Multiple Phenotypic Changes Associated with Large-Scale Horizontal Gene Transfer

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e., changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmids and phage, little is known about the magnitude or number of such costs after the transfer of larger regions. Here we describe numerous phenotypic changes that occur after a large-scale horizontal transfer event (∼1 Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.     

Evolutionary rate heterogeneity between multi- and single-interface hubs across human housekeeping and tissue-specific protein interaction network: Insights from proteins' and its partners' properties

Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slower than SI hubs. Here we explored the evolutionary rate difference between MI and SI proteins within TS- and HK-PPIN and observed that this difference is present only in TS, but not in HK-class. Next, we explored whether proteins' own properties or its partners' properties are more influential in such evolutionary discrepancy. Statistical analyses revealed that this evolutionary rate correlates negatively with protein's own properties like expression level, miRNA count, conformational diversity and functional properties and with its partners' properties like protein disorder and tissue expression similarity. Moreover, partial correlation and regression analysis revealed that both proteins' and its partners' properties have independent effects on protein evolutionary rate.     

Searching and gradualness

Consider the elements of the power set S as the alternatives in a search space. Each element of the set has a value and the goal of a search is to find an element with near-minimum value. If high-valued elements of cardinality i (recall that elements of S are themselves sets) are subsets of high-valued elements of cardinality i + 1, then the search space has a king of gradualness that should facilitate search.A search algorithm might generate a series, S′(1), … S′(k) of samples in S, where all the elements in S′ (i) have cardinality i. I propose a class of search algorithms, where each algorithm A(j) generates S′(i + 1) by emphasizing the j lowest-valued elements in S′(i). I then define search space gradualness and search algorithm performance and formally relate gradualness and performance.     

Energy intensities in ecological and economic systems

The concept of energy intensity (the energy needed, directly and indirectly, to effect the production of a “modity” an be applied to both economic and ecological systems. Hannon (1979) and Constanza (1980) have remarked on the lack of variation of energy intensity between different commodities for an ecosystem and an economic system, respectively. T This is particularly surprising for the ecosystem, since it seems to violate the traditional pyramid view of trophic systems. I show rigorously that Hannon's result is a mathematical consequence of his assumptions which are physically unjustified. I present a similar intuitive argument for Costanza's result, which is based on controversial but not physically unacceptable assumptions. The discussion brings out common threads of input-output economics and ecosystem analysis.     

The expansion of information in ecological systems: Emergence as a quantifiable state

Although the term ‘emergence’ has received wide attention in the literature, most of this attention has been focused on epistemological discussions about the nature of what might be considered emergent behavior in self-organizing systems. For the concept of emergence to have any great utility for biologists, it must (1) be perceptible as a physical, quantitative property rather than just a philosophical one; (2) have a quantitative definition applicable to all levels of biological organization; and (3) be an essential component of biological system performance or evolution. Using an independent, cellular population model (running in the StarLogo system), we have developed a mutual information calculation to measure the information expansion when considering the interactions between a population of herbivores and an environment in comparison to the interactions between the individual herbivores and that environment. In self-organizing biological systems, the collective action of massively parallel units generates a greater potential complexity in the information processing capacity of the ‘whole’ system relative to the ‘individual’ parts, and as such, there is a demonstrable increase in mutual information content. From this perspective, we consider emergence to exist as a simple information expansion that is a default behavior of any system with multiple, component parts governed by a simple, probabilistic rule set. It is not a first principle of self-organizing biological systems, but rather a collective behavior that can be quantitatively described in practical terms for experimental biologists. With a quantitative formulation, the concept of emergence may become a useful information statistic in assessing the structure of biological systems.     

Evolutionary aspects of interaction of sleep and stress: Phylo- and ontogenetic approach

This work considers comparative behavioral, somatoautonomic, and neurophysiological characteristics of three forms of passive defensive behavior included in the amphibian wakefulness-sleep cycle and their dynamics in the ascending vertebrate series. Considered in parallel is sleep formation in early postnatal ontogenesis of mature-and immature-born mammals-from undifferentiated sleep to the mature sleep divided into two phases as well as of stress-reaction. Comparative phylo-and ontogenetic analysis of several aspects of stress-reactions, sleep, and immobility phenomenon of the catalepsy type allows concluding that the immobility state of the catalepsy type in amphibians and reptiles can be considered the preadaptive behavior type that underlies the homoiothermal stress-reaction. It is the genetically programmed to the poikilothermal state characterized by a relatively high animal alertness, a freezing of the animal in the immobile, but active posture, with a possibility of a fast exit into the wakefulness state, which, alongside with other somatoautonomic and neurophysiological characteristics, which determines the entire subsequent complex of evolutionary morphofunctional changes of neuroregulatory and hormonal changes in the homoiothermal organism. In poikilothermal animals, this in many aspects unspecific behavioral adaptive reaction is realized at the corresponding hormonal and neurological levels of development of the organism and promotes fast mobilization and stabilization of constancy of the internal medium. At the higher evolutionary ladder levels, on the background of maturation of most neurotransmitter systems of brain and the hypothalamo-pituitary-adrenal system, the leading role in the stress-reaction regulation begins to be played predominantly by hormones, and only in the phase of the stress-reaction alertness, there are observed elements of activation of extrapyramidal systems of regulation of locomotor activity, which is manifested as the cataleptic freezing reaction. Thus, stress as the general adaptational syndrome reflects evolutionary regularities of development of specific functions supporting the total homeostasis. A scheme of evolutionary development of the wakefulness-sleep cycle in the vertebrate subtype is presented; according to it, the immobility state of the catalepsy type, on one hand, is considered as a part of wakefulness providing mainly specific elements of the stress-reaction, while, on the other hand,—as a certain step of the process of inhibition in CNS for subsequent involvement of the sleep-regulatory systems of compensation and maintenance of recovery reactions.     

Do Correlation Patterns Reflect the Role of Development in Morphological Evolution?

Correlation patterns have been widely used in evolutionary studies for exploring the role of development in channelling morphological evolution. The approach was firstly introduced by Olson and Miller in the 1950s, but it did not gain prominence until the 1980s, due to some extent to Gould and Lewontin’s (Proc R Soc Lond B 205:581–598, 1979) assertion of the importance of considering organisms as integrated entities, where the internal organization of a structure, and not only the selective regime acting upon it, would play a fundamental role in its evolution. Here we show that this approach, mainly focused on the study of small, quantitative shape changes of existing structures, does not deal with a fundamental aspect of developmental systems, that is, their intrinsic capacity of originating morphological novelties. We show that only when the physicochemical processes underlying morphogenesis and pattern formation are taken into account, would the causal role of development be fully incorporated into the evolutionary view.     

Parsimony in evolutionary theory: Law or methodological prescription?

Parsimony (Ockham's razor) is in widespread use in phylogenetic reconstruction (evolution takes the shortest route), however it is not quite obvious which is the rank that this principle should have in evolutionary theory. Parsimony is not of a single kind but, on the contrary, is at least of two kinds: ontological and methodological. Ontological parsimony involves an assumption about the “simplicity of nature”. Methodological parsimony is a purely logical precept, a case of the broad practical principle not to believe anything for which there is no evidence. The two kinds of parsimony are not compatible with one another. The ontological hypotheses that reality is simple has been refuted many times in the history of science, and evolution is not an exception to this. In spite of the fact, that direct evolutionary changes have higher probability than the ones that take “unnecessary” steps, evolutionary parsimony is merely a methodological precept, not a law of evolution. Probability is not enough to give evolutionary parsimony a rank of ontological axiom. Therefore, the reasons to use the principle of evolutionary parsimony are only methodological. A definition of evolutionary parsimony is: as long as no evidence is available to suggest an alternative pathway evolution may be considered to occur in the most parsimonious way.     

What is menstruation for? On the projectibility of functional predicates in menstruation research

In 1993, biologist Margie Profet captured the attention of the popular press with the publication of her radical thesis: menstruation has a function. Traditional theories, she claims, typically view menstruation as a functionless by-product of cyclic flux. The details of Profet’s functional account are similarly radical: she argues that menstruation has been naturally selected to defend the female reproductive tract from sperm-borne pathogens. There are a number of weaknesses in Profet’s evolutionary analysis. However, I focus on a set of pragmatic problems that arise prior to any details of her evolutionary account. In arguing for the importance of pragmatic considerations, I draw from the linguistic analyses of Nelson Goodman. I conclude that critical investigation of the evolutionary details of Profet’s pathogen defense account will be more feasible if and when biologists more frequently feature the female system of pathogen defense in their inductive generalisations. The system needs to be better entrenched before its functional components, such as menstruation, can be thoroughly investigated.     

A levels-of-selection approach to evolutionary individuality

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken in Clarke (J Philos 110(8):413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided.     

Power and limitation of an energy-balance climate model as applied to the astronomical theory of palaeoclimates

From the long-term variatioon of zonal annual mean air-surface temperature, computed through a global model which includes a new determination of the Earth's orbital elements and insolation and is based on Sellers' first climatic model, it is shown that the astronomical elements can only trigger and modulate the climatic changes during the last Ice Age.     

The evolution of matrilineal kinship organization

Matrilineal kinship organization is a human social system that emphasizes interactions between matrilineal kin, i.e. individuals related only through females. The ‘matrilineal puzzle’ refers to the potential for tension characteristic of this social system, owing to the conflict between the interests and responsibilities of men in their roles as brother/uncle versus husband/father. From an evolutionary perspective, matrilineal kinship organization is puzzling when it diverts investment of resources from the individuals who provide the potentially highest reproductive returns. I use a game-theoretic framework to investigate a particular form of matrilineal inheritance—the transfer of property from a maternal uncle to a sororal nephew. The analysis reveals two mechanisms that may make this strategy a stable evolutionary outcome. First, a polygynous male has multiple wives, and hence multiple brothers-in-law; with matrilineal inheritance, each additional brother-in-law may transfer resources to the male''s wife''s offspring, thus potentially contributing to the male''s inclusive fitness. Second, the husband of a polyandrous female is effectively ‘sharing’ paternity with other men; depending on the number of husbands, he may be better off investing in his sister''s offspring. I conclude by discussing how these results address the challenges posed by the occurrence of matrilineal kinship organization.     

Probing Evolutionary Repeatability: Neutral and Double Changes and the Predictability of Evolutionary Adaptation

Background

The question of how organisms adapt is among the most fundamental in evolutionary biology. Two recent studies investigated the evolution of Escherichia coli in response to challenge with the antibiotic cefotaxime. Studying five mutations in the β-lactamase gene that together confer significant antibiotic resistance, the authors showed a complex fitness landscape that greatly constrained the identity and order of intermediates leading from the initial wildtype genotype to the final resistant genotype. Out of 18 billion possible orders of single mutations leading from non-resistant to fully-resistant form, they found that only 27 (1.5×10⁻⁷%) pathways were characterized by consistently increasing resistance, thus only a tiny fraction of possible paths are accessible by positive selection. I further explore these data in several ways.

Principal Findings

Allowing neutral changes (those that do not affect resistance) increases the number of accessible pathways considerably, from 27 to 629. Allowing multiple simultaneous mutations also greatly increases the number of accessible pathways. Allowing a single case of double mutation to occur along a pathway increases the number of pathways from 27 to 259, and allowing arbitrarily many pairs of simultaneous changes increases the number of possible pathways by more than 100 fold, to 4800. I introduce the metric ‘repeatability,’ the probability that two random trials will proceed via the exact same pathway. In general, I find that while the total number of accessible pathways is dramatically affected by allowing neutral or double mutations, the overall evolutionary repeatability is generally much less affected.

Conclusions

These results probe the conceivable pathways available to evolution. Even when many of the assumptions of the analysis of Weinreich et al. (2006) are relaxed, I find that evolution to more highly cefotaxime resistant β-lactamase proteins is still highly repeatable.     

On the Relative Importance of Haplo-Diploidy, Assortative Mating and Social Synergy on the Evolutionary Emergence of Social Behavior

Advances in multiagent simulation techniques make it possible to study more realistic dynamics of complex systems and allow evolutionary theories to be tested. Here I use simulations to assess the relative importance of reproductive systems (haplodiploidy vs. diploidy), mate selection (assortative mating vs. random mating) and social economics (pay-off matrices of evolutionary games) in the evolutionary dynamics leading to the emergence of social cooperation in the provision of parental care. The simulations confirm that haplo-diploid organisms and organisms mating assortatively have a higher probability for fixing alleles and require less favorable conditions for their fixation, than diploids or organisms mating randomly. The simulations showed that social behavior was most likely to emerge a) when the cost for parental investment was much lower than the benefits to the offspring, b) when cooperation improved synergistically the fitness of offspring compared to the corresponding egoistic behavior and c) when alleles coding for altruistic or social behavior could be rapidly fixed in the population, thanks to mechanisms such as haplo-diploidy and/or assortative mating. Cooperative social behavior always appeared if sociality conferred much higher fitness gains compared to non cooperative alternatives suggesting that the most important factors for the emergence and maintenance of social behavior are those based on energetic or efficiency considerations. The simulations, in congruence with the scant experimental evidence available, suggest that economic considerations rather than genetic ones are critical in explaining the emergence and maintenance of sociality.     

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (∼23%) than the other two, COPI (∼9%) and COPII (∼8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes.     

Coordinate Representations for Interference Reduction in Motor Learning

When opposing force fields are presented alternately or randomly across trials for identical reaching movements, subjects learn neither force field, a behavior termed ‘interference’. Studies have shown that a small difference in the endpoint posture of the limb reduces this interference. However, any difference in the limb’s endpoint location typically changes the hand position, joint angles and the hand orientation making it ambiguous as to which of these changes underlies the ability to learn dynamics that normally interfere. Here we examine the extent to which each of these three possible coordinate systems—Cartesian hand position, shoulder and elbow joint angles, or hand orientation—underlies the reduction in interference. Subjects performed goal-directed reaching movements in five different limb configurations designed so that different pairs of these configurations involved a change in only one coordinate system. By specifically assigning clockwise and counter-clockwise force fields to the configurations we could create three different conditions in which the direction of the force field could only be uniquely distinguished in one of the three coordinate systems. We examined the ability to learn the two fields based on each of the coordinate systems. The largest reduction of interference was observed when the field direction was linked to the hand orientation with smaller reductions in the other two conditions. This result demonstrates that the strongest reduction in interference occurred with changes in the hand orientation, suggesting that hand orientation may have a privileged role in reducing motor interference for changes in the endpoint posture of the limb.     

ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12

Anti-restriction and anti-modification (anti-RM) is the ability to prevent cleavage by DNA restriction–modification (RM) systems of foreign DNA entering a new bacterial host. The evolutionary consequence of anti-RM is the enhanced dissemination of mobile genetic elements. Homologues of ArdA anti-RM proteins are encoded by genes present in many mobile genetic elements such as conjugative plasmids and transposons within bacterial genomes. The ArdA proteins cause anti-RM by mimicking the DNA structure bound by Type I RM enzymes. We have investigated ArdA proteins from the genomes of Enterococcus faecalis V583, Staphylococcus aureus Mu50 and Bacteroides fragilis NCTC 9343, and compared them to the ArdA protein expressed by the conjugative transposon Tn916. We find that despite having very different structural stability and secondary structure content, they can all bind to the EcoKI methyltransferase, a core component of the EcoKI Type I RM system. This finding indicates that the less structured ArdA proteins become fully folded upon binding. The ability of ArdA from diverse mobile elements to inhibit Type I RM systems from other bacteria suggests that they are an advantage for transfer not only between closely-related bacteria but also between more distantly related bacterial species.     

Evolution towards oscillation or stability in a predator–prey system

We studied a prey–predator system in which both species evolve. We discuss here the conditions that result in coevolution towards a stable equilibrium or towards oscillations. First, we show that a stable equilibrium or population oscillations with small amplitude is likely to occur if the prey''s (host''s) defence is effective when compared with the predator''s (parasite''s) attacking ability at equilibrium, whereas large-amplitude oscillations are likely if the predator''s (parasite''s) attacking ability exceeds the prey''s (host''s) defensive ability. Second, a stable equilibrium is more likely if the prey''s defensive trait evolves faster than the predator''s attack trait, whereas population oscillations are likely if the predator''s trait evolves faster than that of the prey. Third, when the adaptation rates of both species are similar, the amplitude of the fluctuations in their abundances is small when the adaptation rate is either very slow or very fast, but at an intermediate rate of adaptation the fluctuations have a large amplitude. We also show the case in which the prey''s abundance and trait fluctuate greatly, while those of the predator remain almost unchanged. Our results predict that populations and traits in host–parasite systems are more likely than those in prey–predator systems to show large-amplitude oscillations.     

Information processing in molecular systems

Information processing, or selective dissipation, is mediated by switching elements in classical systems and by enzyme catalysis in biochemical systems. There are important differences in the character of this dissipation (from the standpoint of energy and control) in self-reproducing systems based on molecular interactions and those based on conventional computers. Conventional computers process information in a single level mode, i.e., the state of each unit of the system is accessed independently. This includes the manipulable memory units which store the computer program. In contrast, molecular self-reproducing systems process information in a hierarchical mode, based on the fact of hierarchy in molecular structure. In particular, the enzyme is described genetically at the primary level of structure (amino acid sequence) but functions at the higher, tertiary level on the basis of the interactions of many manipulable units. As a consequence it is not possible to program a biochemical system in any conventional sense. However, this is compensated by an increased capacity for accumulating appropriate information through evolution by variation and natural selection. This is possible because systems operating in the hierarchical mode are amenable to gradual modification of function. The degree of gradualness is itself an evolved property of biological molecules.