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PubMed1989

A hierarchical model of the evolution of cooperation in cultural systems.

In this paper the following problem is addressed: "Under what conditions can a collection of individual organisms learn to cooperate when cooperation appears to outwardly degrade individual performance at the outset. In order to attempt a theoretical solution to this problem, data from a real world problem in anthropology is used. A distributed simulation model of this system was developed to assess its long term behavior using using an approach suggested by Zeigler (Zeigler, B.P., 1984, Multifaceted Modelling and Discrete Event Simulation (Academic Press, London)). The results of the simulation are used to show that although cooperation degrades the performance potential of each individual, it enhances the persistence of the individual's partial solution to the problem in certain situations."

Animals↗
PubMed1998

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

A nonhomogeneous, nonstationary stochastic model of DNA sequence evolution allowing varying equilibrium G + C contents among lineages is devised in order to deal with sequences of unequal base compositions. A maximum-likelihood implementation of this model for phylogenetic analyses allows handling of a reasonable number of sequences. The relevance of the model and the accuracy of parameter estimates are theoretically and empirically assessed, using real or simulated data sets. Overall, a significant amount of information about past evolutionary modes can be extracted from DNA sequences, suggesting that process (rates of distinct kinds of nucleotide substitutions) and pattern (the evolutionary tree) can be simultaneously inferred. G + C contents at ancestral nodes are quite accurately estimated. The new method appears to be useful for phylogenetic reconstruction when base composition varies among compared sequences. It may also be suitable for molecular evolution studies.

Algorithms↗
PubMed1990

N-person games and the evolution of co-operation: a model based on predator inspection in fish.

Two N-person game theoretical models examining the evolution of co-operation during predator inspection in fish are presented. Predator inspection occurs in small shoals of fish, in which one to a few individuals, the "inspectors" (co-operators) break away from the shoal and cautiously approach a predator to obtain information on this potential danger. In the models presented here, remaining with the shoal and not inspecting is considered an act of defection. Both model I and II produce a stable internal polymorphism of inspectors and noninspectors. While the equilibrial frequency of inspectors can be low (i.e. less than 10%) at large shoal size, the proportion of shoals containing any inspectors--and therefore exhibiting the inspection behavior--is much greater. Both models presented here, and N-person games in general are equivalent to intrademic group selection models of evolution in structured populations, in which shoals are trait groups and co-operation evolves by between-shoal selection. While the results are cast in terms of predator inspection, the model itself is general and applies to any multi-group scenario where co-operators benefit entire groups at their own expense. The results presented here add to the mounting theoretical and empirical evidence that co-operation is frequently not a pure evolutionarily stable strategy, and that many metapopulations should be polymorphic for both co-operators and defectors.

Animals↗
PubMed2003

Integration of shelf evolution and river basin models to simulate Holocene sediment dynamics of the Humber Estuary during periods of sea-level change and variations in catchment sediment supply.

Three modelling elements and sedimentary evidence provide an understanding of sediment characteristics, river basin processes, tidal regimes and sea-level changes to explain sediment supply to the Humber Estuary through the Holocene (the last 10,000 years). An upscaled cellular catchment model simulates water and sediment fluxes from river basins, illustrating significant variations in response to climate change, especially precipitation and vegetation changes, principally deforestation. Much of the sediment mobilised remains in stores within the catchment and only a small fraction reaches the Humber tidal system. An empirical model helps to explain sediment erosion, transport and deposition from the offshore and coastal zones through the Holocene and sea-level rise caused the transgression of the continental shelf of the North Sea. Comparison with the sediment fill of the lowlands around of the Humber estuary, that represent the extent of the estuary during the Holocene, demonstrates that most of the fill (approximately 95-98%) was derived from non-fluvial sources. A shelf evolution model, with reconstructions of sea level, palaeogeography and palaeobathymetry for 1,000 year time steps through the Holocene predicts significant changes in tidal regimes, first over wide areas of the coast as the transgression of the continental shelf progresses. The most significant changes occur with the inner reaches of the palaeo-estuaries, especially those of the Humber and the Fenland. Throughout the mid-Holocene they are characterised by significantly lower tidal ranges (MWHST approximately 2.5 m less than present) and low tidal currents. The simulated patterns of tidal currents concur with the transport of fine grain sediment from the coastal zone into the estuaries. The major tidal range changes revise estimates of late Holocene and ongoing relative sea and land level changes.

Journal Article↗
PubMed2001

On the mod resc model and the evolution of Wolbachia compatibility types.

Cytoplasmic incompatibility (CI) is induced by the endocellular bacterium Wolbachia. It results in an embryonic mortality occurring when infected males mate with uninfected females. The mechanism involved is currently unknown, but the mod resc model allows interpretation of all observations made so far. It postulates the existence of two bacterial functions: modification (mod) and rescue (resc). The mod function acts in the males' germline, before Wolbachia are shed from maturing sperm. If sperm is affected by mod, zygote development will fail unless resc is expressed in the egg. Interestingly, CI is also observed in crosses between infected males and infected females when the two partners bear different Wolbachia strains, demonstrating that mod and resc interact in a specific manner: Two Wolbachia strains are compatible with each other only if they harbor the same compatibility type. Here we focus on the evolutionary process involved in the emergence of new compatibility types from ancestral ones. We argue that new compatibility types are likely to evolve under a wider range of conditions than previously thought, through a two-step process. First, new mod variants can arise by mutation and spread by drift. This is possible because mod is expressed in males and Wolbachia is transmitted by females. Second, once such a mod variant achieves a certain frequency, it can create the conditions for the deterministic invasion of a new resc variant, allowing the invasion of a new mod resc pair. Furthermore, we show that a stable polymorphism might be maintained in natural populations, allowing the long-term existence of "suicidal" Wolbachia strains.

Algorithms↗
PubMed1996

Tandemly repeated satellite DNA of Dolichopoda schiavazzii: a test for models on the evolution of highly repetitive DNA.

Three specific satellite DNA families can be detected in the genome of the cave cricket Dolichopoda schiavazzii. The pDoP102 and the pDsPv400 families are species specific for D. schiavazzii; the pDoP500 family is probably present in all Dolichopoda species. The three satellite DNA families were characterized from individuals of three isolated populations of D. schiavazzii with respect to nucleotide sequence, sequence complexity, sequence variability, and copy number. This unique data set on satellite DNAs of D. schiavazzii seems to allow one to test the significance of theoretical approaches to the mode of evolution of noncoding, tandemly arranged satellite DNA. At least for satellite DNAs of D. schiavazzii two clear trends were observed: (1) sequence variability increases with copy number and (2) the repeat length decreases with copy number. The first trend is in good agreement with the theory but the second is not. Thus, a revision of the models is proposed.

Animals↗
PubMed2005

Why are males bad for females? Models for the evolution of damaging male mating behavior.

One explanation for the cost to mating for females caused by damaging male mating behavior is that this causes the females to adaptively modify their subsequent life histories in a way that also increases male fitness. This might occur because the reduction in residual reproductive value of the female increases her optimal oviposition rate or because an increase in the current level of damage increases the female's optimal remating interval. In this article, I present models of a stochastic dynamic game in which males choose the level of mating damage that they inflict on females and females choose their oviposition rate and whether to remate. The models show that some level of damage is always an evolutionarily stable strategy and may even provoke females into making terminal reproductive investment (and hence a semelparous life history), that nondamaging populations are always invaded by damaging male mutants, and that damage evolves because of its effect on oviposition rate and despite its effect on remating interval.

Animals↗
PubMed2003

Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa.

Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.

Algorithms↗
PubMed1996

Heavy-chain variable regions in carcharhine sharks: development of a comprehensive model for the evolution of VH domains among the gnathanstomes.

We determined the sequence of 18 DNA clones encoding VH regions of sandbar shark and bull shark. All of these sequences exhibit key structural coding features characteristic of known VH genes of higher vertebrates. These VH sequences disclosed considerable diversity, and can be divided into six families according to the criterion of 80% DNA sequence identity. The overlapping of some VH gene clones to two or more families is a particular feature found in carcharhine sharks, which suggests that VH diversification is a continuing process. The basic sequence patterns of heavy-chain V regions found in all representative gnathanstomes and in VH of the shark heavy immunoglobulin IgW provides evidence for selection of canonical residues in all VH structures. Elasmobranch VH sequences can be divided into two classes or clans, one comprising the 'classical' VH set and the other comprising VHS related to those of IgW (V omega). Phylogenetic analyses place the VH cluster as the root of all the classic VHS and indicates that the V omega set is most probably that of the primordial heavy chain.

Amino Acid Sequence↗
PubMed2004

A Lagrangian model of the evolution of the particulate size distribution of vehicular emissions.

The emission inventory for London indicates that nearly 80% of the particulate emissions derive from vehicular sources. Most of this mass is in the form of ultrafine submicrometer particles which are of concern because of their influence on lung function. The prediction of their dispersion in the atmosphere coupled to the physical and chemical transformations which affect their size distribution and concentration are of great importance. This paper reports the first results from a new meso-scale Lagrangian model which follows the particulate emissions and the evolution of their size distribution across the city. The vehicular emissions are based on the published inventory, corrected to time of day, while other emissions are assumed steady. The initial size distributions of background and emitted particles are represented by the sum of three lognormal distributions. Meteorological data are derived from Meteorological Office reports and are preprocessed to obtain the hourly values of boundary layer depth, Monin-Obukov (MO) length, friction velocity, etc., needed for the computation of the vertical dispersion process via eddy diffusivities and the aerodynamic component of the dry deposition process. In the vertical direction, three layers are assumed-surface layer (typically 50 m), canopy layer and one further layer up to the prevailing boundary layer depth. Currently, the model includes wet and dry deposition and coagulation but not chemical reaction, nucleation or deliquescence. Trajectories are evolved for several hours across the city and the number size distributions and mass concentrations (PM10, PM2.5, PM1 and PM0.1) output at each step. This enables the vehicular contributions over and above the background concentration in each size range to be studied in detail. Data from the model have been compared with experimental data for one of the London background sites where particle number size distribution up to 450 nm (SMPS), plus PM10 and PM2.5 (TEOM) data are available.

Journal Article↗
PubMed1999

A theoretical model of the evolution of virulence in sexually transmitted HIV/AIDS.

INTRODUCTION: The evolution of virulence in host-parasite relationships has been the subject of several publications. In the case of HIV virulence, some authors suggest that the evolution of HIV virulence correlates with the rate of acquisition of new sexual partners. In contrast some other authors argue that the level of HIV virulence is independent of the sexual activity of the host population. METHODS: Provide a mathematical model for the study of the potential influence of human sexual behaviour on the evolution of virulence of HIV is provided. RESULTS: The results indicated that, when the probability of acquisition of infection is a function both of the sexual activity and of the virulence level of HIV strains, the evolution of HIV virulence correlates positively with the rate of acquisition of new sexual partners. CONCLUSION: It is concluded that in the case of a host population with a low (high) rate of exchange of sexual partners the evolution of HIV virulence is such that the less (more) virulent strain prevails.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Behavioral drive versus behavioral inertia in evolution: a null model approach.

Some biologists embrace the classical view that changes in behavior inevitably initiate or drive evolutionary changes in other traits, yet others note that behavior sometimes inhibits evolutionary changes. Here we develop a null model that quantifies the impact of regulatory behaviors (specifically, thermoregulatory behaviors) on body temperature and on performance of ectotherms. We apply the model to data on a lizard (Anolis cristatellus) and show that thermoregulatory behaviors likely inhibit selection for evolutionary shifts in thermal physiology with altitude. Because behavioral adjustments are commonly used by ectotherms to regulate physiological performance, regulatory behaviors should generally constrain rather than drive evolution, a phenomenon we call the "Bogert effect." We briefly review a few other examples that contradict the classical view of behavior as the inevitable driving force in evolution. Overall, our analysis and brief review challenge the classical view that behavior is invariably the driving force in evolution, and instead our work supports the alternative view that behavior has diverse--and sometimes conflicting--effects on the directions and rates at which other traits evolve.

Altitude↗
PubMed2006

MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution.

BACKGROUND: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences. RESULTS: Here we present an improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences. The method uses an explicit model of indel length frequency distribution which can be specified, and allows any time reversible model of nucleotide substitution. The method uses a deterministic global optimiser to find the alignment with the highest posterior probability. We test MCALIGN2 in simulations, and compare it to a previous Monte Carlo based method (MCALIGN), to the pair HMM method of Knudsen and Miyamoto, and to a heuristic method (AVID) that performed very well in a previous simulation study. We show that the pair HMM methods have excellent performance for all combinations of parameter values we have considered. MCALIGN2 is up to ten times faster than MCALIGN. MCALIGN2 is more accurate in resolving indels given an accurate explicit model than heuristic methods, but is computationally slower. CONCLUSION: MCALIGN2 produces better quality alignments by explicitly using biological knowledge about the indel length distribution and time reversible models of nucleotide substitution. As a result, it can outperform other available sequence alignment methods for the cases we have considered to align non-coding DNA sequences.

Algorithms↗
PubMed2001

Mutation and recombination in cattle satellite DNA: a feedback model for the evolution of satellite DNA repeats.

The cattle genome contains several distinct centromeric satellites with interrelated evolutionary histories. We compared these satellites in Bovini species that diverged 0.2 to about 5 Myr ago. Quantification of hybridization signals by phosphor imaging revealed a large variation in the relative amounts of the major satellites. In the genome of water buffalo this has led to the complete deletion of satellite III. Comparative sequencing and PCR-RFLP analysis of satellites IV, 1.711a, and 1.711b from the related Bos and Bison species revealed heterogeneities in 0.5 to 2% of the positions, again with variations in the relative amounts of sequence variants. Restriction patterns generated by double digestions suggested a recombination of sequence variants. Our results are compatible with a model of the life history of satellites during which homogeneity of interacting repeat units is both cause and consequence of the rapid turnover of satellite DNA. Initially, a positive feedback loop leads to a rapid saltatory amplification of homogeneous repeat units. In the second phase, mutations inhibit the interaction of repeat units and coexisting sequence variants amplify independently. Homogenization by the spreading of one of the variants is prevented by recombination and the satellite is eventually outcompeted by another, more homogeneous tandem repeat sequence.

Animals↗
PubMed2000

Relatedness in trait group models of social evolution.

Genetic relatedness is a central concept in the study of social evolution. Though originally defined in terms of genealogy, the modern version of relatedness accommodates genetic similarity of any origin. This paper examines relatedness in group structured modes, in which a trait affects the fitness of all group members. Such traits can be divided into two types, based on whether their group fitness effects encompass all group members including the actor ("whole-group traits"), or only group members other than the actor ("other-only traits"). Both trait types are common in nature as well as in theoretical models, but they have rarely been distinguished clearly. The average relatedness of recipients to actors differs for the two trait types within the same population and even the same individual, leading to different selection pressures and evolutionary outcomes. Total relatedness in group-structured models can be partitioned into two components: structural relatedness due to the size and number of groups in the population, and assortative relatedness due to the distribution of genotypes among groups. Each component differs for whole-group vs. other-only traits, both in terms of their values and the factors that influence them. Some key differences include: positive relatedness requires positive assortment for other-only but not for whole-group traits; negative relatedness is possible for other-only but not whole-group traits; relatedness depends on average group size for whole-group but not other-only traits, and non-random assortment into groups affects relatedness more strongly for other-only than whole-group traits. Recognizing the distinction between these trait types resolves some apparent contradictions in the literature, and clarifies the limits of some previous results.

Animals↗
PubMed1998

Score-dependent fertility model for the evolution of cooperation in a lattice.

The evolution of cooperation is studied in a lattice-structured population, in which each individual plays the iterated Prisoner's Dilemma game with its neighbors. The population includes Tit-for-Tat (TFT, a cooperative strategy) and All Defect (AD, a selfish strategy) distributed over the lattice points. An individual dies randomly, and the vacant site is filled immediately by a copy of one of the neighbors in which the probability of colonization success by a particular neighbor is proportional to its score accumulated in the game. This "score-dependent fertility model" (or fertility model) behaves very differently from score-dependent viability model (viability model) studied in a previous paper. The model on a one-dimensional lattice is a analysed by invasion probability analysis, pair-edge method mean-field approximation, pair approximation, and computer simulation. Results are: (1) TFT players come to form tight clusters. When the probability of iteration w is large, initially rare TFT can invade and spread in a population dominated by AD, unlike in the complete mixing model. The condition for the increase of TFT is accurately predicted by all the techniques except mean-field approximation; (2) fertility model is much more favorable for the spread of TFT than the corresponding viability model, because spiteful killing of neighbors is favored in the viability model but not in the fertility model; (3) eight lattice games on two-dimensional lattice with different assumptions are examined. Cooperation and defects can coexist in the models of deterministic state change but not in the models of stochastic state change.

Biological Evolution↗