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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. The plasminogen (PLG) activation system is composed by a series of serine proteases, inhibitors and several binding proteins, which together control the temporal and spatial generation of the active serine pro...

    Authors: Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Bendixen and Frank Panitz
    Citation: BMC Evolutionary Biology 2019 19:27
    Content type: Research article Published on:

  2. ALRs (AIM2-like Receptors) are germline encoded PRRs that belong to PYHIN gene family of cytokines, which are having signature N-terminal PYD (Pyrin, PAAD or DAPIN) domain and C-terminal HIN-200 (hematopoietic, i...

    Authors: Sushil Kumar, Jatinder Singh Chera, Ashutosh Vats and Sachinandan De
    Citation: BMC Evolutionary Biology 2019 19:26
    Content type: Research article Published on:

  3. The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plasti...

    Authors: Jong Im Kim, Hyunmoon Shin, Pavel Škaloud, Jaehee Jung, Hwan Su Yoon, John M. Archibald and Woongghi Shin
    Citation: BMC Evolutionary Biology 2019 19:20
    Content type: Research article Published on:

  5. Oligoadenylate synthetases (OASs) are widely distributed in Metazoa including sponges, fish, reptiles, birds and mammals and show large variation, with one to twelve members in any given species. Upon double-s...

    Authors: Jiaxiang Hu, Xiaoxue Wang, Yanling Xing, Enguang Rong, Mengfei Ning, Jacqueline Smith and Yinhua Huang
    Citation: BMC Evolutionary Biology 2018 18:201
    Content type: Research article Published on:

  6. The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of bi...

    Authors: Dorota Matelska, Ivan G. Shabalin, Jagoda Jabłońska, Marcin J. Domagalski, Jan Kutner, Krzysztof Ginalski and Wladek Minor
    Citation: BMC Evolutionary Biology 2018 18:199
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Psychiatry 2019 19:221

  7. Adaptation to local host plants may impact a pollinator’s population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation...

    Authors: Belinda Kahnt, Panagiotis Theodorou, Antonella Soro, Hilke Hollens-Kuhr, Michael Kuhlmann, Anton Pauw and Robert J. Paxton
    Citation: BMC Evolutionary Biology 2018 18:196
    Content type: Research article Published on:

  9. The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid...

    Authors: Małgorzata Wnętrzak, Paweł Błażej, Dorota Mackiewicz and Paweł Mackiewicz
    Citation: BMC Evolutionary Biology 2018 18:192
    Content type: Research article Published on:

  10. Osteoglycin (OGN, a.k.a. mimecan) belongs to cluster III of the small leucine-rich proteoglycans (SLRP) of the extracellular matrix (ECM). In vertebrates OGN is a characteristic ECM protein of bone. In the pre...

    Authors: R. A. Costa, R. S. T. Martins, E. Capilla, L. Anjos and D. M. Power
    Citation: BMC Evolutionary Biology 2018 18:191
    Content type: Research article Published on:

  12. The ascomycete fungus Clonostachys rosea (order Hypocreales) can control several important plant diseases caused by plant pathogenic fungi and nematodes. Subtilisin-like serine proteases are considered to play an...

    Authors: Mudassir Iqbal, Mukesh Dubey, Mikael Gudmundsson, Maria Viketoft, Dan Funck Jensen and Magnus Karlsson
    Citation: BMC Evolutionary Biology 2018 18:171
    Content type: Research article Published on:

  13. The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influe...

    Authors: Milica Mandic, Marina L. Ramon, Aleeza C. Gerstein, Andrew Y. Gracey and Jeffrey G. Richards
    Citation: BMC Evolutionary Biology 2018 18:163
    Content type: Research article Published on:

  14. Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts...

    Authors: Shir Portugez, William F. Martin and Einat Hazkani-Covo
    Citation: BMC Evolutionary Biology 2018 18:162
    Content type: Research article Published on:

  15. Provision of long-chain polyunsaturated fatty acids (LC-PUFA) in vertebrates occurs through the diet or via endogenous production from C18 precursors through consecutive elongations and desaturations. It has been...

    Authors: Mónica Lopes-Marques, Naoki Kabeya, Yu Qian, Raquel Ruivo, Miguel M. Santos, Byrappa Venkatesh, Douglas R. Tocher, L. Filipe C. Castro and Óscar Monroig
    Citation: BMC Evolutionary Biology 2018 18:157
    Content type: Research article Published on:

  17. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  21. 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
    Content type: Research article Published on:

  22. 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
    Content type: Research article Published on:

  23. 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
    Content type: Research article Published on:

  24. 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
    Content type: Research article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research article Published on:

  34. 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
    Content type: Research article Published on:

  35. 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
    Content type: Research article Published on:

  36. 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
    Content type: Research article Published on:

  38. 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 Published on:

  39. 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 Published on:

  40. 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 Published on:

  41. 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 Published on:

  42. 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 Published on:

  45. 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 Published on:

  46. 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 Published on:

  48. 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 Published on:

  49. 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 Published on:

  50. 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 Published on:
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