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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 4 of 10

  1. Maleness in mammals is genetically determined by the Y chromosome. On the Y chromosome SRY is known as the mammalian male-determining gene. Both placental mammals (Eutheria) and marsupial mammals (Metatheria) hav...

    Authors: Yukako Katsura, Hiroko X. Kondo, Janelle Ryan, Vincent Harley and Yoko Satta
    Citation: BMC Evolutionary Biology 2018 18:3
    Content type: Research article Published on:

  2. Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly not...

    Authors: Octavio M. Palacios-Gimenez, Diogo Milani, Bernardo Lemos, Elio R. Castillo, Dardo A. Martí, Erica Ramos, Cesar Martins and Diogo C. Cabral-de-Mello
    Citation: BMC Evolutionary Biology 2018 18:2
    Content type: Research article Published on:

  3. The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPH...

    Authors: Yiyuan Li, Rui Zhang, Shanlin Liu, Alexander Donath, Ralph S. Peters, Jessica Ware, Bernhard Misof, Oliver Niehuis, Michael E. Pfrender and Xin Zhou
    Citation: BMC Evolutionary Biology 2017 17:269
    Content type: Research article Published on:

  4. The Na,K-ATPase is a vital animal cell-membrane protein that maintains the cell’s resting potential, among other functions. Cardenolides, a group of potent plant toxins, bind to and inhibit this pump. The gene...

    Authors: Jennifer N. Lohr, Fee Meinzer, Safaa Dalla, Renja Romey-Glüsing and Susanne Dobler
    Citation: BMC Evolutionary Biology 2017 17:256
    Content type: Research Article Published on:

  5. Genes encoding proteins underlying host-pathogen co-evolution and which are selected for new resistance specificities frequently are under positive selection, a process that maintains diversity. Here, we teste...

    Authors: Mariana Mondragón-Palomino, Remco Stam, Ajay John-Arputharaj and Thomas Dresselhaus
    Citation: BMC Evolutionary Biology 2017 17:255
    Content type: Research Article Published on:

  6. Morphological divergences of snake retinal structure point to complex evolutionary processes and adaptations. The Colubridae family has a remarkable variety of retinal structure that can range from all-cone an...

    Authors: E. Hauzman, D. M. O. Bonci, E. Y. Suárez-Villota, M. Neitz and D. F. Ventura
    Citation: BMC Evolutionary Biology 2017 17:249
    Content type: Research article Published on:

  7. An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytoso...

    Authors: Melania Abrahamian, Meenakshi Kagda, Audrey M. V. Ah-Fong and Howard S. Judelson
    Citation: BMC Evolutionary Biology 2017 17:241
    Content type: Research article Published on:

  8. Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed...

    Authors: Jiawei Li, Wen Zeng, Ye Zhang, Albert Min-Shan Ko, Chunxiang Li, Hong Zhu, Qiaomei Fu and Hui Zhou
    Citation: BMC Evolutionary Biology 2017 17:239
    Content type: Research article Published on:

  9. The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly bet...

    Authors: Rajiv K. Parvathaneni, Victoria L. DeLeo, John J. Spiekerman, Debkanta Chakraborty and Katrien M. Devos
    Citation: BMC Evolutionary Biology 2017 17:238
    Content type: Research article Published on:

  10. The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci ...

    Authors: Sanjarbek Hudaiberdiev, Sergey Shmakov, Yuri I. Wolf, Michael P. Terns, Kira S. Makarova and Eugene V. Koonin
    Citation: BMC Evolutionary Biology 2017 17:232
    Content type: Research article Published on:

  11. Organisms living at high altitudes face low oxygen and temperature conditions; thus, the genetic mechanisms underlying the adaptations in these organisms merit investigation. The glyptosternoid fish, Creteuchilog...

    Authors: Jingliang Kang, Xiuhui Ma and Shunping He
    Citation: BMC Evolutionary Biology 2017 17:229
    Content type: Research article Published on:

  12. Siglecs-11 and -16 are members of the sialic acid recognizing Ig-like lectin family, and expressed in same cells. Siglec-11 functions as an inhibitory receptor, whereas Siglec-16 exhibits activating properties...

    Authors: Toshiyuki Hayakawa, Zahra Khedri, Flavio Schwarz, Corinna Landig, Suh-Yuen Liang, Hai Yu, Xi Chen, Naoko T. Fujito, Yoko Satta, Ajit Varki and Takashi Angata
    Citation: BMC Evolutionary Biology 2017 17:228
    Content type: Research article Published on:

  13. Grass powdery mildew (Blumeria graminis, Ascomycota) is a major pathogen of cereal crops and has become a model organism for obligate biotrophic fungal pathogens of plants. The sequenced genomes of two formae spe...

    Authors: Fabrizio Menardo, Coraline R. Praz, Thomas Wicker and Beat Keller
    Citation: BMC Evolutionary Biology 2017 17:223
    Content type: Research article Published on:

  14. Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathwa...

    Authors: Santiago Fontenla, Gabriel Rinaldi, Pablo Smircich and Jose F. Tort
    Citation: BMC Evolutionary Biology 2017 17:215
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  16. 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
    Content type: Research article Published on:

  17. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research Article Published on:

  24. 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
    Content type: Research Article Published on:

  26. 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
    Content type: Research Article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Research article Published on:

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

  30. 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
    Content type: Research article Published on:

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

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research Article Published on:

  34. 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
    Content type: Research article Published on:

  35. 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
    Content type: Research article Published on:

  36. 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
    Content type: Research article Published on:

  37. 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
    Content type: Research article Published on:

  38. 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
    Content type: Research article Published on:

  39. 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
    Content type: Research article Published on:

  41. 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
    Content type: Research article Published on:

  43. 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
    Content type: Research Article Published on:

  44. 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
    Content type: Research article Published on:

  45. 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
    Content type: Research article Published on:

  46. 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
    Content type: Research article Published on:

  47. 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
    Content type: Research article Published on:

  48. 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
    Content type: Research article Published on:

  50. 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
    Content type: Research article Published on:
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