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  2. Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 an...

    Authors: Maria E Manetti, Magdalena Rossi, Ana PP Costa, Andrea M Clausen and Marie-Anne Van Sluys
    Citation: BMC Evolutionary Biology 2007 7:34
    Content type: Research article Published on:

  3. Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of ...

    Authors: Elena Simionato, Valérie Ledent, Gemma Richards, Morgane Thomas-Chollier, Pierre Kerner, David Coornaert, Bernard M Degnan and Michel Vervoort
    Citation: BMC Evolutionary Biology 2007 7:33
    Content type: Research article Published on:

  4. Genetic studies of the Arabian Peninsula are scarce even though the region was the center of ancient trade routes and empires and may have been the southern corridor for the earliest human migration from Afric...

    Authors: Khaled K Abu-Amero, Ana M González, Jose M Larruga, Thomas M Bosley and Vicente M Cabrera
    Citation: BMC Evolutionary Biology 2007 7:32
    Content type: Research article Published on:

  5. Mitochondrial porins, or voltage-dependent anion-selective channels (VDAC) allow the passage of small molecules across the mitochondrial outer membrane, and are involved in complex interactions regulating orga...

    Authors: Matthew J Young, Denice C Bay, Georg Hausner and Deborah A Court
    Citation: BMC Evolutionary Biology 2007 7:31
    Content type: Research article Published on:

  7. In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models incl...

    Authors: V Lila Koumandou, Joel B Dacks, Richard MR Coulson and Mark C Field
    Citation: BMC Evolutionary Biology 2007 7:29
    Content type: Research article Published on:

  9. Nuclear receptors (NRs) are important transcriptional modulators in metazoans which regulate transcription through binding to the promoter region of their target gene by the DNA binding domain (DBD) and activa...

    Authors: Wenjie Wu, Edward G Niles, Hirohisa Hirai and Philip T LoVerde
    Citation: BMC Evolutionary Biology 2007 7:27
    Content type: Research article Published on:

  11. Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different s...

    Authors: Paul ME Bunje, Marta Barluenga and Axel Meyer
    Citation: BMC Evolutionary Biology 2007 7:25
    Content type: Research article Published on:

  12. The glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) evolved from a common ancestor. Still not completely understood is how specificity for glucocorticoids (e.g. cortisol) and mineralocorticoid...

    Authors: Michael E Baker, Charlie Chandsawangbhuwana and Noah Ollikainen
    Citation: BMC Evolutionary Biology 2007 7:24
    Content type: Research article Published on:

  13. Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified i...

    Authors: Edna C Suárez-Castillo and José E García-Arrarás
    Citation: BMC Evolutionary Biology 2007 7:23
    Content type: Research article Published on:

  14. Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native ...

    Authors: Debra L Fisk, Leigh C Latta IV, Roland A Knapp and Michael E Pfrender
    Citation: BMC Evolutionary Biology 2007 7:22
    Content type: Research article Published on:

  15. Introductions of non-native species can significantly alter the selective environment for populations of native species, which can respond through phenotypic plasticity or genetic adaptation. We examined pheno...

    Authors: Leigh C Latta IV, Jeremy W Bakelar, Roland A Knapp and Michael E Pfrender
    Citation: BMC Evolutionary Biology 2007 7:21
    Content type: Research article Published on:

  16. How are morphological evolution and developmental changes related? This rather old and intriguing question had a substantial boost after the 70s within the framework of heterochrony (changes in rates or timing...

    Authors: Gabriel Marroig
    Citation: BMC Evolutionary Biology 2007 7:20
    Content type: Research article Published on:

  17. In this paper we describe an analysis of the size evolution of both protein domains and their indels, as inferred by changing sizes of whole domains or individual unaligned regions or "spacers". We studied rel...

    Authors: Yuri Wolf, Thomas Madej, Vladimir Babenko, Benjamin Shoemaker and Anna R Panchenko
    Citation: BMC Evolutionary Biology 2007 7:19
    Content type: Research article Published on:

  19. The effectiveness of elimination of slightly deleterious mutations depends mainly on drift and recombination frequency. Here we analyze the influence of these two factors on the strength of the purifying selec...

    Authors: Leila Mamirova, Konstantin Popadin and Mikhail S Gelfand
    Citation: BMC Evolutionary Biology 2007 7:17
    Content type: Research article Published on:

  20. We report an analysis of a protein network of functionally linked proteins, identified from a phylogenetic statistical analysis of complete eukaryotic genomes. Phylogenetic methods identify pairs of proteins t...

    Authors: Mark Pagel, Andrew Meade and Daniel Scott
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  21. Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister...

    Authors: David S Horner, Konstantinos Lefkimmiatis, Aurelio Reyes, Carmela Gissi, Cecilia Saccone and Graziano Pesole
    Citation: BMC Evolutionary Biology 2007 7:16
    Content type: Research article Published on:

  22. Transcription factors regulate gene expression by interacting with their specific DNA binding sites. Some transcription factors, particularly those involved in transcription initiation, always bind close to tr...

    Authors: Brandon Smith, Hung Fang, Youlian Pan, P Roy Walker, A Fazel Famili and Marianna Sikorska
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  23. Widespread transcription activities in the human genome were recently observed in high-resolution tiling array experiments, which revealed many novel transcripts that are outside of the boundaries of known pro...

    Authors: Zhaolei Zhang, Andy Wing Chun Pang and Mark Gerstein
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  24. Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome bi...

    Authors: Michael D Woodhams, Peter F Stadler, David Penny and Lesley J Collins
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  25. Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone to systematic error. Phylogenomic analysis reduces these errors by inferring protein func...

    Authors: Nandini Krishnamurthy, Duncan Brown and Kimmen Sjölander
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  26. The diversity of visual systems in fish has long been of interest for evolutionary biologists and neurophysiologists, and has recently begun to attract the attention of molecular evolutionary geneticists. Seve...

    Authors: Cameron J Weadick and Belinda SW Chang
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  28. Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions loca...

    Authors: Hui Chen and Mathieu Blanchette
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  29. Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the domin...

    Authors: Pradeep Reddy Marri, Weilong Hao and G Brian Golding
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  30. A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this r...

    Authors: Iñaki Comas, Andrés Moya and Fernando González-Candelas
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  31. Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patte...

    Authors: Huai-Chun Wang and Donal A Hickey
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  32. Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolu...

    Authors: Le Bao, Hong Gu, Katherine A Dunn and Joseph P Bielawski
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S5
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  33. Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the...

    Authors: Nicolas Lartillot, Henner Brinkmann and Hervé Philippe
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  34. Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nucle...

    Authors: Michael J Sanderson and Michelle M McMahon
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  35. Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the ...

    Authors: Béatrice Roure, Naiara Rodriguez-Ezpeleta and Hervé Philippe
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S2
    Content type: Software Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  36. The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and pr...

    Authors: Hervé Philippe and Mathieu Blanchette
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  37. One of the important insights of quasi-species theory is an error-threshold. The error-threshold is the error rate of replication above which the sudden onset of the population delocalization from the fittest ...

    Authors: Nobuto Takeuchi and Paulien Hogeweg
    Citation: BMC Evolutionary Biology 2007 7:15
    Content type: Correspondence Published on:

  38. The origin of angiosperms has been under debate since the time of Darwin. While there has been much speculation in past decades about pre-Cretaceous angiosperms, including Archaefructus, these reports are controv...

    Authors: Xin Wang, Shuying Duan, Baoyin Geng, Jinzhong Cui and Yong Yang
    Citation: BMC Evolutionary Biology 2007 7:14
    Content type: Research article Published on:

  41. The parasitic Platyhelminthes (Neodermata) contains three parasitic groups of flatworms, each having a unique morphology, and life style: Monogenea (primarily ectoparasitic), Trematoda (endoparasitic flukes), ...

    Authors: Joong-Ki Park, Kyu-Heon Kim, Seokha Kang, Won Kim, Keeseon S Eom and DTJ Littlewood
    Citation: BMC Evolutionary Biology 2007 7:11
    Content type: Research article Published on:

  42. Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovat...

    Authors: Kohji Mabuchi, Masaki Miya, Yoichiro Azuma and Mutsumi Nishida
    Citation: BMC Evolutionary Biology 2007 7:10
    Content type: Research article Published on:

  43. Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolut...

    Authors: Yoshihiro Kawahara and Tadashi Imanishi
    Citation: BMC Evolutionary Biology 2007 7:9
    Content type: Research article Published on:

  45. The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and bre...

    Authors: Stephan Koblmüller, Nina Duftner, Kristina M Sefc, Mitsuto Aibara, Martina Stipacek, Michel Blanc, Bernd Egger and Christian Sturmbauer
    Citation: BMC Evolutionary Biology 2007 7:7
    Content type: Research article Published on:

  46. Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in A...

    Authors: Margaret E Kellogg, Sandra Burkett, Thomas R Dennis, Gary Stone, Brian A Gray, Peter M McGuire, Roberto T Zori and Roscoe Stanyon
    Citation: BMC Evolutionary Biology 2007 7:6
    Content type: Research article Published on:

  47. In acoustic species, traits such as male calling song are likely to diverge quickly between allopatric populations due to sexual selection, and divergence in parameters such as carrier frequency, chirp structu...

    Authors: Nathan W Bailey, Darryl T Gwynne, William V Bailey and Michael G Ritchie
    Citation: BMC Evolutionary Biology 2007 7:5
    Content type: Research article Published on:

  48. Dispersal between habitat patches is a key process in the functioning of (meta)populations. As distance between suitable habitats increases, the ongoing process of habitat fragmentation is expected to generate...

    Authors: Nicolas Schtickzelle, Augustin Joiris, Hans Van Dyck and Michel Baguette
    Citation: BMC Evolutionary Biology 2007 7:4
    Content type: Research article Published on:

  49. In animals, the biogenesis of some lipoprotein classes requires members of the ancient large lipid transfer protein (LLTP) superfamily, including the cytosolic large subunit of microsomal triglyceride transfer...

    Authors: Jean-Christophe Avarre, Esther Lubzens and Patrick J Babin
    Citation: BMC Evolutionary Biology 2007 7:3
    Content type: Research article Published on:

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