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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 9 of 10

  1. Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencin...

    Authors: Dean M Castillo, Joshua Chang Mell, Kimberly S Box and Justin P Blumenstiel

    Citation: BMC Evolutionary Biology 2011 11:258

    Content type: Research article

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  2. It has been known for over a decade that Plasmodium falciparum proteins are enriched in non-globular domains of unknown function. The potential for these regions of protein sequence to undergo high levels of gene...

    Authors: Kate B Gardner, Ipsita Sinha, Leyla Y Bustamante, Nicholas PJ Day, Nicholas J White and Charles J Woodrow

    Citation: BMC Evolutionary Biology 2011 11:257

    Content type: Research article

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  3. The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochond...

    Authors: Wan-Jun Chen, Yun Bu, Antonio Carapelli, Romano Dallai, Sheng Li, Wen-Ying Yin and Yun-Xia Luan

    Citation: BMC Evolutionary Biology 2011 11:246

    Content type: Research article

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  4. The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of...

    Authors: Christian Rödelsperger and Ralf J Sommer

    Citation: BMC Evolutionary Biology 2011 11:239

    Content type: Research article

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  5. The synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late Precambrian/early Cambrian 545 million years ago. However our understanding o...

    Authors: Daniel J Jackson, Luciana Macis, Joachim Reitner and Gert Wörheide

    Citation: BMC Evolutionary Biology 2011 11:238

    Content type: Research article

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  6. Chemosensory receptors, which are all G-protein-coupled receptors (GPCRs), come in four types: odorant receptors (ORs), vomeronasal receptors, trace-amine associated receptors and formyl peptide receptor-like ...

    Authors: Yingsong Zhou, Xiaojun Yan, Shanliang Xu, Peng Zhu, Xianxing He and Jianxin Liu

    Citation: BMC Evolutionary Biology 2011 11:237

    Content type: Research article

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  7. LNX (Ligand of Numb Protein-X) proteins typically contain an amino-terminal RING domain adjacent to either two or four PDZ domains - a domain architecture that is unique to the LNX family. LNX proteins functio...

    Authors: Michael Flynn, Orthis Saha and Paul Young

    Citation: BMC Evolutionary Biology 2011 11:235

    Content type: Research article

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  8. Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important...

    Authors: Stefan Kurtenbach, Christoph Mayer, Thomas Pelz, Hanns Hatt, Florian Leese and Eva M Neuhaus

    Citation: BMC Evolutionary Biology 2011 11:234

    Content type: Research article

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  9. Biotin-dependent carboxylases are a diverse family of carboxylating enzymes widespread in the three domains of life, and thus thought to be very ancient. This family includes enzymes that carboxylate acetyl-Co...

    Authors: Jonathan Lombard and David Moreira

    Citation: BMC Evolutionary Biology 2011 11:232

    Content type: Research article

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  10. The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular sys...

    Authors: Jaret P Bilewitch and Sandie M Degnan

    Citation: BMC Evolutionary Biology 2011 11:228

    Content type: Research article

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  11. Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are diffic...

    Authors: Giltae Song, Chih-Hao Hsu, Cathy Riemer, Yu Zhang, Hie Lim Kim, Federico Hoffmann, Louxin Zhang, Ross C Hardison, Eric D Green and Webb Miller

    Citation: BMC Evolutionary Biology 2011 11:226

    Content type: Research article

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  12. The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which di...

    Authors: Konstantin V Gunbin, Valentin V Suslov, Igor I Turnaev, Dmitry A Afonnikov and Nikolay A Kolchanov

    Citation: BMC Evolutionary Biology 2011 11:224

    Content type: Research article

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  13. tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on...

    Authors: Lijuan Fan, Zhikang Wang, Jinyu Liu, Weili Guo, Jie Yan and Ying Huang

    Citation: BMC Evolutionary Biology 2011 11:219

    Content type: Research article

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  14. In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences...

    Authors: Qing Lu and George E Fox

    Citation: BMC Evolutionary Biology 2011 11:218

    Content type: Research article

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  15. Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely...

    Authors: Teresa J Crease, Robin Floyd, Melania E Cristescu and David Innes

    Citation: BMC Evolutionary Biology 2011 11:212

    Content type: Research article

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  16. Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs...

    Authors: Alexandra Moosmann, Coen Campsteijn, Pascal WTC Jansen, Carole Nasrallah, Martina Raasholm, Henk G Stunnenberg and Eric M Thompson

    Citation: BMC Evolutionary Biology 2011 11:208

    Content type: Research article

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  17. Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore...

    Authors: Ferran Casals, Martin Sikora, Hafid Laayouni, Ludovica Montanucci, Aura Muntasell, Ross Lazarus, Francesc Calafell, Philip Awadalla, Mihai G Netea and Jaume Bertranpetit

    Citation: BMC Evolutionary Biology 2011 11:202

    Content type: Research article

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  18. Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel

    Authors: Stéphane Audic, Magali Lescot, Jean-Michel Claverie, Axel Cloeckaert and Michel S Zygmunt

    Citation: BMC Evolutionary Biology 2011 11:200

    Content type: Research article

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  19. Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two ori...

    Authors: Dimitris Dimitriadis, V Lila Koumandou, Philip Trimpalis and Sophia Kossida

    Citation: BMC Evolutionary Biology 2011 11:193

    Content type: Research article

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  20. Small insertions and deletions ("indels" with size ≦ 100 bp) whose lengths are not multiples of three (non-3n) are strongly constrained and depleted in protein-coding sequences. Such a constraint has never bee...

    Authors: Chun-Hsi Chen, Ben-Yang Liao and Feng-Chi Chen

    Citation: BMC Evolutionary Biology 2011 11:192

    Content type: Research article

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  21. The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X1X2Y sex systems in Hoplias mal...

    Authors: Marcelo B Cioffi, Antonio Sánchez, Juan A Marchal, Nadezda Kosyakova, Thomas Liehr, Vladimir Trifonov and Luiz AC Bertollo

    Citation: BMC Evolutionary Biology 2011 11:186

    Content type: Research article

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  22. Escherichia coli is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide pol...

    Authors: Shana R Leopold, Stanley A Sawyer, Thomas S Whittam and Phillip I Tarr

    Citation: BMC Evolutionary Biology 2011 11:183

    Content type: Research article

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  23. Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open...

    Authors: Rachele Cagliani, Stefania Riva, Uberto Pozzoli, Matteo Fumagalli, Giacomo P Comi, Nereo Bresolin, Mario Clerici and Manuela Sironi

    Citation: BMC Evolutionary Biology 2011 11:171

    Content type: Research article

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  24. Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differenc...

    Authors: Eleanne Solorzano, Kazufusa Okamoto, Pushpa Datla, Way Sung, RD Bergeron and WK Thomas

    Citation: BMC Evolutionary Biology 2011 11:168

    Content type: Research article

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  25. Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants ...

    Authors: Jie Wang, Yu Wang, Zhuo Wang, Lei Liu, Xin-Guang Zhu and Xiaotu Ma

    Citation: BMC Evolutionary Biology 2011 11:161

    Content type: Research article

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  26. Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction o...

    Authors: Mikhail L Kuravsky, Vladimir V Aleshin, Dmitrij Frishman and Vladimir I Muronetz

    Citation: BMC Evolutionary Biology 2011 11:160

    Content type: Research article

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  27. We have recently discovered that the two tryptophans of human β2-microglobulin have distinctive roles within the structure and function of the protein. Deeply buried in the core, Trp95 is essential for folding...

    Authors: Sara Raimondi, Nicola Barbarini, Palma Mangione, Gennaro Esposito, Stefano Ricagno, Martino Bolognesi, Irene Zorzoli, Loredana Marchese, Cristina Soria, Riccardo Bellazzi, Maria Monti, Monica Stoppini, Mario Stefanelli, Paolo Magni and Vittorio Bellotti

    Citation: BMC Evolutionary Biology 2011 11:159

    Content type: Research article

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  28. Long terminal repeat (LTR) retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale m...

    Authors: Nicole de la Chaux and Andreas Wagner

    Citation: BMC Evolutionary Biology 2011 11:154

    Content type: Research article

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  29. Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been ...

    Authors: Krishna BS Swamy, Wen-Yi Chu, Chun-Yi Wang, Huai-Kuang Tsai and Daryi Wang

    Citation: BMC Evolutionary Biology 2011 11:150

    Content type: Research article

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  30. The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Tol...

    Authors: Yinhua Huang, Nicholas D Temperley, Liming Ren, Jacqueline Smith, Ning Li and David W Burt

    Citation: BMC Evolutionary Biology 2011 11:149

    Content type: Research article

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  31. Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We...

    Authors: Chrysanthi Ainali, Michelle Simon, Shiri Freilich, Octavio Espinosa, Lee Hazelwood, Sophia Tsoka, Christos A Ouzounis and John M Hancock

    Citation: BMC Evolutionary Biology 2011 11:142

    Content type: Research article

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  32. Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-...

    Authors: Edward L Braun, Rebecca T Kimball, Kin-Lan Han, Naomi R Iuhasz-Velez, Amber J Bonilla, Jena L Chojnowski, Jordan V Smith, Rauri CK Bowie, Michael J Braun, Shannon J Hackett, John Harshman, Christopher J Huddleston, Ben D Marks, Kathleen J Miglia, William S Moore, Sushma Reddy…

    Citation: BMC Evolutionary Biology 2011 11:141

    Content type: Research article

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  33. Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of γ1 ERVs to ...

    Authors: Fabrícia F Nascimento, Jaime Gongora, Michael Charleston, Michael Tristem, Stewart Lowden and Chris Moran

    Citation: BMC Evolutionary Biology 2011 11:139

    Content type: Research article

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  34. The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deutero...

    Authors: Marleen Perseke, Joerg Hetmank, Matthias Bernt, Peter F Stadler, Martin Schlegel and Detlef Bernhard

    Citation: BMC Evolutionary Biology 2011 11:134

    Content type: Research article

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  35. Stearoyl-CoA desaturases (SCDs) are key enzymes involved in de novo monounsaturated fatty acid synthesis. They catalyze the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position, generating ...

    Authors: L Filipe C Castro, Jonathan M Wilson, Odete Gonçalves, Susana Galante-Oliveira, Eduardo Rocha and Isabel Cunha

    Citation: BMC Evolutionary Biology 2011 11:132

    Content type: Research article

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  36. The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of gr...

    Authors: Václav Mahelka, David Kopecký and Ladislava Paštová

    Citation: BMC Evolutionary Biology 2011 11:127

    Content type: Research article

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  37. Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary...

    Authors: Benoîte Cazaux, Josette Catalan, Frédéric Veyrunes, Emmanuel JP Douzery and Janice Britton-Davidian

    Citation: BMC Evolutionary Biology 2011 11:124

    Content type: Research article

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  38. Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a...

    Authors: Ovidiu Paun, Richard M Bateman, Michael F Fay, Javier A Luna, Justin Moat, Mikael Hedrén and Mark W Chase

    Citation: BMC Evolutionary Biology 2011 11:113

    Content type: Research article

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  39. Major intrinsic proteins (MIPs) also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in t...

    Authors: Hanna I Anderberg, Jonas ÅH Danielson and Urban Johanson

    Citation: BMC Evolutionary Biology 2011 11:110

    Content type: Research article

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  40. Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation event...

    Authors: Vladimir A Lukhtanov, Vlad Dincă, Gerard Talavera and Roger Vila

    Citation: BMC Evolutionary Biology 2011 11:109

    Content type: Research article

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  41. The SLC11A1/Nramp1 and SLC11A2/Nramp2 genes belong to the SLC11/Nramp family of transmembrane divalent metal transporters, with SLC11A1 being associated with resistance to pathogens and SLC11A2 involved in intest...

    Authors: João V Neves, Jonathan M Wilson, Heiner Kuhl, Richard Reinhardt, L Filipe C Castro and Pedro NS Rodrigues

    Citation: BMC Evolutionary Biology 2011 11:106

    Content type: Research article

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  42. Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, th...

    Authors: Shinichiro Maruyama, Toshinobu Suzaki, Andreas PM Weber, John M Archibald and Hisayoshi Nozaki

    Citation: BMC Evolutionary Biology 2011 11:105

    Content type: Research article

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