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Volume 6;  2006
Commentary
Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements
J Peter Gogarten, Elena Hilario
BMC Evol Biol. 2006; 6: 94. Published online 2006 November 13. doi: 10.1186/1471-2148-6-94
PMCID:
PMC1654191
Abstract Full Text PDF–372K
Database
PHOG: a database of supergenomes built from proteome complements
Igor V Merkeev, Pavel S Novichkov, Andrey A Mironov
BMC Evol Biol. 2006; 6: 52. Published online 2006 June 22. doi: 10.1186/1471-2148-6-52
PMCID:
PMC1523204
Abstract Full Text PDF–294K
Software
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change
Mathieu Fourment, Mark J Gibbs
BMC Evol Biol. 2006; 6: 1. Published online 2006 January 3. doi: 10.1186/1471-2148-6-1
PMCID:
PMC1352388
Abstract Full Text PDF–313K
JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data
Antonio Carvajal-Rodriguez, Emilio Rolan-Alvarez
BMC Evol Biol. 2006; 6: 40. Published online 2006 May 9. doi: 10.1186/1471-2148-6-40
PMCID:
PMC1479385
Abstract Full Text PDF–517K Supplementary Material
PHOG-BLAST – a new generation tool for fast similarity search of protein families
Igor V Merkeev, Andrey A Mironov
BMC Evol Biol. 2006; 6: 51. Published online 2006 June 22. doi: 10.1186/1471-2148-6-51
PMCID:
PMC1522020
Abstract Full Text PDF–296K Supplementary Material
Research Articles
A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns
James W Wilson, Cheryl A Nickerson
BMC Evol Biol. 2006; 6: 2. Published online 2006 January 5. doi: 10.1186/1471-2148-6-2
PMCID:
PMC1360685
Abstract Full Text PDF–633K
Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio
Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle, HW Stokes
BMC Evol Biol. 2006; 6: 3. Published online 2006 January 18. doi: 10.1186/1471-2148-6-3
Correction in:
BMC Evol Biol. 2006; 6: 9.
PMCID:
PMC1382264
Abstract Full Text PDF–402K Correction
Diversity begets diversity: host expansions and the diversification of plant-feeding insects
Niklas Janz, Sören Nylin, Niklas Wahlberg
BMC Evol Biol. 2006; 6: 4. Published online 2006 January 18. doi: 10.1186/1471-2148-6-4
PMCID:
PMC1382262
Abstract Full Text PDF–457K
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
Etienne GJ Danchin, Philippe Gouret, Pierre Pontarotti
BMC Evol Biol. 2006; 6: 5. Published online 2006 January 18. doi: 10.1186/1471-2148-6-5
PMCID:
PMC1382263
Abstract Full Text PDF–350K Supplementary Material
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis
Karolina L Tkaczuk, Agnieszka Obarska, Janusz M Bujnicki
BMC Evol Biol. 2006; 6: 6. Published online 2006 January 24. doi: 10.1186/1471-2148-6-6
PMCID:
PMC1397878
Abstract Full Text PDF–3.7M Supplementary Material
Genome-wide acceleration of protein evolution in flies (Diptera)
Joël Savard, Diethard Tautz, Martin J Lercher
BMC Evol Biol. 2006; 6: 7. Published online 2006 January 25. doi: 10.1186/1471-2148-6-7
PMCID:
PMC1369000
Abstract Full Text PDF–361K
Stable evolutionary signal in a Yeast protein interaction network
Stefan Wuchty, Albert-Laszlo Barabási, Michael T Ferdig
BMC Evol Biol. 2006; 6: 8. Published online 2006 January 30. doi: 10.1186/1471-2148-6-8
PMCID:
PMC1395346
Abstract Full Text PDF–1.0M Supplementary Material
Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification
Fabio S Raposo do Amaral, Matthew J Miller, Luís Fábio Silveira, Eldredge Bermingham, Anita Wajntal
BMC Evol Biol. 2006; 6: 10. Published online 2006 February 7. doi: 10.1186/1471-2148-6-10
PMCID:
PMC1413559
Abstract Full Text PDF–382K Supplementary Material
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes
Daniel J Fairbanks, Peter J Maughan
BMC Evol Biol. 2006; 6: 12. Published online 2006 February 9. doi: 10.1186/1471-2148-6-12
PMCID:
PMC1457002
Abstract Full Text PDF–341K
Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach
Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B Stern, Claude W dePamphilis
BMC Evol Biol. 2006; 6: 13. Published online 2006 February 9. doi: 10.1186/1471-2148-6-13
PMCID:
PMC1421436
Abstract Full Text PDF–438K Supplementary Material
Rate of promoter class turn-over in yeast evolution
Georgii A Bazykin, Alexey S Kondrashov
BMC Evol Biol. 2006; 6: 14. Published online 2006 February 10. doi: 10.1186/1471-2148-6-14
PMCID:
PMC1457003
Abstract Full Text PDF–281K
Tracking the evolution of alternatively spliced exons within the Dscam family
Mack E Crayton, III, Bradford C Powell, Todd J Vision, Morgan C Giddings
BMC Evol Biol. 2006; 6: 16. Published online 2006 February 16. doi: 10.1186/1471-2148-6-16
PMCID:
PMC1397879
Abstract Full Text PDF–406K Supplementary Material
Molecular phylogeny and taxonomic revision of the sportive lemurs (Lepilemur, Primates)
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, Mathias Craul, Jürgen Tomiuk, Ian Tattersall, Yves Rumpler
BMC Evol Biol. 2006; 6: 17. Published online 2006 February 23. doi: 10.1186/1471-2148-6-17
PMCID:
PMC1397877
Abstract Full Text PDF–921K Supplementary Material
The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene
Veiko Krauss, Anne Fassl, Petra Fiebig, Ina Patties, Heinz Sass
BMC Evol Biol. 2006; 6: 18. Published online 2006 March 2. doi: 10.1186/1471-2148-6-18
PMCID:
PMC1435931
Abstract Full Text PDF–481K Supplementary Material
Immune function and parasite resistance in male and polymorphic female Coenagrion puella
Gerrit Joop, Andreas Mitschke, Jens Rolff, Michael T Siva-Jothy
BMC Evol Biol. 2006; 6: 19. Published online 2006 March 7. doi: 10.1186/1471-2148-6-19
PMCID:
PMC1431586
Abstract Full Text PDF–329K
Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region
Santiago García-Vallvé, José R Iglesias-Rozas, Ángel Alonso, Ignacio G Bravo
BMC Evol Biol. 2006; 6: 20. Published online 2006 March 9. doi: 10.1186/1471-2148-6-20
PMCID:
PMC1421437
Abstract Full Text PDF–392K
Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices
Nicolas Corradi, Ian R Sanders
BMC Evol Biol. 2006; 6: 21. Published online 2006 March 10. doi: 10.1186/1471-2148-6-21
PMCID:
PMC1479386
Abstract Full Text PDF–435K
Multi-character perspectives on the evolution of intraspecific differentiation in a neotropical hylid frog
Stephen C Lougheed, James D Austin, James P Bogart, Peter T Boag, Andrew A Chek
BMC Evol Biol. 2006; 6: 23. Published online 2006 March 15. doi: 10.1186/1471-2148-6-23
PMCID:
PMC1434785
Abstract Full Text PDF–703K Supplementary Material
No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation
Michael E Hellberg
BMC Evol Biol. 2006; 6: 24. Published online 2006 March 16. doi: 10.1186/1471-2148-6-24
PMCID:
PMC1431588
Abstract Full Text PDF–328K
Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
Tang Li, Stephen G Chamberlin, M Daniel Caraco, David A Liberles, Eric A Gaucher, Steven A Benner
BMC Evol Biol. 2006; 6: 25. Published online 2006 March 20. doi: 10.1186/1471-2148-6-25
PMCID:
PMC1435776
Abstract Full Text PDF–722K
Multiple lineage specific expansions within the guanylyl cyclase gene family
David A Fitzpatrick, Damien M O'Halloran, Ann M Burnell
BMC Evol Biol. 2006; 6: 26. Published online 2006 March 20. doi: 10.1186/1471-2148-6-26
PMCID:
PMC1435932
Abstract Full Text PDF–576K Supplementary Material
Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes
Jan O Andersson, Robert P Hirt, Peter G Foster, Andrew J Roger
BMC Evol Biol. 2006; 6: 27. Published online 2006 March 21. doi: 10.1186/1471-2148-6-27
PMCID:
PMC1484493
Abstract Full Text PDF–487K Supplementary Material
Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
Charles TT Edwards, Edward C Holmes, Daniel J Wilson, Raphael P Viscidi, Elaine J Abrams, Rodney E Phillips, Alexei J Drummond
BMC Evol Biol. 2006; 6: 28. Published online 2006 March 23. doi: 10.1186/1471-2148-6-28
PMCID:
PMC1444934
Abstract Full Text PDF–375K Supplementary Material
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
Thomas M Keane, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton, James O Mclnerney
BMC Evol Biol. 2006; 6: 29. Published online 2006 March 24. doi: 10.1186/1471-2148-6-29
PMCID:
PMC1435933
Abstract Full Text PDF–379K
A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage
Elena M Kramer, Huei-Jiun Su, Cheng-Chiang Wu, Jer-Ming Hu
BMC Evol Biol. 2006; 6: 30. Published online 2006 March 24. doi: 10.1186/1471-2148-6-30
PMCID:
PMC1513400
Abstract Full Text PDF–513K Supplementary Material
A phylogenomic profile of globins
Serge N Vinogradov, David Hoogewijs, Xavier Bailly, Raúl Arredondo-Peter, Julian Gough, Sylvia Dewilde, Luc Moens, Jacques R Vanfleteren
BMC Evol Biol. 2006; 6: 31. Published online 2006 April 7. doi: 10.1186/1471-2148-6-31
PMCID:
PMC1457004
Abstract Full Text PDF–848K Supplementary Material
Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids
Robert K Jansen, Charalambos Kaittanis, Christopher Saski, Seung-Bum Lee, Jeffrey Tomkins, Andrew J Alverson, Henry Daniell
BMC Evol Biol. 2006; 6: 32. Published online 2006 April 9. doi: 10.1186/1471-2148-6-32
PMCID:
PMC1479384
Abstract Full Text PDF–551K
Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation
Patrick McKenzie, Seetharam C Chadalavada, Justin Bohrer, Josephine C Adams
BMC Evol Biol. 2006; 6: 33. Published online 2006 April 18. doi: 10.1186/1471-2148-6-33
PMCID:
PMC1464143
Abstract Full Text PDF–649K Supplementary Material
A high density of ancient spliceosomal introns in oxymonad excavates
Claudio H Slamovits, Patrick J Keeling
BMC Evol Biol. 2006; 6: 34. Published online 2006 April 25. doi: 10.1186/1471-2148-6-34
PMCID:
PMC1501061
Abstract Full Text PDF–344K
Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes)
Martin Kemler, Markus Göker, Franz Oberwinkler, Dominik Begerow
BMC Evol Biol. 2006; 6: 35. Published online 2006 April 25. doi: 10.1186/1471-2148-6-35
PMCID:
PMC1526759
Abstract Full Text PDF–544K Supplementary Material
A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects
Kathleen M Kay, Justen B Whittall, Scott A Hodges
BMC Evol Biol. 2006; 6: 36. Published online 2006 April 25. doi: 10.1186/1471-2148-6-36
PMCID:
PMC1484492
Abstract Full Text PDF–310K Supplementary Material
The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands
Jean-Charles de Cambiaire, Christian Otis, Claude Lemieux, Monique Turmel
BMC Evol Biol. 2006; 6: 37. Published online 2006 April 25. doi: 10.1186/1471-2148-6-37
PMCID:
PMC1513399
Abstract Full Text PDF–776K
Differential gene transfers and gene duplications in primary and secondary endosymbioses
Stefan Zauner, Peter Lockhart, Bettina Stoebe-Maier, Paul Gilson, Geoffrey I McFadden, Uwe G Maier
BMC Evol Biol. 2006; 6: 38. Published online 2006 April 26. doi: 10.1186/1471-2148-6-38
PMCID:
PMC1550267
Abstract Full Text PDF–325K
Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron
Odd-Gunnar Wikmark, Christer Einvik, Johan F De Jonckheere, Steinar D Johansen
BMC Evol Biol. 2006; 6: 39. Published online 2006 May 2. doi: 10.1186/1471-2148-6-39
PMCID:
PMC1464144
Abstract Full Text PDF–457K
The distribution and evolutionary history of the PRP8 intein
Margaret I Butler, Jeremy Gray, Timothy JD Goodwin, Russell TM Poulter
BMC Evol Biol. 2006; 6: 42. Published online 2006 May 31. doi: 10.1186/1471-2148-6-42
PMCID:
PMC1508164
Abstract Full Text PDF–607K Supplementary Material
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
Ugo Bastolla, Markus Porto, H Eduardo Roman, Michele Vendruscolo
BMC Evol Biol. 2006; 6: 43. Published online 2006 May 31. doi: 10.1186/1471-2148-6-43
PMCID:
PMC1570368
Abstract Full Text PDF–820K
The evolution of activity breaks in the nest cycle of annual eusocial bees: a model of delayed exponential growth
Oliver Mitesser, Norbert Weissel, Erhard Strohm, Hans-Joachim Poethke
BMC Evol Biol. 2006; 6: 45. Published online 2006 June 2. doi: 10.1186/1471-2148-6-45
PMCID:
PMC1533862
Abstract Full Text PDF–422K
Comparative rates of evolution in endosymbiotic nuclear genomes
Nicola J Patron, Matthew B Rogers, Patrick J Keeling
BMC Evol Biol. 2006; 6: 46. Published online 2006 June 14. doi: 10.1186/1471-2148-6-46
PMCID:
PMC1523203
Abstract Full Text PDF–1.5M Supplementary Material
Mitochondrial sequence data expose the putative cosmopolitan polychaete Scoloplos armiger (Annelida, Orbiniidae) as a species complex
Christoph Bleidorn, Inken Kruse, Sylvia Albrecht, Thomas Bartolomaeus
BMC Evol Biol. 2006; 6: 47. Published online 2006 June 15. doi: 10.1186/1471-2148-6-47
PMCID:
PMC1550730
Abstract Full Text PDF–446K
ESTimating plant phylogeny: lessons from partitioning
Jose EB de la Torre, Mary G Egan, Manpreet S Katari, Eric D Brenner, Dennis W Stevenson, Gloria M Coruzzi, Rob DeSalle
BMC Evol Biol. 2006; 6: 48. Published online 2006 June 15. doi: 10.1186/1471-2148-6-48
PMCID:
PMC1564041
Abstract Full Text PDF–884K Supplementary Material
Mitochondrial phylogeny and phylogeography of East African squeaker catfishes (Siluriformes: Synodontis)
Stephan Koblmüller, Christian Sturmbauer, Erik Verheyen, Axel Meyer, Walter Salzburger
BMC Evol Biol. 2006; 6: 49. Published online 2006 June 19. doi: 10.1186/1471-2148-6-49
PMCID:
PMC1543664
Abstract Full Text PDF–1.4M
Differentiated evolutionary rates in alternative exons and the implications for splicing regulation
Mireya Plass, Eduardo Eyras
BMC Evol Biol. 2006; 6: 50. Published online 2006 June 22. doi: 10.1186/1471-2148-6-50
PMCID:
PMC1543662
Abstract Full Text PDF–1.1M Supplementary Material
Highly variable sperm precedence in the stalk-eyed fly, Teleopsis dalmanni
Laura S Corley, Samuel Cotton, Ellen McConnell, Tracey Chapman, Kevin Fowler, Andrew Pomiankowski
BMC Evol Biol. 2006; 6: 53. Published online 2006 June 26. doi: 10.1186/1471-2148-6-53
PMCID:
PMC1543661
Abstract Full Text PDF–286K
No evidence for learned mating discrimination in male Drosophila pseudoobscura
Nikolai P Kandul, Kevin M Wright, Ekaterina V Kandul, Mohamed AF Noor
BMC Evol Biol. 2006; 6: 54. Published online 2006 July 6. doi: 10.1186/1471-2148-6-54
PMCID:
PMC1534054
Abstract Full Text PDF–229K
Tempo and mode of early gene loss in endosymbiotic bacteria from insects
F Delmotte, C Rispe, J Schaber, FJ Silva, A Moya
BMC Evol Biol. 2006; 6: 56. Published online 2006 July 18. doi: 10.1186/1471-2148-6-56
PMCID:
PMC1544356
Abstract Full Text PDF–373K
Environmental stress and reproduction in Drosophila melanogaster: starvation resistance, ovariole numbers and early age egg production
Marta L Wayne, Usha Soundararajan, Lawrence G Harshman
BMC Evol Biol. 2006; 6: 57. Published online 2006 July 18. doi: 10.1186/1471-2148-6-57
PMCID:
PMC1550266
Abstract Full Text PDF–365K
Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome
Debra T Burhans, Lakshmi Ramachandran, Jianxin Wang, Ping Liang, Hugh G Patterton, Michael Breitenbach, William C Burhans
BMC Evol Biol. 2006; 6: 58. Published online 2006 July 21. doi: 10.1186/1471-2148-6-58
PMCID:
PMC1550265
Abstract Full Text PDF–4.1M Supplementary Material
Genetic structure and evolution of the Vps25 family, a yeast ESCRT-II component
Ruth Slater, Naomi E Bishop
BMC Evol Biol. 2006; 6: 59. Published online 2006 August 4. doi: 10.1186/1471-2148-6-59
PMCID:
PMC1579232
Abstract Full Text PDF–502K Supplementary Material
Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage
RP Tucker, K Drabikowski, JF Hess, J Ferralli, R Chiquet-Ehrismann, JC Adams
BMC Evol Biol. 2006; 6: 60. Published online 2006 August 7. doi: 10.1186/1471-2148-6-60
PMCID:
PMC1578592
Abstract Full Text PDF–2.0M Supplementary Material
Evolutionary constraints on yeast protein size
Jonas Warringer, Anders Blomberg
BMC Evol Biol. 2006; 6: 61. Published online 2006 August 15. doi: 10.1186/1471-2148-6-61
PMCID:
PMC1560397
Abstract Full Text PDF–1.4M
Retrotranspositions in orthologous regions of closely related grass species
Chunguang Du, Zuzana Swigoňová, Joachim Messing
BMC Evol Biol. 2006; 6: 62. Published online 2006 August 16. doi: 10.1186/1471-2148-6-62
PMCID:
PMC1560396
Abstract Full Text PDF–358K Supplementary Material
On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
Yanbin Yin, Daniel Fischer
BMC Evol Biol. 2006; 6: 63. Published online 2006 August 16. doi: 10.1186/1471-2148-6-63
PMCID:
PMC1559721
Abstract Full Text PDF–295K Supplementary Material
The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages
Deborah A Johnson, Jeffrey P Hill, Michael A Thomas
BMC Evol Biol. 2006; 6: 64. Published online 2006 August 21. doi: 10.1186/1471-2148-6-64
PMCID:
PMC1578591
Abstract Full Text PDF–3.5M Supplementary Material
Systematics within Gyps vultures: a clade at risk
Jeff A Johnson, Heather RL Lerner, Pamela C Rasmussen, David P Mindell
BMC Evol Biol. 2006; 6: 65. Published online 2006 August 23. doi: 10.1186/1471-2148-6-65
PMCID:
PMC1569873
Abstract Full Text PDF–563K Supplementary Material
The shape of human gene family phylogenies
James A Cotton, Roderic DM Page
BMC Evol Biol. 2006; 6: 66. Published online 2006 August 29. doi: 10.1186/1471-2148-6-66
PMCID:
PMC1618862
Abstract Full Text PDF–388K
Thermal plasticity in Drosophila melanogaster: A comparison of geographic populations
Vincenzo Trotta, Federico CF Calboli, Marcello Ziosi, Daniela Guerra, Maria C Pezzoli, Jean R David, Sandro Cavicchi
BMC Evol Biol. 2006; 6: 67. Published online 2006 August 30. doi: 10.1186/1471-2148-6-67
PMCID:
PMC1569442
Abstract Full Text PDF–676K
Interspecific competition between entomopathogenic nematodes (Steinernema) is modified by their bacterial symbionts (Xenorhabdus)
Mathieu Sicard, Julie Hinsinger, Nathalie Le Brun, Sylvie Pages, Noël Boemare, Catherine Moulia
BMC Evol Biol. 2006; 6: 68. Published online 2006 September 5. doi: 10.1186/1471-2148-6-68
PMCID:
PMC1569874
Abstract Full Text PDF–373K
Phase distribution of spliceosomal introns: implications for intron origin
Hung D Nguyen, Maki Yoshihama, Naoya Kenmochi
BMC Evol Biol. 2006; 6: 69. Published online 2006 September 8. doi: 10.1186/1471-2148-6-69
PMCID:
PMC1574350
Abstract Full Text PDF–757K Supplementary Material
Global similarity and local divergence in human and mouse gene co-expression networks
Panayiotis Tsaparas, Leonardo Mariño-Ramírez, Olivier Bodenreider, Eugene V Koonin, I King Jordan
BMC Evol Biol. 2006; 6: 70. Published online 2006 September 12. doi: 10.1186/1471-2148-6-70
PMCID:
PMC1601971
Abstract Full Text PDF–1.5M Supplementary Material
Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria
Chagai Rot, Itay Goldfarb, Micha Ilan, Dorothée Huchon
BMC Evol Biol. 2006; 6: 71. Published online 2006 September 14. doi: 10.1186/1471-2148-6-71
PMCID:
PMC1618405
Abstract Full Text PDF–1.8M Supplementary Material
A phyloclimatic study of Cyclamen
Chris Yesson, Alastair Culham
BMC Evol Biol. 2006; 6: 72. Published online 2006 September 20. doi: 10.1186/1471-2148-6-72
PMCID:
PMC1599755
Abstract Full Text PDF–6.2M Supplementary Material
Origin of mitochondrial DNA diversity of domestic yaks
Songchang Guo, Peter Savolainen, Jianping Su, Qian Zhang, Delin Qi, Jie Zhou, Yang Zhong, Xinquan Zhao, Jianquan Liu
BMC Evol Biol. 2006; 6: 73. Published online 2006 September 22. doi: 10.1186/1471-2148-6-73
PMCID:
PMC1626082
Abstract Full Text PDF–503K Supplementary Material
Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes
Yajuan J Liu, Matthew C Hodson, Benjamin D Hall
BMC Evol Biol. 2006; 6: 74. Published online 2006 September 29. doi: 10.1186/1471-2148-6-74
PMCID:
PMC1599754
Abstract Full Text PDF–954K Supplementary Material
Dispersal strategies of phytophagous insects at a local scale: adaptive potential of aphids in an agricultural environment
Eric Lombaert, Roger Boll, Laurent Lapchin
BMC Evol Biol. 2006; 6: 75. Published online 2006 October 2. doi: 10.1186/1471-2148-6-75
PMCID:
PMC1622755
Abstract Full Text PDF–627K
Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes
Yasuyuki Hashiguchi, Mutsumi Nishida
BMC Evol Biol. 2006; 6: 76. Published online 2006 October 3. doi: 10.1186/1471-2148-6-76
PMCID:
PMC1601972
Abstract Full Text PDF–468K Supplementary Material
Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids
Zhengqiu Cai, Cynthia Penaflor, Jennifer V Kuehl, James Leebens-Mack, John E Carlson, Claude W dePamphilis, Jeffrey L Boore, Robert K Jansen
BMC Evol Biol. 2006; 6: 77. Published online 2006 October 4. doi: 10.1186/1471-2148-6-77
PMCID:
PMC1626487
Abstract Full Text PDF–1.0M
Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta)
Hwan Su Yoon, Claudia Ciniglia, Min Wu, Josep M Comeron, Gabriele Pinto, Antonino Pollio, Debashish Bhattacharya
BMC Evol Biol. 2006; 6: 78. Published online 2006 October 5. doi: 10.1186/1471-2148-6-78
PMCID:
PMC1626084
Abstract Full Text PDF–909K
Insights into the evolution of the ErbB receptor family and their ligands from sequence analysis
Richard A Stein, James V Staros
BMC Evol Biol. 2006; 6: 79. Published online 2006 October 6. doi: 10.1186/1471-2148-6-79
PMCID:
PMC1618406
Abstract Full Text PDF–468K Supplementary Material
The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies
Thomas Galewski, Marie-ka Tilak, Sophie Sanchez, Pascale Chevret, Emmanuel Paradis, Emmanuel JP Douzery
BMC Evol Biol. 2006; 6: 80. Published online 2006 October 9. doi: 10.1186/1471-2148-6-80
PMCID:
PMC1618403
Abstract Full Text PDF–500K
Evolution of competence and DNA uptake specificity in the Pasteurellaceae
Rosemary J Redfield, Wendy A Findlay, Janine Bossé, J Simon Kroll, Andrew DS Cameron, John HE Nash
BMC Evol Biol. 2006; 6: 82. Published online 2006 October 12. doi: 10.1186/1471-2148-6-82
PMCID:
PMC1626085
Abstract Full Text PDF–1.1M
Deep mtDNA divergences indicate cryptic species in a fig-pollinating wasp
Eleanor R Haine, Joanne Martin, James M Cook
BMC Evol Biol. 2006; 6: 83. Published online 2006 October 13. doi: 10.1186/1471-2148-6-83
PMCID:
PMC1626083
Abstract Full Text PDF–510K
The reach of the genome signature in prokaryotes
Mark WJ van Passel, Eiko E Kuramae, Angela CM Luyf, Aldert Bart, Teun Boekhout
BMC Evol Biol. 2006; 6: 84. Published online 2006 October 13. doi: 10.1186/1471-2148-6-84
PMCID:
PMC1621082
Abstract Full Text PDF–324K Supplementary Material
Molecular polymorphism, differentiation and introgression in the period gene between Lutzomyia intermedia and Lutzomyia whitmani
Camila J Mazzoni, Nataly A Souza, Claudia Andrade-Coelho, Charalambos P Kyriacou, Alexandre A Peixoto
BMC Evol Biol. 2006; 6: 85. Published online 2006 October 27. doi: 10.1186/1471-2148-6-85
PMCID:
PMC1634875
Abstract Full Text PDF–692K
Adaptive evolution of Hox-gene homeodomains after cluster duplications
Vincent J Lynch, Jutta J Roth, Günter P Wagner
BMC Evol Biol. 2006; 6: 86. Published online 2006 November 1. doi: 10.1186/1471-2148-6-86
PMCID:
PMC1636070
Abstract Full Text PDF–1.1M
Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution
April D Harlin-Cognato, Rodney L Honeycutt
BMC Evol Biol. 2006; 6: 87. Published online 2006 November 1. doi: 10.1186/1471-2148-6-87
PMCID:
PMC1635737
Abstract Full Text PDF–902K
Complex host-pathogen coevolution in the Apterostigma fungus-growing ant-microbe symbiosis
Nicole M Gerardo, Ulrich G Mueller, Cameron R Currie
BMC Evol Biol. 2006; 6: 88. Published online 2006 November 3. doi: 10.1186/1471-2148-6-88
PMCID:
PMC1635738
Abstract Full Text PDF–388K
SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily
Ricardo DeMarco, Thiago M Venancio, Sergio Verjovski-Almeida
BMC Evol Biol. 2006; 6: 89. Published online 2006 November 7. doi: 10.1186/1471-2148-6-89
PMCID:
PMC1636069
Abstract Full Text PDF–2.0M
Recurring genomic breaks in independent lineages support genomic fragility
Hanno Hinsch, Sridhar Hannenhalli
BMC Evol Biol. 2006; 6: 90. Published online 2006 November 7. doi: 10.1186/1471-2148-6-90
PMCID:
PMC1636669
Abstract Full Text PDF–596K Supplementary Material
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level
Lipika R Pal, Chittibabu Guda
BMC Evol Biol. 2006; 6: 91. Published online 2006 November 7. doi: 10.1186/1471-2148-6-91
PMCID:
PMC1654190
Abstract Full Text PDF–1.3M
Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family
Anthony Levasseur, Philippe Gouret, Laurence Lesage-Meessen, Michèle Asther, Marcel Asther, Eric Record, Pierre Pontarotti
BMC Evol Biol. 2006; 6: 92. Published online 2006 November 8. doi: 10.1186/1471-2148-6-92
PMCID:
PMC1660568
Abstract Full Text PDF–884K Supplementary Material
A higher-level MRP supertree of placental mammals
Robin MD Beck, Olaf RP Bininda-Emonds, Marcel Cardillo, Fu-Guo Robert Liu, Andy Purvis
BMC Evol Biol. 2006; 6: 93. Published online 2006 November 13. doi: 10.1186/1471-2148-6-93
PMCID:
PMC1654192
Abstract Full Text PDF–381K Supplementary Material
Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions
Nicolaas C Gey van Pittius, Samantha L Sampson, Hyeyoung Lee, Yeun Kim, Paul D van Helden, Robin M Warren
BMC Evol Biol. 2006; 6: 95. Published online 2006 November 15. doi: 10.1186/1471-2148-6-95
PMCID:
PMC1660551
Abstract Full Text PDF–645K Supplementary Material
Assortative mating and differential male mating success in an ash hybrid zone population
Pierre R Gérard, Etienne K Klein, Frédéric Austerlitz, Juan F Fernández-Manjarrés, Nathalie Frascaria-Lacoste
BMC Evol Biol. 2006; 6: 96. Published online 2006 November 15. doi: 10.1186/1471-2148-6-96
PMCID:
PMC1660552
Abstract Full Text PDF–490K
Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics
Ilke van Hazel, Francesco Santini, Johannes Müller, Belinda SW Chang
BMC Evol Biol. 2006; 6: 97. Published online 2006 November 15. doi: 10.1186/1471-2148-6-97
PMCID:
PMC1664589
Abstract Full Text PDF–1.2M Supplementary Material
Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly
Kellie L Heckman, Emilienne Rasoazanabary, Erica Machlin, Laurie R Godfrey, Anne D Yoder
BMC Evol Biol. 2006; 6: 98. Published online 2006 November 16. doi: 10.1186/1471-2148-6-98
PMCID:
PMC1657033
Abstract Full Text PDF–603K
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
David A Fitzpatrick, Mary E Logue, Jason E Stajich, Geraldine Butler
BMC Evol Biol. 2006; 6: 99. Published online 2006 November 22. doi: 10.1186/1471-2148-6-99
PMCID:
PMC1679813
Abstract Full Text PDF–448K Supplementary Material
Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata)
Markus Pfenninger, Mathilde Cordellier, Bruno Streit
BMC Evol Biol. 2006; 6: 100. Published online 2006 November 23. doi: 10.1186/1471-2148-6-100
PMCID:
PMC1679812
Abstract Full Text PDF–610K
The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic
Alexandra Stechmann, Manuela Baumgartner, Jeffrey D Silberman, Andrew J Roger
BMC Evol Biol. 2006; 6: 101. Published online 2006 November 23. doi: 10.1186/1471-2148-6-101
PMCID:
PMC1665464
Abstract Full Text PDF–713K Supplementary Material
Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers
Virginie Roy, Christine Demanche, Alexandre Livet, Myriam Harry
BMC Evol Biol. 2006; 6: 102. Published online 2006 November 23. doi: 10.1186/1471-2148-6-102
PMCID:
PMC1687204
Abstract Full Text PDF–611K
Identification of a gonadotropin-releasing hormone receptor orthologue in Caenorhabditis elegans
Sivan Vadakkadath Meethal, Miguel J Gallego, Ryan J Haasl, Stephen J Petras, III, Jean-Yves Sgro, Craig S Atwood
BMC Evol Biol. 2006; 6: 103. Published online 2006 November 29. doi: 10.1186/1471-2148-6-103
PMCID:
PMC1762030
Abstract Full Text PDF–3.3M Supplementary Material
Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment
Sean C Sleight, Nicholas S Wigginton, Richard E Lenski
BMC Evol Biol. 2006; 6: 104. Published online 2006 December 5. doi: 10.1186/1471-2148-6-104
PMCID:
PMC1698501
Abstract Full Text PDF–457K
Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila
Sònia Casillas, Bárbara Negre, Antonio Barbadilla, Alfredo Ruiz
BMC Evol Biol. 2006; 6: 106. Published online 2006 December 12. doi: 10.1186/1471-2148-6-106
PMCID:
PMC1764764
Abstract Full Text PDF–1.6M Supplementary Material
Insights into the evolutionary history of tubercle bacilli as disclosed by genetic rearrangements within a PE_PGRS duplicated gene pair
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, Helmi Mardassi
BMC Evol Biol. 2006; 6: 107. Published online 2006 December 12. doi: 10.1186/1471-2148-6-107
PMCID:
PMC1762029
Abstract Full Text PDF–741K Supplementary Material
Evolution of secretin family GPCR members in the metazoa
João CR Cardoso, Vanda C Pinto, Florbela A Vieira, Melody S Clark, Deborah M Power
BMC Evol Biol. 2006; 6: 108. Published online 2006 December 13. doi: 10.1186/1471-2148-6-108
PMCID:
PMC1764030
Abstract Full Text PDF–995K Supplementary Material
Insights on the evolution of trehalose biosynthesis
Nelson Avonce, Alfredo Mendoza-Vargas, Enrique Morett, Gabriel Iturriaga
BMC Evol Biol. 2006; 6: 109. Published online 2006 December 19. doi: 10.1186/1471-2148-6-109
PMCID:
PMC1769515
Abstract Full Text PDF–1.0M Supplementary Material
Methodology Articles
Phylogenetic identification of lateral genetic transfer events
Robert G Beiko, Nicholas Hamilton
BMC Evol Biol. 2006; 6: 15. Published online 2006 February 11. doi: 10.1186/1471-2148-6-15
PMCID:
PMC1431587
Abstract Full Text PDF–396K
Core set approach to reduce uncertainty of gene trees
Takahisa Okabayashi, Yasuhiro Kitazoe, Hirohisa Kishino, Teruaki Watabe, Noriaki Nakajima, Yoshiyasu Okuhara, Samantha O'Loughlin, Catherine Walton
BMC Evol Biol. 2006; 6: 41. Published online 2006 May 20. doi: 10.1186/1471-2148-6-41
PMCID:
PMC1508163
Abstract Full Text PDF–441K Supplementary Material
Computing Ka and Ks with a consideration of unequal transitional substitutions
Zhang Zhang, Jun Li, Jun Yu
BMC Evol Biol. 2006; 6: 44. Published online 2006 June 2. doi: 10.1186/1471-2148-6-44
PMCID:
PMC1552089
Abstract Full Text PDF–396K Supplementary Material
Statistical measures for defining an individual's degree of independence within state-dependent dynamic games
Sean A Rands, Rufus A Johnstone
BMC Evol Biol. 2006; 6: 81. Published online 2006 October 12. doi: 10.1186/1471-2148-6-81
PMCID:
PMC1618404
Abstract Full Text PDF–530K
Topology testing of phylogenies using least squares methods
Aleksandra Czarna, Rafael Sanjuán, Fernando González-Candelas, Borys Wróbel
BMC Evol Biol. 2006; 6: 105. Published online 2006 December 6. doi: 10.1186/1471-2148-6-105
PMCID:
PMC1698936
Abstract Full Text PDF–405K
Correction
Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages
Revathi Rajkumar, Jheelam Banerjee, Hima Bindu Gunturi, R Trivedi, VK Kashyap
BMC Evol Biol. 2006; 6: 9. Published online 2006 February 7. doi: 10.1186/1471-2148-6-9
Corrects:
BMC Evol Biol. 2006; 6: 3.
PMCID:
PMC1386706
Correction PDF–155K Original Article
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