MEGASAT: automated inference of microsatellite genotypes from sequence data

MEGASAT is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. MEGASAT reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important fea- ture of MEGASAT is the generation of histograms of the length–frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. MEGASAT is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demon- strate MEGASAT using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0–1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The Holocene optimum (HO) and the response of human activity: A case study of the Huai River Basin in eastern China

There is a controversy regarding the timing of the onset of the Holocene optimum (HO) in the Huai River Basin in eastern China, reflecting the scarcity of well-dated high-resolution sedimentary records in the region. In this study we validate the time-transgressive onset of the HO in the East Asian Monsoon (EAM) region and update a regression model of the onset of the HO versus latitude. We also estimate the onset time of the HO in the Huai River Basin to 9100-8000 yr BP, which is confirmed by other well-dated geological records from within and around the basin. We also compared our age estimate with data from archaeological sites in the Huai River Basin and with the record of rice remains in eastern China. The result indicates that a dramatic increase in the number of archaeological sites and the northward expansion of rice cultivation, which eventually occupied the entire Huai River Basin, corresponds temporally to the onset of the HO. Thus our results suggest that the prosperity of prehistoric culture in the Huai River Basin was enhanced by the initiation of the HO. Our findings reveal a close relationship between the onset of the HO in the Huai River Basin and human activity, and they provide an improved understanding of the response of human activity to climate change in eastern China

Kontraktuele kontrolerechten en bewijsovereenkomsten

This R file contains pseudocode for the main analyses used in the publication "Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus" by Van Wyngaarden, M et al. Not all steps are included in the code but examples of the major analyses (outlier selection, PCA, RDA, and multiple linear regressions) are presented. Running this code will not repeat all the analyses used in the publication but will allow readers to see what functions were used

VanWyngaardenM_etal_SeascapeGen_FinalEnvironmentalData

This file contains data for the final 90 environmental variables used to compare genetic and environmental variation among sea scallop populations as well as the latitude and longitude of all 12 sample sites. Data have been standardized to 0 mean and unit variance

VanWyngaardenM_etal_SeascapeGen_RADseq_SNPs

This VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus. The program stacks v0.9999 was used to call variants