Treasurers Report for Financial Year (FY) 2015: Prepared by Juliette de Meaux, SMBE Treasurer
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Tags: Society Reports Source Type: research
Society for Molecular Biology and Evolution, Council and Business Meetings, 2016, Gold Coast Australia
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: McInerney, J. O. Tags: Society Reports Source Type: research
Ancient Hominid "Hanky Panky" Also Influenced Spread of STIs
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Rotting Away: Getting at the Evolutionary Root of Wood Decay
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Blind as Bats: Bat Echolocation Study Reveals Key Evolutionary Trade-Offs with Other Senses
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
SLiM 2: Flexible, Interactive Forward Genetic Simulations
Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite for this goal is the ability to model realistic evolutionary scenarios and predict their expected patterns in genomic data. To that end, we present SLiM 2: an evolutionary simulation framework that combines a powerful, fast engine for forward population genetic simulations with the capability of modeling a wide variety of complex evolutionary scenarios. SLiM achieves this flexibility through scriptability, which provides control over most aspects of the simulated evol...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Haller, B. C., Messer, P. W. Tags: Resources Source Type: research
CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes
Closely spaced clusters of tandemly duplicated genes (CTDGs) contribute to the diversity of many phenotypes, including chemosensation, snake venom, and animal body plans. CTDGs have traditionally been identified subjectively as genomic neighborhoods containing several gene duplicates in close proximity; however, CTDGs are often highly variable with respect to gene number, intergenic distance, and synteny. This lack of formal definition hampers the study of CTDG evolutionary dynamics and the discovery of novel CTDGs in the exponentially growing body of genomic data. To address this gap, we developed a novel homology-based a...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Ortiz, J. F., Rokas, A. Tags: Methods Source Type: research
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and non-synonymous substitutions. Another modeling approach, known as the mutation–selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some approaches allowing for heterogeneity in these patterns across codon sites. Under such a model, substitutions at a given position occur at the neutral or nearly neutral rate when they are synonymous, or when they correspond to replacements between amino acids of similar fi...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Rodrigue, N., Lartillot, N. Tags: Methods Source Type: research
Reconstruction of Haplotype-Blocks Selected during Experimental Evolution
The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify sel...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Franssen, S. U., Barton, N. H., Schlötterer, C. Tags: Methods Source Type: research
Spontaneous Mutation Accumulation in Daphnia pulex in Selection-Free vs. Competitive Environments
Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics, and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone. By sequencing 30 genomes and implementing a series of validation steps that informed the bioinforma...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Flynn, J. M., Chain, F. J. J., Schoen, D. J., Cristescu, M. E. Tags: Discoveries Source Type: research
Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment
The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L (pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their ...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Xu, J., Li, J.-T., Jiang, Y., Peng, W., Yao, Z., Chen, B., Jiang, L., Feng, J., Ji, P., Liu, G., Liu, Z., Tai, R., Dong, C., Sun, X., Zhao, Z.-X., Zhang, Y., Wang, J., Li, S., Zhao, Y., Yang, J., Sun, X., Xu, P. Tags: Discoveries Source Type: research
Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites
We describe 32 independent coding mutations including common mutations outside the kelch13 propeller associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ~0.079. ART-R allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The frequency with which adaptive alleles arise is determined by the rate of mutation and the population size. Two factors drive this soft sweep: (1) multiple kelch13 amino-acid mutations confer resistance providing a large mutational target—we es...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Anderson, T. J. C., Nair, S., McDew-White, M., Cheeseman, I. H., Nkhoma, S., Bilgic, F., McGready, R., Ashley, E., Pyae Phyo, A., White, N. J., Nosten, F. Tags: Discoveries Source Type: research
Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects
Accurate knowledge of the mutation rate provides a base line for inferring expected rates of evolution, for testing evolutionary hypotheses and for estimation of key parameters. Advances in sequencing technology now permit direct estimates of the mutation rate from sequencing of close relatives. Within insects there have been three prior such estimates, two in nonsocial insects (Drosophila: 2.8 x 10–9 per bp per haploid genome per generation; Heliconius: 2.9 x 10–9) and one in a social species, the honeybee (3.4 x 10–9). Might the honeybee’s rate be ~20% higher because it has an exceptionally high r...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Liu, H., Jia, Y., Sun, X., Tian, D., Hurst, L. D., Yang, S. Tags: Discoveries Source Type: research
Fitness Trade-Offs Lead to Suppressor Tolerance in Yeast
Genetic variation among individuals within a population provides the raw material for phenotypic diversity upon which natural selection operates. Some given variants can act on multiple standing genomic variations simultaneously and release previously inaccessible phenotypes, leading to increased adaptive potential upon challenging environments. Previously, we identified such a variant related to a tRNA nonsense suppressor in yeast. When introduced into other genetic backgrounds, the suppressor led to an increased population phenotypic variance on various culture conditions, conferring background and environment specific s...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Hou, J., Schacherer, J. Tags: Discoveries Source Type: research
Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri
The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural...
Source: Molecular Biology and Evolution - January 3, 2017 Category: Molecular Biology Authors: Dillon, M. M., Sung, W., Sebra, R., Lynch, M., Cooper, V. S. Tags: Discoveries Source Type: research
