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Molecular Biology and Evolution

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https://www.readbyqxmd.com/read/29788493/how-the-central-american-seaway-and-an-ancient-northern-passage-affected-flatfish-diversification
#1
Lisa Byrne, François Chapleau, Stéphane Aris-Brosou
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788479/repeated-cis-regulatory-tuning-of-a-metabolic-bottleneck-gene-during-evolution
#2
Meihua Christina Kuang, Jacek Kominek, William G Alexander, Jan-Fang Cheng, Russell L Wrobel, Chris Todd Hittinger
Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788330/the-evolution-of-gene-expression-underlying-vision-loss-in-cave-animals
#3
David B Stern, Keith A Crandall
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#4
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788252/translation-the-universal-structural-core-of-life
#5
Chad R Bernier, Anton S Petrov, Nicholas A Kovacs, Petar Penev, Loren Dean Williams
The Universal Gene Set of Life (UGSL) is common to genomes of all extant organisms. The UGSL is small, consisting of less than 100 genes, and is dominated by genes encoding the translation system. Here we extend the search for biological universality to three dimensions. We characterize and quantitate the universality of structure of macromolecules that are common to all of life. We determine that around 90% of prokaryotic rRNA forms a common core, which are the structural and functional foundation of rRNAs of all cytoplasmic ribosomes...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29771364/broad-genomic-sampling-reveals-a-smut-pathogenic-ancestry-of-the-fungal-clade-ustilaginomycotina
#6
Teeratas Kijpornyongpan, Stephen J Mondo, Kerrie Barry, Laura Sandor, Juna Lee, Anna Lipzen, Jasmyn Pangilinan, Kurt LaButti, Matthieu Hainaut, Bernard Henrissat, Igor V Grigoriev, Joseph W Spatafora, M Catherine Aime
Ustilaginomycotina is home to a broad array of fungi including important plant pathogens collectively called smut fungi. Smuts are biotrophs that produce characteristic perennating propagules called teliospores, one of which, Ustilago maydis, is a model genetic organism. Broad exploration of smut biology has been hampered by limited phylogenetic resolution of Ustilaginiomycotina as well as an overall lack of genomic data for members of this subphylum. In this study, we sequenced eight Ustilaginomycotina genomes from previously unrepresented lineages, deciphered ordinal-level phylogenetic relationships for the subphylum, and performed comparative analyses...
May 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29762743/lipidome-evolution-in-mammalian-tissues
#7
Ekaterina Khrameeva, Ilia Kurochkin, Katarzyna Bozek, Patrick Giavalisco, Philipp Khaitovich
Lipids are essential structural and functional components of cells. Little is known, however, about the evolution of lipid composition in different tissues. Here, we report a large-scale analysis of the lipidome evolution in six tissues of 32 species representing primates, rodents and bats. While changes in genes' sequence and expression accumulate proportionally to the phylogenetic distances, less than two percent of the lipidome evolves this way. Yet, lipids constituting this two percent cluster in specific functions shared among all tissues...
May 11, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29746697/adaptation-of-s-cerevisiae-to-fermented-food-environments-reveals-remarkable-genome-plasticity-and-the-footprints-of-domestication
#8
Jean-Luc Legras, Virginie Galeote, Frédéric Bigey, Carole Camarasa, Souhir Marsit, Thibault Nidelet, Isabelle Sanchez, Arnaud Couloux, Julie Guy, Ricardo Franco-Duarte, Marcet-Houben Marina, Toni Gabaldon, Dorit Schuller, José Paulo Sampaio, Sylvie Dequin
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups...
May 8, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29722887/mega-x-molecular-evolutionary-genetics-analysis-across-computing-platforms
#9
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura
The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www...
May 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29722880/extensive-differential-splicing-underlies-phenotypically-plastic-aphid-morphs
#10
Mary E Grantham, Jennifer A Brisson
Phenotypic plasticity results in a diversity of phenotypes from a single genotype in response to environmental cues. To understand the molecular basis of phenotypic plasticity, studies have focused on differential gene expression levels between environmentally-determined phenotypes. The extent of alternative splicing differences among environmentally-determined phenotypes has largely been understudied. Here we study alternative splicing differences among plastically-produced morphs of the pea aphid using RNA-sequence data...
May 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29722831/the-neutral-theory-in-light-of-natural-selection
#11
Andrew D Kern, Matthew W Hahn
In this perspective we evaluate the explanatory power of the neutral theory of molecular evolution, 50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.
May 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29722819/non-equilibrium-neutral-theory-for-hitchhikers
#12
Yoko Satta, Naoko T Fujito, Naoyuki Takahata
Selective sweep is a phenomenon of reduced variation at presumably neutrally evolving sites (hitchhikers) in the genome that is caused by the spread of a selected allele at a linked focal site, and is widely used to test for action of positive selection. Nonetheless, selective sweep may also provide an unprecedented opportunity for studying non-equilibrium properties of the neutral variation itself. We have demonstrated this possibility in relation to ancient selective sweep for modern human-specific changes and ongoing selective sweep for local population-specific changes...
May 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29722884/de-novo-mutations-resolve-disease-transmission-pathways-in-clonal-malaria
#13
Seth N Redmond, Bronwyn M MacInnis, Selina Bopp, Amy K Bei, Daouda Ndiaye, Daniel L Hartl, Dyann F Wirth, Sarah K Volkman, Daniel E Neafsey
Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages...
May 1, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29718509/evolution-of-darwin-s-peloric-gloxinia-sinningia-speciosa-is-caused-by-a-null-mutation-in-a-pleiotropic-tcp-gene
#14
Yang Dong, Jing Liu, Peng-Wei Li, Chao-Qun Li, Tian-Feng Lü, Xia Yang, Yin-Zheng Wang
Unlike most crops, which were domesticated through long periods of selection by ancient humans, horticultural plants were primarily domesticated through intentional selection over short time periods. The molecular mechanisms underlying the origin and spread of novel traits in the domestication process have remained largely unexplored in horticultural plants. Gloxinia (Sinningia speciosa), whose attractive peloric flowers influenced the thoughts of Darwin, have been cultivated since the early 19th century, but its origin and genetic basis are currently unknown...
April 27, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29718454/neutral-theory-in-cancer-cell-population-genetics
#15
Atsushi Niida, Watal M Iwasaki, Hideki Innan
No abstract text is available yet for this article.
April 27, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29718409/the-puzzle-of-hiv-neutral-and-selective-evolution
#16
Thomas Leitner
HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell types and using the same replication machinery year after year. Hence, one would think that most mutations that HIV accumulates are neutral. But the picture is more complicated than that...
April 27, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29701800/ancestral-function-and-diversification-of-a-horizontally-acquired-oomycete-carboxylic-acid-transporter
#17
F R Savory, D S Milner, D C Miles, T A Richards
Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonise new environments. However, few studies have characterised the functions of HGT genes experimentally or examined post-acquisition functional divergence. Here we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi...
April 25, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29697849/chance-finiteness-and-history
#18
Naruya Saitou
Importance of chance, finiteness, and history in evolution is pointed out with special reference to the neutral theory.
April 24, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29697819/divergence-of-non-coding-regulatory-elements-explains-gene-phenotype-differences-between-human-and-mouse-orthologous-genes
#19
Seong Kyu Han, Donghyo Kim, Heetak Lee, Inhae Kim, Sanguk Kim
Mice have been widely used as a model organism to investigate human gene-phenotype relationships based on a conjecture that orthologous genes generally perform similar functions and are associated with similar phenotypes. However, phenotypes associated with orthologous genes often turn out to be quite different between human and mouse. Herein, we devised a method to quantitatively compare phenotypes annotations associated with mouse models and human. Using semantic similarity comparisons, we identified orthologous genes with different phenotype annotations, of which the similarity score is on a par with that of random gene pairs...
April 24, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29688481/neutral-theory-and-rapidly-evolving-viral-pathogens
#20
Simon D W Frost, Brittany Rife Magalis, Sergei L Kosakovsky Pond
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance...
April 24, 2018: Molecular Biology and Evolution
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