Effective Population Size and Population Subdivision in Demographically Structured Populations

AbstractA fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.

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A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽

10.1093/genetics/136.2.685 ◽

1994 ◽

Vol 136 (2) ◽

pp. 685-692 ◽

Cited By ~ 1

Author(s):

Y X Fu

Keyword(s):

Population Size ◽

Effective Population Size ◽

Mutation Rate ◽

Dna Sequences ◽

High Efficiency ◽

Minimum Variance ◽

Population Subdivision ◽

Effective Population ◽

Fisher Model ◽

Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

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Historical Analysis of Genetic Variation Reveals Low Effective Population Size in a Northern Pike (Esox lucius) Population

Genetics ◽

10.1093/genetics/147.3.1249 ◽

1997 ◽

Vol 147 (3) ◽

pp. 1249-1258 ◽

Cited By ~ 4

Author(s):

Loren M Miller ◽

Anne R Kapuscinski

Keyword(s):

Population Size ◽

Effective Population Size ◽

Microsatellite Loci ◽

Natural Populations ◽

Historical Analysis ◽

Fish Population ◽

Time Interval ◽

Effective Population ◽

Entire Interval ◽

Census Size

Effective population size (Ne) of a natural fish population was estimated from temporal changes in allele frequencies at seven microsatellite loci. Use of a historical collection of fish scales made it possible to increase the precision of estimates by increasing the time interval between samples and to use an equation developed for discrete generations without correcting for demographic parameters. Estimates of Ne for the time intervals 1961–1977 and 1977–1993 were 35 and 72, respectively. For the entire interval, 1961–1993, the estimate of Ne was 48 when based on a weighted mean derived from the above two estimates or 125 when calculated from 1961 and 1993 samples only. Corresponding ratios of effective size to adult census size ranged from 0.03 to 0.14. An Ne of 48 over a 32-year period would imply that this population lost as much as 8% of its heterozygosity in that time. Results suggest the potential for using genetic methods based on microsatellite loci data to compare historical trends in Ne with population dynamic parameters. Such comparisons will help to evaluate the relationship between genetic diversity and long-term persistence of natural populations.

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The Genetic Effective Size of a Population

10.1093/oso/9780198830870.003.0003 ◽

2018 ◽

Author(s):

Bruce Walsh ◽

Michael Lynch

Keyword(s):

Population Size ◽

Effective Population Size ◽

Genome Structure ◽

Population Subdivision ◽

Effective Population ◽

Entire Genome ◽

History Of ◽

A Site ◽

The Hill ◽

New Mutations

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.

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The effective population size of some age-structured populations

Mathematical Biosciences ◽

10.1016/s0025-5564(00)00041-9 ◽

2000 ◽

Vol 168 (1) ◽

pp. 39-56 ◽

Cited By ~ 14

Author(s):

Edward Pollak

Keyword(s):

Population Size ◽

Effective Population Size ◽

Structured Populations ◽

Effective Population ◽

Age Structured

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Nuclear Gene Genealogies Reveal Historical, Demographic and Selective Factors Associated With Speciation in Field Crickets

Genetics ◽

10.1093/genetics/163.4.1389 ◽

2003 ◽

Vol 163 (4) ◽

pp. 1389-1401 ◽

Cited By ~ 1

Author(s):

Richard E Broughton ◽

Richard G Harrison

Keyword(s):

Population Size ◽

Effective Population Size ◽

Natural Populations ◽

Nuclear Gene ◽

Distinct Species ◽

Effective Population ◽

Ancestral Polymorphisms ◽

History Of ◽

Selective Forces ◽

Shared Polymorphism

Abstract Population genetics theory predicts that genetic drift should eliminate shared polymorphism, leading to monophyly or exclusivity of populations, when the elapsed time between lineage-splitting events is large relative to effective population size. We examined patterns of nucleotide variation in introns at four nuclear loci to relate processes affecting the history of genes to patterns of divergence among natural populations and species. Ancestral polymorphisms were shared among three recognized species, Gryllus firmus, G. pennsylvanicus, and G. ovisopis, and genealogical patterns suggest that successive speciation events occurred recently and rapidly relative to effective population size. High levels of shared polymorphism among these morphologically, behaviorally, and ecologically distinct species indicate that only a small fraction of the genome needs to become differentiated for speciation to occur. Among the four nuclear gene loci there was a 10-fold range in nucleotide diversity, and patterns of polymorphism and divergence suggest that natural selection has acted to maintain or eliminate variation at some loci. While nuclear gene genealogies may have limited applications in phylogeography or other approaches dependent on population monophyly, they provide important insights into the historical, demographic, and selective forces that shape speciation.

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Patterns of Inbreeding Depression and Architecture of the Load in Subdivided Populations

Genetics ◽

10.1093/genetics/165.4.2193 ◽

2003 ◽

Vol 165 (4) ◽

pp. 2193-2212 ◽

Cited By ~ 5

Author(s):

Sylvain Glémin ◽

Joëlle Ronfort ◽

Thomas Bataillon

Keyword(s):

Population Size ◽

Effective Population Size ◽

Inbreeding Depression ◽

Local Population ◽

Population Subdivision ◽

Deleterious Mutations ◽

Effective Population ◽

Subdivided Populations ◽

And Migration ◽

Insight Into

AbstractInbreeding depression is a general phenomenon that is due mainly to recessive deleterious mutations, the so-called mutation load. It has been much studied theoretically. However, until very recently, population structure has not been taken into account, even though it can be an important factor in the evolution of populations. Population subdivision modifies the dynamics of deleterious mutations because the outcome of selection depends on processes both within populations (selection and drift) and between populations (migration). Here, we present a general model that permits us to gain insight into patterns of inbreeding depression, heterosis, and the load in subdivided populations. We show that they can be interpreted with reference to single-population theory, using an appropriate local effective population size that integrates the effects of drift, selection, and migration. We term this the “effective population size of selection” (NeS). For the infinite island model, for example, it is equal to NeS=N(1+m∕hs), where N is the local population size, m the migration rate, and h and s the dominance and selection coefficients of deleterious mutation. Our results have implications for the estimation and interpretation of inbreeding depression in subdivided populations, especially regarding conservation issues. We also discuss the possible effects of migration and subdivision on the evolution of mating systems.

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NATURAL SELECTION FOR WITHIN-GENERATION VARIANCE IN OFFSPRING NUMBER

Genetics ◽

10.1093/genetics/76.3.601 ◽

1974 ◽

Vol 76 (3) ◽

pp. 601-606

Author(s):

John H Gillespie

Keyword(s):

Genetic Variation ◽

Natural Selection ◽

Population Size ◽

Effective Population Size ◽

Variance Component ◽

Fixation Probability ◽

Effective Population ◽

Offspring Number ◽

Selection For

ABSTRACT In this paper it is shown that natural selection can act on the within-generation variance in offspring number. The fitness of a genotype will increase as its variance in offspring number decreases. The intensity of selection on the variance component is inversely proportional to population size, although the fixation probability of a gene which differs from its allele only in the variance in its offspring number is independent of population size. The concept of effective population size is shown to be of limited use when there is genetic variation in the variance in offspring number.

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Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

Canadian Journal of Zoology ◽

10.1139/z00-170 ◽

2001 ◽

Vol 79 (1) ◽

pp. 26-34 ◽

Cited By ~ 10

Author(s):

Michael F Antolin ◽

Beatrice Van Horne ◽

Michael D Berger, Jr. ◽

Alisha K Holloway ◽

Jennifer L Roach ◽

...

Keyword(s):

Genetic Analysis ◽

Population Size ◽

Effective Population Size ◽

Ground Squirrel ◽

Population Genetic ◽

Ground Squirrels ◽

Perennial Grasses ◽

Population Subdivision ◽

Effective Population ◽

Population Genetic Analysis

Piute ground squirrels (Spermophilus mollis) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size (Ne) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 813 km. The ratio of effective population size to census number (Ne/N) was 0.57. Combining Ne/N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Qpopulations [Formula: see text] 0.070.10) between subpopulations and no inbreeding within subpopulations (f = 0.0003). These estimates of population subdivision translate into an effective migration rate (Nem) of 2.33.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.

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