D Penny

Summary

Affiliation: Massey University
Country: New Zealand

Publications

  1. ncbi request reprint Testing fundamental evolutionary hypotheses
    David Penny
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    J Theor Biol 223:377-85. 2003
  2. pmc Rewriting evolution--"been there, done that"
    David Penny
    Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    Genome Biol Evol 5:819-21. 2013
  3. pmc Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis
    Xiaowei S Chen
    Department of Biochemistry, University of Otago, Dunedin, New Zealand
    BMC Genomics 12:550. 2011
  4. pmc Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:188. 2007
  5. pmc LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
    Liat Shavit Grievink
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand
    BMC Evol Biol 8:317. 2008
  6. pmc Bird evolution: testing the Metaves clade with six new mitochondrial genomes
    Mary Morgan-Richards
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 8:20. 2008
  7. pmc RNase MRP and the RNA processing cascade in the eukaryotic ancestor
    Michael D Woodhams
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:S13. 2007
  8. ncbi request reprint Comment on "Hexapod origins: monophyletic or paraphyletic?"
    Frédéric Delsuc
    Allan Wilson Center for Molecular, Ecology and Evolution, Institute of Molecular Biosciences, Science Tower D, Massey University, Post Office Box 11 222, Palmerston North, New Zealand
    Science 301:1482; author reply 1482. 2003
  9. doi request reprint An overview of the introns-first theory
    David Penny
    Allan Wilson Center, Massey University, Palmerston North, New Zealand
    J Mol Evol 69:527-40. 2009
  10. ncbi request reprint Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
    D Penny
    Institute for Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Syst Biol 48:76-93. 1999

Detail Information

Publications78

  1. ncbi request reprint Testing fundamental evolutionary hypotheses
    David Penny
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    J Theor Biol 223:377-85. 2003
    ..The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses...
  2. pmc Rewriting evolution--"been there, done that"
    David Penny
    Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    Genome Biol Evol 5:819-21. 2013
    ..The underlying unrooted tree is probably correct, but the placement of the root just reflects a well-known error from the acceleration in the rate of evolution among some myomorph rodents...
  3. pmc Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis
    Xiaowei S Chen
    Department of Biochemistry, University of Otago, Dunedin, New Zealand
    BMC Genomics 12:550. 2011
    ..In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites Giardia intestinalis and Trichomonas vaginalis...
  4. pmc Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:188. 2007
    ....
  5. pmc LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
    Liat Shavit Grievink
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand
    BMC Evol Biol 8:317. 2008
    ..To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown...
  6. pmc Bird evolution: testing the Metaves clade with six new mitochondrial genomes
    Mary Morgan-Richards
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 8:20. 2008
    ..With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade...
  7. pmc RNase MRP and the RNA processing cascade in the eukaryotic ancestor
    Michael D Woodhams
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:S13. 2007
    ....
  8. ncbi request reprint Comment on "Hexapod origins: monophyletic or paraphyletic?"
    Frédéric Delsuc
    Allan Wilson Center for Molecular, Ecology and Evolution, Institute of Molecular Biosciences, Science Tower D, Massey University, Post Office Box 11 222, Palmerston North, New Zealand
    Science 301:1482; author reply 1482. 2003
  9. doi request reprint An overview of the introns-first theory
    David Penny
    Allan Wilson Center, Massey University, Palmerston North, New Zealand
    J Mol Evol 69:527-40. 2009
    ..e. well established in LECA), and regardless of which is ultimately correct, it pays to separate out various questions and to focus on testing the predictions of sub-theories...
  10. ncbi request reprint Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
    D Penny
    Institute for Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Syst Biol 48:76-93. 1999
    ..Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades...
  11. ncbi request reprint Mathematical elegance with biochemical realism: the covarion model of molecular evolution
    D Penny
    Institute of Molecular Biosciences, P O Box 11222, Massey University, Palmerston North, New Zealand
    J Mol Evol 53:711-23. 2001
    ..The accurate reconstruction of older divergences from sequence data is still a major problem, and molecular evolution still requires mathematical models that also have a sound biochemical basis...
  12. ncbi request reprint The nature of the last universal common ancestor
    D Penny
    Institute of Molecular Biosciences, Massey University, PO Box 11 222, New Zealand
    Curr Opin Genet Dev 9:672-7. 1999
    ..The last universal common ancestor may have been mesophilic and could have had many features of the eukaryote genome, but its cytology is unknown...
  13. ncbi request reprint Coevolution of genomic intron number and splice sites
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    Trends Genet 23:321-5. 2007
    ..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...
  14. ncbi request reprint Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous
    G L Abby Harrison
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 21:974-83. 2004
    ..In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required...
  15. ncbi request reprint Recovering evolutionary trees under a more realistic model of sequence evolution
    P J Lockhart
    School of Biological Sciences, Massey University, New Zealand
    Mol Biol Evol 11:605-12. 1994
    ..Consequently, many published studies may need to be reexamined...
  16. ncbi request reprint Early evolution: prokaryotes, the new kids on the block
    A Poole
    Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Bioessays 21:880-9. 1999
    ..The later derivation of prokaryote RNA metabolism and genome structure can be accounted for by the two complementary mechanisms of r-selection and thermoreduction...
  17. ncbi request reprint Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study
    B R Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Syst Biol 52:229-38. 2003
    ....
  18. ncbi request reprint Estimating changes in mutational mechanisms of evolution
    Rissa Ota
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    J Mol Evol 57:S233-40. 2003
    ..In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change...
  19. ncbi request reprint Hepatitis B virus genotypes: a South Pacific perspective
    G L Harrison
    Institute of Molecular Biosciences, Massey University, PO Box 11222, Palmerston North
    Pac Health Dialog 8:188-92. 2001
    ..HDV is a satellite viroid-like RNA virus that requires HBV for replication. It can either co-infect with, or super-infect upon HBV infection resulting in acute infection and/or chronic infection respectively...
  20. ncbi request reprint Complex spliceosomal organization ancestral to extant eukaryotes
    Lesley Collins
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 22:1053-66. 2005
    ..Although the last common ancestor of extant eukaryotes appears to show much of the molecular complexity seen today, we do not, from this work, infer anything of the properties of the earlier "first eukaryote."..
  21. pmc Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes
    Melanie J Pierson
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:1966-75. 2006
    ....
  22. ncbi request reprint The root of the mammalian tree inferred from whole mitochondrial genomes
    Matthew J Phillips
    Allan Wilson Center for Molecular Ecology and Evolution, Institute of Molecular Biosciences, P O Box 11222, Massey University, Palmerston North, New Zealand
    Mol Phylogenet Evol 28:171-85. 2003
    ..However, a short therian stem lineage is inferred, which is at variance with the traditionally deep placement of monotremes on morphological data...
  23. doi request reprint Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors
    Renae C Pratt
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 26:313-26. 2009
    ..Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes...
  24. ncbi request reprint Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes
    Lesley Collins
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:901-10. 2006
    ....
  25. ncbi request reprint Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria)
    Andrew C Clarke
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:893-900. 2006
    ..This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole...
  26. ncbi request reprint Resolving the root of the avian mitogenomic tree by breaking up long branches
    Kerryn E Slack
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Phylogenet Evol 42:1-13. 2007
    ..Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution...
  27. ncbi request reprint Using ancestral sequences to uncover potential gene homologues
    Lesley J Collins
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Appl Bioinformatics 2:S85-95. 2003
    ..Overall, including ancestral sequences in searches with BLAST and/or HMMER was the most successful approach in the recovery of potential RNase P protein gene homologues, making this a useful technique in early homologue identification...
  28. ncbi request reprint The problem of rooting rapid radiations
    Liat Shavit
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:2400-11. 2007
    ..For all the cases tested here, tree estimation using a two taxon outgroup was more accurate than when using a single-taxon outgroup. However, the ingroup was most accurately recovered when no outgroup was used...
  29. ncbi request reprint Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations
    Gillian C Gibb
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:269-80. 2007
    ..In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids...
  30. pmc Index-free de novo assembly and deconvolution of mixed mitochondrial genomes
    Bennet J McComish
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Genome Biol Evol 2:410-24. 2010
    ..The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes...
  31. ncbi request reprint Prokaryote and eukaryote evolvability
    Anthony M Poole
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
    Biosystems 69:163-85. 2003
    ..Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry...
  32. doi request reprint Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves
    Gillian C Gibb
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222 Palmerston North 4442, New Zealand
    Mol Phylogenet Evol 56:698-706. 2010
    ..The finding that pigeons and sandgrouse may be more closely related to falcons than to previous candidates such as shorebirds or parrots invites further investigation...
  33. ncbi request reprint Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling
    Yu Hsin Lin
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 19:2060-70. 2002
    ..On the basis of our quantitative results, we expect the evolutionary tree for mammals to be resolved quickly, and this will allow other problems to be solved...
  34. ncbi request reprint Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires
    Yu Hsin Lin
    Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Gene 294:119-29. 2002
    ..Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms...
  35. doi request reprint The RNA infrastructure: dark matter of the eukaryotic cell?
    Lesley J Collins
    Allan Wilson Centre for Molecular Ecology and Evolution and Institute of Molecular BioSciences, Private Bag 11222, Massey University, 4442 Palmerston North, New Zealand
    Trends Genet 25:120-8. 2009
    ..The general and ancestral nature of most basic RNA-processing steps places a new focus on the generality of the spatial and temporal steps in RNA processing...
  36. ncbi request reprint LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
    Liat Shavit Grievink
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand
    BMC Evol Biol 9:200. 2009
    ..ABSTRACT: Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1):317...
  37. doi request reprint The modern RNP world of eukaryotes
    Lesley J Collins
    Allan Wilson Center for Molecular Ecology and Evolution, Palmerston North, New Zealand
    J Hered 100:597-604. 2009
    ..Thus, the eukaryote genome may be uniquely informative about the transition from an earlier RNA genome world to the modern DNA genome world...
  38. pmc Optimal alphabets for an RNA world
    Paul P Gardner
    Institute of Fundamental Sciences, Massey University, PB 11 222, Palmerston North, New Zealand
    Proc Biol Sci 270:1177-82. 2003
    ..In higher copy-fidelity experiments, six-letter alphabets outperform the four-letter alphabets, suggesting that the canonical alphabet is indeed a relic of the RNA world...
  39. ncbi request reprint The MinMax Squeeze: guaranteeing a minimal tree for population data
    B R Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand
    Mol Biol Evol 22:235-42. 2005
    ..Namely, a pair of Australian lineages comes deeper in the tree (in agreement with archaeological data), and the non-African part of the tree shows greater agreement with the geographical distribution of lineages...
  40. ncbi request reprint A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1447-57. 2007
    ..These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich...
  41. ncbi request reprint Treeness triangles: visualizing the loss of phylogenetic signal
    W T White
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:2029-39. 2007
    ..The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis...
  42. pmc Intron length distributions and gene prediction
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Nucleic Acids Res 35:4737-42. 2007
    ....
  43. ncbi request reprint Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution
    Kerryn E Slack
    Allan Wilson Center for Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:1144-55. 2006
    ....
  44. ncbi request reprint Widespread intron loss suggests retrotransposon activity in ancient apicomplexans
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1926-33. 2007
    ..By contrast, Cryptosporidium introns are less evolutionary conserved with Toxoplasma than are introns from other apicomplexans; thus the few remaining introns are not simply indispensable ancestral introns...
  45. pmc Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials
    M J Phillips
    Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Proc Biol Sci 268:1533-8. 2001
    ..Further, RY coding was found to nullify AGCT coding nucleotide composition bias...
  46. ncbi request reprint Confounded cytosine! Tinkering and the evolution of DNA
    A Poole
    Institute of Molecular Biosciences, PO Box 11222, Massey University, Palmerston North, New Zealand
    Nat Rev Mol Cell Biol 2:147-51. 2001
    ..Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer. By keeping cytosine and replacing uracil the problem was never eliminated, returning once again with the advent of DNA methylation...
  47. ncbi request reprint The power of relative rates tests depends on the data
    L Bromham
    Institute for Molecular Biosciences, Massey University, P O Box 11 222, Palmerston North, Aotearoa, New Zealand
    J Mol Evol 50:296-301. 2000
    ....
  48. pmc Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis
    Xiaowei Sylvia Chen
    Allan Wilson Centre for Molecular Ecology and Evolution, IMBS, Massey University, Palmerston North, New Zealand
    PLoS ONE 3:e3106. 2008
    ..Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes...
  49. ncbi request reprint On the incidence of intron loss and gain in paralogous gene families
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1579-81. 2007
    ..Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families...
  50. pmc Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis
    Xiaowei Sylvia Chen
    Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand
    Nucleic Acids Res 35:4619-28. 2007
    ..Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized...
  51. pmc Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Genome Res 16:1270-5. 2006
    ..We suggest that intron loss/gain in some eukaryotic lineages may be concentrated in relatively short episodes coincident with occasional TE invasions...
  52. ncbi request reprint Evolutionary conservation of UTR intron boundaries in Cryptococcus
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1140-8. 2007
    ..These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing...
  53. ncbi request reprint Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:171-81. 2007
    ..This pattern implies that rates of intron creation were higher during earlier periods of evolution and further focuses attention on the causes of initial intron proliferation...
  54. pmc Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences
    R P Murray-McIntosh
    Institute for Molecular Biosciences, Massey University, P O Box 11222, Palmerston North, New Zealand
    Proc Natl Acad Sci U S A 95:9047-52. 1998
    ....
  55. pmc The emergence of predators in early life: there was no Garden of Eden
    Silvester de Nooijer
    Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    PLoS ONE 4:e5507. 2009
    ..85~2.7 billion years ago, leads to an unexpected prediction of a long period (approximately 1-3 billion years) with no phagocytotes -- a veritable Garden of Eden...
  56. ncbi request reprint Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:2259-62. 2006
    ....
  57. ncbi request reprint A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
    Christian Esser
    Institute of Botany III, University of Dusseldorf, Dusseldorf, Germany
    Mol Biol Evol 21:1643-60. 2004
    ..Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed...
  58. ncbi request reprint Spectronet: a package for computing spectra and median networks
    Katharina T Huber
    Department of Biometry and Informatics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Appl Bioinformatics 1:159-61. 2002
    ..The package is highly interactive and available for PCs...
  59. ncbi request reprint Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features
    Kerryn E Slack
    Division of Evolutionary Molecular Systematics, Department of Cell and Organism Biology, University of Lund, Solvegatan 29, S 223 62, Lund, Sweden
    Gene 302:43-52. 2003
    ..The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded...
  60. ncbi request reprint Genome-scale phylogeny and the detection of systematic biases
    Matthew J Phillips
    Mol Biol Evol 21:1455-8. 2004
    ..Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error...
  61. ncbi request reprint Evolutionary biology: our relative genetics
    David Penny
    Nature 427:208. 2004
  62. pmc Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
    William Martin
    Institut fur Botanik, Heinrich Heine Universitat, Universitatsstrasse 1, 40225 Dusseldorf, Germany
    Proc Natl Acad Sci U S A 99:12246-51. 2002
    ....
  63. ncbi request reprint A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction
    Sverker Edvardsson
    Department of Information Technology, Mid Sweden University, S 851 70, Sundsvall, Sweden
    Bioinformatics 19:865-73. 2003
    ..Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date...
  64. ncbi request reprint The modern molecular clock
    Lindell Bromham
    Centre for the Study of Evolution, School of Biological Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
    Nat Rev Genet 4:216-24. 2003
    ....
  65. ncbi request reprint The biology of intron gain and loss
    Daniel C Jeffares
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
    Trends Genet 22:16-22. 2006
    ..In this article, we discuss the growing evidence that these differences are subject to selection acting on introns depending on the biology of the organism and the gene involved...
  66. ncbi request reprint Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations
    Matthew J Phillips
    Henry Wellcome Ancient Biomolecules Center, Department of Zoology, Oxford University, South Parks Road, Oxford OX1 3PS, United Kingdom
    Syst Biol 55:122-37. 2006
    ..This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.]...
  67. doi request reprint Origin of introns by 'intronization' of exonic sequences
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
    Trends Genet 24:378-81. 2008
    ..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...
  68. ncbi request reprint Response to Dagan and Martin
    Anthony M Poole
    Bioessays 29:611-4. 2007
  69. ncbi request reprint Evaluating hypotheses for the origin of eukaryotes
    Anthony M Poole
    Department of Molecular Biology and Functional Genomics, Stockholm University, Sweden
    Bioessays 29:74-84. 2007
    ..Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host...
  70. ncbi request reprint Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 24:1604-7. 2007
    ..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...
  71. ncbi request reprint Eukaryote evolution: engulfed by speculation
    Anthony Poole
    Department of Molecular Biology and Functional Genomics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 447:913. 2007
  72. ncbi request reprint A bias in ML estimates of branch lengths in the presence of multiple signals
    David Penny
    Mol Biol Evol 25:239-42. 2008
    ..We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees...
  73. ncbi request reprint Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 25:375-82. 2008
    ..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...
  74. ncbi request reprint Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
    Scott William Roy
    Mol Biol Evol 23:1824-7. 2006
    ..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...
  75. ncbi request reprint Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years
    James W Matheson
    Malaghan Institute of Medical Research, Wellington, New Zealand
    J Med Virol 78:1354-64. 2006
    ..The mutation rate calculated for the RSV B G gene was significantly higher than for RSV A. Together, these data reveal that RSV subgroups exhibit different patterns of evolution, with subgroup B viruses evolving faster than A...
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    David Penny
    Nature 436:183-4. 2005
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    Peter J Lockhart
    Trends Plant Sci 10:201-2. 2005
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    David Penny
    Nature 446:501-2. 2007