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Using Environmental Correlations to Identify Loci Underlying Local Adaptation
A Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers and then uses this as a null model for a test at individual SNPs, which can be used to identify SNPs with unusually large allele frequency differentiation and offers a powerful alternative to tests based on pairwise or global FST.
Robust Identification of Local Adaptation from Allele Frequencies
A set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv are developed.
PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice
The results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome.
Signals of recent positive selection in a worldwide sample of human populations.
Analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel, suggests that there has been selection on loci involved in susceptibility to type II diabetes.
The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
Although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HAPMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.
THE SIGNATURE OF POSITIVE SELECTION ON STANDING GENETIC VARIATION
This work examines what effect this mode of selection has on patterns of variation at linked neutral sites by implementing a new coalescent model of positive directional selection on standing variation, and highlights the importance of an accurate characterization of the effects of positive selection, if the authors are to reliably identify recent adaptations from polymorphism data.
The Geography of Recent Genetic Ancestry across Europe
A genomic survey of recent genealogical relatedness reveals the close ties of kinship and the impact of events across the past 3,000 years of European history.
IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS
- C. Boettiger, G. Coop, Peter L. Ralph
- BiologyEvolution; international journal of organic…
- 23 September 2011
This work describes a Monte Carlo‐based method and provides an open‐source implementation in the pmc (“Phylogenetic Monte Carlo”) package for the R programming language, and hopes such power analysis becomes a routine part of model comparison in comparative methods.
Sequencing and Analysis of Neanderthal Genomic DNA
The characterization of Neanderthals from a new perspective is described, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis, and the finding that the Neanderthal and human genomes are at least 99.5% identical is found.