SMBE Editors and Council
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Associate Editors
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Cover
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Ballesteros, J. A., Hormiga, G. Tags: Erratum Source Type: research
The Telltale Heart of Chordate Evolution: New Study Shows Model Organism Making Do with Less
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
New Insights into Coral Bleaching
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
No One Is an Island: The History of Human Genetic Ancestry in Madagascar
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
The Call of the Sea: Mammalian Transition Back to the Sea Occurred Three Times Independently and Involved Adaptation from Hundreds of Genes
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Researchers Show Nature Conserves Its Most Vital DNA by Multitasking
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast
Interlocus gene conversion (IGC) homogenizes repeats. While genomes can be repeat-rich, the evolutionary importance of IGC is poorly understood. Additional statistical tools for characterizing it are needed. We propose a composite likelihood strategy for incorporating IGC into widely-used probabilistic models for sequence changes that originate with point mutation. We estimated the percentage of nucleotide substitutions that originate with an IGC event rather than a point mutation in 14 groups of yeast ribosomal protein-coding genes, and found values ranging from 20% to 38%. We designed and applied a procedure to determine...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Ji, X., Griffing, A., Thorne, J. L. Tags: Methods Source Type: research
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how m...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: du Plessis, L., Leventhal, G. E., Bonhoeffer, S. Tags: Methods Source Type: research
Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems
Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess similar sets of selenoproteins, Sec biosynthesis is more similar among archaea and eukaryotes. However, SECIS elements are completely different in the three domains of life. Here, we analyze the archaeon Lokiarchaeota that resolves the relationships among Sec insertion systems. This organism has selenoproteins ...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Mariotti, M., Lobanov, A. V., Manta, B., Santesmasses, D., Bofill, A., Guigo, R., Gabaldon, T., Gladyshev, V. N. Tags: Discoveries Source Type: research
Genomic Response to Selection for Predatory Behavior in a Mammalian Model of Adaptive Radiation
If genetic architectures of various quantitative traits are similar, as studies on model organisms suggest, comparable selection pressures should produce similar molecular patterns for various traits. To test this prediction, we used a laboratory model of vertebrate adaptive radiation to investigate the genetic basis of the response to selection for predatory behavior and compare it with evolution of aerobic capacity reported in an earlier work. After 13 generations of selection, the proportion of bank voles (Myodes [=Clethrionomys] glareolus) showing predatory behavior was five times higher in selected lines than in contr...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Konczal, M., Koteja, P., Orlowska-Feuer, P., Radwan, J., Sadowska, E. T., Babik, W. Tags: Discoveries Source Type: research
The Evolution of Photoperiod-Insensitive Flowering in Sorghum, A Genomic Model for Panicoid Grasses
Of central importance in adapting plants of tropical origin to temperate cultivation has been selection of daylength-neutral genotypes that flower early in the temperate summer and take full advantage of its long days. A cross between tropical and temperate sorghums [Sorghum propinquum (Kunth) Hitchc.xS. bicolor (L.) Moench], revealed a quantitative trait locus (QTL), FlrAvgD1, accounting for 85.7% of variation in flowering time under long days. Fine-scale genetic mapping placed FlrAvgD1 on chromosome 6 within the physically largest centiMorgan in the genome. Forward genetic data from "converted" sorghums validated the QTL...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Cuevas, H. E., Zhou, C., Tang, H., Khadke, P. P., Das, S., Lin, Y.-R., Ge, Z., Clemente, T., Upadhyaya, H. D., Hash, C. T., Paterson, A. H. Tags: Discoveries Source Type: research
Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate
The bloom of genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metabolic gene network (RA-MGN) in the chordate Oikopleura dioica as a case study, we combine approaches of comparative genomics, phylogenetics, biochemistry, and developmental biology to investigate the mutational robustness associated to biased patterns of gene loss. We demonstrate the...
Source: Molecular Biology and Evolution - August 16, 2016 Category: Molecular Biology Authors: Marti-Solans, J., Belyaeva, O. V., Torres-Aguila, N. P., Kedishvili, N. Y., Albalat, R., Canestro, C. Tags: Discoveries Source Type: research
