• Corpus ID: 1868831

Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.

  title={Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.},
  author={Jean-Marie Cornuet and Gordon Luikart},
  volume={144 4},
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a… 

Figures and Tables from this paper

Test for a population expansion after a drastic reduction in population size using DNA sequence data

The patterns arising when populations undergo bottlenecks and then slowly recover are analysed, and two new statistical tests for the detection of the bottleneck are used, suggesting that the test is particularly suited for detecting relatively recent and strong bottlenECks and thus may be a valuable tool for identifying population events on a fine temporal scale.

Empirical Evaluation of a Test for Identifying Recently Bottlenecked Populations from Allele Frequency Data

A statistical test (a sign test for heterozygosity excess) for detecting recent historical bottlenecks using allele frequency data (Cornuet & Luikart 1996) is developed and evaluated by analyzing 56 allozyme and 37 microsatellite data sets from bottlenecked and nonbottlenecked natural populations.

Allele excess at neutrally evolving microsatellites and the implications for tests of neutrality

Skews in the observed allele–frequency spectrum are frequently viewed as an indication of non–neutral evolution. Recent surveys of microsatellite variability have used an excess of alleles as a

BOTTLENECK : A Computer Program for Detecting Recent Reductions in the Effective Population Size Using Allele Frequency Data

BOTTLENECK (current version 1.2) is a population genetics computer program that conducts four tests for identifying populations that have recently experienced a severe reduction in effective

Comparison of methods for detecting bottlenecks from microsatellite loci

Simulation tests to compare methods for detecting recent bottlenecks using microsatellite data find that Mk was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large.

Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change

The variance test was most powerful; it provided an 85% probability of detecting a bottleneck of size Ne = 10 when monitoring five microsatellite loci and sampling 30 individuals both before and one generation after the bottleneck.

Reliability of genetic bottleneck tests for detecting recent population declines

Recommendations are provided that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.

Estimating the number of founder lineages from haplotypes of closely linked SNPs

A Monte‐Carlo maximum‐likelihood method for estimating the number of founding individuals from the haplotype frequencies at several SNP (single nucleotide polymorphism) loci in a sample is developed and applied to simulated data and shows that it is unbiased.

Maximum-likelihood inference of population size contractions from microsatellite data.

This work develops a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data, based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM).

Detecting past changes of effective population size

A new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach was developed.



Population bottlenecks and nonequilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck.

It is suggested that populations that have undergone a single bottleneck event, followed by rapid population growth, should have an apparent excess number of alleles, given the observed level of genic heterozygosity and provided that the bottleneck has not occurred very recently.


The reduction in population size results in an accelerated increase in genetic distance in the early generations by using the stepwise mutation model and the method of generating function first used by Nei and Chakraborty (1973) is employed in the study of protein variation and extended considerably by Wehrhahn.

Population bottlenecks and nonequilibrium models in population genetics. I. Allele numbers when populations evolve from zero variability.

Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers.

Allele frequencies at microsatellite loci: the stepwise mutation model revisited.

There is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.


In a population of constant size the expected heterozygosity for a neutral locus when mutation and genetic drift are balanced is given by 4 Nv/(4Nv + 1) under the assumption that new mutations are

Mutation rates, population sizes and amounts of electrophoretic variation of enzyme loci in natural populations.

The hypothesis that differences in the amount of electrophoretic variability among polymorphic loci may reflect Differences in the rate by which electroph theoretically detectable variation is generated in population is supported.


  • R. Lande
  • Biology
    Evolution; international journal of organic evolution
  • 1994
Data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of Ne = 103, may incur a substantial risk of extinction from the fixation of new mutations.

Mutational processes of simple-sequence repeat loci in human populations.

Computer simulations were used to determine expected values of statistics that reflect frequency distributions of allele size for the two-phase model and two alternatives, the one-step and geometric models, and found that estimates of interpopulation distances from SSRs were similar to those derived from analysis of mitochondrial DNA.

Evolutionary relationship of DNA sequences in finite populations.

These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors.