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Molecular Biology and Evolution

Yezi Xiang, Chien-Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, Hong Ma
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution...
November 17, 2016: Molecular Biology and Evolution
Helen K Alexander, Stephanie I Mayer, Sebastian Bonhoeffer
Mutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic population genetic models to allow an arbitrary distribution of mutation rate among individuals, either with or without inheritance...
November 11, 2016: Molecular Biology and Evolution
Yuh Chwen G Lee, Courtney Leek, Mia T Levine
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly...
November 11, 2016: Molecular Biology and Evolution
Beatriz Mello, Qiqing Tao, Koichiro Tamura, Sudhir Kumar
Ongoing advances in sequencing technology have led to an explosive expansion in the available molecular data for building increasingly larger and more comprehensive timetrees. However, Bayesian relaxed-clock approaches frequently used to infer these timetrees impose a large computational burden and discourage critical assessment of the robustness of inferred times to model assumptions, influence of calibrations, and selection of optimal data subsets. We analyzed eight large, recently published, empirical datasets to compare time estimates produced by RelTime (a non-Bayesian method) with those reported by using Bayesian approaches that require many priors and are computationally demanding...
November 11, 2016: Molecular Biology and Evolution
László G Nagy, Robert Riley, Philip J Bergmann, Krisztina Krizsán, Francis M Martin, Igor V Grigoriev, Dan Cullen, David S Hibbett
Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes...
November 10, 2016: Molecular Biology and Evolution
Richard G Dorrell, Christen M Klinger, Robert J Newby, Erin R Butterfield, Elisabeth Richardson, Joel B Dacks, Christopher J Howe, R Ellen R Nisbet, Chris Bowler
Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organisation of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons...
November 4, 2016: Molecular Biology and Evolution
Dong Dong, Ming Lei, Panyu Hua, Yi-Hsuan Pan, Shuo Mu, Guantao Zheng, Erli Pang, Kui Lin, Shuyi Zhang
Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats - the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats...
November 1, 2016: Molecular Biology and Evolution
Geeta N Eick, Jamie T Bridgham, Douglas P Anderson, Michael J Harms, Joseph W Thornton
Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR) - phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the inferred functions and mutational effects are robust to uncertainty about the ancestral sequence has not been studied systematically...
October 30, 2016: Molecular Biology and Evolution
Kai He, Akio Shinohara, Kristofer M Helgen, Mark S Springer, Xue-Long Jiang, Kevin L Campbell
The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them pose outstanding questions regarding the evolutionary history within the family, not only for living but also for fossil taxa. Here we investigate the phylogenetic relationships, divergence times, and biogeographic history of the family using 19 nuclear and two mitochondrial genes (~16 kb) from ~60% of described species representing all 17 genera...
October 30, 2016: Molecular Biology and Evolution
Jullien M Flynn, Frédéric J J Chain, Daniel J Schoen, Melania E Cristescu
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...
October 24, 2016: Molecular Biology and Evolution
John E Pool, Dylan T Braun, Justin B Lack
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude...
October 24, 2016: Molecular Biology and Evolution
Fernando Racimo, Davide Marnetto, Emilia Huerta-Sánchez
Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process - adaptive introgression - may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection...
October 18, 2016: Molecular Biology and Evolution
Lara R Arauna, Javier Mendoza-Revilla, Alex Mas-Sandoval, Hassan Izaabel, Asmahan Bekada, Soraya Benhamamouch, Karima Fadhlaoui-Zid, Pierre Zalloua, Garrett Hellenthal, David Comas
North Africa is characterized by its diverse cultural and linguistic groups and its genetic heterogeneity. Genomic data has shown an amalgam of components mixed since pre-Holocean times. Though no differences have been found in uniparental and classical markers between Berbers and Arabs, the two main ethnic groups in the region, the scanty genomic data available have highlighted the singularity of Berbers. We characterize the genetic heterogeneity of North African groups, focusing on the putative differences of Berbers and Arabs, and estimate migration dates...
October 15, 2016: Molecular Biology and Evolution
Marcus M Dillon, Way Sung, Robert Sebra, Michael Lynch, Vaughn S Cooper
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...
October 15, 2016: Molecular Biology and Evolution
Jaison Arivalagan, Teja Yarra, Benjamin Marie, Victoria A Sleight, Evelyne Duvernois-Berthet, Melody S Clark, Arul Marie, Sophie Berland
Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In this study the shell matrix proteins (SMPs) of four highly divergent bivalves (The Pacific oyster, Crassostrea gigas; the blue mussel, Mytilus edulis; the clam, Mya truncata and the king scallop, Pecten maximus) were analyzed in an identical fashion using proteomics pipeline...
October 15, 2016: Molecular Biology and Evolution
Yuan-Yuan Li, Zhen Liu, Fei-Yan Qi, Xin Zhou, Peng Shi
Molecular basis for mammalian echolocation has been receiving much concerns. Recent findings on the parallel evolution of prestin sequences among echolocating bats and toothed whales suggest that adaptations for high-frequency hearing have occurred during the evolution of echolocation. Here, we report that although the species tree for echolocating bats emitting echolocation calls with frequency modulated (FM) sweeps is paraphyletic, prestin exhibits similar functional changes between FM bats. Site-directed mutagenesis shows that the amino acid 308S in FM bats is responsible for the similar functional changes of prestin We strongly support that the occurrence of serine at position 308 is a case of hemiplasy, caused by incomplete lineage sorting of an ancestral polymorphism...
October 15, 2016: Molecular Biology and Evolution
Nicolas Rodrigue, Nicolas Lartillot
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and nonsynonymous 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 fitness; substitutions from high to low (low to high) fitness amino acids have comparatively low (high) rates...
October 15, 2016: Molecular Biology and Evolution
Susanne U Franssen, Nicholas H Barton, Christian Schlötterer
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...
October 3, 2016: Molecular Biology and Evolution
Benjamin C Haller, Philipp W Messer
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...
October 3, 2016: Molecular Biology and Evolution
Bryan D Clifton, Pablo Librado, Shu-Dan Yeh, Edwin S Solares, Daphne A Real, Suvini U Jayasekera, Wanting Zhang, Mijuan Shi, Ronni V Park, Robert D Magie, Hsiu-Ching Ma, Xiao-Qin Xia, Antonio Marco, Julio Rozas, José M Ranz
Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition...
October 3, 2016: Molecular Biology and Evolution
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