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Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps
Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps. In contrast to a hard selective sweep,Expand
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Molecular evidence for a single evolutionary origin of domesticated rice
Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. AExpand
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An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomicExpand
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Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster
The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkageExpand
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Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population
The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interestedExpand
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Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity
Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity.Expand
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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteriaExpand
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The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens
Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drugExpand
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Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.
Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweepsExpand
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Reply to Ge and Sang: A single origin of domesticated rice
In a recent study using two different methods of analysis and two different datasets, we concluded that domesticated Asian rice had a single origin (1). Ge and Sang (2) suggest that our analyses wereExpand
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