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  1. Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-r...

    Authors: Serge N Vinogradov, David Hoogewijs, Xavier Bailly, Raúl Arredondo-Peter, Julian Gough, Sylvia Dewilde, Luc Moens and Jacques R Vanfleteren
    Citation: BMC Evolutionary Biology 2006 6:31
  2. The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ...

    Authors: Elena M Kramer, Huei-Jiun Su, Cheng-Chiang Wu and Jer-Ming Hu
    Citation: BMC Evolutionary Biology 2006 6:30
  3. In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution m...

    Authors: Thomas M Keane, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton and James O Mclnerney
    Citation: BMC Evolutionary Biology 2006 6:29
  4. Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evo...

    Authors: Charles TT Edwards, Edward C Holmes, Daniel J Wilson, Raphael P Viscidi, Elaine J Abrams, Rodney E Phillips and Alexei J Drummond
    Citation: BMC Evolutionary Biology 2006 6:28
  5. Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the ...

    Authors: Jan O Andersson, Robert P Hirt, Peter G Foster and Andrew J Roger
    Citation: BMC Evolutionary Biology 2006 6:27
  6. The exchange of nucleotides at synonymous sites in a gene encoding a protein is believed to have little impact on the fitness of a host organism. This should be especially true for synonymous transitions, wher...

    Authors: Tang Li, Stephen G Chamberlin, M Daniel Caraco, David A Liberles, Eric A Gaucher and Steven A Benner
    Citation: BMC Evolutionary Biology 2006 6:25
  7. Multi-character empirical studies are important contributions to our understanding of the process of speciation. The relatively conserved morphology of, and importance of the mate recognition system in anurans...

    Authors: Stephen C Lougheed, James D Austin, James P Bogart, Peter T Boag and Andrew A Chek
    Citation: BMC Evolutionary Biology 2006 6:23
  8. While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer...

    Authors: Shaul Shaul, Ruth Nussinov and Tal Pupko
    Citation: BMC Evolutionary Biology 2006 6:22
  9. The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are sp...

    Authors: Nicolas Corradi and Ian R Sanders
    Citation: BMC Evolutionary Biology 2006 6:21
  10. Papillomaviruses (PVs) infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the ...

    Authors: Santiago García-Vallvé, José R Iglesias-Rozas, Ángel Alonso and Ignacio G Bravo
    Citation: BMC Evolutionary Biology 2006 6:20
  11. Colour polymorphisms are widespread and one of the prime examples is the colour polymorphism in female coenagrionid damselflies: one female morph resembles the male colour (andromorph) while one, or more, fema...

    Authors: Gerrit Joop, Andreas Mitschke, Jens Rolff and Michael T Siva-Jothy
    Citation: BMC Evolutionary Biology 2006 6:19
  12. In eukaryotes, histone H3 lysine 9 (H3K9) methylation is a common mechanism involved in gene silencing and the establishment of heterochromatin. The loci of the major heterochromatic H3K9 methyltransferase Su(...

    Authors: Veiko Krauss, Anne Fassl, Petra Fiebig, Ina Patties and Heinz Sass
    Citation: BMC Evolutionary Biology 2006 6:18
  13. The number of species within the Malagasy genus Lepilemur and their phylogenetic relationships is disputed and controversial. In order to establish their evolutionary relationships, a comparative cytogenetic and ...

    Authors: Nicole Andriaholinirina, Jean-Luc Fausser, Christian Roos, Dietmar Zinner, Urs Thalmann, Clément Rabarivola, Iary Ravoarimanana, Jörg U Ganzhorn, Bernhard Meier, Roland Hilgartner, Lutz Walter, Alphonse Zaramody, Christoph Langer, Thomas Hahn, Elke Zimmermann, Ute Radespiel…
    Citation: BMC Evolutionary Biology 2006 6:17
  14. The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17), potent...

    Authors: Mack E Crayton III, Bradford C Powell, Todd J Vision and Morgan C Giddings
    Citation: BMC Evolutionary Biology 2006 6:16
  15. Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer even...

    Authors: Robert G Beiko and Nicholas Hamilton
    Citation: BMC Evolutionary Biology 2006 6:15
  16. Phylogenetic conservation at the DNA level is routinely used as evidence of molecular function, under the assumption that locations and sequences of functional DNA segments remain invariant in evolution. In pa...

    Authors: Georgii A Bazykin and Alexey S Kondrashov
    Citation: BMC Evolutionary Biology 2006 6:14
  17. Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a larg...

    Authors: Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B Stern and Claude W dePamphilis
    Citation: BMC Evolutionary Biology 2006 6:13
  18. The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic posit...

    Authors: James F Parham, Chris R Feldman and Jeffrey L Boore
    Citation: BMC Evolutionary Biology 2006 6:11
  19. The family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. ...

    Authors: Fabio S Raposo do Amaral, Matthew J Miller, Luís Fábio Silveira, Eldredge Bermingham and Anita Wajntal
    Citation: BMC Evolutionary Biology 2006 6:10
  20. The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-prot...

    Authors: Stefan Wuchty, Albert-Laszlo Barabási and Michael T Ferdig
    Citation: BMC Evolutionary Biology 2006 6:8
  21. The rate of molecular evolution varies widely between proteins, both within and among lineages. To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we...

    Authors: Joël Savard, Diethard Tautz and Martin J Lercher
    Citation: BMC Evolutionary Biology 2006 6:7
  22. Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from S-adenosylmethionine to the 2'-OH or 3'-OH group of ...

    Authors: Karolina L Tkaczuk, Agnieszka Obarska and Janusz M Bujnicki
    Citation: BMC Evolutionary Biology 2006 6:6
  23. Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of...

    Authors: Etienne GJ Danchin, Philippe Gouret and Pierre Pontarotti
    Citation: BMC Evolutionary Biology 2006 6:5
  24. Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombina...

    Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle and HW Stokes
    Citation: BMC Evolutionary Biology 2006 6:3
  25. Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear th...

    Authors: James W Wilson and Cheryl A Nickerson
    Citation: BMC Evolutionary Biology 2006 6:2
  26. Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10–20 times lower than in plant nuclear genomes,...

    Authors: Christopher L Parkinson, Jeffrey P Mower, Yin-Long Qiu, Andrew J Shirk, Keming Song, Nelson D Young, Claude W dePamphilis and Jeffrey D Palmer
    Citation: BMC Evolutionary Biology 2005 5:73
  27. Calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients...

    Authors: Steffen Abel, Tatyana Savchenko and Maggie Levy
    Citation: BMC Evolutionary Biology 2005 5:72
  28. Evolutionary analyses of the largest subunit of RNA polymerase II (RPB1) have yielded important and at times provocative results. One particularly troublesome outcome is the consistent inference of independent...

    Authors: John W Stiller and Leslie Harrell
    Citation: BMC Evolutionary Biology 2005 5:71
  29. Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most...

    Authors: Carles Lalueza-Fox, Jose Castresana, Lourdes Sampietro, Tomàs Marquès-Bonet, Josep Antoni Alcover and Jaume Bertranpetit
    Citation: BMC Evolutionary Biology 2005 5:70
  30. Merlin, the product of the Neurofibromatosis type 2 (NF2) tumor suppressor gene, belongs to the ezrin-radixin-moesin (ERM) subgroup of the protein 4.1 superfamily, which links cell surface glycoproteins to the ac...

    Authors: Kseniya Golovnina, Alexander Blinov, Elena M Akhmametyeva, Leonid V Omelyanchuk and Long-Sheng Chang
    Citation: BMC Evolutionary Biology 2005 5:69
  31. Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated i...

    Authors: Debashish Bhattacharya, Valérie Reeb, Dawn M Simon and François Lutzoni
    Citation: BMC Evolutionary Biology 2005 5:68
  32. In Drosophila melanogaster the Enhancer of split-Complex [E(spl)-C] consists of seven highly related genes encoding basic helix-loop-helix (bHLH) repressors and intermingled, four genes that belong to the Bearded...

    Authors: Rebekka Schlatter and Dieter Maier
    Citation: BMC Evolutionary Biology 2005 5:67
  33. Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffold...

    Authors: Annkatrin Rose, Shannon J Schraegle, Eric A Stahlberg and Iris Meier
    Citation: BMC Evolutionary Biology 2005 5:66
  34. Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon i...

    Authors: Sofia Berlin and Nick GC Smith
    Citation: BMC Evolutionary Biology 2005 5:65
  35. Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but ...

    Authors: Charles Chapus, Christine Dufraigne, Scott Edwards, Alain Giron, Bernard Fertil and Patrick Deschavanne
    Citation: BMC Evolutionary Biology 2005 5:63
  36. Prior to the sequencing of the human genome it was typically assumed that, tandem duplication aside, gene order is for the most part random. Numerous observers, however, highlighted instances in which a ligand...

    Authors: Laurence D Hurst and Martin J Lercher
    Citation: BMC Evolutionary Biology 2005 5:62
  37. Confronted with well-defended, novel hosts, should an enemy invest in avoidance of these hosts (behavioral adaptation), neutralization of the defensive innovation (physiological adaptation) or both? Although simu...

    Authors: Corinne Vacher, Sam P Brown and Michael E Hochberg
    Citation: BMC Evolutionary Biology 2005 5:60
  38. Costly structures need to represent an adaptive advantage in order to be maintained over evolutionary times. Contrary to many other conspicuous shell ornamentations of gastropods, the haired shells of several ...

    Authors: Markus Pfenninger, Magda Hrabáková, Dirk Steinke and Aline Dèpraz
    Citation: BMC Evolutionary Biology 2005 5:59
  39. Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiatio...

    Authors: Marina V Omelchenko, Yuri I Wolf, Elena K Gaidamakova, Vera Y Matrosova, Alexander Vasilenko, Min Zhai, Michael J Daly, Eugene V Koonin and Kira S Makarova
    Citation: BMC Evolutionary Biology 2005 5:57
  40. Plastid-bearing cryptophytes like Cryptomonas contain four genomes in a cell, the nucleus, the nucleomorph, the plastid genome and the mitochondrial genome. Comparative phylogenetic analyses encompassing DNA sequ...

    Authors: Kerstin Hoef-Emden, Hoang-Dung Tran and Michael Melkonian
    Citation: BMC Evolutionary Biology 2005 5:56
  41. Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological signifi...

    Authors: Gabriela Guerrero, Humberto Peralta, Alejandro Aguilar, Rafael Díaz, Miguel Angel Villalobos, Arturo Medrano-Soto and Jaime Mora
    Citation: BMC Evolutionary Biology 2005 5:55

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