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Molecular Biology and Evolution

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https://www.readbyqxmd.com/read/29346651/bipartite-network-analysis-of-gene-sharings-in-the-microbial-world
#1
Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O McInerney, Philippe Lopez, Eric Bapteste
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346646/the-evolutionary-history-of-nebraska-deer-mice-local-adaptation-in-the-face-of-strong-gene-flow
#2
Susanne P Pfeifer, Stefan Laurent, Vitor C Sousa, Catherine R Linnen, Matthieu Foll, Laurent Excoffier, Hopi E Hoekstra, Jeffrey D Jensen
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346601/accumulation-of-mutational-load-at-the-edges-of-a-species-range
#3
Yvonne Willi, Marco Fracassetti, Stefan Zoller, Josh Van Buskirk
Why species have geographically restricted distributions is an unresolved question in ecology and evolutionary biology. Here we test a new explanation, that mutation accumulation due to small population size or a history of range expansion can contribute to restricting distributions by reducing population growth rate at the edge. We examined genomic diversity and mutational load across the entire geographic range of the North American plant Arabidopsis lyrata, including old, isolated populations predominantly at the southern edge and regions of postglacial range expansion at the northern and southern edges...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29340700/finding-their-inner-bird-using-modern-genomics-to-turn-alligator-scales-into-birdlike-feathers
#4
Joseph Caspermeyer
No abstract text is available yet for this article.
January 11, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29340696/from-southeast-asia-to-the-sewers-study-determines-new-geographic-origins-of-brown-rats
#5
Joseph Caspermeyer
No abstract text is available yet for this article.
January 11, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29340608/could-increasing-cancer-incidence-be-tied-to-human-adaptation-of-living-in-extreme-environments
#6
Joseph Caspermeyer
No abstract text is available yet for this article.
January 11, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29329419/a-single-mutation-unlocks-cascading-exaptations-in-the-origin-of-a-potent-pitviper-neurotoxin
#7
A Carl Whittington, Andrew J Mason, Darin R Rokyta
Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases (SVMP). Type II venoms are highly neurotoxic and lack SVMP expression and associated hemorrhagic activity. This dichotomy hinges on Mojave toxin (MTx), a phospholipase A2 (PLA2) based ᵝ-neurotoxin expressed in Type II venoms...
January 10, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29329426/a-practical-guide-to-estimating-the-heritability-of-pathogen-traits
#8
Venelin Mitov, Tanja Stadler
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens...
January 9, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29319812/deuterostome-genomics-lineage-specific-protein-expansions-that-enabled-chordate-muscle-evolution
#9
Jun Inoue, Noriyuki Satoh
Fish-like larvae were foundational to the chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree...
January 8, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29301006/datamonkey-2-0-a-modern-web-application-for-characterizing-selective-and-other-evolutionary-processes
#10
Steven Weaver, Stephen D Shank, Stephanie J Spielman, Michael Li, Spencer V Muse, Sergei L Kosakovsky Pond
Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data...
January 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29301001/the-gateway-from-near-into-remote-oceania-new-insights-from-genome-wide-data
#11
Irina Pugach, Ana T Duggan, D Andrew Merriwether, Françoise R Friedlaender, Jonathan S Friedlaender, Mark Stoneking
A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement...
January 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294063/the-4-celled-tetrabaena-socialis-nuclear-genome-reveals-the-essential-components-for-genetic-control-of-cell-number-at-the-origin-of-multicellularity-in-the-volvocine-lineage
#12
Jonathan Featherston, Yoko Arakaki, Erik R Hanschen, Patrick J Ferris, Richard E Michod, Bradley J S C Olson, Hisayoshi Nozaki, Pierre M Durand
Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage - the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes...
December 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294047/substitution-rates-predicted-by-stability-constrained-models-of-protein-evolution-are-not-consistent-with-empirical-data
#13
María José Jimenez, Miguel Arenas, Ugo Bastolla
Protein structures strongly influence molecular evolution. In particular, the evolutionary rate of a protein site depends on the number of its native contacts. Stability constrained models of protein evolution consider this influence of protein structure on evolution by predicting the effect of mutations on the stability of the native state, but they currently neglect how mutations affect the protein structure. These models predict that buried protein sites with more native contacts are more constrained by natural selection and less variable, as observed...
December 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294021/phylogenomic-data-yield-new-and-robust-insights-into-the-phylogeny-and-evolution-of-weevils
#14
Seunggwan Shin, Dave J Clarke, Alan R Lemmon, Emily Moriarty Lemmon, Alexander L Aitken, Stephanie Haddad, Brian D Farrell, Adriana E Marvaldi, Rolf G Oberprieler, Duane D McKenna
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in previous studies, but with some interesting exceptions...
December 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29309671/avoidance-of-toxic-misfolding-and-protein-stability-do-not-explain-the-sequence-constraints-of-highly-expressed-proteins
#15
Germán Plata, Dennis Vitkup
The avoidance of cytotoxic effects associated with protein misfolding has been proposed as a dominant constraint on the sequence evolution and molecular clock of highly expressed proteins. Recently, Leuenberger et al. developed an elegant experimental approach to measure protein thermal stability at the proteome scale. The collected data allow us to rigorously test the predictions of the misfolding avoidance hypothesis that highly expressed proteins have evolved to be more stable, and that maintaining thermodynamic stability significantly constrains their evolution...
December 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29272536/complex-relationships-between-chromatin-accessibility-sequence-divergence-and-gene-expression-in-a-thaliana
#16
C M Alexandre, J R Urton, K Jean-Baptiste, J L Huddleston, M W Dorrity, J T Cuperus, A M Sullivan, F Bemm, D Jolic, A A Arsovski, A Thompson, J L Nemhauser, S Fields, D Weigel, K L Bubb, C Queitsch
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcriptions factors across animal species highlighted a fundamental conundrum: transcriptions factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide...
December 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294071/genetic-architecture-and-selection-of-chinese-cattle-revealed-by-whole-genome-resequencing
#17
Chugang Mei, Hongcheng Wang, Qijun Liao, Lizhong Wang, Gong Cheng, Hongbao Wang, Chunping Zhao, Shancen Zhao, Jiuzhou Song, Xuanmin Guang, George E Liu, Anning Li, Xueli Wu, Chongzhi Wang, Xiaodong Fang, Xin Zhao, Stephen B Smith, Wucai Yang, Wanqiang Tian, Linsheng Gui, Yingying Zhang, Rodney A Hill, Zhongliang Jiang, Yaping Xin, Cunling Jia, Xiuzhu Sun, Shuhui Wang, Huanming Yang, Jian Wang, Wenjuan Zhu, Linsen Zan
The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analysed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle (RAN) genomes, 11 Japanese black cattle (JBC) genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus...
December 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294066/immune-signaling-networks-sources-of-robustness-and-constrained-evolvability-during-coevolution
#18
Edward Schrom, Joaquin M Prada, Andrea L Graham
Defense against infection incurs costs as well as benefits that are expected to shape the evolution of optimal defense strategies. In particular, many theoretical studies have investigated contexts favoring constitutive versus inducible defenses. However, even when one immune strategy is theoretically optimal, it may be evolutionarily unachievable. This is because evolution proceeds via mutational changes to the protein interaction networks underlying immune responses, not by changes to an immune strategy directly...
December 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29294020/experimental-determination-and-prediction-of-the-fitness-effects-of-random-point-mutations-in-the-biosynthetic-enzyme-hisa
#19
Erik Lundin, Po-Cheng Tang, Lionel Guy, Joakim Näsvall, Dan I Andersson
The distribution of fitness effects (DFE) of mutations is a factor of fundamental importance in evolutionary biology. We determined the DFE of 510 mutants that each carried between 1 to 10 mutations (synonymous and non-synonymous) in the hisA gene, encoding an essential enzyme in the L-histidine biosynthesis pathway of Salmonella enterica. For the full set of mutants, the distribution was bimodal with many apparently neutral mutations and many lethal mutations. For a subset of 81 single, non-synonymous mutants most mutations appeared neutral at high expression levels, whereas at low expression levels only a few mutations were neutral...
December 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29253197/genetic-mapping-reveals-an-anthocyanin-biosynthesis-pathway-gene-potentially-influencing-evolutionary-divergence-between-two-subspecies-of-scarlet-gilia-ipomopsis-aggregata
#20
Brandon E Campitelli, Amanda M Kenney, Robin Hopkins, Jacob Soule, John T Lovell, Thomas E Juenger
Immense floral trait variation has likely arisen as an adaptation to attract pollinators. Different pollinator syndromes-suites of floral traits that attract specific pollinator functional groups-are repeatedly observed across closely related taxa or divergent populations. The observation of these trait syndromes suggests that pollinators use floral cues to signal the underlying nectar reward, and that complex trait combinations may persist and evolve through genetic correlations. Here, we explore pollinator preferences and the genetic architecture of floral divergence using an extensive genetic mapping study in the hybrid zone of two Ipomopsis aggregata subspecies that exhibit a hummingbird and a hawkmoth pollinator syndrome...
December 15, 2017: Molecular Biology and Evolution
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