Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

/pdf/stacks-an-analysis-tool-set-for-population-genomics-3dmvyh33iq.pdf

Stacks: an analysis tool set for population genomics

The authors describe the best practices for a growing number of methods that use next-generation sequencing to rapidly discover and assess genetic markers across any genome, with applications from population genomics and quantitative trait locus mapping to marker-assisted selection.

Genome-wide genetic marker discovery and genotyping using next-generation sequencing.

The objective of this paper is to give a comprehensive introduction to applied cryptography with an engineer or computer scientist in mind. The emphasis is on the knowledge needed to create practical systems which supports integrity, confidentiality, or authenticity. Topics covered includes an introduction to the concepts in cryptography, attacks against cryptographic systems, key use and handling, random bit generation, encryption modes, and message authentication codes. Recommendations on algorithms and further reading is given in the end of the paper. This paper should make the reader able to build, understand and evaluate system descriptions and designs based on the cryptographic components described in the paper.

[서평]「Applied Cryptography」

Summary: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (FST, Fisher’s exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer. Availability and Implementation: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/ popoolation2/

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of individuals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of individuals (Pool-seq) provides a cost-effective alternative to sequencing individuals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms. In this Review, we not only demonstrate the breadth of questions that are being addressed by Pool-seq but also discuss its limitations and provide guidelines for users.

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θWatterson, θπ, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.

/pdf/popoolation-a-toolbox-for-population-genetic-analysis-of-s5f3ne4qxi.pdf

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Summary: SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites. Availability: free for use: www.kofler.or.at/Bioinformatics Contact: robert.kofler@boku.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.

/pdf/sciroko-a-new-tool-for-whole-genome-microsatellite-search-19qhq95n93.pdf

SciRoKo: a new tool for whole genome microsatellite search and investigation.

Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North American east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/TOR, ecdysone, torso, EGFR, TGFβ/BMP, JAK/STAT, immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R, especially within the cosmopolitan inversion In(3R)Payne, which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P, we also identify genes that are likely independent of this inversion. Our results provide genome-wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well-known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.

/pdf/genome-wide-patterns-of-latitudinal-differentiation-among-3ay21vspwn.pdf

Robert Kofler

Papers

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

SciRoKo: a new tool for whole genome microsatellite search and investigation.

Genome‐wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America