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Molecular biology and evolution [journal]
- Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Feb 27.
The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20(th) century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in recent decades. Recently, complete P. infestans mitogenome sequences from 19(th)-century herbarium specimens were shown to belong to a unique lineage (HERB-1) predicted to be rare or extinct in modern times. We report 44 additional P. infestans mitogenomes: four from 19(th)-century Europe, three from 1950s U.K. and 34 from modern populations across the New World. We use phylogenetic analyses to identify the HERB-1 lineage in modern populations from both Mexico and South America, and to demonstrate distinct mitochondrial haplotypes were present in 19(th)-century Europe, with this lineage initially diversifying 75 years before the first reports of potato late blight.
- Subscription page. [Journal Article]
- Mol Biol Evol 2014 Mar; 31(3):i4.
- SMBE Editors and Council. [Journal Article]
- Mol Biol Evol 2014 Mar; 31(3):i3.
- Associate editors. [Journal Article]
- Mol Biol Evol 2014 Mar; 31(3):i2.
- Cover. [Journal Article]
- Mol Biol Evol 2014 Mar; 31(3):i1.
- Fight or flight and the evolution of pain. [Journal Article]
- Mol Biol Evol 2014 Mar; 31(3):764.
- A comprehensive, high-resolution map of a gene's fitness landscape. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Feb 23.
Mutations are central to evolution, providing the genetic variation upon which selection acts. A mutation's effect on the suitability of a gene to perform a particular function (gene fitness) can be positive, negative, or neutral. Knowledge of the distribution of fitness effects (DFE) of mutations is fundamental for understanding evolutionary dynamics, molecular-level genetic variation, complex genetic disease, the accumulation of deleterious mutations, and the molecular clock. We present comprehensive DFEs for point and codon mutants of the E. coli TEM-1 β-lactamase gene and missense mutations in the TEM-1 protein. These DFEs provide insight into the inherent benefits of the genetic code's architecture, support for the hypothesis that mRNA stability dictates codon usage at the beginning of genes, an extensive framework for understanding protein mutational tolerance, and evidence that mutational effects on protein thermodynamic stability shape the DFE. Contrary to prevailing expectations, we find that deleterious effects of mutation primarily arise from a decrease in specific protein activity and not protein cellular levels.
- Illuminating the base of the annelid tree using transcriptomics. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Feb 23.
Annelida is one of three animal groups possessing segmentation and is central in considerations about the evolution of different character traits. It has even been proposed that the bilaterian ancestor resembled an annelid. However, a robust phylogeny of Annelida, especially with respect to the basal relationships, has been lacking. Our study based on transcriptomic data comprising 68,750 - 170,497 amino acid sites from 305 - 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, Magelonidae in the basal part of the tree. Myzostomida, which have been indicated to belong to the basal radiation as well, are now found deeply nested within Annelida as sister group to Errantia in most analyses. Based on our reconstruction of a robust annelid phylogeny, we show that the basal branching taxa include a huge variety of life-styles such as tube-dwelling and deposit-feeding, endobenthic and burrowing, tubicolous and filter-feeding, as well as errant and carnivorous forms. Ancestral character state reconstruction suggests that the ancestral annelid possessed a pair of either sensory or grooved palps, bicellular eyes, biramous parapodia bearing simple chaeta and lacked nuchal organs. Since the oldest fossil of Annelida is reported for Sipuncula (520 Mya), we infer that the early diversification of annelids took place at least in the Lower Cambrian.
- Simulation of Genome-wide Evolution under Heterogeneous Substitution models and Complex Multispecies Coalescent Histories. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Feb 19.
Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequencies across genes and rate variation among sites and regions can lead to severe underestimation of the global dN/dS values. The program SGWE -Simulation of Genome-Wide Evolution- is freely available from http://code.google.com/p/sgwe-project/, including extensive documentation and detailed examples.
- Unprecedented heterogeneity in the synonymous substitution rate within a plant genome. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Feb 19.
The synonymous substitution rate varies widely among species, but it is generally quite stable within a genome due to the absence of strong selective pressures. In plants, plastid genes tend to evolve faster than mitochondrial genes, rate variation among species generally correlates between the mitochondrial and plastid genomes, and few examples of intragenomic rate heterogeneity exist. To study the extent of substitution rate variation between and within plant organellar genomes, we sequenced the complete mitochondrial and plastid genomes from the bugleweed, Ajuga reptans, which was previously shown to exhibit rate heterogeneity for several mitochondrial genes. Substitution rates were accelerated specifically in the mitochondrial genome, which contrasts with correlated plastid and mitochondrial rate changes in most other angiosperms. Strikingly, we uncovered a 340-fold range of synonymous substitution rate variation among Ajuga mitochondrial genes. This is by far the largest amount of synonymous rate heterogeneity ever reported for a genome, but the evolutionary forces driving this phenomenon are unclear. Selective effects on synonymous sites in plant mitochondria are generally weak and thus unlikely to generate such unprecedented intragenomic rate heterogeneity. Quickly evolving genes are not clustered in the genome, arguing against localized hypermutation, although it is possible that they were clustered ancestrally given the high rate of genomic rearrangement in plant mitochondria. Mutagenic retroprocessing, involving error-prone reverse transcription and genomic integration of mature transcripts, is hypothesized as another potential explanation.