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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. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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

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  9. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  19. 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

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  20. 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

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  22. 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

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  23. 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

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  24. 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

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  25. 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

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  33. 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

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  34. 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

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  36. 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

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  37. 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

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  38. 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

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  39. 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

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  40. 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

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  41. 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

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  42. 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

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  43. 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

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  45. Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (“T-P spacers”) have been ob...

    Authors: Tor Erik Jørgensen, Ingrid Bakke, Anita Ursvik, Morten Andreassen, Truls Moum and Steinar D Johansen

    Citation: BMC Evolutionary Biology 2014 14:182

    Content type: Research article

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  46. Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical interco...

    Authors: Hong-Hu Meng, Frédéric MB Jacques, Tao Su, Yong-Jiang Huang, Shi-Tao Zhang, Hong-Jie Ma and Zhe-Kun Zhou

    Citation: BMC Evolutionary Biology 2014 14:181

    Content type: Research article

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  47. Dacts are multi-domain adaptor proteins. They have been implicated in Wnt and Tgfβ signaling and serve as a nodal point in regulating many cellular activities. Dact genes have so far only been identified in bony ...

    Authors: Frank Richard Schubert, Débora Rodrigues Sobreira, Ricardo Guerreiro Janousek, Lúcia Elvira Alvares and Susanne Dietrich

    Citation: BMC Evolutionary Biology 2014 14:157

    Content type: Research article

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  48. The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mR...

    Authors: Xiu-Qing Li and Donglei Du

    Citation: BMC Evolutionary Biology 2014 14:162

    Content type: Research article

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  49. The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected...

    Authors: Dianne I Lou, Ross M McBee, Uyen Q Le, Anne C Stone, Gregory K Wilkerson, Ann M Demogines and Sara L Sawyer

    Citation: BMC Evolutionary Biology 2014 14:155

    Content type: Research article

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  50. Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most ch...

    Authors: Hui Huang, Chao Shi, Yuan Liu, Shu-Yan Mao and Li-Zhi Gao

    Citation: BMC Evolutionary Biology 2014 14:151

    Content type: Research article

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