Pervasive Effects of Aging on Gene Expression in Wild Wolves
Gene expression levels change as an individual ages and responds to environmental conditions. With the exception of humans, such patterns have principally been studied under controlled conditions, overlooking the array of developmental and environmental influences that organisms encounter under conditions in which natural selection operates. We used high-throughput RNA sequencing (RNA-Seq) of whole blood to assess the relative impacts of social status, age, disease, and sex on gene expression levels in a natural population of gray wolves (Canis lupus). Our findings suggest that age is broadly associated with gene expressio...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Charruau, P., Johnston, R. A., Stahler, D. R., Lea, A., Snyder-Mackler, N., Smith, D. W., vonHoldt, B. M., Cole, S. W., Tung, J., Wayne, R. K. Tags: Discoveries Source Type: research
Adaptation by Deletogenic Replication Slippage in a Nascent Symbiont
As a consequence of population level constraints in the obligate, host-associated lifestyle, intracellular symbiotic bacteria typically exhibit high rates of molecular sequence evolution and extensive genome degeneration over the course of their host association. While the rationale for genome degeneration is well understood, little is known about the molecular mechanisms driving this change. To understand these mechanisms we compared the genome of Sodalis praecaptivus, a nonhost associated bacterium that is closely related to members of the Sodalis-allied clade of insect endosymbionts, with the very recently derived insec...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Clayton, A. L., Jackson, D. G., Weiss, R. B., Dale, C. Tags: Discoveries Source Type: research
Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements
Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Joly-Lopez, Z., Hoen, D. R., Blanchette, M., Bureau, T. E. Tags: Discoveries Source Type: research
Searching the Evolutionary Origin of Epithelial Mucus Protein Components--Mucins and FCGBP
The gel-forming mucins are large glycosylated proteins that are essential components of the mucus layers covering epithelial cells. Using novel methods of identifying mucins based on profile hidden Markov models, we have found a large number of such proteins in Metazoa, aiding in their classification and allowing evolutionary studies. Most vertebrates have 5–6 gel-forming mucin genes and the genomic arrangement of these genes is well conserved throughout vertebrates. An exception is the frog Xenopus tropicalis with an expanded repertoire of at least 26 mucins of this type. Furthermore, we found that the ovomucin prot...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Lang, T., Klasson, S., Larsson, E., Johansson, M. E. V., Hansson, G. C., Samuelsson, T. Tags: Discoveries Source Type: research
Target-Driven Positive Selection at Hot Spots of Scorpion Toxins Uncovers Their Potential in Design of Insecticides
In this study, we undertook a systematical molecular dissection of nearly all the PSSs newly characterized in the Mesobuthus α-toxin family and a two-residue insertion (19AlaPhe20) located within a positively selected loop via mutational analysis of α-like MeuNaTxα-5, one member affecting both insect and mammalian Nav channels. This allows to identify hot-spot residues on its functional face involved in interaction with the receptor site of Nav channels, which comprises two PSSs (Ile40 and Leu41) and the small insertion, both located on two spatially separated functional loops. Mutations at these hot-spot...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Zhu, L., Peigneur, S., Gao, B., Zhang, S., Tytgat, J., Zhu, S. Tags: Discoveries Source Type: research
How Common Is Parallel Intron Gain? Rapid Evolution Versus Independent Creation in Recently Created Introns in Daphnia
The evolutionary history of the spliceosomal introns that interrupt nuclear genes in eukaryotes has been debated for four decades. Positions of introns show a high degree of coincidence between various eukaryotes, implying either than many modern introns are very old and/or that intron creation is highly biased toward certain sites, leading to rampant parallel intron gain. A series of articles in this and other journals reported evidence for a strikingly high degree of parallel insertion of introns in different alleles of the water flea Daphnia pulex. Here, I report several new analyses of these data. Among the 23 loci rep...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Roy, S. W. Tags: Fast Track Source Type: research
Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution
LINE-1 (long interspersed element-1) retroelements are the only active autonomous endogenous retroelements in human genomes. Their retrotransposition activity has created close to 50% of the current human genome. Due to the apparent costs of this proliferation, host genomes have evolved multiple mechanisms to curb LINE-1 retrotransposition. Here, we investigate the evolution and function of the LINE-1 restriction factor APOBEC3A, a member of the APOBEC3 cytidine deaminase gene family. We find that APOBEC3A genes have evolved rapidly under diversifying selection in primates, suggesting changes in APOBEC3A have been recurren...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: McLaughlin, R. N., Gable, J. T., Wittkopp, C. J., Emerman, M., Malik, H. S. Tags: Fast Track Source Type: research
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Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
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Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
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Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
A Lesson from Wheat Evolution: Wild and Landraces Genetic Diversity the Key to Improving the Nutritional Value of Our Spaghetti Dish
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Are We What We Eat? Evidence of a Vegetarian Diet Permanently Shaping the Human Genome to Change Individual Risk of Cancer and Heart Disease
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
MEGA Evolutionary Software Re-Engineered to Handle Todays Big Data Demands
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we ar...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadlowski, L., Peters, R. S., Petersen, M., Meusemann, K., Liere, K., Wägele, J.-W., Misof, B., Bleidorn, C., Ohl, M., Niehuis, O. Tags: Resources Source Type: research
