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Molecular Biology and Evolution

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https://www.readbyqxmd.com/read/28100792/evolutionary-history-of-the-asian-horned-frogs-megophryinae-integrative-approaches-to-timetree-dating-in-the-absence-of-a-fossil-record
#1
Stephen Mahony, Nicole M Foley, S D Biju, Emma C Teeling
Molecular dating studies typically need fossils to calibrate the analyses. Unfortunately, the fossil record is extremely poor or presently non-existent for many species groups, rendering such dating analysis difficult. One such group is the Asian horned frogs (Megophryinae). Sampling all generic nomina, we combined a novel ∼5kb dataset composed of four nuclear and three mitochondrial gene fragments to produce a robust phylogeny, with an extensive external morphological study to produce a working taxonomy for the group...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100791/the-reliability-and-stability-of-an-inferred-phylogenetic-tree-from-empirical-data
#2
Yukako Katsura, Craig E Stanley, Sudhir Kumar, Masatoshi Nei
The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100790/genome-wide-analysis-in-brazilians-reveals-highly-differentiated-native-american-genome-regions
#3
Josyf C Mychaleckyj, Alexandre Havt, Uma Nayak, Relana Pinkerton, Emily Farber, Patrick Concannon, Aldo A Lima, Richard L Guerrant
Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared to the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh)...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100789/complex-evolutionary-history-of-the-mammalian-histone-h1-1-h1-5-gene-family
#4
Inma Ponte, Devani Romero, Daniel Yero, Pedro Suau, Alicia Roque
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions. We have examined the evolution of the H1.1 to H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100788/genomic-infectious-disease-epidemiology-in-partially-sampled-and-ongoing-outbreaks
#5
Xavier Didelot, Christophe Fraser, Jennifer Gardy, Caroline Colijn
Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28096304/antibiotic-cycling-and-antibiotic-mixing-which-one-best-mitigates-antibiotic-resistance
#6
R E Beardmore, R Pena-Miller, F Gori, J Iredell
Can we exploit our burgeoning understanding of molecular evolution to slow the progress of drug resistance? One role of an infection clinician is exactly that: to foresee trajectories to resistance during antibiotic treatment and to hinder that evolutionary course. But can this be done at a hospital-wide scale? Clinicians and theoreticians tried to when they proposed two conicting behavioural strategies that are expected to curb resistance evolution in the clinic, these are known as 'antibiotic cycling' and 'antibiotic mixing'...
January 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28096303/down-regulation-of-epas1-transcription-and-genetic-adaptation-of-tibetans-to-high-altitude-hypoxia
#7
Yi Peng, Chaoying Cui, Yaoxi He, Ouzhuluobu, Hui Zhang, Deying Yang, Qu Zhang, Bianbazhuoma, Lixin Yang, Yibo He, Kun Xiang, Xiaoming Zhang, Sushil Bhandari, Peng Shi, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Yongyue Pan, Cirenyangji, Baimayangji, Gonggalanzi, Caijuan Bai, Bianba, Basang, Ciwangsangbu, Shuhua Xu, Hua Chen, Shimin Liu, Tianyi Wu, Xuebin Qi, Bing Su
Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans...
January 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087782/mutation-supply-and-relative-fitness-shape-the-genotypes-of-ciprofloxacin-resistant-escherichia-coli
#8
Douglas L Huseby, Franziska Pietsch, Gerrit Brandis, Linnéa Garoff, Angelica Tegehall, Diarmaid Hughes
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087781/deleterious-variants-in-asian-rice-and-the-potential-cost-of-domestication
#9
Qingpo Liu, Yongfeng Zhou, Peter L Morrell, Brandon S Gaut
Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a 'cost of domestication'. Here we investigated the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two varieties (japonica and indica) and their wild relative (O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087780/oncogenes-without-a-neighboring-tumor-suppressor-gene-are-more-prone-to-amplification
#10
William K K Wu, Xiangchun Li, Xiansong Wang, Rudin Z W Dai, Alfred S L Cheng, Maggie H T Wang, Thomas Kwong, Tai C Chow, Jun Yu, Matthew T V Chan, Sunny H Wong
Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of non-cancer genes, suggesting that oncogenes and TSGs tend to be in close physical proximity in the human genome. Such relationship was conserved in mouse and drosophila. Pan-cancer analysis using data from The Cancer Genome Atlas indicated that oncogenes without a nearby TSG are more prone to amplification...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087779/genomics-of-parallel-experimental-evolution-in-drosophila
#11
J L Graves, K L Hertweck, M A Phillips, M V Han, L G Cabral, T T Barter, L F Greer, M K Burke, L D Mueller, M R Rose
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly forty-year laboratory radiation featuring three selection regimes, each shared by ten populations for up to 837 generations, with moderately large effective population sizes. Each of three sets of ten populations that shared a selection regime consist of five populations that have long been maintained under that selection regime, paired with five populations that had only recently been subjected to that selection regime...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087778/no-evidence-for-phylostratigraphic-bias-impacting-inferences-on-patterns-of-gene-emergence-and-evolution
#12
Tomislav Domazet-Lošo, Anne-Ruxandra Carvunis, M Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087777/genome-sequencing-reveals-the-origin-of-the-allotetraploid-arabidopsis-suecica
#13
Polina Yu Novikova, Takashi Tsuchimatsu, Samson Simon, Viktoria Nizhynska, Viktor Voronin, Robin Burns, Olga M Fedorenko, Svante Holm, Torbjörn Säll, Elisa Prat, William Marande, Vincent Castric, Magnus Nordborg
Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual - a bona fide speciation event. The extent to which this happens is not known...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#14
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087775/rapid-expansion-of-immune-related-gene-families-in-the-house-fly-musca-domestica
#15
Timothy B Sackton, Brian P Lazzaro, Andrew G Clark
The house fly, Musca domestica, occupies an unusual diversity of potentially septic niches compared to other sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies upon bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087774/the-origin-of-mitochondrial-cristae-from-alphaproteobacteria
#16
Sergio A Muñoz-Gómez, Jeremy G Wideman, Andrew J Roger, Claudio H Slamovits
Mitochondria are the respiratory organelles of eukaryotes and their evolutionary history is deeply intertwined with that of eukaryotes. The compartmentalization of respiration in mitochondria occurs within cristae, whose evolutionary origin has remained unclear. Recent discoveries, however, have revived the old notion that mitochondrial cristae could have had a pre-endosymbiotic origin. Mitochondrial cristae are likely homologous to the intracytoplasmic membranes (ICMs) used by diverse alphaproteobacteria for harnessing energy...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087773/rwty-r-we-there-yet-an-r-package-for-examining-convergence-of-bayesian-phylogenetic-analyses
#17
LETTER
Dan L Warren, Anthony J Geneva, Robert Lanfear
Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#18
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087771/genome-wide-convergence-during-evolution-of-mangroves-from-woody-plants
#19
Shaohua Xu, Ziwen He, Zixiao Guo, Zhang Zhang, Gerald J Wyckoff, Anthony Greenberg, Chung-I Wu, Suhua Shi
When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia and other stressors in the new habitat might have affected both genomic features and protein structures...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087770/mitochondrial-mutation-rate-spectrum-and-heteroplasmy-in-caenorhabditis-elegans-spontaneous-mutation-accumulation-lines-of-differing-population-size
#20
Anke Konrad, Owen Thompson, Robert H Waterston, Donald G Moerman, Peter D Keightley, Ulfar Bergthorsson, Vaishali Katju
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10 and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection...
January 12, 2017: Molecular Biology and Evolution
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