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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 2 of 8

  1. Content type: Research article

    Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that ...

    Authors: Robin Koch, Anne Kupczok, Karina Stucken, Judith Ilhan, Katrin Hammerschmidt and Tal Dagan

    Citation: BMC Evolutionary Biology 2017 17:209

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  2. Content type: Research article

    Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in siz...

    Authors: Shixia Xu, Xiaohui Sun, Xu Niu, Zepeng Zhang, Ran Tian, Wenhua Ren, Kaiya Zhou and Guang Yang

    Citation: BMC Evolutionary Biology 2017 17:206

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  3. Content type: Research article

    The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in rapid adaptation t...

    Authors: Sabrina M. McNew, Daniel Beck, Ingrid Sadler-Riggleman, Sarah A. Knutie, Jennifer A. H. Koop, Dale H. Clayton and Michael K. Skinner

    Citation: BMC Evolutionary Biology 2017 17:183

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  4. Content type: Research article

    Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domesticatio...

    Authors: Yun-Mei Wang, Hai-Bo Xu, Ming-Shan Wang, Newton Otieno Otecko, Ling-Qun Ye, Dong-Dong Wu and Ya-Ping Zhang

    Citation: BMC Evolutionary Biology 2017 17:192

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  5. Content type: Research article

    Pollen tube growth and fertilization are key processes in angiosperm sexual reproduction. The transmitting tract (TT) of Nicotiana tabacum controls pollen tube growth in part by secreting pistil extensin-like pro...

    Authors: Andrzej K. Noyszewski, Yi-Cheng Liu, Koichiro Tamura and Alan G. Smith

    Citation: BMC Evolutionary Biology 2017 17:186

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  6. Content type: Research article

    The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human imig...

    Authors: Ana Paula Schaan, Lorenna Costa, Diego Santos, Antonio Modesto, Marcos Amador, Camile Lopes, Sílvia Helena Rabenhorst, Raquel Montenegro, Bruno D. A. Souza, Thayson Lopes, France Keiko Yoshioka, Giovanny Pinto, Vivian Silbiger and Ândrea Ribeiro-dos-Santos

    Citation: BMC Evolutionary Biology 2017 17:185

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  7. Content type: Research Article

    Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococc...

    Authors: Nicolas M. Schmelling, Robert Lehmann, Paushali Chaudhury, Christian Beck, Sonja-Verena Albers, Ilka M. Axmann and Anika Wiegard

    Citation: BMC Evolutionary Biology 2017 17:169

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  8. Content type: Research Article

    The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including ...

    Authors: Henrike Indrischek, Sonja J. Prohaska, Vsevolod V. Gurevich, Eugenia V. Gurevich and Peter F. Stadler

    Citation: BMC Evolutionary Biology 2017 17:163

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  9. Content type: Research Article

    The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (ln...

    Authors: Alberto Lopez-Ezquerra, Mark C. Harrison and Erich Bornberg-Bauer

    Citation: BMC Evolutionary Biology 2017 17:155

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  10. Content type: Research article

    Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication. The...

    Authors: Pere Puigbò, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf and Eugene V. Koonin

    Citation: BMC Evolutionary Biology 2017 17:94

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  11. Content type: Research article

    NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a ...

    Authors: Ana Caroline Paiva Gandara, André Torres, Ana Cristina Bahia, Pedro L. Oliveira and Renata Schama

    Citation: BMC Evolutionary Biology 2017 17:92

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    The Erratum to this article has been published in BMC Evolutionary Biology 2017 17:196

  12. Content type: Research article

    Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surf...

    Authors: Mark Lynch, Thomas A. Walsh, Izabela Marszalowska, Andrew E. Webb, Micheál MacAogain, Thomas R. Rogers, Henry Windle, Dermot Kelleher, Mary J. O’Connell and Christine E. Loscher

    Citation: BMC Evolutionary Biology 2017 17:90

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    The Erratum to this article has been published in BMC Evolutionary Biology 2017 17:135

  13. Content type: Research article

    Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive o...

    Authors: Gloria I. Giraldo-Calderón, Michael J. Zanis and Catherine A. Hill

    Citation: BMC Evolutionary Biology 2017 17:84

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  14. Content type: Research article

    Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarian...

    Authors: Astrid Schuster, Jose V. Lopez, Leontine E. Becking, Michelle Kelly, Shirley A. Pomponi, Gert Wörheide, Dirk Erpenbeck and Paco Cárdenas

    Citation: BMC Evolutionary Biology 2017 17:82

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  15. Content type: Research Article

    Changing environmental conditions pose a challenge for the survival of species. To meet this challenge organisms adapt their phenotype by physiological regulation (phenotypic plasticity) or by evolving. Regula...

    Authors: Thomas D. Cuypers, Jacob P. Rutten and Paulien Hogeweg

    Citation: BMC Evolutionary Biology 2017 17:60

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  16. Content type: Research article

    In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diver...

    Authors: Myriam Croze, Andreas Wollstein, Vedran Božičević, Daniel Živković, Wolfgang Stephan and Stephan Hutter

    Citation: BMC Evolutionary Biology 2017 17:15

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  17. Content type: Research article

    Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the dev...

    Authors: Isabelle R. Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara and Mathias Choquer

    Citation: BMC Evolutionary Biology 2016 16:252

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  18. Content type: Research article

    Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive ...

    Authors: Anita J. Porath-Krause, Autum N. Pairett, Davide Faggionato, Bhagyashree S. Birla, Kannan Sankar and Jeanne M. Serb

    Citation: BMC Evolutionary Biology 2016 16:250

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  19. Content type: Research article

    Bacterial endosymbionts are found across the eukaryotic kingdom and profoundly impacted eukaryote evolution. In many endosymbiotic associations with vertically inherited symbionts, highly complementary metabol...

    Authors: Jorge Morales, Sofia Kokkori, Diana Weidauer, Jarrod Chapman, Eugene Goltsman, Daniel Rokhsar, Arthur R. Grossman and Eva C. M. Nowack

    Citation: BMC Evolutionary Biology 2016 16:247

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  20. Content type: Research article

    From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short af...

    Authors: Patricia Marrero, Khaled K. Abu-Amero, Jose M. Larruga and Vicente M. Cabrera

    Citation: BMC Evolutionary Biology 2016 16:246

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  21. Content type: Research article

    Although bats are natural reservoirs of many pathogens, few studies have been conducted on the genetic variation and detection of selection in major histocompatibility complex (MHC) genes. These genes are crit...

    Authors: Arielle Salmier, Benoit de Thoisy, Brigitte Crouau-Roy, Vincent Lacoste and Anne Lavergne

    Citation: BMC Evolutionary Biology 2016 16:229

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  22. Content type: Research article

    In mouse ES cells, the function of Sox2 is essential for the maintenance of pluripotency. Since the Sox-family of transcription factors are well conserved in the animal kingdom, addressing the evolutionary ori...

    Authors: Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka

    Citation: BMC Evolutionary Biology 2016 16:173

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  23. Content type: Research article

    Transitions from marine to intertidal and terrestrial habitats resulted in a significant adaptive radiation within the Panpulmonata (Gastropoda: Heterobranchia). This clade comprises several groups that invade...

    Authors: Pedro E. Romero, Alexander M. Weigand and Markus Pfenninger

    Citation: BMC Evolutionary Biology 2016 16:164

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  24. Content type: Research Article

    The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in...

    Authors: Christian Rödelsperger, Kevin Menden, Vahan Serobyan, Hanh Witte and Praveen Baskaran

    Citation: BMC Evolutionary Biology 2016 16:165

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  25. Content type: Research article

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing ...

    Authors: Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C. Willison, Richard E. Lenski, Orkun S. Soyer and Dominique Schneider

    Citation: BMC Evolutionary Biology 2016 16:163

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  26. Content type: Research article

    A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartil...

    Authors: Ramray Bhat, Mahul Chakraborty, Tilmann Glimm, Thomas A. Stewart and Stuart A. Newman

    Citation: BMC Evolutionary Biology 2016 16:162

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  27. Content type: Research article

    A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was perf...

    Authors: Solomon A. Yimer, Amine Namouchi, Ephrem Debebe Zegeye, Carol Holm-Hansen, Gunnstein Norheim, Markos Abebe, Abraham Aseffa and Tone Tønjum

    Citation: BMC Evolutionary Biology 2016 16:146

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  28. Content type: Research article

    RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previou...

    Authors: Pradeep Yerramsetty, Matt Stata, Rebecca Siford, Tammy L. Sage, Rowan F. Sage, Gane Ka-Shu Wong, Victor A. Albert and James O. Berry

    Citation: BMC Evolutionary Biology 2016 16:141

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  29. Content type: Research article

    The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved...

    Authors: Shandiya Balasubramaniam, Rebecca D. Bray, Raoul A. Mulder, Paul Sunnucks, Alexandra Pavlova and Jane Melville

    Citation: BMC Evolutionary Biology 2016 16:112

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  30. Content type: Research article

    Arthropods have received much attention as a model for studying opsin evolution in invertebrates. Yet, relatively few studies have investigated the diversity of opsin proteins that underlie spectral sensitivit...

    Authors: Nathan P. Lord, Rebecca L. Plimpton, Camilla R. Sharkey, Anton Suvorov, Jonathan P. Lelito, Barry M. Willardson and Seth M. Bybee

    Citation: BMC Evolutionary Biology 2016 16:107

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  31. Content type: Research article

    Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetopla...

    Authors: Ugo Cenci, Daniel Moog, Bruce A. Curtis, Goro Tanifuji, Laura Eme, Julius Lukeš and John M. Archibald

    Citation: BMC Evolutionary Biology 2016 16:109

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  32. Content type: Research article

    The Planar Cell Polarity pathway (PCP) has been described as the main feature involved in patterning cell orientation in bilaterian tissues. Recently, a similar phenomenon was revealed in cnidarians, in which ...

    Authors: Quentin Schenkelaars, Laura Fierro-Constain, Emmanuelle Renard and Carole Borchiellini

    Citation: BMC Evolutionary Biology 2016 16:69

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  33. Content type: Research article

    Neuropeptides are key players in information transfer and act as important regulators of development, growth, metabolism, and reproduction within multi-cellular animal organisms (Metazoa). These short protein-...

    Authors: Christian Derst, Heinrich Dircksen, Karen Meusemann, Xin Zhou, Shanlin Liu and Reinhard Predel

    Citation: BMC Evolutionary Biology 2016 16:51

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  34. Content type: Research article

    Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure tha...

    Authors: Rafał Milanowski, Natalia Gumińska, Anna Karnkowska, Takao Ishikawa and Bożena Zakryś

    Citation: BMC Evolutionary Biology 2016 16:49

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  35. Content type: Research article

    Low complexity regions (LCRs) are a ubiquitous feature in genomes and yet their evolutionary history and functional roles are unclear. Previous studies have shown contrasting evidence in favor of both neutral ...

    Authors: Fabia U. Battistuzzi, Kristan A. Schneider, Matthew K. Spencer, David Fisher, Sophia Chaudhry and Ananias A. Escalante

    Citation: BMC Evolutionary Biology 2016 16:47

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  36. Content type: Research article

    Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations...

    Authors: Mitsuhiko P. Sato, Takashi Makino and Masakado Kawata

    Citation: BMC Evolutionary Biology 2016 16:35

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  37. Content type: Research article

    The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followe...

    Authors: Beatriz Mengual-Chuliá, Stéphanie Bedhomme, Guillaume Lafforgue, Santiago F. Elena and Ignacio G. Bravo

    Citation: BMC Evolutionary Biology 2016 16:32

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  38. Content type: Research article

    Multicellularity evolved multiple times in eukaryotes. In all cases, this required an elaboration of the regulatory mechanisms controlling gene expression. Amongst the conserved eukaryotic transcription factor...

    Authors: Katia Jindrich and Bernard M. Degnan

    Citation: BMC Evolutionary Biology 2016 16:28

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  39. Content type: Research article

    Prions are transmissible, propagating alternative states of proteins, and are usually made from the fibrillar, beta-sheet-rich assemblies termed amyloid. Prions in the budding yeast Saccharomyces cerevisiae propa...

    Authors: Lu An, David Fitzpatrick and Paul M. Harrison

    Citation: BMC Evolutionary Biology 2016 16:24

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  40. Content type: Research article

    RNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30–50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, ...

    Authors: Anke Hein, Monika Polsakiewicz and Volker Knoop

    Citation: BMC Evolutionary Biology 2016 16:23

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  41. Content type: Research article

    Protamines are sperm nuclear proteins with a crucial role in chromatin condensation. Their function is strongly linked to sperm head morphology and male fertility. Protamines appear to be affected by a complex...

    Authors: Lena Lüke, Maximiliano Tourmente, Hernan Dopazo, François Serra and Eduardo R. S. Roldan

    Citation: BMC Evolutionary Biology 2016 16:21

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  42. Content type: Research article

    Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (EL...

    Authors: Krishnadev Oruganty, Eric E. Talevich, Andrew F. Neuwald and Natarajan Kannan

    Citation: BMC Evolutionary Biology 2016 16:7

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2017 Journal Metrics

  • Citation Impact
    3.027 - 2-year Impact Factor
    3.628 - 5-year Impact Factor
    1.16 - Source Normalized Impact per Paper (SNIP)
    1.656 - SCImago Journal Rank (SJR)

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