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  1. 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

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

  2. 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

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

  3. 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

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

  4. 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

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

  5. 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

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

  6. 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

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

  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. The dynamics of antagonistic host-parasite coevolution are believed to be crucially dependent on the rate of migration between populations. We addressed how the rate of simultaneous migration of host and paras...

    Authors: Andrew D Morgan, Michael A Brockhurst, Laura DC Lopez-Pascua, Csaba Pal and Angus Buckling
    Citation: BMC Evolutionary Biology 2007 7:1
  18. The compatible solute trehalose is a non-reducing disaccharide, which accumulates upon heat, cold or osmotic stress. It was commonly accepted that trehalose is only present in extremophiles or cryptobiotic org...

    Authors: Nelson Avonce, Alfredo Mendoza-Vargas, Enrique Morett and Gabriel Iturriaga
    Citation: BMC Evolutionary Biology 2006 6:109
  19. Comparative approaches using protostome and deuterostome data have greatly contributed to understanding gene function and organismal complexity. The family 2 G-protein coupled receptors (GPCRs) are one of the ...

    Authors: João CR Cardoso, Vanda C Pinto, Florbela A Vieira, Melody S Clark and Deborah M Power
    Citation: BMC Evolutionary Biology 2006 6:108
  20. The highly homologous PE_PGRS (Proline-glutamic acid_polymorphic GC-rich repetitive sequence) genes are members of the PE multigene family which is found only in mycobacteria. PE genes are particularly abundan...

    Authors: Anis Karboul, Nicolaas C Gey van Pittius, Amine Namouchi, Véronique Vincent, Christophe Sola, Nalin Rastogi, Philip Suffys, Michel Fabre, Angel Cataldi, Richard C Huard, Natalia Kurepina, Barry Kreiswirth, John L Ho, M Cristina Gutierrez and Helmi Mardassi
    Citation: BMC Evolutionary Biology 2006 6:107
  21. It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, shou...

    Authors: Sònia Casillas, Bárbara Negre, Antonio Barbadilla and Alfredo Ruiz
    Citation: BMC Evolutionary Biology 2006 6:106
  22. The least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) ...

    Authors: Aleksandra Czarna, Rafael Sanjuán, Fernando González-Candelas and Borys Wróbel
    Citation: BMC Evolutionary Biology 2006 6:105
  23. In order to study the dynamics of evolutionary change, 12 populations of E. coli B were serially propagated for 20,000 generations in minimal glucose medium at constant 37°C. Correlated changes in various other t...

    Authors: Sean C Sleight, Nicholas S Wigginton and Richard E Lenski
    Citation: BMC Evolutionary Biology 2006 6:104
  24. The Caenorhabditis elegans genome is known to code for at least 1149 G protein-coupled receptors (GPCRs), but the GPCR(s) critical to the regulation of reproduction in this nematode are not yet known. This study ...

    Authors: Sivan Vadakkadath Meethal, Miguel J Gallego, Ryan J Haasl, Stephen J Petras III, Jean-Yves Sgro and Craig S Atwood
    Citation: BMC Evolutionary Biology 2006 6:103
  25. Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link...

    Authors: Virginie Roy, Christine Demanche, Alexandre Livet and Myriam Harry
    Citation: BMC Evolutionary Biology 2006 6:102
  26. Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, i...

    Authors: Alexandra Stechmann, Manuela Baumgartner, Jeffrey D Silberman and Andrew J Roger
    Citation: BMC Evolutionary Biology 2006 6:101
  27. Reliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of indiv...

    Authors: Markus Pfenninger, Mathilde Cordellier and Bruno Streit
    Citation: BMC Evolutionary Biology 2006 6:100
  28. To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to ...

    Authors: David A Fitzpatrick, Mary E Logue, Jason E Stajich and Geraldine Butler
    Citation: BMC Evolutionary Biology 2006 6:99
  29. The past decade has seen a remarkable increase in the number of recognized mouse lemur species (genus Microcebus). As recently as 1994, only two species of mouse lemur were recognized according to the rules of zo...

    Authors: Kellie L Heckman, Emilienne Rasoazanabary, Erica Machlin, Laurie R Godfrey and Anne D Yoder
    Citation: BMC Evolutionary Biology 2006 6:98
  30. Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebr...

    Authors: Ilke van Hazel, Francesco Santini, Johannes Müller and Belinda SW Chang
    Citation: BMC Evolutionary Biology 2006 6:97
  31. The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, tem...

    Authors: Pierre R Gérard, Etienne K Klein, Frédéric Austerlitz, Juan F Fernández-Manjarrés and Nathalie Frascaria-Lacoste
    Citation: BMC Evolutionary Biology 2006 6:96
  32. The PE and PPE multigene families of Mycobacterium tuberculosis comprise about 10% of the coding potential of the genome. The function of the proteins encoded by these large gene families remains unknown, althoug...

    Authors: Nicolaas C Gey van Pittius, Samantha L Sampson, Hyeyoung Lee, Yeun Kim, Paul D van Helden and Robin M Warren
    Citation: BMC Evolutionary Biology 2006 6:95
  33. The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP super...

    Authors: Robin MD Beck, Olaf RP Bininda-Emonds, Marcel Cardillo, Fu-Guo Robert Liu and Andy Purvis
    Citation: BMC Evolutionary Biology 2006 6:93
  34. There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and fun...

    Authors: Anthony Levasseur, Philippe Gouret, Laurence Lesage-Meessen, Michèle Asther, Marcel Asther, Eric Record and Pierre Pontarotti
    Citation: BMC Evolutionary Biology 2006 6:92
  35. The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functi...

    Authors: Lipika R Pal and Chittibabu Guda
    Citation: BMC Evolutionary Biology 2006 6:91
  36. The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome a...

    Authors: Ricardo DeMarco, Thiago M Venancio and Sergio Verjovski-Almeida
    Citation: BMC Evolutionary Biology 2006 6:89
  37. The fungus-growing ant-microbe symbiosis consists of coevolving microbial mutualists and pathogens. The diverse fungal lineages that these ants cultivate are attacked by parasitic microfungi of the genus Escovops...

    Authors: Nicole M Gerardo, Ulrich G Mueller and Cameron R Currie
    Citation: BMC Evolutionary Biology 2006 6:88
  38. Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relat...

    Authors: April D Harlin-Cognato and Rodney L Honeycutt
    Citation: BMC Evolutionary Biology 2006 6:87
  39. Lutzomyia intermedia and Lutzomyia whitmani (Diptera: Psychodidae) are important and very closely related vector species of cutaneous leishmaniasis in Brazil, which are distinguishable by a few morphological diff...

    Authors: Camila J Mazzoni, Nataly A Souza, Claudia Andrade-Coelho, Charalambos P Kyriacou and Alexandre A Peixoto
    Citation: BMC Evolutionary Biology 2006 6:85
  40. With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. One of these studies suggested good congruence betw...

    Authors: Mark WJ van Passel, Eiko E Kuramae, Angela CM Luyf, Aldert Bart and Teun Boekhout
    Citation: BMC Evolutionary Biology 2006 6:84
  41. Many bacteria can take up DNA, but the evolutionary history and function of natural competence and transformation remain obscure. The sporadic distribution of competence suggests it is frequently lost and/or g...

    Authors: Rosemary J Redfield, Wendy A Findlay, Janine Bossé, J Simon Kroll, Andrew DS Cameron and John HE Nash
    Citation: BMC Evolutionary Biology 2006 6:82
  42. For organisms living or interacting in groups, the decision-making processes of an individual may be based upon aspects of both its own state and the states of other organisms around it. Much research has soug...

    Authors: Sean A Rands and Rufus A Johnstone
    Citation: BMC Evolutionary Biology 2006 6:81

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