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  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Software

    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

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  8. Content type: Research article

    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

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

  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Methodology article

    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

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  26. Content type: Research article

    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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  27. Content type: Research article

    How does intraspecific variation relate to macroevolutionary change in morphology? This question can be addressed in species in which derived characters are present but not fixed. In rhabditid nematodes, the a...

    Authors: Scott Everet Baird, Cynthia R Davidson and Justin C Bohrer

    Citation: BMC Evolutionary Biology 2005 5:3

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  28. Content type: Research article

    Selfish genetic elements that distort the sex ratio are found widely. Notwithstanding the number of records of sex ratio distorters, their incidence is poorly understood. Two factors can prevent a sex ratio di...

    Authors: Zoe Veneti, Masanori J Toda and Gregory DD Hurst

    Citation: BMC Evolutionary Biology 2004 4:52

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  29. Content type: Research article

    The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistent...

    Authors: Johannes Berg, Michael Lässig and Andreas Wagner

    Citation: BMC Evolutionary Biology 2004 4:51

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  30. Content type: Research article

    The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylo...

    Authors: Alex Mira, Ravindra Pushker, Boris A Legault, David Moreira and Francisco Rodríguez-Valera

    Citation: BMC Evolutionary Biology 2004 4:50

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  31. Content type: Research article

    Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome o...

    Authors: Hinrich Schulenburg and Jonathan J Ewbank

    Citation: BMC Evolutionary Biology 2004 4:49

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  32. Content type: Research article

    Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observat...

    Authors: Jean-François Manen

    Citation: BMC Evolutionary Biology 2004 4:46

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  33. Content type: Research article

    Parasite heterogeneity and within-host competition are thought to be important factors influencing the dynamics of host-parasite relationships. Yet, while there have been many theoretical investigations of how...

    Authors: William OH Hughes, Klaus S Petersen, Line V Ugelvig, Dorthe Pedersen, Lene Thomsen, Michael Poulsen and Jacobus J Boomsma

    Citation: BMC Evolutionary Biology 2004 4:45

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  34. Content type: Research article

    The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large ...

    Authors: Fabia U Battistuzzi, Andreia Feijao and S Blair Hedges

    Citation: BMC Evolutionary Biology 2004 4:44

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  35. Content type: Research article

    The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three...

    Authors: Gustavo Glusman, Amardeep Kaur, Leroy Hood and Lee Rowen

    Citation: BMC Evolutionary Biology 2004 4:43

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  36. Content type: Research article

    The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them ...

    Authors: Johannes Berg, Stana Willmann and Michael Lässig

    Citation: BMC Evolutionary Biology 2004 4:42

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  37. Content type: Research article

    The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizant...

    Authors: Daniel L Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell and Frank E Anderson

    Citation: BMC Evolutionary Biology 2004 4:40

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  38. Content type: Research article

    As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer...

    Authors: James R Brown, Kristin K Koretke, Marian L Birkeland, Philippe Sanseau and Denis R Patrick

    Citation: BMC Evolutionary Biology 2004 4:39

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