Weekly Round Up - January 15, 2016

Every week, members of the Wilson Sayres’ lab scour journals for interesting and relevant (to lab research) articles. We're back after taking some time off from the blog for winter break.  This week's list will therefore be fairly long as we catch up on the articles published during the last 3-4 weeks.  We hope you still take the time to skim through the titles though, as there are quite a few really interesting papers.  Here's the list in no particular order:

Sex Chromosomes/Sex Determination

The eutherian pseudoautosomal region. Raudsepp and Chowdhary (2016) in Cytogenetic and Genome Research

Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs Schartl et al. (2015) in Chromosoma

The emerging phylogenetic pattern of parthenogenesis in snakes Booth and Schuett (2016) in Biological Journal of the Linnean Society

Evolutionary stability of sex chromosomes in snakes Rovatsos et al. (2015) in Proc. Roy. Soc. B

Evolution of vertebrate sex chromosomes and dosage compensation Graves (2015) in Nature Reviews Genetics

Developmental dynamics of X-chromosome dosage compensation by the DCC and H4K20me1 in C. elegans Kramer et al. (2015) in PLOS Genetics

Probing Xist RNA structure in cells using targeted structure-seq Fang et al. (2o15) in PLOS Genetics

Cell-specific mRNA profiling of the C. elegans somatic gonadal precursor cells identifies suites of sex-biased and gonad-enriched transcripts Kroetz and Zarkower (2015) in G3

Sxl-dependent, tra/tra2-independent alternative splicing of the D. melanogaster X-linked gene found in neurons Sun et al. (2015) in G3

The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome Hurst et al. (2015) in PLOS Biology

A second transmissible cancer in Tasmanian devils Pye et al. (2016) in PNAS "DFT2 causes facial tumors that are grossly indistinguishable but histologically distinct from those caused by DFT1. DFT2 bears no detectable cytogenetic similarity to DFT1 and carries a Y chromosome, which contrasts with the female origin of DFT1."

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae) Li et al. (2016) in Genome Research

The pig X and Y chromosomes: structure, sequence, and evolution Skinner et al. (2016) in Genome Research

Evolution of haploid selection in predominantly diploid organisms Otto et al. (2015) in PNAS

The sex determination gene transformer regulates male-female differences in Drosophila body size Rideout et al. (2015) in PLoS Genetics

Coalescent times and patterns of genetic diversity in species with facultative sex: effects of gene conversion, population structure, and heterogeneity Hartfield et al. (2016) in Genetics

Genomics

Bayesian molecular clock dating of species divergences in the genomics era dos Reis et al. (2015) in Nature Reviews Genetics

Genome-wide patterns of selection in 230 ancient Eurasians Mathieson et al. (2015) in Nature

Time-dependent estimates of molecular evolutionary rates: evidence and causes Ho et al. (2015) in Molecular Ecology

Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions Qiu et al. (2015) in Nature Communications

DNA methylation: insights into human evolution Hernando-Herraez et al. (2015) in PLOS Genetics

Genomic insights into the ancestry and demographic history of South America Homburder et al. (2015) in PLOS Genetics

Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution Yuan et al. (2015) in PLOS Genetics

The 5300-year-old Helicobacter pylori genome of the Iceman Maixner et al. (2016) in Science

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake Malinsky et al. (2015) in Science

Reassignment of Drosophila willistoni genome scaffolds to chromosome II arms Garcia et al. (2015) in G3

Identification of genes uniquely expressed in the germ-line tissues of the jewel wasp Nasonia vitripennis Ferree et al. (2015) in G3

The hologenome concept: helpful or hollow? Moran and Sloan (2015) in PLOS Biology

Abundant contribution of short tandem repeats to gene expression variation in humans Gymrek et al. (2016) in Nature Genetics

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming Durruthy-Durruthy et al. (2016) in Nature Genetics

POGZ truncating alleles cause syndromic intellectual disability White et al. (2016) in Genome Medicine

Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network Brodrick et al. (2016) in Genome Medicine

Genome editing: the end of the beginning Doudna and Gersbach (2015) in Genome Biology

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction McClay et al. (2015) in Genome Biology

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal sources of human methylome variation Busche et al. (2015) in Genome Biology

Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging Wood et al. (2015) in Genome Biology

Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevances of glucocorticoid Zannas et al. (2015) in Genome Biology

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome Cassidy et al. (2016) in PNAS

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs Mardsen et al. (2016) in PNAS

Evolution of stickleback in 50 years on earthquake-uplifted islands Lescak et al. (2015) in PNAS

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade Boothby et al. (2015)

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) Lamichhaney et al. (2016) in Nature Genetics

Nuclear and mitochondrial DNA sequences from two Denisovan individuals Sawyer et al. (2015) in PNAS

Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication Kistler et al. (2015) in PNAS

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments Librado et al. (2015) in PNAS

Genomic data do not support comb jellies as the sister group to all other animals Pisani et al. (2015) in PNAS

The convergent cancer evolution toward a single cellular destination Chen and He (2016) in Molecular Biology and Evolution

Adaptive evolution favoring KLK4 downregulation in East Asians Marques et al. (2016) Molecular Biology and Evolution

Recombination rate variation modulates gene sequence evolution mainly via GC-biased gene conversion, not Hill-Robertson interference, in an avian system Bolivar et al. (2016) in Molecular Biology and Evolution

DNA methylation: insights into human evolution Hernando-Herraez et al. (2015) in PLoS Genetics

Origins of de novo genes in human and chimpanzee Ruiz-Orera et al. (2015) in PLoS Genetics

Genomic insights into the ancestry and demographic history of South America Homburger et al. (2015) in PLoS Genetics

Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution in primates Yuan et al. (2015) in PLoS Genetics

Combined genetic and genealoic studies uncover a large BAP1 cancer syndrome kindred tracing back nine generations to a common ancestor from the 1700s Carbone et al. (2015) in PLoS Genetics

Maternal modifiers and parent-of-origin bias of the autism-associated 16p11.2 CNV Duyzend et al. (2016) in the American Journal of Human Genetics

Detecting and characterizing the highly divergent plastid geome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae) Naumann et al. (2016) in Genome Biology and Evolution

Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes Warren et al. (2016) in Genome Biology and Evolution

Methods

The January issue of Molecular Ecology was a special issue dedicated to "Detecting selection in natural populations" and contains a number of interesting methodological, theoretical, and emprical papers on the subject

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data Finak et al. (2015) in Genome Biology

Fast and accurate approximate inference of transcript expression from RNA-seq data Hensman et al. (2015) in Bioinformatics

Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations Pybus et al. (2015) in Bioinformatics

Approximately independent linkage disequilibrium blocks in human populations Berisa and Pickrell (2016) in Bioinformatics

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Okonechinikov et al. (2016) in Bioinformatics

Meta-analysis of RNA-seq expression data across species, tissues and studies Sudmant et al. (2015) in Genome Biology

A molecular evolutionary reference for the human variome Liu et al. (2016) in Molecular Biology and Evolution

INTEGRATE: gene fusion discovery using whole genome and trascriptome data Zhang et al. (2016) in Genome Research

A simple model-based approach to inferring and visualizing cancer mutational signatures Shiraishi et al. (2015) in PLoS Genetics

Integration analysis of three Omics data using penalized regression methods: an application to bladder cancer Pineda et al. (2015) in PLoS Genetics

Melanoma cell colony expansion parameters revealed by approximate Bayesian computation Vo et al. (2015) in PLoS Genetics

Inferring bottlenecks from genome-wide samples of short sequence blocks Bunnefeld et al. (2015) in Genetics

Targeted chromosomal transocations and essential gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans Chen et al. (2015) in Genetics

Miscellaneous

Holocene shifts in the assembly of plant and animal communities implicate human impacts Lyons et al. (2016) in Nature

Influence of extreme weather disasters on global crop production Lesk et al. (2016) in Nature

Multidrug evolutionary strategies to reverse antibiotic resistance Baym et al. (2016) in Science

Five selfish reasons to work reproducibly Markowetz (2015) in Genome Biology

Free mate choice enhances conservation breeding in the endangered giant panda Martin-Wintle et al. (2015) in Nature Communications

Rarity in mass extinctions and the future of ecosystems Hull et al. (2015) in Science

The founder strains of the collaborative cross express a complex combination of advantageous and deleterious traits for male reproduction Odet et al. (2015) in G3

Controlled access under review: improving the governance of genomic data access Shabani et al. (2015) in PLOS Biology

 

Weekly Roundup - Week of November 27, 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 27, 2015:

Sex Chromosomes

Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans Rogers (2015) in Molecular Biology and Evolution

Differentiation of sex chromosomes and karyotype characterisation in the dragonsnake Xenodermus javanicus (Squamata: Xenodermatidae) Rovatsos et al. (2015) in Cytogenic and Genome Research

Genomics/Genetics

Allelic mutations of KITLG, encoding KIT ligand, cause asymmetric and unilateral hearing loss and Waardenburg Syndrome Type 2. Zazo Seco et al. (2015) in American Journal of Human Genetics

Family wide molecular adaptations to underground life in African mole-rats revealed by phylogenomic analysis Davies et al. (2015) in Molecular Biology and Evolution

Reintroduction of a homocysteine level-associated allele into East Asians by Neanderthal introgression Hu et al. (2015) in Molecular Biology and Evolution

A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures Olalde et al. (2015) in Molecular Biology and Evolution

Polymerase zeta activity is linked to replication timing in humans: evidence from mutational signatures Seplyarskiy et al. (2015) in Molecular Biology and Evolution

Exploring massive incomplete lineage sorting in Arctoids (Laurasiatheria, Carnivora) Doronina et al. (2015) in Molecular Biology and Evolution

Population level purifying selection and gene expression shape subgenome evolution in maize Pophaly and Tellier (2015) in Molecular Biology and Evolution

The mosaic ancestry of the Drosophila genetic reference panel and the D. melanogaster reference genome reveals a network of epistatic fitness interactions Pool (2015) in Molecular Biology and Evolution

Inferring selective constraint from population genomic data suggest recent regulatory turnover in the human brain Schrider and Kern (2015) in Molecular Biology and Evolution

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors Asgharian et al. (2015) in Proceedings of the Royal Society: B

Identification and characterization of essential genes in the human genome Wang et al. (2015) in Science

Hemichordate genomes and deuterostome origins Simakov et al. (2015) in Nature

Stable recombination hotspots in birds Singhal et al. (2015) in Science

Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration Liu et al. (2015) in Nature Communications

Methods/Data

A comparative study of RNA-seq analysis strategies Jänes et al. (2015) in Briefings in Bioinformatics

Assessing the consistency of public human tissue RNA-seq data sets Danielsson et al. (2015) in Briefings in Bioinformatics

Beyond fruit-flies: population genomic advances in non-Drosohpila arthropods Hasselmann et al. (2015) in Briefings in Functional Genomics

Miscellaneous

Hybridization and the origin of contagious asexuality in Daphnia pulex Xu et al. (2015) in Molecular Biology and Evolution

Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders Sahin and Sur (2015) in Science

The effects of life history and sexual selection on male and female plumage colouration Dale et al. (2015) in Nature

 

Weekly Roundup - Week of November 13, 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 13, 2015:

Sex Chromosomes

The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex systems Charlesworth (2015) in Evolutionary Applications

Genetics/Genomics

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens Galen et al. (2015) in PNAS

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia Tackney et al. (2015) in PNAS

Allelic variation of cytochrome P450s drives resistance to bednet insecticides in a major malaria vector Ibrahim et al. (2015) in PLoS Genetics

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence Sonay et al (2015) in Genome Research

GC skew defines distinct RNA polymerase pause sites in CpG island promoters Kellner et al. (2015) in Genome Research

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background Elvers et al. (2015) in Genome Research

Genetic adaptation to climate in white spruce involves small to moderate allele frequency shifts in functionally diverse genes Hornoy et al. (2015) in Genome Biology and Evolution

Calibrating the human mutation rate via ancestral recombination density in diploid genomes Lipson et al. (2015) in PLoS Genetics

The genomics of ecological vicariance in threespine stickleback fish Roesti et al. (2015) in Nature Communications

Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent Gallego Llorente et al. (2015) in Nature

Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding the LCT gene De Fanti et al. (2015) in American Journal of Physical Anthropology

CRISPR

This week, Genome Biology published a series of articles on CRISPR-Cas9:

Research Highlights

The Cpf1 CRISPR-Cas protein expands genome-editing tools Fagerlund et al. (2015) in Genome Biology

Pop in, pop out: a novel gene-targeting strategy for use with CRISPR-Cas9 Kühn and Chu (2015) in Genome Biology

CRISPR sabotage van der Oost and Brouns (2015) in Genome Biology

Reviews and Research Articles

Diversity of CRISPR-Cas immune systems and molecular machines Barrangou (2015) in Genome Biology

A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression Xi et al. (2015) in Genome Biology

CRISPR/Cas9-mediated viral interference in plants Ali et al. (2015) in Genome Biology

Methods

Dating tips for divergence-time estimation O'Reilly et al. (2015) in Trends in Genetics

A new Fst-based method to uncover local adaptation using environmental variables de Villemereuil and Gaggiotti (2015) in Methods in Ecology and Evolution

Miscellaneous

Why significant variables aren't automatically good predictors Lo et al. (2015) in PNAS

Evolution and dispersal of mammoths across the Northern Hemisphere Lister and Sher (2015) in Science

Public data archiving in ecology and evolution: how well are we doing? Roche et al. (2015) in PLoS Biology

Widespread exploitation of the honeybee by early Neolithic farmers Roffet-Salque et al. (2015) in Nature

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

Genomics

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

Methods

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

Miscellaneous

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

Weekly Roundup - October 23, 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 23, 2015 (apologies for the inconsistent formatting below, I'm still trying to get a handle on Wordpress's autoformatting behavior):

Sex Chromosomes

Genomics

Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems Patten et al (2015) in Molecular Ecology

Genetic variation and the de novo assembly of human genomes Chaisson et al. (2015) in Nature Reviews Genetics

Boharcek and Mansuy (2015) in Nature Reviews Genetics
Extremely high mutation rate of HIV-1 in vivo Cuevas et al. (2015) in PLoS Biology
DNA methylation landscapes of human fetal development Slieker et al. (2015) in PLoS Genetics
Schmich et al. (2015) in Genome Biology

Evolutionary Biology

Fitness benefits of mate choice for compatibility in a socially monogamous species Ihle et al. (2015) in PLoS Biology

Miyata et al. (2015) in Science Also see accompanying perspective: Towards a rapid and reversible male pill

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

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."
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."

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

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

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."

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"

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

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

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