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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Simultaneous inference of selection and population growth from patterns of variation in the human genome
TL;DR: A model-based approach to developing predictions for patterns of polymorphism in the presence of both population size change and natural selection, which is more robust to assumptions regarding the true underlying demography than previous approaches to detecting and analyzing selection.
Grinding up Wheat: A Massive Loss of Nucleotide Diversity Since Domestication
Annabelle Haudry,Alberto Cenci,Catherine Ravel,Thomas Bataillon,Dominique Brunel,Charles Poncet,Isabelle Hochu,Sebastien Poirier,Sylvain Santoni,Sylvain Glémin,Jacques David +10 more
TL;DR: Whether some of the genes departed from the empirical distribution of most loci are investigated, suggesting that they might have been selected during domestication or breeding, and a departure from the null model of demographic bottleneck for the hypothetical gene HgA is detected.
386
Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestication of Rice
TL;DR: Consistent with the dramatic reduction in nucleotide diversity, a severe domestication bottleneck is detected and the sequence diversity currently found in the rice genome could be explained by a founding population of 1,500 individuals if the initial domestication event occurred over a 3,000-year period.
Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest
Tingcai Cheng,Jiaqi Wu,Wu Yuqian,Rajendra V. E. Chilukuri,Lihua Huang,Kohji Yamamoto,Li Feng,Wanshun Li,Zhiwei Chen,Huizhen Guo,Jianqiu Liu,Shenglong Li,Xiaoxiao Wang,Li Peng,Duolian Liu,Youbing Guo,Bohua Fu,Zhiqing Li,Chun Liu,Yuhui Chen,Archana Tomar,Frédérique Hilliou,Nicolas Montagné,Emmanuelle Jacquin-Joly,Emmanuelle d'Alençon,Rakesh Kumar Seth,Raj K. Bhatnagar,Akiya Jouraku,Takahiro Shiotsuki,Keiko Kadono-Okuda,Amornrat Promboon,Guy Smagghe,Guy Smagghe,Kallare P. Arunkumar,Hirohisa Kishino,Marian R. Goldsmith,Qili Feng,Qingyou Xia,Kazuei Mita +38 more
TL;DR: The gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds.
Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants
TL;DR: Simulations indicate that D and H in combination can be most effective in detecting positive selection while being insensitive to other perturbations, and a joint test, referred to as the DH test, is proposed.
381
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