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

Codecademy intro to command line

One of the challenges of learning (or teaching) the command line is that different operating systems  have default access to a command line terminal, whereas others will not (e.g., Windows versus Mac versus Linux). In a classroom session, this is especially frustrating, because time must be spent bringing all computers to the same starting position. Browser emulator Codecademy offers a fantastic alternative to this challenge because it has a terminal emulator directly in the browser, so you can practice and execute all the commands in the emulator, regardless of what operating system you have.


In practice Another feature of codecademy command line interface that I like is that tutorials have students first implement a command, then afterwards there is an explanation of what the command does. This allows students to practice first, observe what happens, and then read through a detailed explanation.

So far, students in the lab have liked this tutorial. We start with Codecademy, then work on installing local terminal/Linux-like environments (e.g., cygwin for people with Windows machines).

Intro to Python: Check out Codecademy

An undergraduate in the lab with no prior programming experience has tried out a couple tutorials for "Intro to Python." The student said that this introduction, from CodeAcademy has been the most accessible: https://www.codecademy.com/learn/python


Nov 6 update: One great feature of the codecademy is that it has a terminal emulator, so you can run all of your commands in the browser, and don't need to be concerned about what operating system you have.

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


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

Managing multiple Python environments using Anaconda

Because members of the lab are working with different versions of Python (e.g., 2.7 vs. 3.4), I thought I’d run through a quick and easy way to manage multiple Python environments on a single computer.  There are a number of options for doing this, but I recommend using Anaconda because it is very user-friendly.

Anaconda First of all, if you aren’t using Anaconda, you should check it out.  It’s a free, easy-to-use package and environment manager for Python.  You can download it here.  It, by default, installs to your home directory, allowing you to easily work with and manage Python in environments where you don’t have root privileges.  It also automatically installs over 100 packages, and allows you to install many more using the simple command:

conda install <packagename>

If you want to install a package that Anaconda doesn't handle, you can also use pip. The version of pip (simply another package manager for Python) that comes with the Anaconda distribution will install to Anaconda's directories, thereby making the package available in any of your Anaconda environments.  You can check the version of pip you’re using with the command:

which pip

If it says something like "~/anaconda/bin/pip", where ~ is your home directory, then you can install packages with the command:

pip install <packagename>

Creating and managing environments with Anaconda I'm going to assume you’ve already downloaded and installed the Python 2.7 version of Anaconda and you want to create an environment for Python 3.4.(this will work with any other version as well, just swap out the version in the commands below).  You can download Anaconda and find installation instructions here.

If you allowed Anaconda to install to your home directory and add itself to your PATH, typing the following command in your shell or terminal should point to the Anaconda distribution in your home directory:

which conda

(for me, this results in: /Users/thw/anaconda/bin/conda)

If this worked, then conda is in your PATH and you can simply enter the command to set up a new Python environment:

conda create -n python34 python=3.4 anaconda

where “-n python34” indicates the name you want to give the environment.  It can be anything you want: “-n boa_constrictor”, “-n python3.4”, etc.  I recommend something similar to python34, which is both easy to remember and informative. The "python=3.4" part indicates the version of Python you want to use in your environment, other examples might be "python=2.7" or "python=3.3"

Then, to activate the new environment, simply use the command:

(Linux, Mac OS X) source activate python34

(Windows) activate python34

You can easily deactivate the environment and revert to your root Python by typing

(Linux, Mac OS X) source deactivate

(Windows) I don't have a Windows computer to test this on, but according to Anaconda's documentation, try: deactivate python34

This, of course, is only scratching the surface of what you can do with Anaconda.  Be sure to check out the documentation for more information.

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


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

Hello, world!

Welcome to the official blog of the Wilson Sayres Lab!  This blog will primarily serve as a repository for links to scientific articles of interest to the lab and its members.  However, we'll also occasionally post in-depth discussions of articles, tutorials, links to resources, and other material relevant to genomics, bioinformatics, evolution, and programming.  Stay tuned, we should post our first round of articles later this week! -Tim