The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice

A genome-wide scan for signatures of directional selection in domesticated pigs

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Background Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs

Cetaceans evolution:insights from the genome sequences of common minke whales

Background: Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water. Results: We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 - 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales. Conclusions: This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth

Allele Frequency Distribution Under Recurrent Selective Sweeps

The allele frequency of a neutral variant in a population is pushed either upward or downward by directional selection on a linked beneficial mutation (“selective sweeps”). DNA sequences sampled after the fixation of the beneficial allele thus contain an excess of rare neutral alleles. This study investigates the allele frequency distribution under selective sweep models using analytic approximation and simulation. First, given a single selective sweep at a fixed time, I derive an expression for the sampling probabilities of neutral mutants. This solution can be used to estimate the time of the fixation of a beneficial allele from sequence data. Next, I obtain an approximation to mean allele frequencies under recurrent selective sweeps. Under recurrent sweeps, the frequency spectrum is skewed toward rare alleles. However, the excess of high-frequency derived alleles, previously shown to be a signature of single selective sweeps, disappears with recurrent sweeps. It is shown that, using this approximation and multilocus polymorphism data, genomewide parameters of directional selection can be estimated

Data from: Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude

A fundamental question in evolutionary biology is what promotes genetic variation at non-neutral loci, a major precursor to adaptation in changing environments. In particular, balanced polymorphism under realistic evolutionary models of temporally varying environments in finite natural populations remains to be demonstrated. Here, we propose a novel mechanism of balancing selection under temporally varying fitnesses. Using forward-in-time computer simulations and mathematical analysis, we show that cyclic selection that spatially varies in magnitude, such as along an environmental gradient, can lead to elevated levels of non-neutral genetic polymorphism in finite populations. Balanced polymorphism is more likely with an increase in gene flow, magnitude and period of fitness oscillations, and spatial heterogeneity. This polymorphism-promoting effect is robust to small systematic fitness differences between competing alleles or to random environmental perturbation. Furthermore, we demonstrate analytically that protected polymorphism arises as spatially heterogeneous cyclic fitness oscillations generate a type of storage effect that leads to negative frequency-dependent selection. Our findings imply that spatially variable cyclic environments can promote elevated levels of non-neutral genetic variation in natural populations

Linkage disequilibrium as a signature of selective sweeps.

The hitchhiking effect of a beneficial mutation, or a selective sweep, generates a unique distribution of allele frequencies and spatial distribution of polymorphic sites. A composite-likelihood test was previously designed to detect these signatures of a selective sweep, solely on the basis of the spatial distribution and marginal allele frequencies of polymorphisms. As an excess of linkage disequilibrium (LD) is also known to be a strong signature of a selective sweep, we investigate how much statistical power is increased by the inclusion of information regarding LD. The expected pattern of LD is predicted by a genealogical approach. Both theory and simulation suggest that strong LD is generated in narrow regions at both sides of the location of beneficial mutation. However, a lack of LD is expected across the two sides. We explore various ways to detect this signature of selective sweeps by statistical tests. A new composite-likelihood method is proposed to incorporate information regarding LD. This method enables us to detect selective sweeps and estimate the parameters of the selection model better than the previous composite-likelihood method that does not take LD into account. However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms

Signatures of Recent Directional Selection Under Different Models of Population Expansion During Colonization of New Selective Environments

A major problem in population genetics is understanding how the genomic pattern of polymorphism is shaped by natural selection and the demographic history of populations. Complex population dynamics confounds patterns of variation and poses serious challenges for identifying genomic imprints of selection. We examine patterns of polymorphism using computer simulations and provide analytical predictions for hitchhiking effects under two models of adaptive niche expansion. The population split (PS) model assumes the separation of a founding population followed by directional selection in the new environment. Here, the new population undergoes a bottleneck and later expands in size. This model has been used in previous studies to account for demographic effects when testing for signatures of selection under colonization or domestication. The genotype-dependent colonization and introgression (GDCI) model is proposed in this study and assumes that a small number of migrants carrying adaptive genotype found a new population, which then grows logistically. The GDCI model also allows for constant migration between the parental and the new population. Both models predict reduction in variation and excess of high frequency of derived alleles relative to neutral expectations, with and without hitchhiking. Under comparable conditions, the GDCI model results in greater reduction in expected heterozygosity and more skew of the site frequency spectrum than the PS model. We also find that soft selective sweeps (fixation of multiple copies of a beneficial mutation) occurs less often in the GDCI model than in the PS model. This result demonstrates the importance of correctly modeling the ecological process in inferring adaptive evolution using DNA sequence polymorphism