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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 1 of 8

  1. Content type: Research article

    Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not b...

    Authors: Ismael L. Hernández-González, Gabriel Moreno-Hagelsieb and Gabriela Olmedo-Álvarez

    Citation: BMC Evolutionary Biology 2018 18:148

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  2. Content type: Research article

    Confined within the freezing Southern Ocean, the Antarctic notothenioids have evolved to become both cold adapted and cold specialized. A marked signature of cold specialization is an apparent loss of the cell...

    Authors: Kevin T. Bilyk, Luis Vargas-Chacoff and C.-H.Christina Cheng

    Citation: BMC Evolutionary Biology 2018 18:143

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  3. Content type: Research article

    Disparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in ...

    Authors: Steven J. Micheletti, Jon E. Hess, Joseph S. Zendt and Shawn R. Narum

    Citation: BMC Evolutionary Biology 2018 18:140

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  4. Content type: Research article

    Phylogenetic relationships among Eastern Hemisphere cypresses, Western Hemisphere cypresses, junipers, and their closest relatives are controversial, and generic delimitations have been in flux for the past de...

    Authors: Andan Zhu, Weishu Fan, Robert P. Adams and Jeffrey P. Mower

    Citation: BMC Evolutionary Biology 2018 18:137

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  5. Content type: Research article

    As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controve...

    Authors: Dong Zhang, Hong Zou, Shan G. Wu, Ming Li, Ivan Jakovlić, Jin Zhang, Rong Chen, Wen X. Li and Gui T. Wang

    Citation: BMC Evolutionary Biology 2018 18:133

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  6. Content type: Research article

    The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which all plant cell wall components are degraded, inclu...

    Authors: Franz-Sebastian Krah, Claus Bässler, Christoph Heibl, John Soghigian, Hanno Schaefer and David S. Hibbett

    Citation: BMC Evolutionary Biology 2018 18:119

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  7. Content type: Research article

    The adaptive immune system of vertebrates has an extraordinary potential to sense and neutralize foreign antigens entering the body. De novo evolution of genes implies that the genome itself expresses novel antig...

    Authors: Cemalettin Bekpen, Chen Xie and Diethard Tautz

    Citation: BMC Evolutionary Biology 2018 18:121

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  8. Content type: Research article

    Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, ...

    Authors: Marina Pais, Kentaro Yoshida, Artemis Giannakopoulou, Mathieu A. Pel, Liliana M. Cano, Ricardo F. Oliva, Kamil Witek, Hannele Lindqvist-Kreuze, Vivianne G. A. A. Vleeshouwers and Sophien Kamoun

    Citation: BMC Evolutionary Biology 2018 18:93

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  9. Content type: Research article

    Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modificat...

    Authors: Katharina E. Bräuer, Kevin Brockers, Jasmin Moneer, Annette Feuchtinger, Evi Wollscheid-Lengeling, Andreas Lengeling and Alexander Wolf

    Citation: BMC Evolutionary Biology 2018 18:96

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  10. Content type: Research article

    An essential question in evolutionary biology is whether shifts in a set of polygenic behaviors share a genetic basis across species. Such a behavioral shift is seen in the cave-dwelling Mexican tetra, Astyanax m...

    Authors: Masato Yoshizawa, Alexander Settle, Meredith C. Hermosura, Lillian J. Tuttle, Nicolas Cetraro, Courtney N. Passow and Suzanne E. McGaugh

    Citation: BMC Evolutionary Biology 2018 18:89

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  11. Content type: Research article

    Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolutio...

    Authors: Bochra A. Bahri, Guillaume Daverdin, Xiangyang Xu, Jan-Fang Cheng, Kerrie W. Barry, E. Charles Brummer and Katrien M. Devos

    Citation: BMC Evolutionary Biology 2018 18:91

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  12. Content type: Research article

    C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a p...

    Authors: Anke Hein and Volker Knoop

    Citation: BMC Evolutionary Biology 2018 18:85

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  13. Content type: Research article

    It is thought that after whole-genome duplications (WGDs), a large fraction of the duplicated gene copies is lost over time while few duplicates are retained. Which factors promote survival or death of a dupli...

    Authors: Elisabeth Kaltenegger, Svetlana Leng and Alexander Heyl

    Citation: BMC Evolutionary Biology 2018 18:76

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  14. Content type: Research article

    Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evo...

    Authors: Manuela Sann, Oliver Niehuis, Ralph S. Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn and Michael Ohl

    Citation: BMC Evolutionary Biology 2018 18:71

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  15. Content type: Research article

    One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that rec...

    Authors: Niladri Banerjee, Tatiana Polushina, Francesco Bettella, Sudheer Giddaluru, Vidar M. Steen, Ole A. Andreassen and Stephanie Le Hellard

    Citation: BMC Evolutionary Biology 2018 18:63

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  16. Content type: Research article

    Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. ...

    Authors: Hanan Arafat, Ada Alamaru, Carmela Gissi and Dorothée Huchon

    Citation: BMC Evolutionary Biology 2018 18:65

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  17. Content type: Research article

    The role of chromosomal arrangements in adaptation is supported by the repeatable clinal variation in inversion frequencies across continents in colonizing species such as Drosophila subobscura. However, there is...

    Authors: Pedro Simões and Marta Pascual

    Citation: BMC Evolutionary Biology 2018 18:60

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Methodology article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research Article

    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

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  32. Content type: Research Article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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  42. 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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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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    Social Media Impact
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