Frequency Spectrum Neutrality Tests: One for All and All for One
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Summary
The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution.
- Type
- article
- Published
- 2009-09-01
- Cited by
- 148
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W2039656278
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:16341966
Keywords
Neutrality, Goodness of fit, Biology, Population, Statistical hypothesis testing
References
- Coalescent Theory: An Introduction
- A phylogenetic estimator of effective population size or mutation rate.
- Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences.
- New statistical tests of neutrality for DNA samples from a population.
- Effect of misoriented sites on neutrality tests with outgroup.
- Evolutionary relationship of DNA sequences in finite populations.
- Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
- Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data
- Statistical properties of segregating sites.
- Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates.
- Population genetic inference using a fixed number of segregating sites: a reassessment.
- On a test of Depaulis and Veuille.
- Simple method for analyzing the pattern of DNA polymorphism and its application to SNP data of human.
- Haplotype tests using coalescent simulations conditional on the number of segregating sites.
- Statistical properties of new neutrality tests against population growth.
- On the number of segregating sites in genetical models without recombination.
- Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection.
- Neutrality tests based on the distribution of haplotypes under an infinite-site model.
- Genomic scans for selective sweeps using SNP data.
- Coalescent simulations and statistical tests of neutrality.
Cited by
- Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster
- Genetic variation in natural populations: a modeller's perspective
- Anàlisi multilocus del polimorfisme nucleotídic al llarg del cromosoma J de Drosophila subobscura
- Théorèmes limites pour les processus de branchement avec mutations
- Properties of neutrality tests based on allele frequency spectrum
- jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors
- A simple route to single‐nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)
- Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps
- Intron retention in the Drosophila melanogaster Rieske iron sulphur protein gene generated a new protein
- The site frequency spectrum of dispensable genes.
- Demography-adjusted tests of neutrality based on genome-wide SNP data.
- Neutrality Tests for Sequences with Missing Data
- Statistical Properties of the Site-Frequency Spectrum Associated with Λ-Coalescents
- Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France
- Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity
- Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders.
- Tests of Selection in Pooled Case-Control Data: An Empirical Study
- Inferring population size changes with sequence and SNP data: lessons from human bottlenecks
- Evidence for positive selection in the gene fruitless in Anastrepha fruit flies
- A developmental switch coupled to the evolution of plasticity acts through a sulfatase.
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