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  3. Robustness is a fundamental property of biological systems and is defined as the ability to maintain stable functioning in the face of various perturbations. Understanding how robustness has evolved has become...

    Authors: Wenjie Shu, Xiaochen Bo, Ming Ni, Zhiqiang Zheng and Shengqi Wang
    Citation: BMC Evolutionary Biology 2007 7:223
    Content type: Research article Published on:

  4. The vitamin D receptor (VDR) and pregnane X receptor (PXR) are nuclear hormone receptors of the NR1I subfamily that show contrasting patterns of cross-species variation. VDR and PXR are thought to have arisen ...

    Authors: Erica J Reschly, Afonso Celso Dias Bainy, Jaco Joaquim Mattos, Lee R Hagey, Nathan Bahary, Sripal R Mada, Junhai Ou, Raman Venkataramanan and Matthew D Krasowski
    Citation: BMC Evolutionary Biology 2007 7:222
    Content type: Research article Published on:

  5. Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the function of the ancestral mole...

    Authors: João CR Cardoso, Edwin CJM de Vet, Bruno Louro, Greg Elgar, Melody S Clark and Deborah M Power
    Citation: BMC Evolutionary Biology 2007 7:221
    Content type: Research article Published on:

  6. Circum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survi...

    Authors: Karel Janko, Guillaume Lecointre, Arthur DeVries, Arnaud Couloux, Corinne Cruaud and Craig Marshall
    Citation: BMC Evolutionary Biology 2007 7:220
    Content type: Research article Published on:

  7. Protein secretion is a universal cellular process involving vesicles which bud and fuse between organelles to bring proteins to their final destination. Vesicle budding is mediated by protein coats; vesicle ta...

    Authors: Dominique Swennen and Jean-Marie Beckerich
    Citation: BMC Evolutionary Biology 2007 7:219
    Content type: Research article Published on:

  8. Analysis of interspecific gene flow is crucial for the understanding of speciation processes and maintenance of species integrity. Oaks (genus Quercus, Fagaceae) are among the model species for the study of hybri...

    Authors: Alexandru L Curtu, Oliver Gailing and Reiner Finkeldey
    Citation: BMC Evolutionary Biology 2007 7:218
    Content type: Research article Published on:

  9. Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids wit...

    Authors: Xin-Yu Zhu, Mark W Chase, Yin-Long Qiu, Hong-Zhi Kong, David L Dilcher, Jian-Hua Li and Zhi-Duan Chen
    Citation: BMC Evolutionary Biology 2007 7:217
    Content type: Research article Published on:

  10. Phylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped sp...

    Authors: Jeff W Higdon, Olaf RP Bininda-Emonds, Robin MD Beck and Steven H Ferguson
    Citation: BMC Evolutionary Biology 2007 7:216
    Content type: Research article Published on:

  11. When orthologous sequences from species distributed throughout an optimal range of divergence times are available, comparative genomics is a powerful tool to address problems such as the identification of the ...

    Authors: Damiano Porcelli, Paolo Barsanti, Graziano Pesole and Corrado Caggese
    Citation: BMC Evolutionary Biology 2007 7:215
    Content type: Research article Published on:

  12. The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, an...

    Authors: Alexei J Drummond and Andrew Rambaut
    Citation: BMC Evolutionary Biology 2007 7:214
    Content type: Software Published on:

  13. The duplication-degeneration-complementation (DDC) model has been proposed as an explanation for the unexpectedly high retention of duplicate genes. The hypothesis proposes that, following gene duplication, th...

    Authors: Thomas MacCarthy and Aviv Bergman
    Citation: BMC Evolutionary Biology 2007 7:213
    Content type: Research article Published on:

  15. The Red Queen Hypothesis (RQH) suggests that the coevolutionary dynamics of host-parasite systems can generate selection for increased host recombination. Since host-parasite interactions often have a strong g...

    Authors: Roger D Kouyos, Marcel Salathé and Sebastian Bonhoeffer
    Citation: BMC Evolutionary Biology 2007 7:211
    Content type: Research article Published on:

  16. The NODULATION RECEPTOR KINASE (NORK) gene encodes a Leucine-Rich Repeat (LRR)-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrenc...

    Authors: Stéphane De Mita, Sylvain Santoni, Joëlle Ronfort and Thomas Bataillon
    Citation: BMC Evolutionary Biology 2007 7:210
    Content type: Research article Published on:

  18. Several studies have investigated the relationships between selective constraints in introns and their length, GC content and location within genes. To date, however, no such investigation has been done in pla...

    Authors: Xingyi Guo, Yu Wang, Peter D Keightley and Longjiang Fan
    Citation: BMC Evolutionary Biology 2007 7:208
    Content type: Research article Published on:

  19. Males that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolis...

    Authors: Alain Jacob, Sébastien Nusslé, Adrian Britschgi, Guillaume Evanno, Rudolf Müller and Claus Wedekind
    Citation: BMC Evolutionary Biology 2007 7:207
    Content type: Research article Published on:

  20. The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the comm...

    Authors: Yan Zhou, Nicolas Rodrigue, Nicolas Lartillot and Hervé Philippe
    Citation: BMC Evolutionary Biology 2007 7:206
    Content type: Research article Published on:

  22. The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization)....

    Authors: Yukuto Sato and Mutsumi Nishida
    Citation: BMC Evolutionary Biology 2007 7:204
    Content type: Research article Published on:

  24. Levels of molecular diversity in Drosophila have repeatedly been shown to be higher in ancestral, African populations than in derived, non-African populations. This pattern holds for both coding and noncoding ...

    Authors: Nadia D Singh, J Michael Macpherson, Jeffrey D Jensen and Dmitri A Petrov
    Citation: BMC Evolutionary Biology 2007 7:202
    Content type: Research article Published on:

  25. Dicyemid mesozoans (Phylum Dicyemida) are simple (8–40-cell) cephalopod endoparasites. They have neither body cavities nor differentiated organs, such as nervous and gastrointestinal systems. Whether dicyemids...

    Authors: Jun Aruga, Yuri S Odaka, Akiko Kamiya and Hidetaka Furuya
    Citation: BMC Evolutionary Biology 2007 7:201
    Content type: Research article Published on:

  26. One of the greatest challenges facing the early land vertebrates was the need to effectively interpret a terrestrial environment. Interpretation was based on ocular adaptations evolved for an aquatic environme...

    Authors: Helena J Bailes, Wayne L Davies, Ann EO Trezise and Shaun P Collin
    Citation: BMC Evolutionary Biology 2007 7:200
    Content type: Research article Published on:

  27. Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic anal...

    Authors: Aurora Ruiz-Herrera and Terence J Robinson
    Citation: BMC Evolutionary Biology 2007 7:199
    Content type: Research article Published on:

  28. Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspeci...

    Authors: Li Yu, Yi-Wei Li, Oliver A Ryder and Ya-Ping Zhang
    Citation: BMC Evolutionary Biology 2007 7:198
    Content type: Research article Published on:

  29. Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuc...

    Authors: Elena G Gonzalez and Rafael Zardoya
    Citation: BMC Evolutionary Biology 2007 7:197
    Content type: Research article Published on:

  30. Although the impact of pathogens on the evolution of the mammalian immune system is still under debate, proteins, which both regulate immune responses and serve as cellular receptors for pathogens should be at...

    Authors: Robert Kammerer, Tanja Popp, Stefan Härtle, Bernhard B Singer and Wolfgang Zimmermann
    Citation: BMC Evolutionary Biology 2007 7:196
    Content type: Research article Published on:

  31. Cichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus Perissodus are known for their unique feeding habit of scale eating with specialized ...

    Authors: Rieko Takahashi, Katsutoshi Watanabe, Mutsumi Nishida and Michio Hori
    Citation: BMC Evolutionary Biology 2007 7:195
    Content type: Research article Published on:

  32. In a number of species males damage females during copulation, but the reasons for this remain unclear. It may be that males are trying to manipulate female mating behaviour or their life histories. Alternativ...

    Authors: Y Teuschl, DJ Hosken and WU Blanckenhorn
    Citation: BMC Evolutionary Biology 2007 7:194
    Content type: Research article Published on:

  33. Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate...

    Authors: Izabela Makałowska, Chiao-Feng Lin and Krisitina Hernandez
    Citation: BMC Evolutionary Biology 2007 7:193
    Content type: Research article Published on:

  34. The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction ...

    Authors: Liran Carmel, Igor B Rogozin, Yuri I Wolf and Eugene V Koonin
    Citation: BMC Evolutionary Biology 2007 7:192
    Content type: Research article Published on:

  35. Insertions and deletions of DNA segments (indels) are together with substitutions the major mutational processes that generate genetic variation. Here we focus on recent DNA insertions and deletions in protein...

    Authors: Nicole de la Chaux, Philipp W Messer and Peter F Arndt
    Citation: BMC Evolutionary Biology 2007 7:191
    Content type: Research article Published on:

  36. The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last d...

    Authors: Jan Ole Kriegs, Andreas Matzke, Gennady Churakov, Andrej Kuritzin, Gerald Mayr, Jürgen Brosius and Jürgen Schmitz
    Citation: BMC Evolutionary Biology 2007 7:190
    Content type: Research article Published on:

  38. Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independen...

    Authors: Manuel Irimia, Jakob Lewin Rukov, David Penny and Scott William Roy
    Citation: BMC Evolutionary Biology 2007 7:188
    Content type: Research article Published on:

  39. Progressive diversification of paralogs after gene expansion is essential to increase their functional specialization. However, mode and tempo of this divergence remain mostly unclear. Here we report the compa...

    Authors: Irene Fumasoni, Natalia Meani, Davide Rambaldi, Gaia Scafetta, Myriam Alcalay and Francesca D Ciccarelli
    Citation: BMC Evolutionary Biology 2007 7:187
    Content type: Research article Published on:

  40. The water buffalo- Bu balus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poor...

    Authors: Satish Kumar, Muniyandi Nagarajan, Jasmeet S Sandhu, Niraj Kumar and Vandana Behl
    Citation: BMC Evolutionary Biology 2007 7:186
    Content type: Research article Published on:

  41. Because the systems of social organisation in the various species of Pemphigus aphids span the continuum from asociality through to advanced sociality (typified by the possession of morphologically specialised so...

    Authors: Nathan Pike, John A Whitfield and William A Foster
    Citation: BMC Evolutionary Biology 2007 7:185
    Content type: Research article Published on:

  42. The Mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. For example, M. haemolytica + M. glucosida are potential pathogens of the respiratory ...

    Authors: Jesper Larsen, Peter Kuhnert, Joachim Frey, Henrik Christensen, Magne Bisgaard and John E Olsen
    Citation: BMC Evolutionary Biology 2007 7:184
    Content type: Research article Published on:

  43. Microcystins are small cyclic heptapeptide toxins produced by a range of distantly related cyanobacteria. Microcystins are synthesized on large NRPS-PKS enzyme complexes. Many structural variants of microcysti...

    Authors: David P Fewer, Leo Rouhiainen, Jouni Jokela, Matti Wahlsten, Kati Laakso, Hao Wang and Kaarina Sivonen
    Citation: BMC Evolutionary Biology 2007 7:183
    Content type: Research article Published on:

  44. Tetrapods exhibit great diversity in limb structures among species and also between forelimbs and hindlimbs within species, diversity which frequently correlates with locomotor modes and life history. We aim t...

    Authors: Olaf RP Bininda-Emonds, Jonathan E Jeffery, Marcelo R Sánchez-Villagra, James Hanken, Matthew Colbert, Claude Pieau, Lynne Selwood, Carel ten Cate, Albert Raynaud, Casmile K Osabutey and Michael K Richardson
    Citation: BMC Evolutionary Biology 2007 7:182
    Content type: Research article Published on:

  45. Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allo...

    Authors: Javier Tamames, Rosario Gil, Amparo Latorre, Juli Peretó, Francisco J Silva and Andrés Moya
    Citation: BMC Evolutionary Biology 2007 7:181
    Content type: Research article Published on:

  46. Urodele amphibians like the axolotl are unique among vertebrates in their ability to regenerate and their resistance to develop cancers. It is unknown whether these traits are linked at the molecular level.

    Authors: Éric Villiard, Henner Brinkmann, Olga Moiseeva, Frédérick A Mallette, Gerardo Ferbeyre and Stéphane Roy
    Citation: BMC Evolutionary Biology 2007 7:180
    Content type: Research article Published on:

  47. Alternative splicing (AS) has been regarded capable of altering selection pressure on protein subsequences. Particularly, the frequency of reading frame preservation (FRFP), as a measure of selection pressure,...

    Authors: Feng-Chi Chen and Trees-Juen Chuang
    Citation: BMC Evolutionary Biology 2007 7:179
    Content type: Research article Published on:

  48. Comparative genomics has greatly improved our understanding of the evolution of pathogenic mycobacteria such as Mycobacterium tuberculosis. Here we have used data from a genome microarray analysis to explore inse...

    Authors: Michael Käser, Simona Rondini, Martin Naegeli, Tim Stinear, Francoise Portaels, Ulrich Certa and Gerd Pluschke
    Citation: BMC Evolutionary Biology 2007 7:177
    Content type: Research article Published on:

  50. Snake venom composition varies widely both among closely related species and within the same species, based on ecological variables. In terrestrial snakes, such variation has been proposed to be due to snakes'...

    Authors: Susanta Pahari, David Bickford, Bryan G Fry and R Manjunatha Kini
    Citation: BMC Evolutionary Biology 2007 7:175
    Content type: Research article Published on:

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