journal
MENU ▼
Read by QxMD icon Read
search

Molecular Biology and Evolution

journal
https://www.readbyqxmd.com/read/28651357/using-viral-gene-sequences-to-compare-and-explain-the-heterogeneous-spatial-dynamics-of-virus-epidemics
#1
Simon Dellicour, Rebecca Rose, Nuno Rodrigues Faria, Luiz Fernando Pereira Vieira, Hervé Bourhy, Marius Gilbert, Philippe Lemey, Oliver G Pybus
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We have compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and detect and compare those environmental factors that impact the velocity of viral spread in continuous spatial landscapes...
June 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645195/mutational-biases-influence-parallel-adaptation
#2
Arlin Stoltzfus, David M McCandlish
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled 2 sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645168/genomic-reconstruction-of-the-history-of-native-sheep-reveals-the-peopling-patterns-of-nomads-and-the-expansion-of-early-pastoralism-in-east-asia
#3
Yong-Xin Zhao, Ji Yang, Feng-Hua Lv, Xiao-Ju Hu, Xing-Long Xie, Min Zhang, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Ling Ren, Feng Wang, EEr Hehua, Juha Kantanen, Johannes Arjen Lenstra, Jian-Lin Han, Meng-Hua Li
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in more than 1,000 modern samples. Population genomic analyses combined with archaeological records and historical ethnic demographics data revealed genetic signatures of their origins, secondary expansions and admixtures, thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28637217/experimental-support-that-natural-selection-has-shaped-the-latitudinal-distribution-of-mitochondrial-haplotypes-in-australian-drosophila-melanogaster
#4
M Florencia Camus, Jonci N Wolff, Carla M Sgrò, Damian K Dowling
Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude or climatic regions across species distributions, led to the hypothesis that thermal selection has played a role in shaping standing variation in the mitochondrial DNA (mtDNA) sequence. This hypothesis, however, remains controversial, and requires evidence that the distribution of haplotypes observed in nature corresponds with the capacity of these haplotypes to confer differences in thermal tolerance...
June 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28637270/in-planta-recapitulation-of-isoprene-synthases-evolution-from-ocimene-synthases
#5
Mingai Li, Jia Xu, Alberto Algarra Alarcon, Silvia Carlin, Enrico Barbaro, Luca Cappellin, Violeta Velikova, Urska Vrhovsek, Francesco Loreto, Claudio Varotto
Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated.We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases...
June 16, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28595347/genetic-history-of-xinjiang-s-uyghurs-suggests-bronze-age-multiple-way-contacts-in-eurasia
#6
Qidi Feng, Yan Lu, Xumin Ni, Kai Yuan, Yajun Yang, Xiong Yang, Chang Liu, Haiyi Lou, Zhilin Ning, Yuchen Wang, Dongsheng Lu, Chao Zhang, Ying Zhou, Meng Shi, Lei Tian, Xiaoji Wang, Xi Zhang, Jing Li, Asifullah Khan, Yaqun Guan, Kun Tang, Sijia Wang, Shuhua Xu
The Uyghur people residing in Xinjiang, a territory located in the far west of China and crossed by the Silk Road, are a key ethnic group for understanding the history of human dispersion in Eurasia. Here we assessed the genetic structure and ancestry of 951 Xinjiang's Uyghurs (XJU) representing 14 geographical subpopulations. We observed a southwest and northeast differentiation within XJU, which was likely shaped jointly by the Tianshan Mountains, which traverses from east to west as a natural barrier, and gene flow from both east and west directions...
June 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28595344/metabolism-and-the-evolution-of-social-behavior
#7
Kerry E Boyle, Hilary T Monaco, Maxime Deforet, Jinyuan Yan, Zhe Wang, Kyu Rhee, Joao Xavier
HASH(0x3a615a8)
June 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28595308/pneumococcal-capsule-synthesis-locus-cps-as-evolutionary-hotspot-with-potential-to-generate-novel-serotypes-by-recombination
#8
Rafal J Mostowy, Nicholas J Croucher, Nicola De Maio, Claire Chewapreecha, Susannah J Salter, Paul Turner, David M Aanensen, Stephen D Bentley, Xavier Didelot, Christophe Fraser
Diversity of the polysaccharide capsule in Streptococcus pneumoniae -- main surface antigen and the target of the currently used pneumococcal vaccines -- constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates...
June 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28591857/adaptive-patterns-of-mitogenome-evolution-are-associated-with-the-loss-of-shell-scutes-in-turtles
#9
Tibisay Escalona, Cameron J Weadick, Agostinho Antunes
The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration...
June 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575409/giant-reverse-transcriptase-encoding-transposable-elements-at-telomeres
#10
Irina R Arkhipova, Irina A Yushenova, Fernando Rodriguez
Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif...
May 30, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575404/evolution-of-the-banana-genome-musa-acuminata-is-impacted-by-large-chromosomal-translocations
#11
Guillaume Martin, Françoise Carreel, Olivier Coriton, Catherine Hervouet, Céline Cardi, Paco Derouault, Danièle Roques, Frédéric Salmon, Mathieu Rouard, Julie Sardos, Karine Labadie, Franc-Christophe Baurens, Angélique D'Hont
Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in inter-subspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny...
May 30, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575451/intra-and-inter-specific-variations-of-gene-expression-levels-in-yeast-are-largely-neutral
#12
Jian-Rong Yang, Calum J Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments...
May 29, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28549194/disentangling-timing-of-admixture-patterns-of-introgression-and-phenotypic-indicators-in-a-hybridizing-wolf-population
#13
M Galaverni, R Caniglia, L Pagani, E Fabbri, A Boattini, E Randi
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favouring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analysed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture...
May 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28549159/a-non-photosynthetic-diatom-reveals-early-steps-of-reductive-evolution-in-plastids
#14
Ryoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe-G Maier, John M Archibald, Yuji Inagaki
Non-photosynthetic plastids retain important biological functions and are indispensable for cell viability. However, the detailed processes underlying the loss of plastidal functions other than photosynthesis remain to be fully understood. In this study, we used transcriptomics, subcellular localization, and phylogenetic analyses to characterize the biochemical complexity of the non-photosynthetic plastids of the apochlorotic diatom Nitzschia sp. NIES-3581. We found that these plastids have lost isopentenyl pyrophosphate (IPP) biosynthesis and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-based carbon fixation but have retained various proteins for other metabolic pathways, including amino acid biosynthesis, and a portion of the Calvin-Benson cycle comprised only of glycolysis/gluconeogenesis, and the reductive pentose phosphate pathway (rPPP)...
May 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541576/rapidly-evolving-toll-3-4-genes-encode-male-specific-toll-like-receptors-in-drosophila
#15
Tera C Levin, Harmit S Malik
Animal Toll-like receptors (TLRs) have evolved through a pattern of duplication and divergence. Whereas mammalian TLRs directly recognize microbial ligands, Drosophila Tolls bind endogenous ligands downstream of both developmental and immune signaling cascades. Here, we find that most Toll genes in Drosophila evolve slowly with little gene turnover (gains/losses), consistent with their important roles in development and indirect roles in microbial recognition. In contrast, we find that the Toll-3/4 genes have experienced an unusually rapid rate of gene gains and losses, resulting in lineage-specific Toll-3/4s and vastly different gene repertoires among Drosophila species, from zero copies (e...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#16
Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541480/alternative-evolutionary-paths-to-bacterial-antibiotic-resistance-cause-distinct-collateral-effects
#17
C Barbosa, V Trebosc, C Kemmer, P Rosenstiel, R Beardmore, H Schulenburg, G Jansen
When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To date, the presence and molecular basis of collateral sensitivity has only been studied in few bacterial species and is unknown for opportunistic human pathogens such as Pseudomonas aeruginosa. In the present study, we assessed patterns of collateral effects by experimentally evolving 160 independent populations of P...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535261/recruitment-of-a-lineage-specific-virulence-regulatory-pathway-promotes-intracellular-infection-by-a-plant-pathogen-experimentally-evolved-into-a-legume-symbiont
#18
Delphine Capela, Marta Marchetti, Camille Clérissi, Anthony Perrier, Dorian Guetta, Carine Gris, Marc Valls, Alain Jauneau, Stéphane Cruveiller, Eduardo P C Rocha, Catherine Masson-Boivin
Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#19
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28525580/a-new-formulation-of-random-genetic-drift-and-its-application-to-the-evolution-of-cell-populations
#20
Yuxin Chen, Ding Tong, Chung-I Wu
Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When drift is defined by the WF model, it becomes stronger as the population size, N, decreases. However, the intensity of competition decreases when N decreases and, hence, drift might become weaker...
May 19, 2017: Molecular Biology and Evolution
journal
journal
28957
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"