Weekly Roundup - October 16, 2015

Every week, members of the Wilson Sayres' lab scour the most recent issues of dozens of journals for interesting and relevant (to lab research) articles. Here's what we found the week of October 16, 2015 (in no particular order within categories):

Sex Chromosomes

Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome

Coolon et al. (2015) in Molecular Biology and Evolution "Here, we test the hypothesis that accelerated adaptive evolution of cis-regulatory sequences on the X chromosome is responsible for this pattern by comparing the relative contributions of cis- and trans-regulatory changes to patterns of faster-X expression divergence observed between strains and species of Drosophila with a range of divergence times. We find support for this hypothesis, especially among male-biased genes, when comparing different species. However, we also find evidence that trans-regulatory differences contribute to a faster-X pattern of expression divergence both within and between species."

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds

Dean et al. (2015) in Molecular Biology and Evolution

"Our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex."

Conservation of regional variation in sex-specific chromosome regulation Wright et al. (2015) in Genetics

Population Genetics/Genomics

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele Ronen et al. (2015) in PLoS Genetics " The main contribution of this paper is the development and analysis of a new statistic (the HAF score), assigned to individual haplotypes. Using both theoretical analyses and simulations, we describe how the HAF scores differ for carriers and non-carriers of the favored allele, and how they change dynamically during a selective sweep."

Effects of interference between selected loci on the mutation load, inbreeding depression, and heterosis Roze (2015) in Genetics

A coalescent model for a sweep of a unique standing variant Berg and Coop (2015) in Genetics

Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.

Ingram et al. (2015) in Molecular Ecology "Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species’ unusual mating system."

Miscellaneous Genomics

Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots Baker et al. (2015) in PloS Genetics

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses Gasmi et al. (2015) in PLos Genetics "We show here that in several lineages, lepidopteran genomes have acquired genes from a bracovirus that is symbiotically used by parasitic wasps to inhibit caterpillar host immune defences. Integration of parts of the viral genome into host caterpillar DNA strongly suggests that integration can sporadically occur in the germline, leading to the production of lepidopteran lineages that harbor bracovirus sequences."

The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe Farlow et al. (2015) in Genetics

The genomics of organismal diversification illuminated by adaptive radiations Berner and Salzburger (2015) in Trends in Genetics

Genomic insights into a contagious cancer in Tasmanian devils Grueber et al. (2015) in Trends in Genetics

Human structural variation: mechanisms of chromosome rearrangements Weckselblatt and Rudd (2015) in Trends in Genetics

This Month in Genetics Garber (2015) in American Journal of Human Genetics

Genome-wide study of Down Syndrome-associated atrioventricular septal defects Ramachandran et al. (2015) in G3

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Frantz et al. (2015) in Nature Genetics

Multilane family evolution: perspectives from insect chemoreceptors. Benton (2015) in Trends in Ecology and Evolution

Methods

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer Foo et al. (2015) in PLOS Computational Biology "We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer."

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity Petrovski et al. (2015) in PloS Genetics "Here, we present two approaches intended to help identify noncoding regions of the genome that may carry mutations influencing disease. The first approach is based on comparing observed and predicted levels of standing human variation in the noncoding exome sequence of a gene. The second approach is based on the phylogenetic conservation of a gene’s noncoding exome sequence using GERP++. We find that both approaches can predict genes known to cause disease through changes in expression level, genes depleted of loss-of-function alleles in the general population, and genes permissive of copy number variants in the general population."

Evaluating the Performance of Fine-Mapping Strategies at Common Variant GWAS Loci

van de Bunt at al. (2015) in PLoS Genetics "In this study, we used extensive simulations to show that statistical fine-mapping can indeed accurately reduce the number of likely causal variants at common GWAS loci"

Genotype-frequency estimation from high-throughput sequencing data Maruki and Lynch (2015) in Genetics

Alternative splicing QTLs in European and African populations. Ongen and Dermitzakis (2015) in American Journal of Human Genetics

Risk of bias in reports of in vivo research: a focus for improvement Macleod et al. (2015) in PLoS Biology

Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability.

Das et al. (2015) in Nature Communications "We introduce a coupled Bayesian regression approach—eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combination of regulatory single-nucleotide polymorphisms (SNPs) that explain the gene expression variance."

Evolutionary Biology

Sperm competition and the evolution of precopulatory weapons: increasing male density promotes sperm competition and reduces selection on arm strength in a chorusing frog. Buzatto et al. (2015) in Evolution

Paleophysiology: from fossils to the future Vermeij (2015) in Trends in Ecology and Evolution

Ape parasite origins of human malaria virulence genes. Larremore et al. (2015) in Nature Communications

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake.

López-Bueno et al. (2015) in Molecular Ecology