ResearchPad - evolutionary-theory https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories]]> https://www.researchpad.co/article/elastic_article_13873 Comparative social science has a long history of attempts to classify societies and cultures in terms of shared characteristics. However, only recently has it become feasible to conduct quantitative analysis of large historical datasets to mathematically approach the study of social complexity and classify shared societal characteristics. Such methods have the potential to identify recurrent social formations in human societies and contribute to social evolutionary theory. However, in order to achieve this potential, repeated studies are needed to assess the robustness of results to changing methods and data sets. Using an improved derivative of the Seshat: Global History Databank, we perform a clustering analysis of 271 past societies from sampling points across the globe to study plausible categorizations inherent in the data. Analysis indicates that the best fit to Seshat data is five subclusters existing as part of two clearly delineated superclusters (that is, two broad “types” of society in terms of social-ecological configuration). Our results add weight to the idea that human societies form recurrent social formations by replicating previous studies with different methods and data. Our results also contribute nuance to previously established measures of social complexity, illustrate diverse trajectories of change, and shed further light on the finite bounds of human social diversity.

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<![CDATA[The continuing evolution of ownership]]> https://www.researchpad.co/article/5c6c7577d5eed0c4843cfddd

The evolution in animals of a first possession convention, in which individuals retain what they are the first to acquire, has often been taken as a foundation for the evolution of human ownership institutions. However, among humans, individuals actually only seldom retain an item they have acquired from the environment, instead typically transferring what they possess to other members of the community, to those in command, or to those who hold a contractual title. This paper presents a novel game-theoretic model of the evolution of ownership institutions as rules governing resource transfers. Integrating existing findings, the model contributes a new perspective on the emergence of communal transfers among hominin large game hunters around 200,000 years ago, of command ownership among sedentary humans in the millennia prior to the transition to agriculture, and of titled property ownership around 5,500 years ago. Since today’s property institutions motivate transfers through the promise of future returns, the analysis presented here suggests that these institutions may be placed under considerable pressure should resources become significantly constrained.

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<![CDATA[Basic color categories and Mandarin Chinese color terms]]> https://www.researchpad.co/article/5c0841bfd5eed0c484fcaa2e

Basic color terms used in Mandarin Chinese have been controversial since first discussed by Berlin and Kay in 1969. Previous studies showed much inconsistency on what should be considered as basic color terms in Mandarin Chinese. In the present study, we investigated categories of color rather than merely the color terms used by Taiwanese native Mandarin speakers. Using samples conforming to the Berlin and Kay survey, various colors were chosen from a collection of Natural Color System (NCS) colored papers and mounted on a piece of neutral gray card. The card was then mounted on a touch-screen, under D65 illumination. Thirty-two single-character color related Mandarin terms were selected from a Chinese character database according to frequency of use. Participants were required to select the color sample that matched the term by pressing a virtual button on the touch screen. The results show that certain terms can be directly correlated to basic color terms in English, comparable with the results of Berlin and Kay’s original study and those that followed. However, some terms, such as Mo (墨 ink), Tie (鐵 iron), and Cai (菜vegetable), show a wide spread of term maps and inconsistent use among subjects. Principle component analysis (PCA) procedures were used to analysis the commodity of data among subjects. The findings suggest that the basic color categories among Mandarin Chinese speakers are similar to those found in the World Color Survey (WCS), but are represented by wide-spread and inconsistent color terms among speakers.

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<![CDATA[The Many Landscapes of Recombination in Drosophila melanogaster]]> https://www.researchpad.co/article/5989d9dcab0ee8fa60b68040

Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricted to qualitative trends due to the lack of detailed characterization of recombination rate variation across genomes and within species. The use of imprecise recombination rates can also skew population genetic analyses designed to assess the presence and mode of selection across genomes. Here we report the first integrated high-resolution description of genomic and population variation in recombination, which also distinguishes between the two outcomes of meiotic recombination: crossing over (CO) and gene conversion (GC). We characterized the products of 5,860 female meioses in Drosophila melanogaster by genotyping a total of 139 million informative SNPs and mapped 106,964 recombination events at a resolution down to 2 kilobases. This approach allowed us to generate whole-genome CO and GC maps as well as a detailed description of variation in recombination among individuals of this species. We describe many levels of variation in recombination rates. At a large-scale (100 kb), CO rates exhibit extreme and highly punctuated variation along chromosomes, with hot and coldspots. We also show extensive intra-specific variation in CO landscapes that is associated with hotspots at low frequency in our sample. GC rates are more uniformly distributed across the genome than CO rates and detectable in regions with reduced or absent CO. At a local scale, recombination events are associated with numerous sequence motifs and tend to occur within transcript regions, thus suggesting that chromatin accessibility favors double-strand breaks. All these non-independent layers of variation in recombination across genomes and among individuals need to be taken into account in order to obtain relevant estimates of recombination rates, and should be included in a new generation of population genetic models of the interaction between selection and linkage.

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<![CDATA[Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?]]> https://www.researchpad.co/article/5989d9efab0ee8fa60b6ddea

With the recent revolution in sequencing, we revisit the unresolved question of what influences the range and values of genetic diversity across taxa.

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<![CDATA[Holobiont&#8211;Holobiont Interactions: Redefining Host&#8211;Parasite Interactions]]> https://www.researchpad.co/article/5989daf8ab0ee8fa60bc3cd6 ]]> <![CDATA[Sex Determination: Why So Many Ways of Doing It?]]> https://www.researchpad.co/article/5989d9fcab0ee8fa60b72896

Sex is universal amongst most eukaryotes, yet a remarkable diversity of sex determining mechanisms exists. We review our current understanding of how and why sex determination evolves in animals and plants.

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<![CDATA[Larger Mammalian Body Size Leads to Lower Retroviral Activity]]> https://www.researchpad.co/article/5989d9feab0ee8fa60b72f94

Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). The abundance of ERVs is partly determined by their mode of replication, but it has also been suggested that host life history traits could enhance or suppress their activity. We show that larger bodied species have lower levels of ERV activity by reconstructing the rate of ERV integration across 38 mammalian species. Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. Furthermore, 68% of the variance in the mean age of ERVs per genome can also be explained by body size. These results indicate that body size limits the number of recently replicating ERVs due to their detrimental effects on their host. To comprehend the possible mechanistic links between body size and ERV integration we built a mathematical model, which shows that ERV abundance is favored by lower body size and higher horizontal transmission rates. We argue that because retroviral integration is tumorigenic, the negative correlation between body size and ERV numbers results from the necessity to reduce the risk of cancer, under the assumption that this risk scales positively with body size. Our model also fits the empirical observation that the lifetime risk of cancer is relatively invariant among mammals regardless of their body size, known as Peto's paradox, and indicates that larger bodied mammals may have evolved mechanisms to limit ERV activity.

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<![CDATA[The Evolutionary Ecology of Biotic Association in a Megadiverse Bivalve Superfamily: Sponsorship Required for Permanent Residency in Sediment]]> https://www.researchpad.co/article/5989da29ab0ee8fa60b81b2e

Background

Marine lineage diversification is shaped by the interaction of biotic and abiotic factors but our understanding of their relative roles is underdeveloped. The megadiverse bivalve superfamily Galeommatoidea represents a promising study system to address this issue. It is composed of small-bodied clams that are either free-living or have commensal associations with invertebrate hosts. To test if the evolution of this lifestyle dichotomy is correlated with specific ecologies, we have performed a statistical analysis on the lifestyle and habitat preference of 121 species based on 90 source documents.

Methodology/Principal Findings

Galeommatoidea has significant diversity in the two primary benthic habitats: hard- and soft-bottoms. Hard-bottom dwellers are overwhelmingly free-living, typically hidden within crevices of rocks/coral heads/encrusting epifauna. In contrast, species in soft-bottom habitats are almost exclusively infaunal commensals. These infaunal biotic associations may involve direct attachment to a host, or clustering around its tube/burrow, but all commensals locate within the oxygenated sediment envelope produced by the host’s bioturbation.

Conclusions/Significance

The formation of commensal associations by galeommatoidean clams is robustly correlated with an abiotic environmental setting: living in sediments (). Sediment-dwelling bivalves are exposed to intense predation pressure that drops markedly with depth of burial. Commensal galeommatoideans routinely attain depth refuges many times their body lengths, independent of siphonal investment, by virtue of their host’s burrowing and bioturbation. In effect, they use their much larger hosts as giant auto-irrigating siphon substitutes. The evolution of biotic associations with infaunal bioturbating hosts may have been a prerequisite for the diversification of Galeommatoidea in sediments and has likely been a key factor in the success of this exceptionally diverse bivalve superfamily.

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<![CDATA[Religion and the Unmaking of Prejudice toward Muslims: Evidence from a Large National Sample]]> https://www.researchpad.co/article/5989db08ab0ee8fa60bc9456

In the West, anti-Muslim sentiments are widespread. It has been theorized that inter-religious tensions fuel anti-Muslim prejudice, yet previous attempts to isolate sectarian motives have been inconclusive. Factors contributing to ambiguous results are: (1) failures to assess and adjust for multi-level denomination effects; (2) inattention to demographic covariates; (3) inadequate methods for comparing anti-Muslim prejudice relative to other minority group prejudices; and (4) ad hoc theories for the mechanisms that underpin prejudice and tolerance. Here we investigate anti-Muslim prejudice using a large national sample of non-Muslim New Zealanders (N = 13,955) who responded to the 2013 New Zealand Attitudes and Values Study. We address previous shortcomings by: (1) building Bayesian multivariate, multi-level regression models with denominations modeled as random effects; (2) including high-resolution demographic information that adjusts for factors known to influence prejudice; (3) simultaneously evaluating the relative strength of anti-Muslim prejudice by comparing it to anti-Arab prejudice and anti-immigrant prejudice within the same statistical model; and (4) testing predictions derived from the Evolutionary Lag Theory of religious prejudice and tolerance. This theory predicts that in countries such as New Zealand, with historically low levels of conflict, religion will tend to increase tolerance generally, and extend to minority religious groups. Results show that anti-Muslim and anti-Arab sentiments are confounded, widespread, and substantially higher than anti-immigrant sentiments. In support of the theory, the intensity of religious commitments was associated with a general increase in tolerance toward minority groups, including a poorly tolerated religious minority group: Muslims. Results clarify religion’s power to enhance tolerance in peaceful societies that are nevertheless afflicted by prejudice.

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<![CDATA[Hidden Epistastic Interactions Can Favour the Evolution of Sex and Recombination]]> https://www.researchpad.co/article/5989dad3ab0ee8fa60bb709d

Deleterious mutations can have a strong influence on the outcome of evolution. The nature of this influence depends on how mutations combine together to affect fitness. “Negative epistasis” occurs when a new deleterious mutation causes the greatest loss in fitness in a genome that already contains many deleterious mutations. Negative epistasis is a key ingredient for some of the leading hypotheses regarding the evolution of recombination, the evolution of sex, and a variety of other phenomena. In general, laboratory studies have not supported the idea that negative epistasis is ubiquitous, and this has led to doubts about its importance in biological evolution. Here, we show that these experimental results may be misleading, because negative epistasis can produce evolutionary advantages for sex and recombination while simultaneously being almost impossible to detect using current experimental methods. Under asexual reproduction, such hidden epistasis influences evolutionary outcomes only if the fittest individuals are present in substantial numbers, while also forming a very small proportion of the population as a whole. This implies that our results for asexuals will apply only for very large populations, and also limits the extent of the fitness benefits that hidden epistasis can provide. Despite these caveats, our results show that the fitness consequences of sex and recombination cannot always be inferred from observable epistasis alone.

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<![CDATA[Inference of Transposable Element Ancestry]]> https://www.researchpad.co/article/5989da06ab0ee8fa60b75ee0

Most common methods for inferring transposable element (TE) evolutionary relationships are based on dividing TEs into subfamilies using shared diagnostic nucleotides. Although originally justified based on the “master gene” model of TE evolution, computational and experimental work indicates that many of the subfamilies generated by these methods contain multiple source elements. This implies that subfamily-based methods give an incomplete picture of TE relationships. Studies on selection, functional exaptation, and predictions of horizontal transfer may all be affected. Here, we develop a Bayesian method for inferring TE ancestry that gives the probability that each sequence was replicative, its frequency of replication, and the probability that each extant TE sequence came from each possible ancestral sequence. Applying our method to 986 members of the newly-discovered LAVA family of TEs, we show that there were far more source elements in the history of LAVA expansion than subfamilies identified using the CoSeg subfamily-classification program. We also identify multiple replicative elements in the AluSc subfamily in humans. Our results strongly indicate that a reassessment of subfamily structures is necessary to obtain accurate estimates of mutation processes, phylogenetic relationships and historical times of activity.

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<![CDATA[Incompatibility and Competitive Exclusion of Genomic Segments between Sibling Drosophila Species]]> https://www.researchpad.co/article/5989dae4ab0ee8fa60bbca9a

The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.

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<![CDATA[Sex Allocation in Relation to Host Races in the Brood-Parasitic Common Cuckoo (Cuculus canorus)]]> https://www.researchpad.co/article/5989db0bab0ee8fa60bca3c6

Sex allocation theory and empirical evidence both suggest that natural selection should favour maternal control of offspring sex ratio in relation to their ability to invest in the offspring. Generalist parasites constitute a particularly interesting group to test this theory as different females commonly utilize different host species showing large variation in provisioning ability. The common cuckoo (Cuculus canorus) is a generalist brood parasite that lays its eggs in the nest of many different passerine birds, but each female tends to specialize on one particular host species giving rise to highly specialized host races. The different host species show large variation in their ability to invest in the parasitic offspring, presenting an opportunity for female cuckoos to bias offspring sex ratio in relation to host species quality. Here, we investigate host-race specific sex allocation controlling for maternal identity in the common cuckoo. We found no evidence of any significant relationship between host race and sex ratio in one sympatric population harbouring three different host races, or in a total of five geographically separated populations. There was also no significant association between host quality, as determined by species-specific female host body mass, and cuckoo sex ratio. Finally, we found no significant relationship between individual cuckoo maternal quality, as determined by her egg volume, and sex ratio within each host race. We conclude that the generalist brood-parasitic common cuckoo show no significant sex-ratio bias in relation to host race and discuss this finding in light of gene flow and host adaptations.

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<![CDATA[Redescription and Phylogenetic Analysis of the Mandible of an Enigmatic Pennsylvanian (Late Carboniferous) Tetrapod from Nova Scotia, and the Lability of Meckelian Jaw Ossification]]> https://www.researchpad.co/article/5989da30ab0ee8fa60b844ac

The lower jaw of an unidentified Pennsylvanian (Late Carboniferous) tetrapod from Nova Scotia – the “Parrsboro jaw”- is redescribed in the light of recent tetrapod discoveries and work on evolution of tetrapod mandibular morphology and placed for the first time in a numerical cladistics analysis. All phylogenetic analyses place the jaw in a crownward polytomy of baphetids, temnospondyls, and embolomeres. Several features resemble baphetids and temnospondyls including dermal ornamentation, absence of coronoid teeth, and presence of coronoid shagreen. Dentary dentition is most similar to Baphetes. An adsymphysial toothplate may not preclude temnospondyl affinity. An apparent large exomeckelian fenestra, with the dorsal foraminal margins formed by an unossified element, echoes the morphology of the stem tetrapod Sigournea and is unusually primitive given the other features of the jaw. The jaw may thus provide an example of an intermediate stage in Meckelian element evolution.

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<![CDATA[An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)]]> https://www.researchpad.co/article/5989db03ab0ee8fa60bc7594

Limnanthes floccosa ssp. floccosa and L. floccosa ssp. grandiflora are two of five subspecies within Limnanthes floccosa endemic to vernal pools in southern Oregon and northern California. Three seasons of monitoring natural populations have quantified that L. floccosa ssp. grandiflora is always found growing sympatrically with L. floccosa ssp. floccosa and that their flowering times overlap considerably. Despite their subspecific rank within the same species crossing experiments have confirmed that their F1 hybrids are sterile. An analysis of twelve microsatellite markers, with unique alleles in each taxon, also shows exceedingly low levels of gene flow between populations of the two subspecies. Due to the lack of previous phylogenetic resolution among L. floccosa subspecies, we used Illumina next generation sequencing to identify single nucleotide polymorphisms from genomic DNA libraries of L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora. These data were used to identify single nucleotide polymorphisms in the chloroplast, mitochondrial, and nuclear genomes. From these variable loci, a total of 2772 bp was obtained using Sanger sequencing of ten individuals representing all subspecies of L. floccosa and an outgroup. The resulting phylogenetic reconstruction was fully resolved. Our results indicate that although L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora are closely related, they are not sister taxa and therefore likely did not diverge as a result of a sympatric speciation event.

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<![CDATA[The Consistency of Beneficial Fitness Effects of Mutations across Diverse Genetic Backgrounds]]> https://www.researchpad.co/article/5989dafeab0ee8fa60bc5a0e

Parallel and convergent evolution have been remarkably common observations in molecular adaptation but primarily in the context of the same genotype adapting to the same conditions. These phenomena therefore tell us about the stochasticity and limitations of adaptation. The limited data on convergence and parallelism in the adaptation of different genotypes conflict as to the importance of such events. If the effects of beneficial mutations are highly context dependent (i.e., if they are epistatic), different genotypes should adapt through different mutations. Epistasis for beneficial mutations has been investigated but mainly through measurement of interactions between individually beneficial mutations for the same genotype. We examine epistasis for beneficial mutations at a broader genetic scale by measuring the fitness effects of two mutations beneficial for the ssDNA bacteriophage ID11 in eight different, related genotypes showing 0.3–3.7% nucleotide divergence from ID11. We found no evidence for sign epistasis, but the mutations tended to have much smaller or no effects on fitness in the new genotypes. We found evidence for diminishing-returns epistasis; the effects were more beneficial for lower-fitness genotypes. The patterns of epistasis were not determined by phylogenetic relationships to the original genotype. To improve our understanding of the patterns of epistasis, we fit the data to a model in which each mutation had a constant, nonepistatic phenotypic effect across genotypes and the phenotype-fitness map had a single optimum. This model fit the data well, suggesting that epistasis for these mutations was due to nonlinearity in the phenotype-fitness mapping and that the likelihood of parallel evolution depends more on phenotype than on genotype.

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<![CDATA[Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks]]> https://www.researchpad.co/article/5989dab5ab0ee8fa60baca05

The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence) and phenotype (approximated by the secondary structure fold) are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 412 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described.

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<![CDATA[Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games]]> https://www.researchpad.co/article/5989daeaab0ee8fa60bbec63

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

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<![CDATA[Instability in Evolutionary Games]]> https://www.researchpad.co/article/5989daa6ab0ee8fa60ba7c25

Background

Phenomena of instability are widely observed in many dissimilar systems, with punctuated equilibrium in biological evolution and economic crises being noticeable examples. Recent studies suggested that such instabilities, quantified by the abrupt changes of the composition of individuals, could result within the framework of a collection of individuals interacting through the prisoner's dilemma and incorporating three mechanisms: (i) imitation and mutation, (ii) preferred selection on successful individuals, and (iii) networking effects.

Methodology/Principal Findings

We study the importance of each mechanism using simplified models. The models are studied numerically and analytically via rate equations and mean-field approximation. It is shown that imitation and mutation alone can lead to the instability on the number of cooperators, and preferred selection modifies the instability in an asymmetric way. The co-evolution of network topology and game dynamics is not necessary to the occurrence of instability and the network topology is found to have almost no impact on instability if new links are added in a global manner. The results are valid in both the contexts of the snowdrift game and prisoner's dilemma.

Conclusions/Significance

The imitation and mutation mechanism, which gives a heterogeneous rate of change in the system's composition, is the dominating reason of the instability on the number of cooperators. The effects of payoffs and network topology are relatively insignificant. Our work refines the understanding on the driving forces of system instability.

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