the classical theory of Einstein’s gravity. In the new formulation of quantum theory, an invariant parameter of the evolutionary time of the universe is defined, which is a generalization of the classical geodesic time measured by a standard clock along time-like geodesics.

Naïve and Experienced Honeybee Foragers Learn Normally Configured Flowers More Easily Than Non-configured or Highly Contrasted Flowers

Angiosperms have evolved to attract and/or deter specific pollinators. Flowers provide signals and cues such as scent, colour, size, pattern, and shape, which allow certain pollinators to more easily find and visit the same type of flower. Over evolutionary time, bees and angiosperms have co-evolved resulting in flowers being more attractive to bee vision and preferences, and allowing bees to recognise specific flower traits to make decisions on where to forage. Here we tested whether bees are instinctively tuned to process flower shape by training both flower-experienced and flower-naïve honeybee foragers to discriminate between pictures of two different flower species when images were either normally configured flowers or flowers which were scrambled in terms of spatial configuration. We also tested whether increasing picture contrast, to make flower features more salient, would improve or impair performance. We used four flower conditions: (i) normally configured greyscale flower pictures, (ii) scrambled flower configurations, (iii) high contrast normally configured flowers, and (iv) asymmetrically scrambled flowers. While all flower pictures contained very similar spatial information, both experienced and naïve bees were better able to learn to discriminate between normally configured flowers than between any of the modified versions. Our results suggest that a specialisation in flower recognition in bees is due to a combination of hard-wired neural circuitry and experience-dependent factors.

Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria

Protein post-translational modifications (PTMs) add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than one billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared to products of likely endosymbiont gene transfer, mitochondrial proteins and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.

The supernumerary B chromosome of maize: drive and genomic conflict

The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.

The Dynamic Hypercube as a Niche Community Model

Different models of community dynamics, such as the MacArthur–Wilson theory of island biogeography and Hubbell’s neutral theory, have given us useful insights into the workings of ecological communities. Here, we develop the niche-hypervolume concept of the community into a powerful model of community dynamics. We describe the community’s size through the volume of the hypercube and the dynamics of the populations in it through the fluctuations of the axes of the niche hypercube on different timescales. While the community’s size remains constant, the relative volumes of the niches within it change continuously, thus allowing the populations of different species to rise and fall in a zero-sum fashion. This dynamic hypercube model reproduces several key patterns in communities: lognormal species abundance distributions, 1/f-noise population abundance, multiscale patterns of extinction debt and logarithmic species-time curves. It also provides a powerful framework to explore significant ideas in ecology, such as the drift of ecological communities into evolutionary time.