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  1. Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many indepe...

    Authors: Chenhong Li, Guillermo Ortí, Gong Zhang and Guoqing Lu

    Citation: BMC Evolutionary Biology 2007 7:44

    Content type: Methodology article

    Published on:

  2. The function and structure of protein translocons at the outer and inner envelope membrane of chloroplasts (Toc and Tic complexes, respectively) are a subject of intensive research. One of the proteins that ha...

    Authors: Mónica Balsera, Anna Stengel, Jürgen Soll and Bettina Bölter

    Citation: BMC Evolutionary Biology 2007 7:43

    Content type: Research article

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  3. Despite its pervasiveness, the genetic basis of adaptation resulting in variation directly or indirectly related to temperature (climatic) gradients is poorly understood. By using 3-fold replicated laboratory ...

    Authors: Hafid Laayouni, Francisco García-Franco, Blanca E Chávez-Sandoval, Vincenzo Trotta, Sergi Beltran, Montserrat Corominas and Mauro Santos

    Citation: BMC Evolutionary Biology 2007 7:42

    Content type: Research article

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  4. In order to obtain insights into the functionality of the human 4q35.2 domain harbouring the facioscapulohumeral muscular dystrophy (FSHD) locus, we investigated in African apes genomic and chromatin organisat...

    Authors: Beatrice Bodega, Maria Francesca Cardone, Stefan Müller, Michaela Neusser, Francesca Orzan, Elena Rossi, Elena Battaglioli, Anna Marozzi, Paola Riva, Mariano Rocchi, Raffaella Meneveri and Enrico Ginelli

    Citation: BMC Evolutionary Biology 2007 7:39

    Content type: Research article

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  5. Paedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic pos...

    Authors: Lukas Rüber, Maurice Kottelat, Heok Hui Tan, Peter KL Ng and Ralf Britz

    Citation: BMC Evolutionary Biology 2007 7:38

    Content type: Research article

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  6. The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ a...

    Authors: Benjamin Yee, Feras F Lafi, Brian Oakley, James T Staley and John A Fuerst

    Citation: BMC Evolutionary Biology 2007 7:37

    Content type: Research article

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  7. 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:

  8. 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:

  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  18. 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

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  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

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  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

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  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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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:

  37. 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:

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