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 sweep, which single adaptive haplotype rises high population frequency, sweep multiple haplotypes through the simultaneously, producing distinct patterns of vicinity site. Current statistical methods were expressly designed detect sweeps and most lack power This is particularly unfortunate for study adaptation species...

Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies indica japonica, were from the wild rice O. rufipogon. In contrast, multiple independent domestication proposes these major types separately in different parts species range rice. This latter view has gained much support observation strong genetic...

We present the M etagenomic I ntra-species D iversity A nalysis S ystem (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 reference genomes that we clustered into groups. These cover majority abundant in human microbiome but only small proportion microbes other...

Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the dynamics have been extensively studied, much less is known about how species gut bacteria evolve over time. Here, we introduce model-based framework for quantifying within across hosts using panel metagenomic samples. We use this approach to study evolution in approximately 40 prevalent human gut. Although patterns between-host diversity consistent with quasi-sexual purifying selection on long...

Abstract Positive natural selection can lead to a decrease in genomic diversity at the selected site and linked sites, producing characteristic signature of elevated expected haplotype homozygosity. These selective sweeps be hard or soft. In case sweep, single adaptive rises high population frequency, whereas multiple haplotypes sweep through simultaneously soft distinct patterns genetic variation vicinity site. Measures homozygosity have previously been used detect study systems. However,...

Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize gut microbiome of a single individual at high temporal genetic resolution through period health, disease, treatment, recovery. We used deep, linked-read metagenomic sequencing track longitudinal trajectories thousands nucleotide variants within 36...

Although the ecological dynamics of infant gut microbiome have been intensely studied, relatively little is known about evolutionary in microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over first year life find that microbiomes are distinct those adults. We evidence for a 10-fold increase rate evolution strain turnover compared with healthy adults, mother-infant transition at delivery being particularly dynamic period which gene...

The human gut microbiome harbors substantial ecological diversity at the species level as well strain within species. In healthy hosts, abundance fluctuations in are thought to be stable, and these can described by macroecological laws. However, it is less clear how abundances change over time. An open question whether individual strains behave like themselves, exhibiting stability following relationships known hold level, or have different dynamics, perhaps due relatively close phylogenetic...

Whether hard sweeps or soft dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both and with similar power (ii) classify the detected as soft. The application our method to population genomic data from natural Drosophila melanogaster (DGRP) allowed us rediscover three known cases at loci Ace, Cyp6g1, CHKov1 be driven by sweeps, additional candidate for recent strong sweeps. Surprisingly, all top 50 candidates...

The human gut microbiome contains a diversity of microbial species that varies in composition over time and across individuals. These (and strains within species) can migrate hosts evolve by mutation recombination hosts. How the ecological process community assembly interacts with intra-species evolutionary change is longstanding question. Two contrasting hypotheses have been proposed based on observations theory: Diversity Begets (DBD), which taxa tend to become more diverse already...

Abstract The extent to which selection and demography impact patterns of genetic diversity in natural populations Drosophila melanogaster is yet be fully understood. We previously observed that linkage disequilibrium (LD) at scales ∼10 kb the Genetic Reference Panel (DGRP), consisting 145 inbred strains from Raleigh, North Carolina, measured both between pairs sites as haplotype homozygosity, elevated above neutral demographic expectations. also demonstrated signatures strong recent soft...

Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are bacterial cell surface proteins facilitate attachment to tissues often virulence factors for opportunistic pathogens. However, attachments transient nonspecific, additional mechanisms required infection. In this work, we use live imaging of individual cells colonizing living Drosophila...

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 interested in the demographic history populations, information is rarely available historical records. Methods have been developed infer parameters genomic data, but it not well understood how inferred compare true population or depend on aspects experimental design. Here, we present and evaluate a method...

Abstract Patterns of nucleotide polymorphism within populations Drosophila melanogaster suggest that insecticides have been the selective agents driving strongest recent bouts positive selection. However, there is a need to explicitly link sweeps particular insecticide phenotypes could plausibly account for drastic responses are observed in these non-target insects. Here, we screen Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a...

Genetic variation in the human gut microbiome is responsible for conferring a number of crucial phenotypes like ability to digest food and metabolize drugs. Yet, our understanding how this arises maintained remains relatively poor. Thus, largely untapped resource, as large coexisting species presents unique opportunity compare contrast evolutionary processes across identify universal trends deviations. Here we outline features that, while not isolation, an assemblage make it system with...

Abstract Animals throughout the metazoa selectively acquire specific symbiotic gut bacteria from their environment that aid host fitness. Current models of colonization suggest these use weakly receptors to stick tissues and results when they in a region overlaps with nutritional niche. An alternative model is unique receptor-ligand binding interactions provide specificity for target niches. Here we live imaging individual bacterial cells colonizing living Drosophila melanogaster show...

Abstract Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including demographic histories and distributions fitness effects (DFE) mutations. Here, we infer DFEs for amino-acid changing mutations 39 most prevalent abundant microbial species found in Westernized individuals over timescales exceeding generations. Some display contractions population size others expansions, with several these events coinciding key...

Abstract Environmental gradients exist throughout the digestive tract, driving spatial variation in membership and abundance of bacterial species along gut. However, less is known about distribution genetic diversity within Understanding this important because variants confer traits for functioning microbiome are also to impart phenotypes hosts, including local inflammation gut ability digest food. Thus, be able understand how functions at a mechanistic level, it essential organized...

Oral potentially malignant disorders (OPMDs) are a group of conditions that carry risk oral squamous cell carcinoma (OSCC) development. Recent studies indicate periodontal disease-associated pathogenic bacteria may play role in the transition from healthy mucosa to dysplasia and OSCC. Yet, microbial signatures associated with have not been established. To characterize at these different sites, we performed 16S sequencing analysis both swab formalin-fixed, paraffin-embedded tissue (FFPE)...

Abstract Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the dynamics have been extensively studied, much less is known about how species gut bacteria evolve over time. Here we introduce model-based framework for quantifying within across hosts using panel metagenomic samples. We use this approach to study evolution in ∼30 prevalent human gut. Although patterns between-host diversity consistent with quasi-sexual purifying selection on long timescales,...

In a recent study using two different methods of analysis and datasets, we concluded that domesticated Asian rice had single origin (1). Ge Sang (2) suggest our analyses were flawed the remains an open question.