# Quantitative Biology

## New submissions

[ total of 11 entries: 1-11 ]
[ showing up to 2000 entries per page: fewer | more ]

### New submissions for Mon, 25 Sep 17

[1]
Title: Eco-evolutionary dynamics and collective dispersal: implications for salmon metapopulation robustness
Comments: 22 pages, 6 figures, 14 supplementary figures
Subjects: Populations and Evolution (q-bio.PE)

The spatial dispersal of individuals is known to play an important role in the dynamics of populations, and is central to metapopulation theory. At the same time, local adaptation to environmental conditions creates a geographic mosaic of evolutionary forces, where the combined drivers of selection and gene flow interact. Although the dispersal of individuals from donor to recipient populations provides connections within the metapopulation, promoting demographic and evolutionary rescue, it may also introduce maladapted individuals into habitats host to different environmental conditions, potentially lowering the fitness of the recipient population. Here we explore a model of the eco-evolutionary dynamics between two populations connected by dispersal, where the productivity of each is defined by a trait complex that is subject to local selection. Although general in nature, our model is inspired by salmon metapopulations, where dispersal between populations is defined in terms of the straying rate, which has been shown to be density-dependent. The results of our model reveal that increased straying between evolving populations leads to alternative stable states, which has large and nonlinear effects on two measures of metapopulation robustness: the portfolio effect and the time to recovery following an induced disturbance. We show that intermediate levels of straying result in large gains in robustness, and that increased habitat heterogeneity promotes robustness when straying rates are low, and erodes robustness when straying rates are high. Finally, we show that density-dependent straying promotes robustness, particularly when the aggregate biomass is low and straying is correspondingly high, which has important ramifications for the conservation of salmon metapopulations facing both natural and anthropogenic disturbances.

[2]
Title: Neutral dynamics and cell renewal of colonic crypts in homeostatic regime
Subjects: Tissues and Organs (q-bio.TO); Biological Physics (physics.bio-ph)

The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: a) We distinguish different classes of cells: stem cells, 6 generations of transit amplifying cells and the differentiated cells. b) In order to take into account the monoclonal character of the crypts in homeostatic regime we include symmetric divisions of the stem cells. We first consider the dynamic differential equations that describe the evolution of the mean values of the populations but the small observed value of the total number of cells involved plus the huge dispersion of experimental data found in the literature leads us to study the stochastic discrete process. This analysis allows us to study fluctuations, the neutral drift that leads to monoclonality and the effects of the fixation of mutant clones.

[3]
Title: Strategy intervention for the evolution of fairness
Subjects: Populations and Evolution (q-bio.PE)

Masses of experiments have shown individual preference for fairness which seems irrational. The reason behind it remains a focus for research. The effect of spite (individuals are only concerned with their own relative standing) on the evolution of fairness has attracted increasing attention from experiments, but only has been implicitly studied in one evolutionary model. The model did not involve high-offer rejections, which have been found in the form of non-monotonic rejections (rejecting offers that are too high or too low) in experiments. Here, we introduce a high offer and a non-monotonic rejection in structured populations of finite size, and use strategy intervention to explicitly study how spite influences the evolution of fairness: five strategies are in sequence added into the competition of a fair strategy and a selfish strategy. We find that spite promotes fairness, altruism inhibits fairness, and the non-monotonic rejection can cause fairness to overcome selfishness, which cannot happen without high-offer rejections. Particularly for the group-structured population with seven discrete strategies, we analytically study the effect of population size, mutation, and migration on fairness, selfishness, altruism, and spite. A larger population size cannot change the dominance of fairness, but it promotes altruism and inhibits selfishness and spite. Intermediate mutation maximizes selfishness and fairness, and minimizes spite; intermediate mutation maximizes altruism for intermediate migration and minimizes altruism otherwise. The existence of migration inhibits selfishness and fairness, and promotes altruism; sufficient migration promotes spite. Our study may provide important insights into the evolutionary origin of fairness.

### Cross-lists for Mon, 25 Sep 17

[4]  arXiv:1709.07630 (cross-list from math.PR) [pdf, ps, other]
Title: On the genealogy and coalescence times of Bienaymé-Galton-Watson branching processes
Comments: 23 pages. This is an Accepted Manuscript of an article to be published by Taylor & Francis in Stochastic Models
Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

Coalescence processes have received a lot of attention in the context of conditional branching processes with fixed population size and non-overlapping generations. Here we focus on similar problems in the context of the standard unconditional Bienaym\'e-Galton-Watson branching processes, either (sub)-critical or supercritical. Using an analytical tool, we derive the structure of some counting aspects of the ancestral genealogy of such processes, including: the transition matrix of the ancestral count process and an integral representation of various coalescence times distributions, such as the time to most recent common ancestor of a random sample of arbitrary size, including full size.
We illustrate our results on two important examples of branching mechanisms displaying either finite or infinite reproduction mean, their main interest being to offer a closed form expression for their probability generating functions at all times. Large time behaviors are investigated.

[5]  arXiv:1709.07633 (cross-list from math.PR) [pdf, ps, other]
Title: On a coalescence process and its branching genealogy
Journal-ref: Journal of Applied Probability, 53(4), 1156-1165 (2016)
Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

We define and analyze a coalescent process as a recursive box-filling process whose genealogy is given by an ancestral time-reversed, time-inhomogeneous Bienyam\'{e}-Galton-Watson process. Special interest is on the expected size of a typical box and its probability of being empty. Special cases leading to exact asymptotic computations are investigated when the coalescing mechanisms are either linear-fractional or quadratic.

[6]  arXiv:1709.07674 (cross-list from physics.soc-ph) [pdf, other]
Title: Epidemic prevalence information on social networks mediates emergent collective outcomes in voluntary vaccine schemes
Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

The success of a vaccination program is crucially dependent on its adoption by a critical fraction of the population, as the resulting herd immunity prevents future outbreaks of an epidemic. However, the effectiveness of a campaign can engender its own undoing if individuals choose to not get vaccinated in the belief that they are protected by herd immunity. Although this may appear to be an optimal decision, based on a rational appraisal of cost and benefits to the individual, it exposes the population to subsequent outbreaks. We investigate if voluntary vaccination can emerge in a an integrated model of an epidemic spreading on a social network of rational agents that make informed decisions whether to be vaccinated. The information available to each agent includes the prevalence of the disease in their local network neighborhood and/or globally in the population, as well as the fraction of their neighbors that are protected against the disease. Crucially, the payoffs governing the decision of agents evolve with disease prevalence, resulting in the co-evolution of vaccine uptake behavior with the spread of the contagion. The collective behavior of the agents responding to local prevalence can lead to a significant reduction in the final epidemic size, particularly for less contagious diseases having low basic reproduction number $R_0$. Near the epidemic threshold ($R_0\approx1$) the use of local prevalence information can result in a dichotomous response in final vaccine coverage. The implications of our results suggest the nature of information used by individuals is a critical factor determining the success of public health intervention schemes that involve mass vaccination.

### Replacements for Mon, 25 Sep 17

[7]  arXiv:1603.01880 (replaced) [pdf, ps, other]
Title: Optimal sequence memory in driven random networks
Subjects: Neurons and Cognition (q-bio.NC); Chaotic Dynamics (nlin.CD)
[8]  arXiv:1612.08064 (replaced) [pdf, ps, other]
Title: Cell reprogramming modelled as transitions in a hierarchy of cell cycles
Journal-ref: J. Phys. A: Math. Theor. 50 (2017) 425601 (23pp)
Subjects: Cell Behavior (q-bio.CB); Disordered Systems and Neural Networks (cond-mat.dis-nn); Molecular Networks (q-bio.MN)
[9]  arXiv:1702.01364 (replaced) [pdf, ps, other]
Title: Solving Moment Hierarchies for Chemical Reaction Networks
Journal-ref: J. Phys. A: Math. Theor. 50 425002 (2017)
Subjects: Statistical Mechanics (cond-mat.stat-mech); Chemical Physics (physics.chem-ph); Molecular Networks (q-bio.MN)
[10]  arXiv:1702.02621 (replaced) [pdf, ps, other]
Title: Relationships Between Characteristic Path Length, Efficiency, Clustering Coefficients, and Graph Density
Comments: Figure 1 seems to have been dropped during formatting. It can be found at this https URL Figure 5.8
Subjects: Combinatorics (math.CO); Neurons and Cognition (q-bio.NC)
[11]  arXiv:1709.04702 (replaced) [pdf, other]
Title: Trait evolution with jumps: illusionary normality