Generating samples under a Wright-Fisher neutral model of genetic variation.
TL;DR: A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model, and the samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.
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Abstract: A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.
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QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time.
TL;DR: Several demographic, genetic and selective parameters can be fine-tuned in QuantiNemo 2: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography and mating system are the main features.
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Marbled inflation from population structure in gene-based association studies with rare variants.
TL;DR: It is shown that, different from single‐SNP inference, genes with diverse composition of rare and common variants may suffer from population stratification to various extent, and caution needs to be exercised when using principal component adjustment.
Reconsidering Association Testing Methods Using Single-Variant Test Statistics as Alternatives to Pooling Tests for Sequence Data with Rare Variants
TL;DR: It is concluded that efficient locus-wide inference using single-variant test statistics should be reconsidered as a useful framework for devising powerful association tests in sequence data with rare variants.
An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study
TL;DR: A new, efficiently computed lower bound is established on the minimum number of recombination events in the evolutionary history of DNA sequences, applicable to many biological phenomena other than recombination, when gene conversions or recurrent or back mutations or cross-species hybridizations cause the phylogenetic history to deviate from a tree structure.
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Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana.
TL;DR: This article infer the rates of gene conversion and crossing over in Arabidopsis thaliana from population genetic data and finds that even if some components of the model clearly do not fit, the pattern of LD conforms to theoretical expectations quite well.
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Warren J. Ewens
- 01 Jan 1979
TL;DR: In this paper, the authors present a model based on the Wright-Fisher In.nitely Many Alleles Model and the Cannings (Exchangeable) Model: Two-Alleles 3.4.