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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. The primate-specific Alu elements, which originated 65 million years ago, exist in over a million copies in the human genome. These elements have been involved in genome shuffling and various diseases not only...

    Authors: Ravi Shankar, Deepak Grover, Samir K Brahmachari and Mitali Mukerji
    Citation: BMC Evolutionary Biology 2004 4:37
  18. Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Recently, it has been proposed that autoindu...

    Authors: Jibin Sun, Rolf Daniel, Irene Wagner-Döbler and An-Ping Zeng
    Citation: BMC Evolutionary Biology 2004 4:36
  19. Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major excep...

    Authors: Saša Stefanović, Danny W Rice and Jeffrey D Palmer
    Citation: BMC Evolutionary Biology 2004 4:35
  20. The clear dominance of two-gender sex in recent species is a notorious puzzle of evolutionary theory. It has at least two layers: besides the most fundamental and challenging question why sex exists at all, th...

    Authors: Tamás L Czárán and Rolf F Hoekstra
    Citation: BMC Evolutionary Biology 2004 4:34
  21. Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary ...

    Authors: Wei Cai, Jimin Pei and Nick V Grishin
    Citation: BMC Evolutionary Biology 2004 4:33
  22. The size distribution of gene families in a broad range of genomes is well approximated by a generalized Pareto function. Evolution of ensembles of gene families can be described with Birth, Death, and Innovat...

    Authors: Georgy P Karev, Yuri I Wolf, Faina S Berezovskaya and Eugene V Koonin
    Citation: BMC Evolutionary Biology 2004 4:32
  23. Evolutionary theory suggests that the selection pressure on parasites to maximize their transmission determines their optimal host exploitation strategies and thus their virulence. Establishing the adaptive ba...

    Authors: REL Paul, T Lafond, CDM Müller-Graf, S Nithiuthai, PT Brey and JC Koella
    Citation: BMC Evolutionary Biology 2004 4:30
  24. DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is support...

    Authors: Marinalva Martins-Pinheiro, Rodrigo S Galhardo, Claudia Lage, Keronninn M Lima-Bessa, Karina A Aires and Carlos FM Menck
    Citation: BMC Evolutionary Biology 2004 4:29
  25. Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylo...

    Authors: Gavin H Thomas, Matthew A Wills and Tamás Székely
    Citation: BMC Evolutionary Biology 2004 4:28
  26. The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic wor...

    Authors: Mary E Cosner, Linda A Raubeson and Robert K Jansen
    Citation: BMC Evolutionary Biology 2004 4:27
  27. With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are severa...

    Authors: MyLo L Thao, Linda Baumann and Paul Baumann
    Citation: BMC Evolutionary Biology 2004 4:25
  28. Aromatic L-amino acid decarboxylase (AADC) enzymes catalyze the synthesis of biogenic amines, including the neurotransmitters serotonin and dopamine, throughout the animal kingdom. These neurotransmitters typi...

    Authors: Emily E Hare and Curtis M Loer
    Citation: BMC Evolutionary Biology 2004 4:24
  29. The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly ...

    Authors: Martin Irestedt, Jon Fjeldså, Johan AA Nylander and Per GP Ericson
    Citation: BMC Evolutionary Biology 2004 4:23
  30. The outbreak of severe acute respiratory syndrome (SARS) caused a severe global epidemic in 2003 which led to hundreds of deaths and many thousands of hospitalizations. The virus causing SARS was identified as...

    Authors: Zhongming Zhao, Haipeng Li, Xiaozhuang Wu, Yixi Zhong, Keqin Zhang, Ya-Ping Zhang, Eric Boerwinkle and Yun-Xin Fu
    Citation: BMC Evolutionary Biology 2004 4:21
  31. In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimat...

    Authors: Tobias Müller, Sven Rahmann, Thomas Dandekar and Matthias Wolf
    Citation: BMC Evolutionary Biology 2004 4:20
  32. Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience.

    Authors: Gangolf Jobb, Arndt von Haeseler and Korbinian Strimmer
    Citation: BMC Evolutionary Biology 2004 4:18

    The Retraction Note to this article has been published in BMC Evolutionary Biology 2015 15:243

  33. Mitochondrial DNA has been detected in the nuclear genome of eukaryotes as pseudogenes, or Numts. Human and plant genomes harbor a large number of Numts, some of which have high similarity to mitochondrial fragme...

    Authors: Sérgio L Pereira and Allan J Baker
    Citation: BMC Evolutionary Biology 2004 4:17
  34. Examination of ancient gene families can provide an insight into how the evolution of gene structure can relate to function. Functional homologs of the evolutionarily conserved transforming acidic coiled coil (TA...

    Authors: Ivan H Still, Ananthalakshmy K Vettaikkorumakankauv, Anthony DiMatteo and Ping Liang
    Citation: BMC Evolutionary Biology 2004 4:16
  35. The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsectio...

    Authors: Maile C Neel and Michael P Cummings
    Citation: BMC Evolutionary Biology 2004 4:15
  36. Anopheles (Nyssorhynchus) albitarsis (Diptera: Culicidae) is one of the very few South American mosquito vectors of malaria successfully colonized in the laboratory. These vectors are very hard to breed because t...

    Authors: José BP Lima, Denise Valle and Alexandre A Peixoto
    Citation: BMC Evolutionary Biology 2004 4:12
  37. Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have s...

    Authors: Frédéric Delsuc, Sergio F Vizcaíno and Emmanuel JP Douzery
    Citation: BMC Evolutionary Biology 2004 4:11

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