The most viewed posts on Haldane’s Sieve this month were:

• Investigating the Evolutionary Importance of Denisovan Introgressions in Papua New Guineans and Australians. Hu et al. identify haplotypes in Oceanians that appear to have introgressed from interbreeding with Denisovans.
• Flawed evidence for convergent evolution of the circadian CLOCK gene in mole-rats. Delsuc critiques a paper on convergent evolution in mole rats.
• Early modern human dispersal from Africa: genomic evidence for multiple waves of migration. Tassi et al. argue that Australo-Melanesian populations partially descend from an early out-of-Africa migration of modern humans.
• Author post: Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila. Castellano and Eyre-Walker discuss their preprint on the consequences of Hill-Robertson interference.
• Origins of de novo genes in human and chimpanzee. Ruiz-Orera et al. use RNA-seq to identify newly-evolved genes in primates.

The most viewed preprints on Haldane’s Sieve in June 2015 were:

• The next 20 years of genome research. Schatz discusses his vision for the future of genomics.
• Approximately independent linkage disequilibrium blocks in human populations. Berisa and Pickrell describe an approach for identifying approximately uncorrelated blocks of genetic variants for use in association studies.
• Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data. Rocke et al. benchmark the performance of methods for detecting differential expression using RNA-seq data.
• Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans. Rogers identifies changes in genome structure during recent human evolution.
• Exact simulation of the Wright-Fisher diffusion. Jenkins and Spano present a new approach to simulation from a Wright-Fisher model.

The most viewed posts on Haldane’s Sieve in May 2015 were:

• Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans. Rebekah Rogers describes an analysis of chromosomal rearrangements in the Neandertal and Denisovan genomes.
• An empirical approach to demographic inference. Peter Ralph describes a new approach to thinking about demographic inference in the context of a fixed pedigree.
• Sharing and specificity of co-expression networks across 35 human tissues. Pierson et al. develop methods for inferring gene co-expression networks, and apply them to the GTEx data.
• Author post: Coalescent times and patterns of genetic diversity in species with facultative sex. Matthew Hartfield describes his preprint (with co-authors) on coalescent modeling in species that switch between sexual and asexual reproduction.
• A Coalescent Model of a Sweep from a Uniquely Derived Standing Variant. Berg and Coop develop analytical theory to describe the effects of a selective sweep from standing variation on patterns of genomic diversity.

The most viewed posts this month were:

• Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Duforet-Frebourg et al. develop a method to detect positive selection in genomic data using principal component analysis, and apply the method to human populations.
• Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia. Galinsky et al. develop a fast version of principal component analysis and methods to use it to detect positive selection, with application to human populations.
• Author post: Bayesian Model Comparison in Genetic Association Analysis: Linear Mixed Modeling and SNP Set Testing. William Wen describes his preprint on model comparison in association studies.
• Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation. Choi et al. develop a population genetic/network approach to identifying pathways important in disease risk.
• FermiKit: assembly-based variant calling for Illumina resequencing data. Heng Li describes a new variant calling pipeline for genome sequence data.

The most viewed posts on Haldane’s Sieve this month were:

• Efficient computation of the joint sample frequency spectra for multiple populations. Kamm et al. introduce new methods for learning about demographic history from the site frequency spectrum.
• Eight thousand years of natural selection in Europe. Mathieson et al. use ancient DNA to identify loci and phenotypes under selection in recent European history.
• Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Schep et al. develop a new genomic method for assaying nucleosome positioning, and apply it to measure nucleosome occupancy in three species.
• Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Sonay et al. compare divergence patterns at short genomic repeats with divergence patterns in gene expression.
• The interplay between DNA methylation and sequence divergence in recent human evolution. Hernando-Herraez et al. study the evolution of DNA methylation in the primate phylogeny using bisulphite sequencing.

The most viewed posts on Haldane’s Sieve this month were:

• Author post: Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance. Pleuni Pennings describes her paper (with co-authors) on the evolution of drug resistance in infectious disease.
• Massive migration from the steppe is a source for Indo-European languages in Europe. Haak et el. present a large study of ancient DNA in Europe, and show that a post-Neolithic migration from the steppe has had a dramatic impact on the population structure of Europe today.
• Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. This post by Greg Cooper and colleagues was one of the most viewed posts last month as well. Adam Siepel’s initial post on this paper was also highly viewed this month.
• Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes. Lipson et al. propose a new method for estimating mutation rates, and apply the method to humans.
• Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations
  Haber et al. present an analysis of the population genetic history of Armenian populations.

The most viewed posts on Haldane’s Sieve this month were:

• Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. This critical commentary on Gulko et al. was highly viewed this month after Adam Siepel responded to the critiques on his lab blog.
• An Atlas of Genetic Correlations across Human Diseases and Traits. Bulik-Sullivan et al. systematically estimate the genetic correlation between a large set of human traits, and identify a number of novel shared connections.
• The Time-Scale of Recombination Rate Evolution in Great Apes. Stevison et al. examine the evolution of recombination across the ape phylogeny, and find a major role for the gene PRDM9 in driving recombination rate variation at this scale.
• A Spatial Framework for Understanding Population Structure and Admixture. Bradburd et al. present a new method for identifying and visualizing spatial patterns of genetic structure in a population, with applications to warblers and humans.
• The origin and evolution of maize in the American Southwest. da Fonseca et al. use ancient DNA from archaeological maize samples to learn about the domestication history of the crop.

2014 was the second full year of Haldane’s Sieve, which we started in 2012 to bring attention to preprints in population and evolutionary genetics. This year we had over 100,000 visitors from across the globe; the most viewed posts were:

• Author post: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. Adam Siepel writes about the motivation for his group’s preprint. The preprint contained a comparison of the authors’ new method to CADD. The CADD authors disagreed with some aspects of this comparison and posted their detailed comments as Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome.
• Our paper: Sashimi plots: Quantitative visualization of RNA sequencing read alignments. This post by Yarden Katz from 2013 describes a method for visualizing RNA sequencing data.
• Author post: Genome Sequencing Highlights the Dynamic Early History of Dogs. Ilan Gronau describes some of the computational details of a preprint on dog domestication. This paper was published in PLOS Genetics.
• LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies. Bulik-Sullivan et al. describe a new method to correct for population stratification in genome-wide association studies.
• Our Paper: Genome-wide inference of ancestral recombination graphs. This post was the most viewed post last year, and the paper was published this year in PLOS Genetics.
• The Landscape of Human STR Variation. Willems et al. discuss a survey of microsatellite variation in humans; Karl Broman posted a review of the paper in the comments. The paper was published in Genome Research.
• Author post: Inferring human population size and separation history from multiple genome sequences. Stephan Schiffels describes his preprint on extensions of the PSMC model. The paper was published in Nature Genetics.
• Author post: qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Stephen Turner describes his preprint on visualization methods for genome-wide association studies.
• The existence and abundance of ghost ancestors in biparental populations. Gravel and Steel explore the differences between genealogical and genetic ancestry.
• Author post: Long non-coding RNAs as a source of new peptides. Mar Alba discusses her group’s preprint on the evolution of gene content. This paper was published in eLife.

The most viewed posts on Haldane’s Sieve this month were:

• Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. Cooper et al. dispute some technical aspects of a paper by Gulko et al. on predicting deleterious mutations.
• Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis. Thomas et al. sequence 37 isolates of C. briggsae and use these sequences to infer the history of the species.
• Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia. Vyas et al. analyze 113 mitochondrial genomes from Yemeni populations in the context of data from other populations across the world.
• Current data show no signal of Ebola virus adapting to humans. Spielman et al. perform a re-analysis of Ebola genome sequences from the most recent outbreak.
• A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing. Schwartz et al. develop a method for phylogenetic inference in the absence of a reference genome.

The most viewed preprints this month were:

• Thoughts on: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. Cooper et al. dispute some technical aspects of a paper by Gulko et al. on predicting deleterious mutations.
• Author post: Probabilities of Fitness Consequences for Point Mutations Across the Human Genome. Adam Siepel describes the story behind the Gulko et al. paper.
• Second-generation PLINK: rising to the challenge of larger and richer datasets. Chang et al. describe a new and much faster version of the popular software package PLINK.
• Ancestry Composition: A Novel, Efficient Pipeline for Ancestry Deconvolution. Durand et al. describe the ancestry inference pipeline used by the personal genomics company 23andMe.
• An extended reply to Mendez et al.: The ‘extremely ancient’ chromosome that still isn’t. On this surface, this paper by Elhaik et al. appears to be a debate about estimates of the Y chromosome mutation rate. Look just a bit deeper, however, and what this paper is “about” becomes considerably less clear.