This theoretical proposal applies evolutionary aesthetic, animal signalling and sexual selection to understand our artistic cognition, especially rock art aesthetics. Iconographic motifs, universally found in rock art, indicate which set of pre-artistic aesthetic psychological bias has been co-opted to catch the viewer`s attention. The co-evolutionary process of sexual selection could have shaped the design features of both rock art images and their aesthetic cognition by conferring mutual benefits on both producers, via manipulation, and receivers, via information extraction. We show some strategic techniques identified in rock art and art that indicate the occurrence of this co-evolution between producers and receivers.
Schistosomes, ancestors and recent species, have pervaded many hosts and several phylogenetic levels of immunity, causing an evolutionary pressure to eosinophil lineage expression and response. Schistosoma mansoni adult worms have capitalized on the apparent adversity of living within the mesenteric veins, using the dispersion of eggs and antigens to other tissues besides intestines to set a systemic activation of several haematopoietic lineages, specially eosinophils and monocytes/macrophages. This activation occurs in bone marrow, spleen, liver, lymph nodes, omental and mesenteric milky spots (activation of the old or primordial and recent or new lymphomyeloid tissue), increasing and making easy the migration of eosinophils, monocytes and other cells to the intestinal periovular granulomas. The exudative perigranulomatous stage of the periovular reaction, which present hystolitic characteristics, is then exploited by the parasites, to release the eggs into the intestinal lumen. The authors hypothesize here that eosinophils, which have a long phylogenic story, could participate in the parasite - host co-evolution, specially with S. mansoni, operating together with monocytes/ macrophages, upon parasite transmission.
The evolutionary relationships of sand flies and Leishmania are discussed in this report, which draws distinctions between co-association, co-evolution and co-speciation (or co-cladogenesis). Examples focus on Phlebotomus vectors of Le. infantum and Le. major in the Mediterranean subregion.
Understanding the evolution of altruism requires knowledge of both its constraints and its drivers. Here we show that, paradoxically, ecological constraints on altruism may ultimately be its strongest driver. We construct a two-trait, co-evolutionary adaptive dynamics model of social evolution in a genetically structured population with local resource competition. The intensity of local resource competition, which influences the direction and strength of social selection and which is typically treated as a static parameter, is here allowed to be an evolvable trait. Evolution of survival/fecundity altruism, which requires weak local competition, increases local competition as it evolves, creating negative environmental feedback that ultimately inhibits its further evolutionary advance. Alternatively, evolution of resource-based altruism, which requires strong local competition, weakens local competition as it evolves, also ultimately causing its own evolution to stall. When evolving independently, these altruistic strategies are intrinsically self-limiting. However, the co-existence of these two altruism types transforms the negative eco-evolutionary feedback generated by each strategy on itself into positive feedback on the other, allowing the presence of one trait to drive the evolution of the other. We call this feedback conversion “reciprocal niche construction”. In the absence of constraints...
Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm...
The exon junction complex (EJC) plays important roles in RNA metabolisms and the development of eukaryotic organisms. MAGO (short form of MAGO NASHI) and Y14 (also Tsunagi or RBM8) are the EJC core components. Their biological roles have been well investigated in various species, but the evolutionary patterns of the two gene families and their protein-protein interactions are poorly known. Genome-wide survey suggested that the MAGO and Y14 two gene families originated in eukaryotic organisms with the maintenance of a low copy. We found that the two protein families evolved slowly; however, the MAGO family under stringent purifying selection evolved more slowly than the Y14 family that was under relative relaxed purifying selection. MAGO and Y14 were obliged to form heterodimer in a eukaryotic organism, and this obligate mode was plesiomorphic. Lack of binding of MAGO to Y14 as functional barrier was observed only among distantly species, suggesting that a slow co-evolution of the two protein families. Inter-protein co-evolutionary signal was further quantified in analyses of the Tol-MirroTree and co-evolution analysis using protein sequences. About 20% of the 41 significantly correlated mutation groups (involving 97 residues) predicted between the two families was clade-specific. Moreover...
Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.
Most Old World mice and rats, subfamily Murinae, have a spermatozoon with an apical hook, a long tail and, as seen typically in eutherian mammals, a bilaterally flattened head. Dramatically different from this are the sperm of the Greater Bandicoot Rat, Bandicota indica. Here, we ask the question has the structure of the sperm head co-evolved with that of the egg coat, the zona pellucida? For this, we first summarise the morphological features of the spermatozoon of B. indica that may relate to zona pellucida penetration at the time of fertilisation, and we confirm that the sperm head is generally round, not bilaterally flattened, in profile and has a huge acrosome. We then show that the zona pellucida around oocytes in tertiary follicles also differs from that of the other murine rodents in being only about 4 μm thick and, as demonstrated by lectin staining, has an unusual abundance of alpha-L-fucose. These findings indicate that both the male and female gametes of this South-East Asian murine rodent are highly divergent in their structural organisation. One of the functional implications of this probably relates to sperm–zona interactions and the release of acrosomal enzymes that probably facilitate penetration by digestion of the zona matrix at the time of fertilisation.; Fiona Dorman...
Unter dem Begriff "Koevolution" werden in der evolutionsbiologischen Literatur sehr unterschiedliche Phänomene eingeordnet, die von wechselseitigen Einflüssen auf den Genpool der Populationen zweier assoziierter Organismen einerseits bis zum Vergleich von Stammbäumen andererseits reichen. Die Begriffsverwirrung wird komplettiert durch Kausalbeziehungen, die zwischen verschiedenen dieser Phänomene postuliert wurden. Um dem babylonischen Chaos entgegenzutreten, wird hier zunächst in einem begriffshistorischen Abriss geklärt, welche der sich derzeit im Umlauf befindenden Definitionen von "Koevolution" der ursprünglichen gleichkommt. Es schließt sich die Diskussion der Frage an, ob sich diese originale Definition als Oberbegriff für die verschiedenen Phänomen eignet. Zweitens wird gefragt, ob sich die in der Literatur postulierten Kausalzusammenhänge empirisch oder theoretisch plausibel machen lassen. Beide Fragen werden verneint. Vor diesem Hintergrund wird für eine Nomenklatur für den Vergleich von Stammbäumen plädiert, die vom begrifflichen Ballast aus dem Umfeld von "Koevolution" befreit ist.; The term "co-evolution" is frequently used in evolutionary biology and covers extremely heterogeneous phenomena, ranging from the reciprocal impact of two associated populations of distinct species on each other's gene pool on the one hand to the comparison of phylogenies on the other hand. The nomenclature is further complicated by the fact the causal relationships have been postulated between some of these phenomena. To counter this kind of terminological confusion...
It has been almost 150 years since Darwin’s “The Origin of Species” was published, yet the mechanisms that lead to the creation of new species are still a topic of fervent research in Evolutionary Biology. In the last several decades, there has been considerable interest in how genetic drift and adaptive processes internal to populations may lead to population divergence. It has been recognized that intersexual co-evolution may drive the rapid evolution of reproductive traits, leading to reproductive isolation between populations in allopatry. To explore the nature of this process, I conducted a series of interpopulation interaction experiments using a set of laboratory-evolved Drosophila melanogaster populations. These “B” (for baseline) populations share a common ancestor and had evolved in identical habitats in allopatry for 650-700 generations prior to my experiments. When different populations were combined in competitive fitness assays, I found that foreign males usually suffer depressed fitness when competing with males who share a common evolutionary history with the focal females. I selected a subset of B populations to investigate potential sources of variation that could explain this result. I examined; 1) characters involved in post-copulatory interactions between mates and 2) traits involved in mating behaviour. I found that sperm precedence patterns varied significantly depending on female population of origin and suggestive evidence that males between populations vary in ability to compete in sperm offence. Males also varied in mating behaviour between populations...
Les logiciels sont en constante évolution, nécessitant une maintenance et un développement continus. Ils subissent des changements tout au long de leur vie, que ce soit pendant l'ajout de nouvelles fonctionnalités ou la correction de bogues.
Lorsque les logiciels évoluent, leurs architectures ont tendance à se dégrader et deviennent moins adaptables aux nouvelles spécifications des utilisateurs. En effet, les architectures de ces logiciels deviennent plus complexes et plus difficiles à maintenir à cause des nombreuses dépendances entre les artefacts.
Par conséquent, les développeurs doivent comprendre les dépendances entre les artefacts des logiciels
pour prendre des mesures proactives qui facilitent les futurs changements et ralentissent la dégradation des architectures des logiciels.
D'une part, le maintien d'un logiciel sans la compréhension des les dépendances entre ses artefacts peut conduire à l'introduction de défauts.
D'autre part, lorsque les développeurs manquent de connaissances sur l'impact de leurs activités de maintenance, ils peuvent introduire des défauts de conception, qui ont un impact négatif sur l'évolution du logiciel. Ainsi, les développeurs ont besoin de mécanismes pour comprendre comment le changement d'un artefact impacte le reste du logiciel.
Dans cette thèse...
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way...
Patterns of nestedness and specialization asymmetry, where specialist species
interact mainly with generalists while generalists interact with both
generalists and specialists, are often observed in mutualistic and antagonistic
bi-partite ecological networks. These have been explained in terms of the
relative abundance of species, using a null model that assigns links in
proportion to abundance, but doubts have been raised as to whether this offers
a complete explanation. In particular, host-parasite networks offer a variety
of examples in which the reverse patterns are observed.
We propose that the link between specificity and species-richness may also be
driven by the co-evolution of hosts and parasites, as hosts allocate resources
to optimize defence against parasites, and parasites to optimize attack on
hosts. In this hypothesis, species interactions are a result of resource
allocations. This novel concept, linking together many different arguments for
network structures, is introduced through the adaptive dynamics of a simple
ecological toy system of two hosts and two parasites.
We analyse the toy model and its functionality, demonstrating that
co-evolution leads to specialization asymmetry in networks with closely related
parasites or fast host mutation rates...
The vertebrate adaptive immune system provides a flexible and diverse set of
molecules to neutralize pathogens. Yet, viruses that cause chronic infections,
such as HIV, can survive by evolving as quickly as the adaptive immune system,
forming an evolutionary arms race within a host. Here we introduce a
mathematical framework to study the co-evolutionary dynamics of antibodies with
antigens within a patient. We focus on changes in the binding interactions
between the antibody and antigen populations, which result from the underlying
stochastic evolution of genotype frequencies driven by mutation, selection, and
drift. We identify the critical viral and immune parameters that determine the
distribution of antibody-antigen binding affinities. We also identify
definitive signatures of co-evolution that measure the reciprocal response
between the antibody and viruses, and we introduce experimentally measurable
quantities that quantify the extent of adaptation during continual co-evolution
of the two opposing populations. Finally, we analyze competition between clonal
lineages of antibodies and characterize the fate of a given lineage dependent
on the state of the antibody and viral populations. In particular, we derive
the conditions that favor the emergence of broadly neutralizing antibodies...
Co-evolution of two coupled quasispecies is studied, motivated by the
competition between viral evolution and adapting immune response. In this
co-adaptive model, besides the classical error catastrophe for high virus
mutation rates, a second ``adaptation-'' catastrophe occurs, when virus
mutation rates are too small to escape immune attack. Maximizing both regimes
of viral error catastrophes is a possible strategy for an optimal immune
response, reducing the range of allowed viral mutation rates to a minimum. From
this requirement one obtains constraints on B-cell mutation rates and receptor
lengths, yielding an estimate of somatic hypermutation rates in the germinal
center in accordance with observation.; Comment: 4 pages RevTeX including 2 figures
Markov models are extensively used in the analysis of molecular evolution. A
recent line of research suggests that pairs of proteins with functional and
physical interactions co-evolve with each other. Here, by analyzing hundreds of
orthologous sets of three fungi and their co-evolutionary relations, we
demonstrate that co-evolutionary assumption may violate the Markov assumption.
Our results encourage developing alternative probabilistic models for the cases
of extreme co-evolution.
We study an abstract model for the co-evolution between mutating viruses and
the adaptive immune system. In sequence space, these two populations are
localized around transiently dominant strains. Delocalization or error
thresholds exhibit a novel interdependence because immune response is
conditional on the viral attack. An evolutionary chase is induced by stochastic
fluctuations and can occur via periodic or intermittent cycles. Using
simulations and stochastic analysis, we show how the transition between these
two dynamic regimes depends on mutation rate, immune response, and population
size.; Comment: 5 pages, 3 figures, 11 pages supplementary material; updated
formatting; accepted at Phys. Rev. Lett
In this paper, we extend a model of host-parasite co-evolution to incorporate
the semi-conservative nature of DNA replication for both the host and the
parasite. We find that the optimal mutation rate for the semi-conservative and
conservative hosts converge for realistic genome lengths, thus maintaining the
admirable agreement between theory and experiment found previously for the
conservative model and justifying the conservative approximation in some cases.
We demonstrate that, while the optimal mutation rate for a conservative and
semi-conservative parasite interacting with a given immune system is similar to
that of a conservative parasite, the properties away from this optimum differ
significantly. We suspect that this difference, coupled with the requirement
that a parasite optimize survival in a range of viable hosts, may help explain
why semi-conservative viruses are known to have significantly lower mutation
rates than their conservative counterparts.
Incluye una figura.; Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories
(similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecularmechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation’) from other forces that...
8 pages, 11 figures.-- PMID: 18714343 [PubMed].-- PMCID: PMC2500161.; [Background] It is normally thought that deep corolla tubes evolve when a plant's successful reproduction is contingent on having a corolla tube longer than the tongue of the flower's pollinators, and that pollinators evolve ever-longer tongues because individuals with longer tongues can obtain more nectar from flowers. A recent model shows that, in the presence of pollinators with long and short tongues that experience resource competition, coexisting plant species can diverge in corolla-tube depth, because this increases the proportion of pollen grains that lands on co-specific flowers.; [Methodology/Principal Findings] We have extended the model to study whether resource competition can trigger the co-evolution of tongue length and corolla-tube depth. Starting with two plant and two pollinator species, all of them having the same distribution of tongue length or corolla-tube depth, we show that variability in corolla-tube depth leads to divergence in tongue length, provided that increasing tongue length is not equally costly for both species. Once the two pollinator species differ in tongue length, divergence in corolla-tube depth between the two plant species ensues.; [Conclusions/Significance] Co-evolution between tongue length and corolla-tube depth is a robust outcome of the model...