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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 7 of 10

  1. One of the most striking features of avian vision is the variation in spectral sensitivity of the short wavelength sensitive (SWS1) opsins, which can be divided into two sub-types: violet- and UV- sensitive (V...

    Authors: Ilke van Hazel, Amir Sabouhanian, Lainy Day, John A Endler and Belinda SW Chang
    Citation: BMC Evolutionary Biology 2013 13:250
  2. Many long non-coding RNA (lncRNA) genes identified in mammals have multiple exons and functional domains, allowing them to bind to polycomb proteins, DNA methyltransferases, and specific DNA sequences to regul...

    Authors: Sha He, Weiling Gu, Yize Li and Hao Zhu
    Citation: BMC Evolutionary Biology 2013 13:247
  3. Pseudogenes are traditionally considered “dead” genes, therefore lacking biological functions. This view has however been challenged during the last decade. This is the case of the Protein phosphatase 1 regula...

    Authors: Luís Korrodi-Gregório, Joana Abrantes, Thorsten Muller, José Melo-Ferreira, Katrin Marcus, Odete AB da Cruz e Silva, Margarida Fardilha and Pedro J Esteves
    Citation: BMC Evolutionary Biology 2013 13:242
  4. Hydrophobins are small secreted cysteine-rich proteins that play diverse roles during different phases of fungal life cycle. In basidiomycetes, hydrophobin-encoding genes often form large multigene families wi...

    Authors: Anthony C Mgbeahuruike, Andriy Kovalchuk, Hongxin Chen, Wimal Ubhayasekera and Fred O Asiegbu
    Citation: BMC Evolutionary Biology 2013 13:240
  5. Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1...

    Authors: David Lagman, Daniel Ocampo Daza, Jenny Widmark, Xesús M Abalo, Görel Sundström and Dan Larhammar
    Citation: BMC Evolutionary Biology 2013 13:238
  6. Guanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuabl...

    Authors: Wanping Chen, Yanchun Shao and Fusheng Chen
    Citation: BMC Evolutionary Biology 2013 13:219
  7. The glycolytic pathway is central to cellular energy production. Selection on individual enzymes within glycolysis, particularly phosphoglucose isomerase (Pgi), has been associated with metabolic performance in n...

    Authors: Luke T Dunning, Alice B Dennis, Geoffrey Thomson, Brent J Sinclair, Richard D Newcomb and Thomas R Buckley
    Citation: BMC Evolutionary Biology 2013 13:215
  8. Horizontal gene transfer (HGT) allows for rapid spread of genetic material between species, increasing genetic and phenotypic diversity. Although HGT contributes to adaptation and is widespread in many bacteri...

    Authors: Sara E Hester, Jihye Park, Laura L Goodfield, Heather A Feaga, Andrew Preston and Eric T Harvill
    Citation: BMC Evolutionary Biology 2013 13:209
  9. The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date bac...

    Authors: Stefanie Mühlhausen and Martin Kollmar
    Citation: BMC Evolutionary Biology 2013 13:202
  10. In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand...

    Authors: Alena Fornůsková, Michal Vinkler, Marie Pagès, Maxime Galan, Emmanuelle Jousselin, Frederique Cerqueira, Serge Morand, Nathalie Charbonnel, Josef Bryja and Jean-François Cosson
    Citation: BMC Evolutionary Biology 2013 13:194
  11. Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played ...

    Authors: João MP Alves, Cecilia C Klein, Flávia Maia da Silva, André G Costa-Martins, Myrna G Serrano, Gregory A Buck, Ana Tereza R Vasconcelos, Marie-France Sagot, Marta MG Teixeira, Maria Cristina M Motta and Erney P Camargo
    Citation: BMC Evolutionary Biology 2013 13:190
  12. Osmoregulation was a primary challenge for cetaceans during the evolutionary transition from a terrestrial to a mainly hyperosmotic environment. Several physiological mechanisms have been suggested to maintain...

    Authors: Shixia Xu, Yunxia Yang, Xuming Zhou, Junxiao Xu, Kaiya Zhou and Guang Yang
    Citation: BMC Evolutionary Biology 2013 13:189
  13. Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organis...

    Authors: Catherine Putonti, Bogdan Nowicki, Michael Shaffer, Yuriy Fofanov and Stella Nowicki
    Citation: BMC Evolutionary Biology 2013 13:184
  14. Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosp...

    Authors: Lorenzo Carretero-Paulet, Agnieszka Lipska, Jordi Pérez-Gil, Félix J Sangari, Victor A Albert and Manuel Rodríguez-Concepción
    Citation: BMC Evolutionary Biology 2013 13:180
  15. Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed ch...

    Authors: Wei Shi, Xiao-Li Dong, Zhong-Ming Wang, Xian-Guang Miao, Shu-Ying Wang and Xiao-Yu Kong
    Citation: BMC Evolutionary Biology 2013 13:173
  16. Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic struct...

    Authors: Jing Ren, Liang Chen, Daokun Sun, Frank M You, Jirui Wang, Yunliang Peng, Eviatar Nevo, Avigdor Beiles, Dongfa Sun, Ming-Cheng Luo and Junhua Peng
    Citation: BMC Evolutionary Biology 2013 13:169
  17. In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involvi...

    Authors: Jian-Bo Yuan, Xiao-Jun Zhang, Cheng-Zhang Liu, Jian-Kai Wei, Fu-Hua Li and Jian-Hai Xiang
    Citation: BMC Evolutionary Biology 2013 13:165
  18. Synonymous or silent mutations are usually thought to evolve neutrally. However, accumulating recent evidence has demonstrated that silent mutations may destabilize RNA structures or disrupt cis regulatory motifs...

    Authors: Itay Mayrose, Adi Stern, Ela O Burdelova, Yosef Sabo, Nihay Laham-Karam, Rachel Zamostiano, Eran Bacharach and Tal Pupko
    Citation: BMC Evolutionary Biology 2013 13:164
  19. Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. In this study, we have assessed the effects of 1...

    Authors: Wen Wei, Tao Zhang, Dan Lin, Zu-Jun Yang and Feng-Biao Guo
    Citation: BMC Evolutionary Biology 2013 13:162
  20. The intention of this editorial is to steer researchers through methodological choices in molecular evolution, drawing on the combined expertise of the authors. Our aim is not to review the most advanced metho...

    Authors: Maria Anisimova, David A Liberles, Hervé Philippe, Jim Provan, Tal Pupko and Arndt von Haeseler
    Citation: BMC Evolutionary Biology 2013 13:161
  21. Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequence...

    Authors: Carlos Henrique Schneider, Maria Claudia Gross, Maria Leandra Terencio, Edson Junior do Carmo, Cesar Martins and Eliana Feldberg
    Citation: BMC Evolutionary Biology 2013 13:152
  22. Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for t...

    Authors: Sébastien Halary, James O McInerney, Philippe Lopez and Eric Bapteste
    Citation: BMC Evolutionary Biology 2013 13:146
  23. Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with...

    Authors: Most Mauluda Akhtar, Giovanni Scala, Sergio Cocozza, Gennaro Miele and Antonella Monticelli
    Citation: BMC Evolutionary Biology 2013 13:145
  24. GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have ...

    Authors: Xinshuai Qi, André S Chanderbali, Gane Ka-Shu Wong, Douglas E Soltis and Pamela S Soltis
    Citation: BMC Evolutionary Biology 2013 13:143
  25. Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolut...

    Authors: Pravech Ajawatanawong and Sandra L Baldauf
    Citation: BMC Evolutionary Biology 2013 13:140
  26. Prospero (Hyacinthaceae) provides a unique system to assess the impact of genome rearrangements on plant diversification and evolution. The genus exhibits remarkable chromosomal variation but very little morpholo...

    Authors: Tae-Soo Jang, Khatere Emadzade, John Parker, Eva M Temsch, Andrew R Leitch, Franz Speta and Hanna Weiss-Schneeweiss
    Citation: BMC Evolutionary Biology 2013 13:136
  27. Previous experiments have shown that the reduced gravity aboard the International Space Station (ISS) causes important alterations in Drosophila gene expression. These changes were shown to be intimately linked t...

    Authors: Raul Herranz, Oliver J Larkin, Richard JA Hill, Irene Lopez-Vidriero, Jack JWA van Loon and F Javier Medina
    Citation: BMC Evolutionary Biology 2013 13:133
  28. Although gene overlapping is a common feature of prokaryote and mitochondria genomes, such genes have also been identified in many eukaryotes. The overlapping genes in eukaryotes are extensively rearranged eve...

    Authors: Susanta K Behura and David W Severson
    Citation: BMC Evolutionary Biology 2013 13:124
  29. The physiological functions of the human Sterile Alpha Motif Domain-containing 9 (SAMD9) gene and its chromosomally adjacent paralogue, SAMD9-like (SAMD9L), currently remain unknown. However, the direct links bet...

    Authors: Ana Lemos de Matos, Jia Liu, Grant McFadden and Pedro J Esteves
    Citation: BMC Evolutionary Biology 2013 13:121
  30. The widespread protozoan parasite Toxoplasma gondii interferes with host cell functions by exporting the contents of a unique apical organelle, the rhoptry. Among the mix of secreted proteins are an expanded, lin...

    Authors: Eric Talevich and Natarajan Kannan
    Citation: BMC Evolutionary Biology 2013 13:117
  31. Comparison of major histocompatibility complex (MHC) genes across vertebrate species can reveal molecular mechanisms underlying the evolution of adaptive immunity-related proteins. As the first terrestrial tet...

    Authors: Mian Zhao, Yongzhen Wang, Hang Shen, Chenliang Li, Cheng Chen, Zhenhua Luo and Hua Wu
    Citation: BMC Evolutionary Biology 2013 13:113
  32. The var genes of the human malaria parasite Plasmodium falciparum are highly polymorphic loci coding for the erythrocyte membrane proteins 1 (PfEMP1), which are responsible for the cytoaherence of P. falciparum i...

    Authors: Martine M Zilversmit, Ella K Chase, Donald S Chen, Philip Awadalla, Karen P Day and Gil McVean
    Citation: BMC Evolutionary Biology 2013 13:110
  33. Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask...

    Authors: Václav Janoušek, Robert C Karn and Christina M Laukaitis
    Citation: BMC Evolutionary Biology 2013 13:107
  34. PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. ...

    Authors: Lingli He, Man Zhao, Yan Wang, Junyi Gai and Chaoying He
    Citation: BMC Evolutionary Biology 2013 13:103
  35. Retrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefo...

    Authors: Abigail L Savage, Vivien J Bubb, Gerome Breen and John P Quinn
    Citation: BMC Evolutionary Biology 2013 13:101
  36. Tyrosinases, tyrosinase-related proteins, catechol oxidases and hemocyanins comprise the type-3 copper protein family and are involved in a variety of biological processes, including pigment formation, innate ...

    Authors: Felipe Aguilera, Carmel McDougall and Bernard M Degnan
    Citation: BMC Evolutionary Biology 2013 13:96
  37. The Ran GTPase Activating Protein 2 (RanGAP2) was first described as a regulator of mitosis and nucleocytoplasmic trafficking. It was then found to interact with the Coiled-Coil domain of the Rx and GPA2 resis...

    Authors: Jean Carpentier, Eric Grenier, Magalie Esquibet, Louis-Philippe Hamel, Peter Moffett, Maria J Manzanares-Dauleux and Marie-Claire Kerlan
    Citation: BMC Evolutionary Biology 2013 13:87
  38. Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS se...

    Authors: Tânia Keiko Shishido, Ulla Kaasalainen, David P Fewer, Leo Rouhiainen, Jouni Jokela, Matti Wahlsten, Marli Fátima Fiore, João Sarkis Yunes, Jouko Rikkinen and Kaarina Sivonen
    Citation: BMC Evolutionary Biology 2013 13:86
  39. The ability to produce physiologically critical LC-PUFA from dietary fatty acids differs greatly among teleost species, and is dependent on the possession and expression of fatty acyl desaturase and elongase g...

    Authors: Greta Carmona-Antoñanzas, Douglas R Tocher, John B Taggart and Michael J Leaver
    Citation: BMC Evolutionary Biology 2013 13:85
  40. The S-domain serine/threonine receptor-like kinases (SRLKs) comprise one of the largest and most rapidly expanding subfamilies in the plant receptor-like/Pelle kinase (RLKs) family. The founding member of this...

    Authors: Shilai Xing, Mengya Li and Pei Liu
    Citation: BMC Evolutionary Biology 2013 13:69
  41. Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has also revealed correlations between substi...

    Authors: David Duchene and Lindell Bromham
    Citation: BMC Evolutionary Biology 2013 13:65
  42. The Southeast Asian deletion (--SEA) is the most commonly observed mutation among diverse α-thalassemia alleles in Southeast Asia and South China. It is generally argued that mutation --SEA, like other variants c...

    Authors: Qin-Wei Qiu, Dong-Dong Wu, Li-Hua Yu, Ti-Zhen Yan, Wen Zhang, Zhe-Tao Li, Yan-Hui Liu, Ya-Ping Zhang and Xiang-Min Xu
    Citation: BMC Evolutionary Biology 2013 13:63
  43. Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system. This system has shown marked evolution during mammalian divergence in such complex attributes as activa...

    Authors: Brandon M Invergo, Ludovica Montanucci, Hafid Laayouni and Jaume Bertranpetit
    Citation: BMC Evolutionary Biology 2013 13:52
  44. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is ...

    Authors: Misty L Kuhn, Carlos M Figueroa, Alberto A Iglesias and Miguel A Ballicora
    Citation: BMC Evolutionary Biology 2013 13:51

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