Dr Barbara Holland

Research Interests

• Phylogenetics - the estimation of evolutionary trees (family trees for species). Molecular phylogenetics primarily uses patterns in modern DNA sequence data to make inferences about the past. I have a particular interest in developing tools that can assess if sequence data is well explained by a simple tree model or if more complex processes such as hybridisation are at work.
• Other topics in mathematical biology including population genetics and epidemiology.

Teaching

• KMA153 - Data Handling & Statistics 1
• KMA414 - Honours unit in Phylogenetics

Recent Publications

• Eytan, R.I., Hastings, P.A., Holland, B.R., and Hellberg M.E. 2012. Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria). Molecular Phylogenetics and Evolution 62:159-173.
• Johnson, K.A., B.R. Holland, M. M. Heslewood, D. M. Crayn. 2012. Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data. Molecular Phylogenetics and Evolution 62: 146-158.
• Sumner, J.G., B.R. Holland, and P.D Jarvis. 2011. The algebra of the general Markov model on phylogenetic trees and networks. Bulletin of Mathematical Biology (published online 6 October 2011, DOI 10.1007/s11538-011-9691-z).
• White, W.T.J and B.R. Holland. 2011. Faster Exact Maximum Parsimony Search with XMP. Bioinf. 27: 1359-1367.
• McGraughran A., Stevens, M.I., Holland B.R. 2010. Biogeography of Circum-Antarctic Springtails. Mol. Phyl. Evol. 57: 48-58.
• McGaughran, B. R. Holland. 2010. Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level. PLoS ONE 5(3): e9686. doi:10.1371/journal.pone.0009686
• N. Zhang, R. D. Cannon, B. R. Holland, M. L. Patchett and J. Schmid. 2010. Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2. PLoS ONE 5(3): e9614. doi:10.1371/journal.pone.0009614
• B. R. Holland, H. G. Spencer, T. H. Worthy, and M. Kennedy. 2010. Identifying cliques of convergent characters: concerted evolution in the cormorants and shags. Syst. Biol. doi: 10.1093/sysbio/syq023
• Shavit, L., D. Penny, M. D. Hendy, B. R. Holland. 2010. Phylogenetic Tree Reconstruction Accuracy and Model Fit When Proportions of Variable Sites Change Across the Tree. Syst. Biol 59:288-297.
• S. de Nooijer, B. R. Holland and D. Penny. 2009. The Emergence of Predators in Early Life: There was No Garden of Eden. PLoS ONE 4(6): e5507. doi:10.1371/journal.pone.0005507
• N. Zhang, J. E. Upritchard, B. Holland, L. E. Fenton, M. M. Ferguson, R.D. Cannon, and J. Schmid. 2009. Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes. Infection, Genetics and Evolution 9:493-500.
• French, N., A. Midwinter, B. Holland, J. Collins-Emerson, R. Pattison, P. Carter. 2009. Molecular epidemiology of Campylobacter jejuni isolated from wild bird faecal material in children's play areas. Applied and Environmental Microbiology 75:779-783.
• Shavit Grievink L., Penny D., Hendy M.D. and Holland B.R. 2008. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evolutionary Biology 8:317
• Holland, S. Bentham, P. Lockhart, V. Moulton, K. Huber. 2008. The power of supernetworks to distinguish hybridisation from lineage-sorting via collections of gene trees. BMC Evol. Biol. 8:202 doi:10.1186/1471-2148-8-202
• Holland, B.R., A.C. Clarke, H. M. Meudt. 2008. Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution. Syst. Biol. 57:347-366.
• L. Shepherd, B. Holland, L. Perrie. 2008. Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns. Mol. Phyl. Evol. 48:176-187.
• Shavit, L., D. Penny, M. D. Hendy, B. R. Holland. 2007. The Problem of Rooting Rapid Radiations. Mol. Biol. Evol. 24:2400-2411.
• White, W.T. , S.F. Hills, R. Gaddam, B.R. Holland, and David Penny. 2007. Treeness Triangles: Visualizing the loss of phylogenetic signal. Mol. Biol. Evol. 24:2029-2039.
• Holland, B. R., G. Conner, K. Huber, V. Moulton. 2007. Imputing supertrees and supernetworks from quartets. Syst. Biol. 56:57-67.
• Holmes, A. R., S. Tsao, S. Ong, E. Lamping, K. Niimi, B.C. Monk, M. Niimi, A. Kaneko, B. Holland, J. Schmid, and R.D. Cannon. 2006. Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2. Mol. Micro. 62:170:186.
• Pierson, M., R. Martinez-Arias, B. Holland, N.J. Gemmell, M. Hurles, and D. Penny. 2006. Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes. Mol. Biol. Evol. 23:1966-1975.
• F. Auch, S. R. Henz, B. R. Holland, and M.Göker. 2006. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics 7:350.
• Holland, B. R., L. S. Jermiin, and V. Moulton. 2006. Improved consensus network techniques for genome-scale phylogeny. Molecular Biology and Evolution 23: 848 - 855.