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Theoretical Population Biology

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https://www.readbyqxmd.com/read/28143695/population-structure-and-coalescence-in-pedigrees-comparisons-to-the-structured-coalescent-and-a-framework-for-inference
#1
Peter R Wilton, Pierre Baduel, Matthieu M Landon, John Wakeley
Contrary to what is often assumed in population genetics, independently segregating loci do not have completely independent ancestries, since all loci are inherited through a single, shared population pedigree. Previous work has shown that the non-independence between gene genealogies of independently segregating loci created by the population pedigree is weak in panmictic populations, and predictions made from standard coalescent theory are accurate for populations that are at least moderately sized. Here, we investigate patterns of coalescence in pedigrees of structured populations...
January 28, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28130147/theory-of-partitioning-of-disease-prevalence-and-mortality-in-observational-data
#2
I Akushevich, A P Yashkin, J Kravchenko, F Fang, K Arbeev, F Sloan, A I Yashin
In this study, we present a new theory of partitioning of disease prevalence and incidence-based mortality and demonstrate how this theory practically works for analyses of Medicare data. In the theory, the prevalence of a disease and incidence-based mortality are modeled in terms of disease incidence and survival after diagnosis supplemented by information on disease prevalence at the initial age and year available in a dataset. Partitioning of the trends of prevalence and mortality is calculated with minimal assumptions...
January 24, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28111186/sex-versus-asex-an-analysis-of-the-role-of-variance-conversion
#3
Andrew E M Lewis-Pye, Antonio Montalbán
The question as to why most complex organisms reproduce sexually remains a very active research area in evolutionary biology. Theories dating back to Weismann have suggested that the key may lie in the creation of increased variability in offspring, causing enhanced response to selection. Under appropriate conditions, selection is known to result in the generation of negative linkage disequilibrium, with the effect of recombination then being to increase genetic variance by reducing these negative associations between alleles...
January 19, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28110065/stochasticity-heterogeneity-and-variance-in-longevity-in-human-populations
#4
Nienke Hartemink, Trifon I Missov, Hal Caswell
Inter-individual variance in longevity (or any other demographic outcome) may arise from heterogeneity or from individual stochasticity. Heterogeneity refers to differences among individuals in the demographic rates experienced at a given age or stage. Stochasticity refers to variation due to the random outcome of demographic rates applied to individuals with the same properties. The variance due to individual stochasticity can be calculated from a Markov chain description of the life cycle. The variance due to heterogeneity can be calculated from a multistate model that incorporates the heterogeneity...
January 18, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28041892/an-alternative-derivation-of-the-stationary-distribution-of-the-multivariate-neutral-wright-fisher-model-for-low-mutation-rates-with-a-view-to-mutation-rate-estimation-from-site-frequency-data
#5
Dominik Schrempf, Asger Hobolth
Recently, Burden and Tang (2016) provided an analytical expression for the stationary distribution of the multivariate neutral Wright-Fisher model with low mutation rates. In this paper we present a simple, alternative derivation that illustrates the approximation. Our proof is based on the discrete multivariate boundary mutation model which has three key ingredients. First, the decoupled Moran model is used to describe genetic drift. Second, low mutation rates are assumed by limiting mutations to monomorphic states...
December 29, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/28039030/sexually-transmitted-infections-and-mate-finding-allee-effects
#6
Luděk Berec, Eva Janoušková, Michal Theuer
Infectious diseases can seriously impact dynamics of their host species. In this study, we model and analyze an interaction between a sexually transmitted infection and its animal host population affected by a mate-finding Allee effect. Since mating drives both host reproduction and infection transmission, the Allee effect shapes the transmission rate of the infection which we show takes a saturating form. Our model combining sexually transmitted infections with the mate-finding Allee effect in the host produces quite rich dynamics, including oscillations, several multistability regimes, and infection-induced host extinction...
December 27, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/28007580/revisiting-the-logistic-map-a-closer-look-at-the-dynamics-of-a-classic-chaotic-population-model-with-ecologically-realistic-spatial-structure-and-dispersal
#7
Laura S Storch, James M Pringle, Karen E Alexander, David O Jones
There is an ongoing debate about the applicability of chaotic and nonlinear models to ecological systems. Initial introduction of chaotic population models to the ecological literature was largely theoretical in nature and difficult to apply to real-world systems. Here, we build upon and expand prior work by performing an in-depth examination of the dynamical complexities of a spatially explicit chaotic population, within an ecologically applicable modeling framework. We pair a classic chaotic growth model (the logistic map) with explicit dispersal length scale and shape via a Gaussian dispersal kernel...
December 19, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27998798/recursions-for-the-exchangeable-partition-function-of-the-seedbank-coalescent
#8
Noemi Kurt, Mathias Rafler
For the seedbank coalescent with mutation under the infinite alleles assumption, which describes the gene genealogy of a population with a strong seedbank effect subject to mutations, we study the distribution of the final partition with mutation. This generalizes the coalescent with freeze by Dong et al. (2007) to coalescents where ancestral lineages are blocked from coalescing. We derive an implicit recursion which we show to have a unique solution and give an interpretation in terms of absorption problems of a random walk...
December 18, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27998797/how-optimally-foraging-predators-promote-prey-coexistence-in-a-variable-environment
#9
Simon Maccracken Stump, Peter Chesson
Optimal foraging is one of the major predictive theories of predator foraging behavior. However, how an optimally foraging predator affects the coexistence of competing prey is not well understood either in a constant or variable environment, especially for multiple prey species. We study the impact of optimal foraging on prey coexistence using an annual plant model, with and without annual variation in seed germination. Seed predators are modeled using Charnov's model of adaptive diet choice. Our results reveal that multiple prey species can coexist because of this type of predator, and that their effect is not greatly modified by environmental variation...
December 18, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27964915/fisher-wright-model-with-deterministic-seed-bank-and-selection
#10
Bendix Koopmann, Johannes Müller, Aurélien Tellier, Daniel Živković
Seed banks are common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. The applied techniques outline a path of approximating a stochastic delay differential equation by an appropriately rescaled stochastic differential equation...
December 10, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27940023/adaptive-diversification-in-heterogeneous-environments
#11
Olivier David, Christian Lannou, Hervé Monod, Julien Papaïx, Djidi Traore
The role of environmental heterogeneity in the evolution of biological diversity has been studied only for simple types of heterogeneities and dispersals. This article broadens previous results by considering heterogeneities and dispersals that are structured by several environmental factors. It studies the evolution of a metapopulation, living in a network of patches connected by dispersal, under the effects of mutation, selection and migration. First, it is assumed that patches are equally connected and that they carry habitats characterized by several factors exerting selection pressures on several individual traits...
December 7, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27915040/differences-in-the-effective-population-sizes-of-males-and-females-do-not-require-differences-in-their-distribution-of-offspring-number
#12
Fernando L Mendez
Difference in male and female effective population sizes has, at times, been attributed to both sexes having unequal variance in their number of offspring. Such difference is paralleled by the relative effective sizes of autosomes, sex chromosomes, and mitochondrial DNA. I develop a simple framework to calculate the inbreeding effective population sizes for loci with different modes of inheritance. In this framework, I separate the effects due to mating strategy and those due to genetic transmission. I then show that, in addition to differences in the variance in offspring number, skew in the male/female effective sizes can also be caused by family composition...
November 30, 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27916679/equivalent-probability-density-moments-determine-equivalent-epidemics-in-an-sirs-model-with-temporary-immunity
#13
Thomas W Carr
In an SIRS compartment model for a disease we consider the effect of different probability distributions for remaining immune. We show that to first approximation the first three moments of the corresponding probability densities are sufficient to well describe oscillatory solutions corresponding to recurrent epidemics. Specifically, increasing the fraction who lose immunity, increasing the mean immunity time, and decreasing the heterogeneity of the population all favor the onset of epidemics and increase their severity...
February 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/27866981/multiple-coexistence-equilibria-in-a-two-parasitoid-one-host-model
#14
Ferdinand Pfab, Odo Diekmann, Souvik Bhattacharya, Andrea Pugliese
Briggs et al. (1993) introduced a host-parasitoid model for the dynamics of a system with two parasitoids that attack different juvenile stages of a common host. Their main result was that coexistence of the parasitoids is only possible when there is sufficient variability in the maturation delays of the host juvenile stages. Here, we analyze the phenomenon of coexistence in that model more deeply. We show that with some distribution families for the maturation delays, the coexistence equilibrium is unique, while with other distributions multiple coexistence equilibria can be found...
February 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/27825765/rate-matrix-estimation-from-site-frequency-data
#15
Conrad J Burden, Yurong Tang
A procedure is described for estimating evolutionary rate matrices from observed site frequency data. The procedure assumes (1) that the data are obtained from a constant size population evolving according to a stationary Wright-Fisher or decoupled Moran model; (2) that the data consist of a multiple alignment of a moderate number of sequenced genomes drawn randomly from the population; and (3) that within the genome a large number of independent, neutral sites evolving with a common mutation rate matrix can be identified...
February 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/27693412/autocratic-strategies-for-alternating-games
#16
Alex McAvoy, Christoph Hauert
Repeated games have a long tradition in the behavioral sciences and evolutionary biology. Recently, strategies were discovered that permit an unprecedented level of control over repeated interactions by enabling a player to unilaterally enforce linear constraints on payoffs. Here, we extend this theory of "zero-determinant" (or, more generally, "autocratic") strategies to alternating games, which are often biologically more relevant than traditional synchronous games. Alternating games naturally result in asymmetries between players because the first move matters or because players might not move with equal probabilities...
February 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/27664440/harsh-environments-and-the-evolution-of-multi-player-cooperation
#17
Kris De Jaegher
The game-theoretic model in this paper provides micro-foundations for the effect a harsher environment on the probability of cooperation among multiple players. The harshness of the environment is alternatively measured by the degree of complementarity between the players' cooperative efforts in producing a public good, and by the number of attacks on an existing public good that the players can collectively defend, where it is shown that these two measures of the degree of adversity facing the players operate in a similar fashion...
February 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/27634366/effective-sizes-and-time-to-migration-drift-equilibrium-in-geographically-subdivided-populations
#18
O Hössjer, Linda Laikre, Nils Ryman
Many versions of the effective population size (Ne) exist, and they are important in population genetics in order to quantify rates of change of various characteristics, such as inbreeding, heterozygosity, or allele frequencies. Traditionally, Ne was defined for single, isolated populations, but we have recently presented a mathematical framework for subdivided populations. In this paper we focus on diploid populations with geographic subdivision, and present new theoretical results. We compare the haploid and diploid versions of the inbreeding effective size (NeI) with novel expression for the variance effective size (NeV), and conclude that for local populations NeV is often much smaller than both versions of NeI, whenever they exist...
December 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27619485/deterministic-evolution-of-an-asexual-population-under-the-action-of-beneficial-and-deleterious-mutations-on-additive-fitness-landscapes
#19
Kavita Jain, Sona John
We study a continuous time model for the frequency distribution of an infinitely large asexual population in which both beneficial and deleterious mutations occur and fitness is additive. When beneficial mutations are ignored, the exact solution for the frequency distribution is known to be a Poisson distribution. Here we include beneficial mutations and obtain exact expressions for the frequency distribution at all times using an eigenfunction expansion method. We find that the stationary distribution is non-Poissonian and related to the Bessel function of the first kind...
December 2016: Theoretical Population Biology
https://www.readbyqxmd.com/read/27609405/stabilization-of-species-coexistence-in-spatial-models-through-the-aggregation-segregation-effect-generated-by-local-dispersal-and-nonspecific-local-interactions
#20
Matteo Detto, Helene C Muller-Landau
Spatial interactions are widely acknowledged to play a significant role in sustaining diversity in ecological communities. However, theoretical work on this topic has focused on how spatial processes affect coexistence of species that differ in their strategies, with less attention to how spatial processes matter when competitors are equivalent. Furthermore, though it is recognized that models with local dispersal and local competition may sustain higher diversities of equivalent competitors than models in which these are not both localized, there is debate as to whether this reflects merely equalizing effects or whether there is also a stabilizing component...
December 2016: Theoretical Population Biology
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