Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Levin, R. A., Beltran, V. H., Hill, R., Kjelleberg, S., McDougald, D., Steinberg, P. D., van Oppen, M. J. H. Tags: Errata Source Type: research
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Moyers, B., Zhang, J. Tags: Errata Source Type: research
Bad Seeds: How the Parental Lineage May Determine Viability in Tomato Hybrids
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Reconstructing the Sixth Century Plague from a Victim
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Where the Buffalo Have Evolutionarily Roamed
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data
Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift by assuming allele frequencies evolve deterministically i...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Jewett, E. M., Steinrücken, M., Song, Y. S. Tags: Methods Source Type: research
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint
The mutation–selection model of coding sequence evolution has received renewed attention for its use in estimating site-specific amino acid propensities and selection coefficient distributions. Two computationally tractable mutation–selection inference frameworks have been introduced: One framework employs a fixed-effects, highly parameterized maximum likelihood approach, whereas the other employs a random-effects Bayesian Dirichlet Process approach. While both implementations follow the same model, they appear to make distinct predictions about the distribution of selection coefficients. The fixed-effects fram...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Spielman, S. J., Wilke, C. O. Tags: Methods Source Type: research
Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites
We present an alternative to BEB called smoothed bootstrap aggregation (SBA), which bootstraps site patterns from an alignment of protein coding DNA sequences to accommodate the uncertainty in the parameter estimates. We show that deriving the correction for parameter uncertainty from the data in hand, in combination with kernel smoothing techniques, improves site specific inference of positive selection. We compare BEB to SBA by simulation and real data analysis. Simulation results show that SBA balances accuracy and power at least as well as BEB, and when parameter estimates are unstable, the performance gap between BEB ...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Mingrone, J., Susko, E., Bielawski, J. Tags: Methods Source Type: research
Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data
This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Tripathi, A., Gupta, K., Khare, S., Jain, P. C., Patel, S., Kumar, P., Pulianmackal, A. J., Aghera, N., Varadarajan, R. Tags: Discoveries Source Type: research
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution
How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Mendizabal, I., Shi, L., Keller, T. E., Konopka, G., Preuss, T. M., Hsieh, T.-F., Hu, E., Zhang, Z., Su, B., Yi, S. V. Tags: Discoveries Source Type: research
Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds
Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviable seeds due to endosperm failure and arrested embryo development. Based on differences of seed size in reciprocal hybrid crosses and developmental evidence implicating endosperm failure, we hypothesized that perturbed genomic imprinting is involved in this strong postzygotic bar...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Florez-Rueda, A. M., Paris, M., Schmidt, A., Widmer, A., Grossniklaus, U., Städler, T. Tags: Discoveries Source Type: research
Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa
A specialized insulin was recently found in the venom of a fish-hunting cone snail, Conus geographus. Here we show that many worm-hunting and snail-hunting cones also express venom insulins, and that this novel gene family has diversified explosively. Cone snails express a highly conserved insulin in their nerve ring; presumably this conventional signaling insulin is finely tuned to the Conus insulin receptor, which also evolves very slowly. By contrast, the venom insulins diverge rapidly, apparently in response to biotic interactions with prey and also possibly the cones’ own predators and competitors. Thus, the inw...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Safavi-Hemami, H., Lu, A., Li, Q., Fedosov, A. E., Biggs, J., Showers Corneli, P., Seger, J., Yandell, M., Olivera, B. M. Tags: Discoveries Source Type: research
A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim
We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Feldman, M., Harbeck, M., Keller, M., Spyrou, M. A., Rott, A., Trautmann, B., Scholz, H. C., Päffgen, B., Peters, J., McCormick, M., Bos, K., Herbig, A., Krause, J. Tags: Discoveries Source Type: research
Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar
Deleterious alleles are expected to be purged by purifying selection or maintained at low frequency. However, many additional evolutionary forces may shape the pattern of deleterious mutations across the genome and among populations, including selection, hitchhiking, recombination, and demographic history. We used exome capture data to estimate the genome-wide distribution of deleterious alleles across natural populations of the model tree black cottonwood (Populus trichocarpa). Although deleterious alleles were on average present at low frequency suggesting purifying selection, they were preferentially enriched both withi...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Zhang, M., Zhou, L., Bawa, R., Suren, H., Holliday, J. A. Tags: Discoveries Source Type: research
A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)
Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as d...
Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Derelle, R., Lopez-Garcia, P., Timpano, H., Moreira, D. Tags: Discoveries Source Type: research
