Barbara R Holland

Summary

Affiliation: Massey University
Country: New Zealand

Publications

  1. pmc Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
    Alexander F Auch
    Center for Bioinformatics ZBIT, Sand 14, Tubingen, University of Tubingen, Germany
    BMC Bioinformatics 7:350. 2006
  2. ncbi 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
  3. pmc Using supernetworks to distinguish hybridization from lineage-sorting
    Barbara R Holland
    Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 8:202. 2008
  4. ncbi Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny
    Barbara R Holland
    Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, New Zealand
    Mol Biol Evol 23:848-55. 2006
  5. pmc Selecting representative model micro-organisms
    B R Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Microbiol 5:26. 2005
  6. ncbi Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods
    Barbara Holland
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222, Palmerston North, New Zealand
    Syst Biol 54:66-76. 2005
  7. ncbi 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
  8. ncbi Identifying cliques of convergent characters: concerted evolution in the cormorants and shags
    Barbara R Holland
    Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
    Syst Biol 59:433-45. 2010
  9. ncbi Imputing supertrees and supernetworks from quartets
    B Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Syst Biol 56:57-67. 2007
  10. ncbi Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
    Martyn Kennedy
    Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
    Syst Biol 54:620-33. 2005

Collaborators

Detail Information

Publications31

  1. pmc Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
    Alexander F Auch
    Center for Bioinformatics ZBIT, Sand 14, Tubingen, University of Tubingen, Germany
    BMC Bioinformatics 7:350. 2006
    ..Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study...
  2. ncbi 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
    ....
  3. pmc Using supernetworks to distinguish hybridization from lineage-sorting
    Barbara R Holland
    Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 8:202. 2008
    ..However, this approach may be confounded by factors such as poor taxon-sampling and/or incomplete lineage-sorting...
  4. ncbi Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny
    Barbara R Holland
    Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, New Zealand
    Mol Biol Evol 23:848-55. 2006
    ..We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa...
  5. pmc Selecting representative model micro-organisms
    B R Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    BMC Microbiol 5:26. 2005
    ..To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species...
  6. ncbi Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods
    Barbara Holland
    The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222, Palmerston North, New Zealand
    Syst Biol 54:66-76. 2005
    ....
  7. ncbi 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...
  8. ncbi Identifying cliques of convergent characters: concerted evolution in the cormorants and shags
    Barbara R Holland
    Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
    Syst Biol 59:433-45. 2010
    ..We suggest, therefore, that these cliques of characters are the result of similar selective pressures and are a signature of concerted convergence...
  9. ncbi Imputing supertrees and supernetworks from quartets
    B Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Syst Biol 56:57-67. 2007
    ..Through simulations and application to real data sets, we compare Q-imputation to the matrix representation with parsimony (MRP) supertree method and Z-closure, and demonstrate that it provides a useful complementary tool...
  10. ncbi Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
    Martyn Kennedy
    Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
    Syst Biol 54:620-33. 2005
    ..These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data...
  11. doi Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes
    Ningxin Zhang
    Institute for Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Infect Genet Evol 9:493-500. 2009
    ....
  12. ncbi Upper bounds on maximum likelihood for phylogenetic trees
    Michael D Hendy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Bioinformatics 19:ii66-72. 2003
    ..The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed-up factor of between 12 and 44...
  13. pmc Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2
    Ningxin Zhang
    Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    PLoS ONE 5:e9614. 2010
    ..Nevertheless the large number of alleles observed indicates that mutability of PNG2 may assist C. albicans strains from different genetic backgrounds optimize their interaction with the host in the long term...
  14. ncbi 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...
  15. 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...
  16. doi Biogeography of circum-Antarctic springtails
    Angela McGaughran
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Phylogenet Evol 57:48-58. 2010
    ..We conclude that these isotomid springtails have a varied and diverse evolutionary history in the circum-Antarctic that consists of both ancient and recent elements and is reflected in a dynamic contemporary fauna...
  17. doi Faster exact maximum parsimony search with XMP
    W Timothy J White
    Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
    Bioinformatics 27:1359-67. 2011
    ..This is, in part, because currently available programs fail to take advantage of parallelism...
  18. 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
    ....
  19. ncbi Optimizing automated AFLP scoring parameters to improve phylogenetic resolution
    Barbara R Holland
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Syst Biol 57:347-66. 2008
    ..This is true not only when AFLP data are used for phylogenetics, but also for other applications, including linkage mapping and population genetics...
  20. pmc Testing the effect of metabolic rate on DNA variability at the intra-specific level
    Angela McGaughran
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    PLoS ONE 5:e9686. 2010
    ....
  21. pmc Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand
    Vathsala Mohan
    mEpiLab, Infectious Disease Research Centre, Institute of Veterinary and Biomedical Sciences, Massey University, Palmerston North, New Zealand
    Microbiologyopen 2:659-73. 2013
    ..The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas...
  22. 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...
  23. ncbi 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...
  24. doi Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli
    Shoukai Yu
    Infectious Disease Research Centre, Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Palmerston North, New Zealand
    J Mol Evol 74:273-80. 2012
    ..A parametric bootstrap method was applied to calculate the uncertainty of these estimates...
  25. pmc Reconstructing past changes in locus-specific recombination rates
    Murray P Cox
    Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
    BMC Genet 14:11. 2013
    ..Such estimates can be misleading, but no analytical framework to infer recombination rates that have changed over time is currently available...
  26. pmc Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus
    Ningxin Zhang
    Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
    Genome Res 13:2005-17. 2003
    ..Our results provide evidence that ALS7 is a hypermutable contingency locus and important for the success of C. albicans as an opportunistic pathogen of humans...
  27. 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...
  28. ncbi 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...
  29. ncbi Using consensus networks to visualize contradictory evidence for species phylogeny
    Barbara R Holland
    Mol Biol Evol 21:1459-61. 2004
    ..We propose an approach to do this using consensus networks. We compare gene trees for eight yeast genomes and show that consensus networks have potential for helping to visualize contradictory evidence for species phylogenies...
  30. ncbi Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns
    Lara D Shepherd
    Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington, New Zealand
    Mol Phylogenet Evol 48:176-87. 2008
    ..Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed...
  31. ncbi Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2
    Ann R Holmes
    Department of Oral Sciences, School of Dentistry, University of Otago, Dunedin, New Zealand
    Mol Microbiol 62:170-86. 2006
    ..Collectively, these results indicate that possession of two functionally different CDR2 alleles in individual strains may confer a selective advantage, but that this is not necessarily due to azole resistance...