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  1. HIV-1 is a retrovirus with high rate of recombination. Increasing experimental studies in vitro indicated that local hairpin structure of RNA was associated with recombination by favoring RT pausing and promoting...

    Authors: Chi-Yu Zhang, Ji-Fu Wei and Shao-Heng He
    Citation: BMC Evolutionary Biology 2005 5:53
  2. The advent of live-attenuated vaccines against measles virus during the 1960'ies changed the circulation dynamics of the virus. Earlier the virus was indigenous to countries worldwide, but now it is mediated b...

    Authors: Mikkel H Schierup, Carl H Mordhorst, Claude P Muller and Laurids S Christensen
    Citation: BMC Evolutionary Biology 2005 5:52
  3. Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however,...

    Authors: David A Ray and Mark A Batzer
    Citation: BMC Evolutionary Biology 2005 5:51
  4. Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Br...

    Authors: Hervé Philippe, Yan Zhou, Henner Brinkmann, Nicolas Rodrigue and Frédéric Delsuc
    Citation: BMC Evolutionary Biology 2005 5:50
  5. The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal...

    Authors: Ross DE MacPhee, Alexei N Tikhonov, Dick Mol and Alex D Greenwood
    Citation: BMC Evolutionary Biology 2005 5:49
  6. Translation initiation in eukaryotes involves the recruitment of mRNA to the ribosome which is controlled by the translation factor eIF4E. eIF4E binds to the 5'-m7Gppp cap-structure of mRNA. Three dimensional str...

    Authors: Bhavesh Joshi, Kibwe Lee, Dennis L Maeder and Rosemary Jagus
    Citation: BMC Evolutionary Biology 2005 5:48
  7. We investigated genetic variation of a major histcompatibility complex (MHC) pseudogene (Anvi-DAB1) in the little greenbul (Andropadus virens) from four localities in Cameroon and one in Ivory Coast, West Africa....

    Authors: Andres Aguilar, Thomas B Smith and Robert K Wayne
    Citation: BMC Evolutionary Biology 2005 5:47
  8. Only one spliceosomal-type intron has previously been identified in the unicellular eukaryotic parasite, Giardia lamblia (a diplomonad). This intron is only 35 nucleotides in length and is unusual in possessing a...

    Authors: Anthony G Russell, Timothy E Shutt, Russell F Watkins and Michael W Gray
    Citation: BMC Evolutionary Biology 2005 5:45
  9. A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evoluti...

    Authors: Claus O Wilke
    Citation: BMC Evolutionary Biology 2005 5:44
  10. The cytochrome P450 aromatase (CYP19), catalyses the aromatisation of androgens to estrogens, a key mechanism in vertebrate reproductive physiology. A current evolutionary hypothesis suggests that CYP19 gene aros...

    Authors: L Filipe C Castro, Miguel M Santos and Maria A Reis-Henriques
    Citation: BMC Evolutionary Biology 2005 5:43
  11. The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus, as evidenced both by recent and extensive gene duplication and by high ratio...

    Authors: Christina M Laukaitis, Stephen R Dlouhy, Richard D Emes, Chris P Ponting and Robert C Karn
    Citation: BMC Evolutionary Biology 2005 5:40
  12. Rodent and primate pregnancy-specific glycoprotein (PSG) gene families have expanded independently from a common ancestor and are expressed virtually exclusively in placental trophoblasts. However, within each sp...

    Authors: Andrew S McLellan, Wolfgang Zimmermann and Tom Moore
    Citation: BMC Evolutionary Biology 2005 5:39
  13. Internal reproductive organ size is an important determinant of male reproductive success. While the response of testis length to variation in the intensity of sperm competition is well documented across many ...

    Authors: David W Rogers, Tracey Chapman, Kevin Fowler and Andrew Pomiankowski
    Citation: BMC Evolutionary Biology 2005 5:37
  14. The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debat...

    Authors: Céline Brochier, Patrick Forterre and Simonetta Gribaldo
    Citation: BMC Evolutionary Biology 2005 5:36
  15. Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life ...

    Authors: E Bapteste, E Susko, J Leigh, D MacLeod, RL Charlebois and WF Doolittle
    Citation: BMC Evolutionary Biology 2005 5:33
  16. We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mouse. For the first time these data allow us to examine selective epis...

    Authors: Colin AM Semple, Alison Maxwell, Philippe Gautier, Fiona M Kilanowski, Hayden Eastwood, Perdita E Barran and Julia R Dorin
    Citation: BMC Evolutionary Biology 2005 5:32
  17. Integrins are a functionally significant family of metazoan cell surface adhesion receptors. The receptors are dimers composed of an alpha and a beta chain. Vertebrate genomes encode an expanded set of integri...

    Authors: Richard Ewan, Julie Huxley-Jones, A Paul Mould, Martin J Humphries, David L Robertson and Raymond P Boot-Handford
    Citation: BMC Evolutionary Biology 2005 5:31
  18. The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful coloni...

    Authors: Sho T Yano, Bahman Panbehi, Arpita Das and Howard M Laten
    Citation: BMC Evolutionary Biology 2005 5:30
  19. To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudini...

    Authors: Antoinette C van der Kuyl, Donato LP Ballasina and Fokla Zorgdrager
    Citation: BMC Evolutionary Biology 2005 5:29
  20. When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinf...

    Authors: Dave MacLeod, Robert L Charlebois, Ford Doolittle and Eric Bapteste
    Citation: BMC Evolutionary Biology 2005 5:27
  21. Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In ...

    Authors: Revathi Rajkumar, Jheelam Banerjee, Hima Bindu Gunturi, R Trivedi and VK Kashyap
    Citation: BMC Evolutionary Biology 2005 5:26

    The Erratum to this article has been published in BMC Evolutionary Biology 2006 6:9

  22. The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free ...

    Authors: Stefan Wuchty and Eivind Almaas
    Citation: BMC Evolutionary Biology 2005 5:24
  23. Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there ...

    Authors: Ino Agrafioti, Jonathan Swire, James Abbott, Derek Huntley, Sarah Butcher and Michael PH Stumpf
    Citation: BMC Evolutionary Biology 2005 5:23
  24. Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs). Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting b...

    Authors: Michael E Bradley and Steven A Benner
    Citation: BMC Evolutionary Biology 2005 5:22
  25. The f factor is a new parameter for accommodating the influence of both the starting and ending states in the rate matrices of "generalized weighted frequencies" (+gwF) models for sequence evolution. In this stud...

    Authors: Bjarne Knudsen and Michael M Miyamoto
    Citation: BMC Evolutionary Biology 2005 5:21
  26. Of the major families of long terminal repeat (LTR) retrotransposons, the Pao/BEL family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic ele...

    Authors: Claudia S Copeland, Victoria H Mann, Maria E Morales, Bernd H Kalinna and Paul J Brindley
    Citation: BMC Evolutionary Biology 2005 5:20
  27. Yellowfin and skipjack tuna are globally distributed in the world's tropical and sub-tropical oceans. Since little, if any, migration of these fishes occurs between the Atlantic and Indo-Pacific Oceans, one mi...

    Authors: Bert Ely, Jordi Viñas, Jaime R Alvarado Bremer, Donna Black, Luciano Lucas, Kelly Covello, Alexis V Labrie and Eric Thelen
    Citation: BMC Evolutionary Biology 2005 5:19
  28. Alu elements are short (~300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and fun...

    Authors: Abdel-Halim Salem, David A Ray, Dale J Hedges, Jerzy Jurka and Mark A Batzer
    Citation: BMC Evolutionary Biology 2005 5:18
  29. The adaptive radiations of cichlid fishes in East Africa are well known for their spectacular diversity and their astonishingly fast rates of speciation. About 80% of all 2,500 cichlid species in East Africa, ...

    Authors: Walter Salzburger, Tanja Mack, Erik Verheyen and Axel Meyer
    Citation: BMC Evolutionary Biology 2005 5:17
  30. The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of gen...

    Authors: Nelson D Young and Claude W dePamphilis
    Citation: BMC Evolutionary Biology 2005 5:16
  31. Mammalian ribosomes contain 79 different proteins encoded by widely scattered single copy genes. Coordinate expression of these genes at transcriptional and post-transcriptional levels is required to ensure a ...

    Authors: Robert P Perry
    Citation: BMC Evolutionary Biology 2005 5:15
  32. The relaxin-like peptide family belongs in the insulin superfamily and consists of 7 peptides of high structural but low sequence similarity; relaxin-1, 2 and 3, and the insulin-like (INSL) peptides, INSL3, IN...

    Authors: Tracey N Wilkinson, Terence P Speed, Geoffrey W Tregear and Ross AD Bathgate
    Citation: BMC Evolutionary Biology 2005 5:14
  33. In yeast, birds and mammals, the SAPK-interacting protein 1 (Sin1) gene product has been implicated as a component of the stress-activated protein kinase (SAPK) signal transduction pathway. Recently, Sin1 has ...

    Authors: Shu-Zong Wang and R Michael Roberts
    Citation: BMC Evolutionary Biology 2005 5:13
  34. The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs) proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 s...

    Authors: Ainsley C Nicholson, Shehre-Banoo Malik, John M Logsdon Jr and Erwin G Van Meir
    Citation: BMC Evolutionary Biology 2005 5:11
  35. The error threshold puts a limit on the amount of information maintainable in Darwinian evolution. The error threshold was first formulated in terms of genotypes. However, if a genotype-phenotype map involves ...

    Authors: Nobuto Takeuchi, Petrus H Poorthuis and Paulien Hogeweg
    Citation: BMC Evolutionary Biology 2005 5:9
  36. Bayesian phylogenetic inference holds promise as an alternative to maximum likelihood, particularly for large molecular-sequence data sets. We have investigated the performance of Bayesian inference with empir...

    Authors: Jessica C Mar, Timothy J Harlow and Mark A Ragan
    Citation: BMC Evolutionary Biology 2005 5:8
  37. Many properties of organisms show great robustness against genetic and environmental perturbations. The terms canalization and developmental stability were originally proposed to describe the ability of an org...

    Authors: Mauro Santos, Pedro Fernández Iriarte and Walkiria Céspedes
    Citation: BMC Evolutionary Biology 2005 5:7
  38. Coalescent theory is a general framework to model genetic variation in a population. Specifically, it allows inference about population parameters from sampled DNA sequences. However, most currently employed v...

    Authors: Rainer Opgen-Rhein, Ludwig Fahrmeir and Korbinian Strimmer
    Citation: BMC Evolutionary Biology 2005 5:6
  39. In this report we re-examine some recent experiments with digital organisms to test some predictions of quasispecies theory. These experiments revealed that under high mutation rates populations of less fit or...

    Authors: Iñaki Comas, Andrés Moya and Fernando González-Candelas
    Citation: BMC Evolutionary Biology 2005 5:5

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