Weekly Roundup - November 6, 2015

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. Here’s what we found the week of November 6, 2015:

Sex Chromosomes

Sex bias and maternal contribution to gene expression divergence in Drosophila blastoderm embryos Paris et al. (2015) in PLoS Genetics

Silencing of X-linked microRNAs by meiotic sex chromosome inactivation Royo et al. (2015) in PLoS Genetics

The pseudoautosomal regions of the U/V sex chromosomes of the brown alga Ectocarpus exhibit unusual features Luthringer et al. (2015) in Molecular Biology and Evolution

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards Lavretsky et al. (2015) in Molecular Ecology

Impact of repetitive DNA on sex chromosome evolution in plants Hobza et al. (2015) in Chromosome Research

No interstitial telomeres on autosomes but remarkable amplification of telomeric repeats on the W sex chromosome in the sand lizard (Lacerta agilis) Matsubara et al. (2015) in Journal of Heredity

Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki Murata et al. (2015) in BMC Evolutionary Biology

Genomic instability of the sex-determining locus in Atlantic salmon (Salmo salar) Lubieniecki et al. (2015) in G3

Phylogenomic evidence for ancient hybridization in the genome of living cats (Felidae) Li et al. (2015) in Genome Research

Preferential breakpoints in the recovery of broken dicentric chromosomes in Drosophila melanogaster Hill and Golic (2015) in Genetics


Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria. Bershtein et al. (2015) in PLoS Genetics

How do genomes create novel phenotypes? Insights from the loss of the worker caste in ant social parasites Smith et al. (2015) in Molecular Biology and Evolution

Ecological and lineage-specific factors drive the molecular evolution of rhodopsin in cichlid fishes Torres-Dowdall et al. (2015) in Molecular Biology and Evolution

The evolutionary landscape of intergenic trans-splicing events in insect Kong et al. (2015) in Nature Communications

Allelic variation contributes to bacterial host specificity Xue et al. (2015) in Nature Communications

Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins Bazykin (2015) in Biology Letters

Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species Potter et al. (2015) in Biology Letters

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance Alexander et al. (2015) in Biology Letters

Genetic diversity in humans and non-human primates and its evolutionary consequences Osada (2015) in Genes and Genetic Systems

Tempo and mode of genomic mutations unveil human evolutionary history Hara (2015) in Genes and Genetic Systems

The transcriptional landscape of age in human peripheral blood Peters et al. (2015) in Nature Communications

Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication Yang et al. (2015) in PNAS

Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia Di et al. (2015) in BMC Evolutionary Biology

Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals Davies et al. (2015) in BMC Evolutionary Biology

Potential mechanisms for cancer resistance in elephants and comparative cellular response to DNA damage in humans Abegglen et al. (2015) in JAMA

Functional and structural consequence of rare exonic single nucleotide polymorphisms: one story, two tales Gu et al. (2015) in Genome Biology and Evolution

Recombining without hotspots: a comprehensive evolutionary portrait of recombination in two closely related species of Drosophila Heil et al. (2015) in Genome Biology and Evolution

TLE6 mutation causes the earliest known human embryonic lethality Alazami et al. (2015) in Genome Biology

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogenography and evolution of cattle Park et al. (2015) in Genome Biology

An atlas of genetic correlations across human diseases and traits Bulik-Sullivan et al. (2015) in Nature Genetics

Height-reducing variants and selection for short stature in Sardinia Zoledziewska et al. (2015) in Nature Genetics

Population genetic differentiation of height and body mass index across Europe Robinson et al. (2015) in Nature Genetics

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control Kretzmer et al. (2015) in Nature Genetics

RNAseq analysis highlights specific transcriptome signatures of yeast mycelial growth phases in the Dutch elm disease fungus Ophiostoma novo-ulmi Nigg et al. (2015) in G3

Whole-genome sequencing suggest schizophrenia risk mechanisms in humans with 22q11.2 deletion syndrome Merico et al. (2015) in G3

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans Cenik et al. (2015) in Genome Research

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers Burri et al. (2015) in Genome Research

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii Ness et al. (2015) in Genome Research

The genome of the vervet (Chlorocebus aethiops sabeus) Warren et al. (2015) in Genome Research

A probabilistic method for testing and estimating selection differences between populations He et al. (2015) in Genome Research

Germline heterozygous variants in SEC23B are associated with Cowden Syndrome and enriched in apparently sporadic thyroid cancer Yehia et al. (2015) in American Journal of Human Genetics

Population genomics of Mycobacterium tuberculosis in the Inuit Lee et al. (2015) in PNAS

Genetic basis of transcriptome diversity in Drosophila melanogaster Huang et al. (2015) in PNAS


Evaluating the adequacy of molecular clock models using posterior predictive simulations Duchene et al. (2015) in Molecular Biology and Evolution

Inferring very recent population growth rate from population-scale sequencing data: using a large-sample coalescent simulator Chen et al. (2015) in Molecular Biology and Evolution

hapbin: an efficient program for performing haplotype-based scans for positive selection in large genomic datasets Maclean et al. (2015) in Molecular Biology and Evolution

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudooxyrhophiine snakes Ruane et al. (2015) in BMC Evolutionary Biology

Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data Forni et al. (2015) in BMC Genomics

Getting the most out of RNA-seq data analysis Khang and Lau (2015) in PeerJ

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes Wang et al. (2015) in Genome Biology

WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system Wong et al. (2015) in Genome Biology

Network analysis of gene essentiality in functional genomics experiments Jiang et al. (2015) in Genome Biology

bz-rates: a web tool to estimate mutation rates from fluctuation analysis Gillet-Markowska et al. (2015) in G3

The human gene damage index as a gene-level approach to prioritizing exome variants Itan et al. (2015) in PNAS

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets Jin et al. (2015) in Bioinformatics

SomaticSignatures: inferring mutational signatures from single-nucleotide variants Gehring et al. (2015) in Bioinformatics

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data Nelson et al. (2015) in Bioinformatics

FermiKit: assembly-based variant calling for Illumina resequencing data Li (2015) in Bioinformatics


Damsel in distress: captured damselfish prey emit chemical cues that attract secondary predators and improve escape chances Lönnstedt and McCormick (2015) in Proceedings of the Royal Society B

Suction-based propulsion as a basis for efficient animal swimming Gemmell et al. (2015) in Nature Communications

Experimental resource pulses influence social network dynamics and the potential for information flow in tool-using crows St Clair et al. (2015) in Nature Communications

Ebola virus disease in the Democratic Republic of the Congo, 1976-2014 Rosello et al. (2015) in eLIFE

The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex Fuchs et al. (2015) in Molecular Ecology

Peer effects on worker output in the laboratory generalize to the field Herbst and Mas (2015) in Science

Miocene small-bodied ape from Eurasia sheds light on hominoid evolution Alba et al. (2015) in Science

I'm sexy and I glow it: female ornamentation in a nocturnal capital breeder Hopkins et al. (2015) in Biology Letters

Reduced birth intervals following the birth of children with long-term illness: evidence supporting a conditional evolved response Waynforth (2015) in Biology Letters

Testing modern human out-of-Africa dispersal models and implications for modern human origins Reyes-Centeno et al. (2015) in Journal of Human Evolution

The earliest unequivocally modern humans in southern China Liu et al. (2015) in Nature

Bantu expansion shows that habitat alters the route and pace of human dispersals Grollemund et al. (2015) in PNAS

DNA capture reveals transoceanic gene flow in endangered river sharks Li et al. (2015) in PNAS

Context-dependent associations between heterozygosity and immune variation in a wild carnivore Brock et al. (2015) in BMC Evolutionary Biology

Quotation accuracy in medical journal articles - a systematic review and meta-analysis Jergas and Baethge (2015) in PeerJ

Mammoth 2.0: will genome engineering resurrect extinct species Shapiro (2015) in Genome Biology

Nonmedical uses of antibiotics: time to restrict their use? Meek et al. (2015) in PLoS Biology

Live fast, die young: experimental evidence of population extinction risk due to climate change Bestion et al. (2015) in PLoS Biology

Combining search, social media, and traditional data sources to improve influenza surveillance Santillana et al. (2015) in PLoS Computational Biology "Our findings suggest that the information from multiple data sources such as Google searches, Twitter microblogs, nearly real-time hospital visit records, and data from a participatory surveillance system complement each other and produce the most accurate and robust set of flu predictions when combined optimally."

Sexual selection drives asymmetric introgression in wall lizards While et al. (2015) in Ecology Letters

Open Questions on the Origins of Eukaryotes López-García et al. (2015) in Trends in Ecology and Evolution

Genetic structure in village dogs reveals a Central Asian domestication origin Shannon et al. (2015) in PNAS