New methods to calculate concordance factors for phylogenomic datasets, bioRxiv, 2018-12-05
Summary We introduce and implement two measures for quantifying genealogical concordance in phylogenomic datasets the gene concordance factor (gCF) and the site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of decisive gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. Availability and Implementation An easy to use implementation and tutorial is freely available in the IQ-TREE software (httpwww.iqtree.org). Supplementary information Data are available at httpsdoi.org10.5281zenodo.1949290
biorxiv bioinformatics 100-200-users 2018Non-academic employability of life science PhDs the importance of training beyond the bench, bioRxiv, 2018-12-05
ABSTRACTTo better understand how PhD graduates have prepared for the non-academic job market, we surveyed life science PhD and postdoctoral graduates from the University of Toronto who were employed in non-academic sectors. We also surveyed life science PhD and postdoctoral trainees to assess their engagement in career preparation activities. PhD professionals employed in non-academic sectors had engaged in various career preparation activities during their training. Some activities had a higher perceived impact on the path to employment than others. Trainees had also engaged in such activities, but those rated by professionals as having a highly positive impact on their path to employment were engaged in by only a minority of trainees. The proportion of trainees who wished to work in a non-academic sector was higher among those who were closer to program completion. Like professionals, many trainees reported facing barriers to pursuing career development activities. Our findings suggest that PhD trainees seeking to work in non-academic sectors should engage in career preparation activities, particularly those that involve experiential learning. By supporting co-curricular programming and reducing barriers to participation in career development activities, academic administrators and faculty have the opportunity to support trainees’ professional development beyond the laboratory.
biorxiv scientific-communication-and-education 0-100-users 2018Posture controls mechanical tuning in the black widow spider mechanosensory system, bioRxiv, 2018-12-05
Spiders rely on mechanical vibration sensing for sexual signalling, prey capture and predator evasion. The sensory organs underlying vibration detection, called slit sensilla, resemble cracks in the spider's exoskeleton, and are distributed all over the spider body. Those crucial to sensing web- and other substrate-borne vibrations are called lyriform organs and are densely distributed around leg joints. It has been shown that forces that cause bending at leg joints also activate these lyriform organs. Little is known of how the biomechanics of the body of a freely-suspended spider in its natural posture interact with vibrations introduced into the body and how this affects vibration perception. Female black widow spiders, in particular, have a striking body-form; their long thin legs support a large pendulous abdomen. Here, we show that in their natural posture, the large abdominal mass of black widow females, interacts with the spring-like behaviour of their leg joints and determines the mechanical behaviour of different leg joints. Furthermore, we find that adopting different body postures enables females to alter both the level and tuning of the mechanical input to lyriform organs. Therefore, we suggest that posture may be used to flexibly and reversibly focus attention to different classes or components of web vibration. Postural effects thus emphasize the dynamic loop of interactions between behaviour and perception, i.e. between 'brain' and body.
biorxiv animal-behavior-and-cognition 100-200-users 2018RNase L reprograms translation by widespread mRNA turnover escaped by antiviral mRNAs, bioRxiv, 2018-12-05
SUMMARYIn response to foreign and endogenous double-stranded RNA (dsRNA), protein kinase R (PKR) and ribonuclease L (RNase L) reprogram translation in mammalian cells. PKR inhibits translation initiation through eIF2α phosphorylation, which triggers stress granule (SG) formation and promotes translation of stress responsive mRNAs. The mechanisms of RNase L-driven translation repression, its contribution to SG assembly, and its regulation of dsRNA stress-induced mRNAs are unknown. We demonstrate that RNase L drives translational shut-off in response to dsRNA by promoting widespread turnover of mRNAs. This alters stress granule assembly and reprograms translation by only allowing for the translation of mRNAs resistant to RNase L degradation, including numerous antiviral mRNAs such as IFN-β. Individual cells differentially activate dsRNA responses revealing variation that can affect cellular outcomes. This identifies bulk mRNA degradation and the resistance of antiviral mRNAs as the mechanism by which RNaseL reprograms translation in response to dsRNA.
biorxiv immunology 0-100-users 2018Geographic variation and bias in polygenic scores of complex diseases and traits in Finland, bioRxiv, 2018-12-04
AbstractPolygenic scores (PS) are becoming a useful tool to identify individuals with high genetic risk for complex diseases and several projects are currently testing their utility for translational applications. It is also tempting to use PS to assess whether genetic variation can explain a part of the geographic distribution of a phenotype. However, it is not well known how population genetic properties of the training and target samples affect the geographic distribution of PS. Here, we evaluate geographic differences, and related biases, of PS in Finland with geographically well-defined sample of 2,376 individuals from the National FINRISK study. First, we detect geographic differences in PS for coronary artery disease (CAD), rheumatoid arthritis, schizophrenia, waits-hip ratio (WHR), body-mass index (BMI) and height, but not for Crohn’s disease or ulcerative colitis. Second, we use height as a model trait to thoroughly assess the possible population genetic biases in PS and apply similar approaches to the other phenotypes. Most importantly, we detect suspiciously large accumulation of geographic differences for CAD, WHR, BMI and height, suggesting bias arising from population genetic structure rather than from a direct genotype-phenotype association. This work demonstrates how sensitive the geographic patterns of current PS are for small biases even within relatively homogenous populations and provides simple tools to identify such biases. A thorough understanding of the effects of population genetic structure on PS is essential for translational applications of PS.
biorxiv genetics 100-200-users 2018Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia, bioRxiv, 2018-12-04
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001002, as the Yamal strains. Despite the remoteness of Yamal from Yakutia, whole genome sequence analysis showed that the B.Br.001002 strains are very closely related. The two other strains contribute to two different branches of A.Br.008011, one of the remarkable polytomies described so far in B. anthracis population. The geographic distribution of the strains belonging to this polytomy is suggesting that this polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
biorxiv microbiology 100-200-users 2018