Abstract:
:The distribution of allele frequencies obtained from diffusion approximations to Wright-Fisher models is useful in developing intuition about the population level effects of evolutionary processes. The statistical properties of the stationary distributions of K-allele models have been extensively studied under neutrality or under selection. Here, we introduce a new family of Wright-Fisher models in which there are two hierarchical levels of genetic variability. The genotypes composed of alleles differing from each other at the selected level have fitness differences with respect to each other and evolve under selection. The genotypes composed of alleles differing from each other only at the neutral level have the same fitness and evolve under neutrality. We show that with an appropriate scaling of the mutation parameter with respect to the number of alleles at each level, the frequencies of alleles at the selected and the neutral level are conditionally independent of each other, conditional on knowing the number of alleles at all levels. This conditional independence allows us to simulate from the joint stationary distribution of the allele frequencies. We use these simulated frequencies to perform inference on parameters of the model with two levels of genetic variability using Approximate Bayesian Computation.
journal_name
Theor Popul Bioljournal_title
Theoretical population biologyauthors
Ferguson JM,Buzbas EOdoi
10.1016/j.tpb.2018.03.004subject
Has Abstractpub_date
2018-07-01 00:00:00pages
78-87eissn
0040-5809issn
1096-0325pii
S0040-5809(18)30060-1journal_volume
122pub_type
杂志文章abstract::The epidemiology of acute infections is strongly influenced by the immune status of individuals. In-host models can provide quantitative predictions of immune status and can thus offer valuable insights into the factors that influence transmission between individuals and the effectiveness of vaccination protocols with...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2007.10.003
更新日期:2008-02-01 00:00:00
abstract::We generalize a recently introduced graphical framework to compute the probability that haplotypes or genotypes of two individuals drawn from a finite, subdivided population match. As in the previous work, we assume an infinite-alleles model. We focus on the case of a population divided into two subpopulations, but th...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2011.01.003
更新日期:2011-05-01 00:00:00
abstract::The effect of population structure on the probability of fixation of a newly introduced mutant under weak selection is studied using a coalescent approach. Wright's island model in a framework of a finite number of demes is assumed and two selection regimes are considered: a beneficial allele model and a linear game a...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2007.04.001
更新日期:2007-11-01 00:00:00
abstract::A dispersal model for airborne pollen based on assumptions about wind directionality, gravity, and a wind threshold at which pollen is taken by the wind is developed, using a three dimensional diffusion approximation. The bivariate probability distribution of pollen receipt by flowers at the same height as the pollen ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1006/tpbi.1997.1306
更新日期:1997-08-01 00:00:00
abstract::The effects of parasites on the behavior of their hosts are well documented. For example, parasites may affect the habitat selection of the host individual. We used variables aggregation methods to investigate the way in which parasites affect the spatial pattern of susceptible hosts. We developed a simple epidemiolog...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1006/tpbi.2002.1598
更新日期:2002-09-01 00:00:00
abstract::A plankton-fish model, comprising phosphorus, algae, zooplankton, and young fish, with light intensity and water temperature varying periodically with the seasons, is analyzed in this paper. For realistic values of the parameters the model behaves chaotically, but its dynamics within the strange attractor can be descr...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1006/tpbi.1998.1368
更新日期:1998-08-01 00:00:00
abstract::Pertussis, or whooping cough, is an important respiratory infection causing considerable infant mortality worldwide. Recently, incidence has risen in countries with strong vaccine programmes and there are concerns about antigenic shift resulting in vaccine evasion. Interactions between pertussis and non-vaccine-preven...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2015.05.003
更新日期:2015-08-01 00:00:00
abstract::In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evolutionary trees with those predicted by neutral models. A key ingredient in this approach is the ability to compute and quantify distributions ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2015.11.004
更新日期:2016-04-01 00:00:00
abstract::There are many examples of male mate choice for female traits that tend to be associated with high fertility. I develop quantitative genetic models of a female trait and a male preference to show when such a male preference can evolve. I find that a disagreement between the fertility maximum and the viability maximum ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2008.06.001
更新日期:2008-09-01 00:00:00
abstract::A four-parameter model describing mortality as the first passage of an abstract measure of survival capacity, vitality, is developed and used to explore four classic problems in demography: (1) medfly demographic paradox, (2) effect of diet restriction on longevity, (3) cross-life stage effects on survival curves and ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2009.05.004
更新日期:2009-09-01 00:00:00
abstract::We provide a general framework for estimating persistence in populations which may be affected by catastrophic events, and which are either unbounded or have very large ceilings. We model the population using a birth-death process modified to allow for downward jumps of arbitrary size. For such processes, it is typica...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2005.02.002
更新日期:2005-08-01 00:00:00
abstract::We develop a theory of generalist predation showing how alternative prey species are affected by changes in both mean abundance and variability (coefficient of variation) of their predator's primary prey. The theory is motivated by the indirect effects of cyclic rodent populations on ground-breeding birds, and develop...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2015.04.002
更新日期:2015-08-01 00:00:00
abstract::All known lambdoid prophages of Escherichia coli have the same orientation with respect to direction of chromosomal replication. This includes 12 prophages that are replicated in one direction and five in the other. Among candidate explanations, the most amenable to experimental study is an effect on dif site function...
journal_title:Theoretical population biology
pub_type: 杂志文章,评审
doi:10.1006/tpbi.2002.1604
更新日期:2002-06-01 00:00:00
abstract::The evolution of social traits remains one of the most fascinating and feisty topics in evolutionary biology even after half a century of theoretical research. W.D. Hamilton shaped much of the field initially with his 1964 papers that laid out the foundation for understanding the effect of genetic relatedness on the e...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2015.05.002
更新日期:2015-08-01 00:00:00
abstract::A forward diffusion equation describing the evolution of the allele frequency spectrum is presented. The influx of mutations is accounted for by imposing a suitable boundary condition. For a Wright-Fisher diffusion with or without selection and varying population size, the boundary condition is lim(x downward arrow0)x...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2006.06.005
更新日期:2007-02-01 00:00:00
abstract::For a sample of two genes from a population divided into an arbitrary number of allele classes, a general mathematical framework is developed to address the expectation and variance of the time of the most recent common ancestor. Depending on the meaning of allele classes and the manner in which genes can change among...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/0040-5809(91)90039-i
更新日期:1991-02-01 00:00:00
abstract::In spatially distributed populations, global panmixia can be regarded as the limiting case of long-distance migration. The effect of incorporating partial panmixia into single-locus clines maintained by migration and selection is investigated. In a diallelic, two-deme model without dominance, partial panmixia can incr...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2011.09.006
更新日期:2012-02-01 00:00:00
abstract::Many herbivore populations fluctuate temporally, but the causes of those fluctuations remain unclear. Plant inducible resistance can theoretically cause herbivore population fluctuations, because herbivory may induce plant changes that reduce the survival or reproduction of later-feeding herbivores. Herbivory can also...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2007.09.006
更新日期:2008-02-01 00:00:00
abstract::How long a newly emerging trait will stay in a population is a fundamental but rarely asked question in cultural evolution. To tackle this question, the distribution and mean of the time to extinction of a discrete cultural trait are derived for models with overlapping generations, in which trait transmission occurs f...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2021.01.002
更新日期:2021-01-19 00:00:00
abstract::The genealogical consequences of temporally fluctuating selection at linked neutrally-evolving sites are studied using coalescent processes structured by genetic backgrounds. Surprisingly, although between-generation fluctuating selection and within-generation fecundity variance polymorphism lead to indistinguishable ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2013.03.004
更新日期:2013-08-01 00:00:00
abstract::Quantitative fishery harvest strategies in many countries throughout the world are based on maximum sustainable yield (MSY) reference points (RPs); in particular, the fishing mortality rate that produces MSY (i.e. Fmsy) and the population biomass (Bmsy) that results from fishing at Fmsy. There is often great interest ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2019.07.010
更新日期:2019-12-01 00:00:00
abstract::With the acquisition of genetic, physical, and sequence maps, linkage relationships among genes (markers) may be more accurately approached in terms of global models for the distribution of recombination events that take into account interference. There are two principal analytical methods used for ascertaining linkag...
journal_title:Theoretical population biology
pub_type: 杂志文章,评审
doi:10.1006/tpbi.1994.1025
更新日期:1994-10-01 00:00:00
abstract::We find the evolutionarily stable dispersal behaviour of a population that inhabits a heterogeneous environment where patches differ in safety (the probability that a juvenile individual survives until reproduction) and productivity (the total competitive weight of offspring produced by the local individual), assuming...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2011.02.004
更新日期:2011-06-01 00:00:00
abstract::Host-parasite interactions in the form of infectious diseases are a topic of interest in both evolutionary biology and public health. Both fields have relied on mathematical models to predict and understand the dynamics and consequences of these interactions. Yet few models explicitly incorporate both epidemiological ...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2017.12.003
更新日期:2018-07-01 00:00:00
abstract::Questions surrounding the prevalence of complex population dynamics form one of the central themes in ecology. Limit cycles and spatiotemporal chaos are examples that have been widely recognised theoretically, although their importance and applicability to natural populations remains debatable. The ecological processe...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2016.04.004
更新日期:2016-08-01 00:00:00
abstract::This paper explores the effects of increasing spatial subdivision of habitat on competition between two species. An increase in the degree of subdivision without any increase in the total amount of resources in the environment leads to smaller patch sizes, and thus, fewer individuals supported per patch. This fact sug...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2018.01.002
更新日期:2018-03-01 00:00:00
abstract::Maladapted individuals can only colonise a new habitat if they can evolve a positive growth rate fast enough to avoid extinction, a process known as evolutionary rescue. We treat log fitness at low density in the new habitat as a single polygenic trait and use the infinitesimal model to follow the evolution of the gro...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2017.11.007
更新日期:2018-07-01 00:00:00
abstract::Character displacement of competing species is studied. A model, originally developed by MacArthur and Levins (Proc. Natl. Acad. Sci. USA 51 (1964), 1207-1210) and further analyzed by Lawlor and Maynard Smith (Amer. Nat. 110 (1976), 70-99), has been reanalyzed. In the present paper, a more formally correct analysis of...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/0040-5809(85)90006-1
更新日期:1985-04-01 00:00:00
abstract::Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical mode...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2010.06.007
更新日期:2010-11-01 00:00:00
abstract::We investigate the properties of a Wright-Fisher diffusion process starting at frequency x at time 0 and conditioned to be at frequency y at time T. Such a process is called a bridge. Bridges arise naturally in the analysis of selection acting on standing variation and in the inference of selection from allele frequen...
journal_title:Theoretical population biology
pub_type: 杂志文章
doi:10.1016/j.tpb.2013.08.005
更新日期:2013-11-01 00:00:00