journal
MENU ▼
Read by QxMD icon Read
search

Molecular Biology and Evolution

journal
https://www.readbyqxmd.com/read/28666382/the-structured-coalescent-and-its-approximations
#1
Nicola F Müller, David A Rasmussen, Tanja Stadler
Phylogeographic methods can help reveal the movement of genes between populations of organisms. This has been widely done to quantify pathogen movement between different host populations, the migration history of humans, and the geographic spread of languages or the gene flow between species using the location or state of samples alongside sequence data. Phylogenies therefore offer insights into migration processes not available from classic epidemiological or occurrence data alone. Phylogeographic methods have however several known shortcomings...
June 28, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28873957/more-to-the-bunch-study-finds-large-chromosomal-swaps-key-to-banana-domestication
#2
Joseph Caspermeyer
No abstract text is available yet for this article.
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28873956/the-estimation-of-alzheimer-s-disease-causative-genes-by-applying-an-evolutionary-approach-to-medicine
#3
Joseph Caspermeyer
No abstract text is available yet for this article.
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28873955/erratum
#4
(no author information available yet)
No abstract text is available yet for this article.
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28873954/bad-clade-deletion-supertrees-a-fast-and-accurate-supertree-algorithm
#5
Markus Fleischauer, Sebastian Böcker
Supertree methods merge a set of overlapping phylogenetic trees into a supertree containing all taxa of the input trees. The challenge in supertree reconstruction is the way of dealing with conflicting information in the input trees. Many different algorithms for different objective functions have been suggested to resolve these conflicts. In particular, there exist methods based on encoding the source trees in a matrix, where the supertree is constructed applying a local search heuristic to optimize the respective objective function...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28873953/genome-wide-dna-methylation-profiling-reveals-epigenetic-adaptation-of-stickleback-to-marine-and-freshwater-conditions
#6
Artem V Artemov, Nikolai S Mugue, Sergey M Rastorguev, Svetlana Zhenilo, Alexander M Mazur, Svetlana V Tsygankova, Eugenia S Boulygina, Daria Kaplun, Artem V Nedoluzhko, Yulia A Medvedeva, Egor B Prokhortchouk
The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution-adaptation to a freshwater environment. Although genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28666362/inference-of-causative-genes-for-alzheimer-s-disease-due-to-dosage-imbalance
#7
Mizuka Sekine, Takashi Makino
Copy number variations (CNVs) have recently drawn attention as an important genetic factor for diseases, especially common neuropsychiatric disorders including Alzheimer's disease (AD). Because most of the pathogenic CNV regions overlap with multiple genes, it has been challenging to identify the true disease-causing genes amongst them. Notably, a recent study reported that CNV regions containing ohnologs, which are dosage-sensitive genes, are likely to be deleterious. Utilizing the unique feature of ohnologs could be useful for identifying causative genes with pathogenic CNVs, however its effectiveness is still unclear...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28655155/evolution-of-cytochrome-c-oxidase-in-hypoxia-tolerant-sculpins-cottidae-actinopterygii
#8
Gigi Y Lau, Milica Mandic, Jeffrey G Richards
Vertebrate hypoxia tolerance can emerge from modifications to the oxygen (O2) transport cascade, but whether there is adaptive variation to O2 binding at the terminus of this cascade, mitochondrial cytochrome c oxidase (COX), is not known. In order to address the hypothesis that hypoxia tolerance is associated with enhanced O2 binding by mitochondria we undertook a comparative analysis of COX O2 kinetics across species of intertidal sculpins (Cottidae, Actinopterygii) that vary in hypoxia tolerance. Our analysis revealed a significant relationship between hypoxia tolerance (critical O2 tension of O2 consumption rate; Pcrit), mitochondrial O2 binding affinity (O2 tension at which mitochondrial respiration was half maximal; P50), and COX O2-binding affinity (apparent Michaelis-Menten constant for O2 binding to COX; Km,app O2)...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645195/mutational-biases-influence-parallel-adaptation
#9
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 overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory...
September 1, 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
#10
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 > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28595344/metabolism-and-the-evolution-of-social-behavior
#11
Kerry E Boyle, Hilary T Monaco, Maxime Deforet, Jinyuan Yan, Zhe Wang, Kyu Rhee, Joao B Xavier
How does metabolism influence social behavior? This fundamental question at the interface of molecular biology and social evolution is hard to address with experiments in animals, and therefore, we turned to a simple microbial system: swarming in the bacterium Pseudomonas aeruginosa. Using genetic engineering, we excised a locus encoding a key metabolic regulator and disrupted P. aeruginosa's metabolic prudence, the regulatory mechanism that controls expression of swarming public goods and protects this social behavior from exploitation by cheaters...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575451/intra-and-interspecific-variations-of-gene-expression-levels-in-yeast-are-largely-neutral-nei-lecture-smbe-2016-gold-coast
#12
Jian-Rong Yang, Calum J Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
It is commonly, although not universally, accepted that most intra and interspecific 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...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575409/giant-reverse-transcriptase-encoding-transposable-elements-at-telomeres
#13
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...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28575404/evolution-of-the-banana-genome-musa-acuminata-is-impacted-by-large-chromosomal-translocations
#14
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 intersubspecies 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...
September 1, 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
#15
Marco Galaverni, Romolo Caniglia, Luca Pagani, Elena Fabbri, Alessio Boattini, Ettore Randi
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring 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 analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28549159/a-non-photosynthetic-diatom-reveals-early-steps-of-reductive-evolution-in-plastids
#16
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
Nonphotosynthetic 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 nonphotosynthetic plastids of the apochlorotic diatom Nitzschia sp. NIES-3581. We found that these plastids have lost isopentenyl pyrophosphate biosynthesis and ribulose-1,5-bisphosphate carboxylase/oxygenase-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)...
September 1, 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
#17
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...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541480/alternative-evolutionary-paths-to-bacterial-antibiotic-resistance-cause-distinct-collateral-effects
#18
Camilo Barbosa, Vincent Trebosc, Christian Kemmer, Philip Rosenstiel, Robert Beardmore, Hinrich Schulenburg, Gunther 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...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#19
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...
September 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#20
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...
September 1, 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"