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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 3 of 10

  1. Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signa...

    Authors: A. D. Lokits, H. Indrischek, J. Meiler, H. E. Hamm and P. F. Stadler

    Citation: BMC Evolutionary Biology 2018 18:51

    Content type: Research article

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  2. Genome reduction in intracellular pathogens and endosymbionts is usually compensated by reliance on the host for energy and nutrients. Free-living taxa with reduced genomes must however evolve strategies for g...

    Authors: Huan Qiu, Alessandro W. Rossoni, Andreas P. M. Weber, Hwan Su Yoon and Debashish Bhattacharya

    Citation: BMC Evolutionary Biology 2018 18:41

    Content type: Research article

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  3. Protein-coding genes expressed in sperm evolve at different rates. To gain deeper insight into the factors underlying this heterogeneity we examined the relative importance of a diverse set of previously descr...

    Authors: Julia Schumacher and Holger Herlyn

    Citation: BMC Evolutionary Biology 2018 18:35

    Content type: Research article

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  4. The CEA gene family is one of the most rapidly evolving gene families in the human genome. The founder gene of the family is thought to be an ancestor of the inhibitory immune checkpoint molecule CEACAM1. Compreh...

    Authors: Sophie Mißbach, Denis Aleksic, Lisa Blaschke, Timm Hassemer, Kyung Jin Lee, Martin Mansfeld, Jana Hänske, Johannes Handler and Robert Kammerer

    Citation: BMC Evolutionary Biology 2018 18:32

    Content type: Research article

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  5. Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxo...

    Authors: Jia-Yong Zhang, Le-Ping Zhang, Dan-Na Yu, Kenneth B. Storey and Rong-Quan Zheng

    Citation: BMC Evolutionary Biology 2018 18:26

    Content type: Research article

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  6. Exaggerated signals, such as brilliant colours, are usually assumed to evolve through antagonistic coevolution between senders and receivers, but the underlying genetic mechanisms are rarely known. Here we exp...

    Authors: Hanlu Twyman, Staffan Andersson and Nicholas I. Mundy

    Citation: BMC Evolutionary Biology 2018 18:22

    Content type: Research article

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  7. Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipeli...

    Authors: Sarah M. Hücker, Sonja Vanderhaeghen, Isabel Abellan-Schneyder, Romy Wecko, Svenja Simon, Siegfried Scherer and Klaus Neuhaus

    Citation: BMC Evolutionary Biology 2018 18:21

    Content type: Research article

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  8. The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, ...

    Authors: Diep Thi Hoang, Le Sy Vinh, Tomáš Flouri, Alexandros Stamatakis, Arndt von Haeseler and Bui Quang Minh

    Citation: BMC Evolutionary Biology 2018 18:11

    Content type: Methodology article

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  9. Universal stress proteins (USPs) are present in all domains of life. Their expression is upregulated in response to a large variety of stress conditions. The functional diversity found in this protein family, ...

    Authors: Sergio Martin Espinola, Martin Pablo Cancela, Lauís Brisolara Corrêa and Arnaldo Zaha

    Citation: BMC Evolutionary Biology 2018 18:10

    Content type: Research article

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  10. Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations...

    Authors: Jianhai Chen, Pan Ni, Xinyun Li, Jianlin Han, Ivan Jakovlić, Chengjun Zhang and Shuhong Zhao

    Citation: BMC Evolutionary Biology 2018 18:4

    Content type: Research article

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  18. 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

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  19. 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

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  20. 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

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  21. 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

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  22. 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

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  23. 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

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  24. 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

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  25. 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

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

  36. 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

  37. 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

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  38. 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

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  39. 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

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  40. 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

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  41. 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:

  42. 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:

  43. 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:

2018 Journal Metrics

  • Citation Impact
    3.045 - 2-year Impact Factor
    3.559 - 5-year Impact Factor
    1.15 - Source Normalized Impact per Paper (SNIP)
    1.687 - SCImago Journal Rank (SJR)

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