Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.
These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci.
Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data
GENECLASS2: a software for genetic assignment and first-generation migrant detection.
- S. Piry, A. Alapetite, J. Cornuet, D. Paetkau, L. Baudouin, A. Estoup
- Computer ScienceJournal of Heredity
- 1 November 2004
GENECLASS2 is a software that computes various genetic assignment criteria to assign or exclude reference populations as the origin of diploid or haploid individuals, as well as of groups of individuals, on the basis of multilocus genotype data, for the specific task of first-generation migrant detection.
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…
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
DIYABC v2.0 implements a number of new features and analytical methods, including efficient Bayesian model choice using linear discriminant analysis on summary statistics and the serial launching of multiple post-processing analyses.
New methods employing multilocus genotypes to select or exclude populations as origins of individuals.
It becomes possible to exclude a population as the origin of an individual, a useful extension of the currently available assignment methods, after the distribution of the assignment criterion was used to define the probability that an individual belongs to the population.
Distortion of allele frequency distributions provides a test for recent population bottlenecks.
It is demonstrated that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci, and a qualitative graphical method is illustrated and evaluated for detecting a bottleneck-induced distortion of allele frequency distributions.
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation
Key methods used in DIY ABC, a computer program for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples, are described.
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.
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)
New developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms.