SMBE Editors and Council
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Associate Editors
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Cover
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Large-Scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honey Bees
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Jasper, W. C., Linksvayer, T. A., Atallah, J., Friedman, D., Chiu, J. C., Johnson, B. R. Tags: Errata Source Type: research
A Comprehensive, High-Resolution Map of a Genes Fitness Landscape
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Firnberg, E., Labonte, J. W., Gray, J. J., Ostermeier, M. Tags: Errata Source Type: research
Scientists Explore a Master Genetic Switch That Plays a Key Role in Energy Metabolism and Human Brain Evolution and Function
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
First Genome-Wide Mutational Map of Macaques a Boon for Evolutionary Studies
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
Although population genetics studies have significantly accelerated the evolutionary and functional interrogations of genes and regulations, limited polymorphism data are available for rhesus macaque, the model animal closely related to human. Here, we report the first genome-wide effort to identify and visualize the population genetics profile in rhesus macaque. On the basis of the whole-genome sequencing of 31 independent macaque animals, we profiled a comprehensive polymorphism map with 46,146,548 sites. The allele frequency for each polymorphism site, the haplotype structure, as well as multiple population genetics par...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Zhong, X., Peng, J., Shen, Q. S., Chen, J.-Y., Gao, H., Luan, X., Yan, S., Huang, X., Zhang, S.-J., Xu, L., Zhang, X., Tan, B. C.-M., Li, C.-Y. Tags: Resource Source Type: research
"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements
Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their e...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Marcovitz, A., Jia, R., Bejerano, G. Tags: Methods Source Type: research
Robust Estimation of Evolutionary Distances with Information Theory
Methods for measuring genetic distances in phylogenetics are known to be sensitive to the evolutionary model assumed. However, there is a lack of established methodology to accommodate the trade-off between incorporating sufficient biological reality and avoiding model overfitting. In addition, as traditional methods measure distances based on the observed number of substitutions, their tend to underestimate distances between diverged sequences due to backward and parallel substitutions. Various techniques were proposed to correct this, but they lack the robustness against sequences that are distantly related and of unequa...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Cao, M. D., Allison, L., Dix, T. I., Boden, M. Tags: Methods Source Type: research
Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp
Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other popu...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Chen, C., Liu, Z., Pan, Q., Chen, X., Wang, H., Guo, H., Liu, S., Lu, H., Tian, S., Li, R., Shi, W. Tags: Discoveries Source Type: research
Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster
Clines in chromosomal inversion polymorphisms—presumably driven by climatic gradients—are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo, and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summ...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Kapun, M., Fabian, D. K., Goudet, J., Flatt, T. Tags: Discoveries Source Type: research
Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster
Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance fo...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Schrider, D. R., Hahn, M. W., Begun, D. J. Tags: Discoveries Source Type: research
Gap Gene Regulatory Dynamics Evolve along a Genotype Network
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as "system drift." System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is e...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Crombach, A., Wotton, K. R., Jimenez-Guri, E., Jaeger, J. Tags: Discoveries Source Type: research
p53 mRNA and p53 Protein Structures Have Evolved Independently to Interact with MDM2
The p53 tumor suppressor and its key regulator MDM2 play essential roles in development, ageing, cancer, and cellular stress responses in mammals. Following DNA damage, MDM2 interacts with p53 mRNA in an ATM kinase-dependent fashion and stimulates p53 synthesis, whereas under normal conditions, MDM2 targets the p53 protein for degradation. The peptide- and RNA motifs that interact with MDM2 are encoded by the same conserved BOX-I sequence, but how these interactions have evolved is unknown. Here, we show that a temperature-sensitive structure in the invertebrate Ciona intestinalis (Ci) p53 mRNA controls its interaction wit...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Karakostis, K., Ponnuswamy, A., Fusee, L. T. S., Bailly, X., Laguerre, L., Worall, E., Vojtesek, B., Nylander, K., Fahraeus, R. Tags: Discoveries Source Type: research
