Data from: Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus

Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation-selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency-dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated for Mendelian traits, but there is little comparable data for loci affecting quantitative characters. Here, we report a three-year field study of selection on intra-population Quantitative Trait Loci (QTL) of flower size, a highly polygenic trait of Mimulus guttatus. The QTL exhibit antagonistic pleiotropy: alleles that increase flower size reduce viability but increase fecundity. The magnitude and direction of selection fluctuates yearly and on a spatial scale of meters. This study provides direct evidence of balancing selection mechanisms on QTL of an ecologically relevant trait

Phenotype and Fitness data

This file provides the raw phenotype and fitness (survivorship and fecundity) data for each of the transplanted Nearly Isogenic Lines as described in Mojica et al 2012

Comparative study on beliefs and practices regarding cough and colds among people living in upland and lowland Cavite

This is a non-experimental, quantitative, descriptive study. Simple random sampling was used to select 100 respondents. Data was obtained using a self-made questionnaire and analyzed through median, standard deviation, variance, Mann-Whitney U Test, Kruskal-Wallis and Spearman’s Rank correlation coefficient. The study concluded that, 1) Most of the respondents were female, 30 years old and below, married and had monthly family income of P10,000 and below. There was an equal number of respondents from upland and lowland; 2) The respondents had a good level of belief regarding cough and colds with the overall mean of 3.06; 3) The respondents often performed the practices with an overall mean of 3.4; 4) There was no significant difference in the beliefs of the respondents regarding cough and colds when they were grouped according to gender, civil status and monthly family income. However, there was a significant difference when grouped according to age in the following statements: “Incidence of cough and colds is greater in upland than in lowland Cavite” and “Taking foods rich in Vitamin C.” There was also a significant difference when grouped according to location with the following beliefs: “Water therapy alleviates cough and colds” and “Taking hot shower baths alleviates cough and colds;” 5) There was no significant difference in the practices of the respondents regarding cough and colds when they were grouped according to age, gender and civil status. However, there was a significant difference when they were grouped according to monthly family income with regard the following practices: visit crowded places whenever they have cough and colds, visit the doctor or health center whenever they have cough and colds and eat sweets whenever they have cough and colds. There was a significant difference when grouped according to location with regard to the following practices: cover their nose or mouth whenever they have cough and colds, wash their hands after sneezing and visit crowded places whenever they have cough and colds; 6) There was a significant relationship in some of the beliefs and practices of the respondents regarding cough and colds among people living in upland and lowland Cavite

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

BackgroundGenomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species.ResultsUsing whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms.ConclusionsOur results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Following publication of the original article [1], the authors reported that the Availability of data and materials section required updating. The updated text reads as follows

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

BackgroundGenomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species.ResultsUsing whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms.ConclusionsOur results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation

SNPs genotyped in this study

This file contains 4,125,395 high-quality SNPs genotyped in this study. For each SNP, the location (Scaffold name and position on scaffold), and reference and alternative alleles were provided

Geographical location of 517 sequenced Boechera stricta accessions.

This file contains geographical information of 517 sequenced B. stricta accessions. 484 genotypes were each assigned into a genetic group based on populaton structure analyses. 33 genotypes were excluded from data analyses due to low data quality, duplicates or incomplete sampling information

Data from: Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution