Research Topics
| Barbara R HollandSummaryAffiliation: Massey University Country: New Zealand Publications
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Detail Information
Publications
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequencesAlexander 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...- Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation studyB R Holland
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Syst Biol 52:229-38. 2003.... - Using supernetworks to distinguish hybridization from lineage-sortingBarbara 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... - Identifying cliques of convergent characters: concerted evolution in the cormorants and shagsBarbara 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... - Imputing supertrees and supernetworks from quartetsB 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... - The MinMax Squeeze: guaranteeing a minimal tree for population dataB 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... - Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapodsBarbara 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.... - Selecting representative model micro-organismsB 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... - Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogenyBarbara 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... - Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networksMartyn 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... - Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypesNingxin Zhang
Institute for Molecular Biosciences, Massey University, Palmerston North, New Zealand
Infect Genet Evol 9:493-500. 2009.... - Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2Ningxin 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... - Upper bounds on maximum likelihood for phylogenetic treesMichael 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... - The problem of rooting rapid radiationsLiat 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... - LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sitesLiat 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... - Biogeography of circum-Antarctic springtailsAngela 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... - Faster exact maximum parsimony search with XMPW 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... - Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomesMelanie J Pierson
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 23:1966-75. 2006.... - Optimizing automated AFLP scoring parameters to improve phylogenetic resolutionBarbara 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... - Testing the effect of metabolic rate on DNA variability at the intra-specific levelAngela McGaughran
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
PLoS ONE 5:e9686. 2010.... - Optimal alphabets for an RNA worldPaul 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... - Treeness triangles: visualizing the loss of phylogenetic signalW 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... - Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locusNingxin 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... - LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sitesLiat 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... - The emergence of predators in early life: there was no Garden of EdenSilvester 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... - Using consensus networks to visualize contradictory evidence for species phylogenyBarbara 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... - Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2Ann 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... - Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium fernsLara 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...