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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 5 of 10

  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Research article Published on:

  4. 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
    Content type: Research article Published on:

  5. 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
    Content type: Research article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Research article Published on:

  13. 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
    Content type: Research article Published on:

  14. 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
    Content type: Research article Published on:

  15. Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signallin...

    Authors: Andriy Kovalchuk, Annegret Kohler, Francis Martin and Fred O. Asiegbu
    Citation: BMC Evolutionary Biology 2015 15:249
    Content type: Research article Published on:

  17. Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. ...

    Authors: Dorothée Huchon, Amir Szitenberg, Sigal Shefer, Micha Ilan and Tamar Feldstein
    Citation: BMC Evolutionary Biology 2015 15:278
    Content type: Research article Published on:

  18. A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such pa...

    Authors: Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi and João Pedro de Magalhães
    Citation: BMC Evolutionary Biology 2015 15:259
    Content type: Research article Published on:

  19. Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and ...

    Authors: Maria-Elisabeth Böhm, Christopher Huptas, Viktoria Magdalena Krey and Siegfried Scherer
    Citation: BMC Evolutionary Biology 2015 15:246
    Content type: Research article Published on:

  20. Sex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent...

    Authors: Chie Murata, Yoko Kuroki, Issei Imoto, Masaru Tsukahara, Naoto Ikejiri and Asato Kuroiwa
    Citation: BMC Evolutionary Biology 2015 15:234
    Content type: Research article Published on:

  21. Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative v...

    Authors: Russell A. Hermansen, Brian K. Mannakee, Wolfgang Knecht, David A. Liberles and Ryan N. Gutenkunst
    Citation: BMC Evolutionary Biology 2015 15:232
    Content type: Research article Published on:

  22. USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partiall...

    Authors: Caitlyn Vlasschaert, Xuhua Xia, Josée Coulombe and Douglas A. Gray
    Citation: BMC Evolutionary Biology 2015 15:230
    Content type: Research article Published on:

  23. Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniquenes...

    Authors: Cibele G. Sotero-Caio, Marianne Volleth, Federico G. Hoffmann, LuAnn Scott, Holly A. Wichman, Fengtang Yang and Robert J. Baker
    Citation: BMC Evolutionary Biology 2015 15:220
    Content type: Research article Published on:

  25. Poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that have important functions in the regulation of translation and the control of mRNA stability in eukaryotes. Most PABPs encode a C-term...

    Authors: Domingo Jiménez-López, Jaime Bravo and Plinio Guzmán
    Citation: BMC Evolutionary Biology 2015 15:195
    Content type: Research article Published on:

  26. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of vir...

    Authors: Izza Nasrullah, Azeem M Butt, Shifa Tahir, Muhammad Idrees and Yigang Tong
    Citation: BMC Evolutionary Biology 2015 15:174
    Content type: Research article Published on:

  28. Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in pr...

    Authors: Thorsten Thiergart, Giddy Landan and William F Martin
    Citation: BMC Evolutionary Biology 2014 14:266
    Content type: Research article Published on:

  29. Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nons...

    Authors: Karen B Barnard-Kubow, Daniel B Sloan and Laura F Galloway
    Citation: BMC Evolutionary Biology 2014 14:268
    Content type: Research article Published on:

  30. X chromosome inactivation is the transcriptional silencing of one X chromosome in the somatic cells of female mammals. In eutherian mammals (e.g. humans) one of the two X chromosomes is randomly chosen for sil...

    Authors: Claudia L Rodríguez-Delgado, Shafagh A Waters and Paul D Waters
    Citation: BMC Evolutionary Biology 2014 14:267
    Content type: Research article Published on:

  31. G protein-coupled receptors (GPCRs) play a central role in eukaryotic signal transduction. However, the GPCR component of this signalling system, at the early origins of metazoans is not fully understood. Here...

    Authors: Arunkumar Krishnan, Rohit Dnyansagar, Markus Sällman Almén, Michael J Williams, Robert Fredriksson, Narayanan Manoj and Helgi B Schiöth
    Citation: BMC Evolutionary Biology 2014 14:270
    Content type: Research article Published on:

  32. The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundan...

    Authors: Kalina TJ Davies, Georgia Tsagkogeorga and Stephen J Rossiter
    Citation: BMC Evolutionary Biology 2014 14:261
    Content type: Research article Published on:

  33. Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the ...

    Authors: Lei Wei, Jian He, Xian Jia, Qi Qi, Zhisheng Liang, Hao Zheng, Yao Ping, Shuyu Liu and Jingchen Sun
    Citation: BMC Evolutionary Biology 2014 14:262
    Content type: Research article Published on:

  34. Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of r...

    Authors: Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang and Qi Zhou
    Citation: BMC Evolutionary Biology 2014 14:250
    Content type: Research article Published on:

  35. Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We h...

    Authors: Matthew J Greenwold, Weier Bao, Erich D Jarvis, Haofu Hu, Cai Li, M Thomas P Gilbert, Guojie Zhang and Roger H Sawyer
    Citation: BMC Evolutionary Biology 2014 14:249
    Content type: Research article Published on:

  36. The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs i...

    Authors: Niles Lehman, Tess Bernhard, Brian C Larson, Andrew JN Robinson and Christopher CB Southgate
    Citation: BMC Evolutionary Biology 2014 14:248
    Content type: Research article Published on:

  37. Young genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Early developmental stages are very important for establishing phenotypes, which might be helpful for studyi...

    Authors: He-Qun Liu, Yan Li, David M Irwin, Ya-Ping Zhang and Dong-Dong Wu
    Citation: BMC Evolutionary Biology 2014 14:241
    Content type: Research article Published on:

  39. Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of th...

    Authors: Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin
    Citation: BMC Evolutionary Biology 2014 14:237
    Content type: Research article Published on:

  40. Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability a...

    Authors: Amanda M Larracuente
    Citation: BMC Evolutionary Biology 2014 14:233
    Content type: Research article Published on:

  42. Elucidating the mechanisms underlying coevolution of ligands and receptors is an important challenge in molecular evolutionary biology. Peptide hormones and their receptors are excellent models for such effort...

    Authors: Barry L Williams, Yasuhisa Akazome, Yoshitaka Oka and Heather L Eisthen
    Citation: BMC Evolutionary Biology 2014 14:215
    Content type: Research article Published on:

  43. Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathway...

    Authors: Juanjuan Chai, Guruprasad Kora, Tae-Hyuk Ahn, Doug Hyatt and Chongle Pan
    Citation: BMC Evolutionary Biology 2014 14:207
    Content type: Research article Published on:

  44. The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous st...

    Authors: Evan K Maxwell, Christine E Schnitzler, Paul Havlak, Nicholas H Putnam, Anh-Dao Nguyen, R Travis Moreland and Andreas D Baxevanis
    Citation: BMC Evolutionary Biology 2014 14:212
    Content type: Research article Published on:

  45. Myxozoa are a diverse group of metazoan parasites with a very simple organization, which has for decades eluded their evolutionary origin. Their most prominent and characteristic feature is the polar capsule: ...

    Authors: Erez Shpirer, E Sally Chang, Arik Diamant, Nimrod Rubinstein, Paulyn Cartwright and Dorothée Huchon
    Citation: BMC Evolutionary Biology 2014 14:205
    Content type: Research article Published on:

  46. MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, inclu...

    Authors: Pedro Gabriel Nachtigall, Marcos Correa Dias and Danillo Pinhal
    Citation: BMC Evolutionary Biology 2014 14:196
    Content type: Research article Published on:

  47. Human bitter taste receptors are encoded by a gene family consisting of 25 functional TAS2R loci. In addition, humans carry 11 TAS2R pseudogenes, some of which display evidence for substantial diversification amo...

    Authors: Davide Risso, Sergio Tofanelli, Gabriella Morini, Donata Luiselli and Dennis Drayna
    Citation: BMC Evolutionary Biology 2014 14:198
    Content type: Research article Published on:

  48. Lysozyme g is an antibacterial enzyme that was first found in the eggs of some birds, but recently has been found in additional species, including non-vertebrates. Some previously characterized lysozyme g sequenc...

    Authors: David M Irwin
    Citation: BMC Evolutionary Biology 2014 14:188
    Content type: Research article Published on:

  49. Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this...

    Authors: Lihong Guan, Wei Chi, Wuhan Xiao, Liangbiao Chen and Shunping He
    Citation: BMC Evolutionary Biology 2014 14:192
    Content type: Research article Published on:
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