The most viewed posts on Haldane’s Sieve in December 2013 were:

• Evolution of female choice and age-dependent male traits with paternal germ-line mutation. Joel James Adamson sets out a model of age dependent mutation rates and the good genes hypothesis for female choice.
• Author post: Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Joe Pickrell writes about his arXived paper linking GWAS data to functional annotations.
• Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture. Bhatia et al. look for deviations in admixture proportions across the genome, this paper is in part a response to Jin et al. who reported signals of selection (post admixture) in African Americans.
• Variational Inference of Population Structure in Large SNP Datasets. Raj, Stephens, and Pritchard develop a variational Bayesian framework implementation to speed up the popular STRUCTURE algorithm.
• Probabilistic models of genetic variation in structured populations applied to global human studies . Hao, Song, and Storey present new approaches to population structure.

The most viewed posts on Haldane’s Sieve in November 2013 were:

• The evolution of sex differences in disease genetics. Gilks et al. review quantitative and evolutionary genetics results on the evolution of sex-specific genetic architectures underlying traits.
• Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis. Durand et al. use a large genomic dataset from the personal genetics company 23andMe to calibrate false positive rates in analysis of genomic regions identified as identical-by-descent, and introduce a method to reduce false positives.
• Data Mining of Online Genealogy Datasets for Revealing Lifespan Patterns in Human Population. Fire and Elovici use online genealogy databases to estimate the heritability of human lifespan. Note that Yaniv Erlich suggests this study is in violation of the terms of service of the database used.
• The Functional Consequences of Variation in Transcription Factor Binding. The comment thread on the Cusanovich et al. preprint (which was the most viewed preprint last month) continued this month with comments from Casey Brown.
• Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Pickrell presents a method for choosing the types of functional genomic data that are relevant for a given trait, and applies the method to genome-wide association studies of 18 traits.

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

• The Functional Consequences of Variation in Transcription Factor Binding. Cusanovich et al. use RNAi knockdowns of transcription factors followed by expression profiling to argue that most transcription factor binding in humans is not relevant to gene expression. This conclusion inspired a lively conversation on Twitter.
• Thoughts on: The date of interbreeding between Neandertals and modern humans. Graham Coop‘s post on Sankararaman et al. was mentioned by David Reich during his plenary talk at ASHG this month (he now thinks the data rejects the model proposed in the post).
• Thoughts on: Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle. Joe Pickrell posted his review of a preprint by Decker et al. on using genetics to learn about the history of cattle domestication.
• Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers. Yan et al. report sequencing of Y chromosomes from 78 east Asian men, and conclude that there was an important population expansion in China during the Neolithic.
• Our Paper: Genome-wide inference of ancestral recombination graphs. Adam Siepel describes his preprint (with Matt Rasmussen) on a new model for inferring ancestral recombination graphs.

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

• Our Paper: Genome-wide inference of ancestral recombination graphs. Adam Siepel’s post on his preprint with Matthew Rasmussen describing a new method for inferring ancestral recombination graphs is the most viewed post for the third month in a row.
• Author post: The identifiability of piecewise demographic models from the sample frequency spectrum. Bhaskar and Song describe their preprint showing that some classes of demographic histories are indeed identifiable from the allele frequency spectrum alone. Graham Coop provides some context in this post.
• Author post: The Population Genetic Signature of Polygenic Local Adaptation. Berg and Coop discuss their preprint on testing for polygenic adaptation using alleles identified in genome-wide association studies.
• Biological Averaging in RNA-Seq. Biswas et al. propose that pooling samples in RNA-seq experiments is a cost-effective alternative to sequencing individual samples.
• Our paper: An integrative genomic approach illuminates the causes and consequences of genetic background effects. Chris Chandler describes his work with colleagues (Chandler et al.) exploring the causes of variation in the effects of a mutation in different genetic backgrounds.

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

• Our Paper: Genome-wide inference of ancestral recombination graphs. Adam Siepel’s post on his preprint with Matthew Rasmussen describing a new method for inferring ancestral recombination graphs repeated as the most viewed post this month, and is now the most viewed post IN THE HISTORY OF THE WORLD*.
• Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. Patro et al. present a novel algorithm for quantifying gene expression using RNA-seq that avoids the computationally expensive step of read alignment.
• The Population Genetic Signature of Polygenic Local Adaptation. Berg and Coop present a method for detecting selection on complex phenotypes by using loci identified in genome-wide association studies.
• A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers. Smith et al. develop a test for selection on enhancers that combines comparative genomic data with data from saturation mutagenesis experiments.
• Our Paper: The genomic impacts of drift and selection for hybrid performance in maize. Jeff Ross-Ibarra describes his work with colleagues (Gerke et al.) tracking allele frequency changes in maize over multiple rounds of selection for hybrid performance.

*”The world” is defined for these purposes as Haldane’s Sieve.

The most viewed preprints in July 2013 were:

• Our Paper: Genome-wide inference of ancestral recombination graphs. Adam Siepel gives a nice overview of ancestral recombination graphs, and discusses his preprint with Matthew Rasmussen on a new method for inferring them.
• Our paper: Assemblathon 2 and pizza. The Assemblathon 2 paper was officially published this month. In this popular post from January, Keith Bradnam describes why assembling a genome is like making a pizza.
• Genetics of single-cell protein abundance variation in large yeast populations. Albert et al. develop a new method for mapping genetic loci that influence protein levels in yeast, and identify a number of hotspots that control levels of multiple proteins.
• Evolution on genotype networks leads to phenotypic entrapment. Manrubia and Cuesta argue that the structure of genetic networks plays a role in evolutionary dynamics.
• Cloudbreak: Accurate and Scalable Genomic Structural Variation Detection in the Cloud with MapReduce. Whelan et al. develop a computational tool for efficient and large-scale detection of structural variants.

This month was the most active yet on Haldane’s Sieve, with over 10,000 page views and several active comment threads. The most viewed preprints were:

• Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs. Freedman et al. perform genome sequencing of several wolves and dogs, and use this data to examine gene flow and selection during the initial domestication of dog breeds.
• Reconstructing the Population Genetic History of the Caribbean. Moreno-Estrada et al. use genomic data from populations throughout the Caribbean to examine their history. They argue that there were at least two pulses of admixture with African populations, and that there is a signature of genetic drift in the European colonists that settled the area.
• Sashimi plots: Quantitative visualization of RNA sequencing read alignments. Katz et al. present a method for visualization of RNA-seq experiments from many samples. An “Our paper” post is here.
• On the accumulation of deleterious mutations during range expansions. Peischl et al. show that populations expanding into a new habitat can accumulate deleterious mutations, and argue that this may be a relevant phenomenon for understanding human variation.
• Populations in statistical genetic modelling and inference. Lawson reviews the fundamental question of how to define a “population” in “population genetics”.

The most viewed posts on Haldane’s Sieve in May 2013 were:

• The deleterious mutation load is insensitive to recent population history. Simons et al. use population genetic modeling and analysis of exome sequencing data to argue against an important role for population history in altering the burden of deleterious mutations in different human populations.
• Bayesian test for co-localisation between pairs of genetic association studies using summary statistics. Giambartolomei et al. present a method for testing whether association signals found in two studies are driven by the same genetic variant. An “Our paper” post is here.
• Our paper: The geography of recent genetic ancestry across Europe. This preprint from Ralph and Coop was formally published last month; they discussed their results in this post from last October.
• The role of twitter in the life cycle of a scientific publication. Darling et al. discuss the use of Twitter as a platform for scientific communication.
• Our paper: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Weigel and Burbano discuss a preprint on using genetic data from different time points to resolve the history of the pathogen that caused the Irish potato famine.

Below are the most viewed posts on Haldane’s Sieve in April 2013. We’ve listed six instead of our usual five posts because the last two posts had identical numbers of views at the time of writing.

• Our paper: The causal meaning of Fisher’s average effect. James Lee discusses the story behind his paper clarifying RA Fisher’s presentation of the fundamental theorem of natural selection.
• Our paper: Improving transcriptome assembly through error correction of high-throughput sequence reads. Matt MacManes discusses his paper on de novo transcriptome assembly.
• Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. This preprint from Bergland et al. on seasonal variation in selective pressure in Drosophila was also one of the most viewed preprints last month.
• Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al. Melissa Wilson Sayres comments on a recent paper describing a new basal lineage of the human Y chromosome genealogy.
• Thoughts on: Loss and Recovery of Genetic Diversity in Adapting Populations of HIV. An exchange between Richard Neher and the authors of a preprint on the population genetics of HIV.
• Our paper: The effects of transcription factor competition on gene regulation. Radu Zabet describes two preprints on applications of a stochastic model for transcription factor binding.

The most viewed preprints on Haldane’s Sieve in March 2013 were:

• RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates. Pyrkosz et al. evaluate the performance of RNA-seq to measure gene expression in organisms where the database of reference transcripts is incomplete. An “Our paper” post is here, and see the discussion on Titus Brown’s blog.
• Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. Bergland et al. sequence wild Drosophila populations at various times over several years, and provide provide evidence for hundreds of loci under temporally-varying selection.
• Soft selective sweeps are the primary mode of recent adaptation in Drosophila melanogaster. Garud et al. develop a population genetic method to search for the genetic signature of “soft” selective sweeps, and argue that such sweeps are widespread. An “Our paper” post is here.
• Sensitive Long-Indel-Aware Alignment of Sequencing Reads. Marschall and Schönhuth present a new alignment algorithm for short read data.
• Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq. Cromie et al. perform a large-scale analysis of genetic diversity in yeast populations.

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