2013 was the first full year of Haldane’s Sieve, which we started in 2012 to bring attention to preprints in evolutionary and population genetics. Perhaps the most exciting development of the year was the expansion of preprint server options–instead of arXiv, some biologists are now using bioRxiv or PeerJ Preprints. This year at Haldane’s Sieve, we received over 100,000 visitors from all over the world. Our most viewed posts of the year were:

• Our Paper: Genome-wide inference of ancestral recombination graphs. Adam Siepel (@asiepel) writes about his paper with Matthew Rasmussen, now posted on the arxiv as a significantly expanded revision.
• Our paper: Assemblathon 2 and pizza. Keith Bradnam writes about genome assembly and finding the right pizza in Davis. The preprint described in the post was published in GigaScience.
• Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs. Freedman et al present work on the timing and history of domestication of dogs and adaptation during this process.
• Reconstructing the Population Genetic History of the Caribbean. Moreno-Estrada et al. use genomic data to learn about the history of the people living in the Caribbean. This paper was published in PLoS Genetics.
• The deleterious mutation load is insensitive to recent population history. Simons et al. show that demographic events on the time scale of recent human evolution are unlikely to have an impact on the number of deleterious alleles carried by an individual.
• Our paper: The causal meaning of Fisher’s average effect. James Lee writes about his paper with Carson Chow on different definitions of the average effect on an allele on the phenotype. There’s also a post by Chow here. Published in Genetics Research (pdf here).
• Our paper: The geography of recent genetic ancestry across Europe. Peter Ralph and Graham Coop write about using Identity By Descent to understand recent history. The paper was published in PLoS Biology.
• Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. Patro et al. report a new algorithm for estimating gene expression levels using RNA-seq.
• The Functional Consequences of Variation in Transcription Factor Binding. Cusanovich et al. present work studying the relationship between transcription factor binding and gene expression.
• The Population Genetic Signature of Polygenic Local Adaptation. Jeremy Berg and Graham Coop develop methods to identify signals of selection on polygenic phenotypes using GWAS data. They also wrote a guest post on their work.

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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.