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Barbara Holland

Senior Lecturer in Mathematics/ Research Officer in Allan Wilson Centre

Email

B.R.Holland@massey.ac.nz

Phone

+64 6 (06) 356-9099  Ext 7939

Fax

+64 6 350-5682

Location

Science Tower B3.25
Turitea Site
Palmerston North Campus
Private Bag 11222
Palmerston North 4442
New Zealand

 

Qualifications and Achievement

NZST Postdoctoral Fellow at the Allan Wilson Centre, Massey University, NZ, 2002-2006; Post Doctoral Researcher, Ruhr-University Bochum, Germany, 2001-2002; PhD, Massey University, New Zealand, 1998-2001; BInfSci. Honours (1st Class) 1997; BSc (Operations Research) 1996.

Aitken Prize (2001); DAAD Short Term Research Scholarship (2000); SMBE Young Investigator (2005); Hamilton Memorial prize (2005), College of Sciences Research Medal - Early Career (2006), Massey University Research Medal - Early Career (2006), NZMS Early Career Award (2008).

Teaching

  • 160.102 Linear Mathematics extramurally in Semester 1
  • 160.102 Linear Mathematics internally in Semester 1
  • 160.319 Mathematical Modelling internally in Semester 2
  • 203.752 Computational Biology internally in Semester 12
  • 203.763 Phylogenetics internally in Semester 12

Research Interests

My research cluster(s):


Mathematical Phylogeny

I enjoy doing collaborative research in Mathematical Biology, particular on problems in evolution, and phylogenetics.

I am interested in methods of displaying phylogenetic data that can show conflicting signals, one such method we have developed is consensus networks. I am currently collaborating with Pete Lockhart and others to see if consensus networks may be a useful tool for studying hybridisation in plants.

How best to assess the goodness-of-fit of models of nucleotide substitution to real data is another important question in phylogenetics. The commonly used models do not account for the fact that processes of evolution can change across different lineages in the tree; it is not clear how serious a problem this is likely to be for phylogenetic estimation methods.

In cases where models are misspecified it seems to be very important to select taxa "wisely". I am currently supervising some projects that look at the effect of tree shape on the accuracy of phylogenetic methods, we want to apply these results to the case of the angiosperms where taxon-sampling appears to critically effect the estimate of the most basal angiosperm.


Recent Grants

  • Marsden (2009) of $519,000 over 3 years for the project Untangling complex evolution: when the Tree of Life is not a tree at all
  • Marsden (2006) over 3 years for the project Candida albicans: Survival without sex? (in collaboration with Jan Schmid (PI, IMBS), Richard Cannon (Otago))
  • Marsden (2005) of $480000 over 3 years for the project Genome-scale plant phylogeny and the challenge of lineage-specific sequence evolution (in collaboration with David Penny (IMBS), Mike Steel (Canterbury))

Former Graduate Students

  • Liat Shavit Grievink to March, 2009

Recent Publications

  • Shavit Grievink L, Penny D, Hendy MD, Holland BR (2008) LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites BMC Evol Biol 8 1 317
  • P.P. Gardner, B.R. Holland, V. Moulton, M.D. Hendy and D. Penny, (2003) Optimal alphabets for an RNA-world Proc. Roy. Soc. Lond. (Series B) 270 1177-1182
  • M.D. Hendy and B.R. Holland (2003) Upper bounds on maximum likelihood for phylogenetic trees Bioinformatics 19 ii66-ii72
  • B.R. Holland, D. Penny, and M.D. Hendy, (0) Outgroup misplacement and phylogenetic inaccuracy under a molecular clock - a simulation study Syst Biol. 52 229-238

Selected Publications

  • Grievink L. S., Holland B. R., Hendy M. D., Penny E. D., (2008) Lineage specific sequence evolution New Zealand Phylogenetics Conference 2008 17
  • Penny E. D., Hendy M. D., Holland B. R., (2007) Phylogenetics: Parsimony, networks, and distance methods Handbook of Statistical Genetics (3rd Ed.) John Wiley and Sons Chichester, UK 489-532
  • Shavit L., Penny E. D., Hendy M. D., Holland B. R., (2007) The problem of rooting rapid radiations Molecular Biology and Evolution 24 2400-2411
  • Dress, A., Holland, B. R., Huber, K. T., Koolen, J. H., Moulton, V., Weyer-Menkhoff, J. (2005). Ä additive and Ä ultra-additive maps, Gromov's trees and the Farris transform Discete Applied Mathematics 146 51-73
  • Goremykin, V. V., Holland, B. R., Hirsch-Ernst, K. I., Hellwig, F. H (2005). Analysis of Acorus calamus chloroplast Ggenome and its phylogenetic implications. Molecular Biology and Evolution 22 (9) 1813-1822.
  • Holland, B. R., Huber, K. T., Penny, D. D., Moulton, V. (2005). The MinMax Squeeze: Guaranteeing a minimal tree for population data Molecular Biology and Evolution 22 (2) 235-242
  • Holland, B. R., Jermiin, L. S., Moulton, V. (2005). Improved concensus network techniques for genome-scale phylogeny Molecular Biology and Evolution unpaged November 9 Advance access
  • Holland, B. R., Schmid, J. (2005). Selecting representative model micro-organisms BMC Microbiology 5 (26) 1-11
  • Kennedy, M., Holland, B. R., Gray, R D., Spencer, H G. (2005). Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks Systematic Biology 54 (4), 620-633
  • Holland, B. R., Huber, K. T., Moulton, V., Lockhart, P. J. (2004). Using consensus networks to visualize contradictory evidence for species phylogeny Molecular Biology and Evolution 21 (7), 1459-1461
  • Schmid, J., Cannon, R. D., Holland, B. R. (2004). A futile act? Thoughts on the reproductive biology of Candida albicans Mycologist 18 (4) 158-163 November DOI: 10.1017
  • Zhang, L., Harrex, A. L., Holland, B. R., Fenton, L., Cannon, R. D., Schmid, J. (2004). Key features distinguishing more pathogenic, general-purpose genotype, strains from less pathogenic Candida albicans strains: A genomic comparison (87-87). American Society for Microbiology Conference: Candida and candidiasis March 18-22, Austin, TX. American Society for Microbiology
  • Zhang, N., Harrex, A. L., Holland, B. R., Fenton, L., Cannon, R. D., Schmid, J. (2004). Genomic markers associated with the increased pathogenicity on Candida albicans Poster at New Zealand Microbiological Society Conference 2004 November 17-19, RichText, Palmerston North, NZ
  • Zhang, N., Harrex, A. L., Holland, B. R., Fenton, L., Cannon, R. D., Schmid, J. (2004). Key features distinguishing more pathogenic, general-purpose genotype, strains from less pathogenic Candida albicans strains: A genomic comparison Poster at Americal Society for Microbiology Conference: Candida and Candidiasis March 18-22, RichText, Austin, TX
  • Gardner, P. P., Holland, B. R., Moulton, V., Hendy, D., Penny, D. (2003). Optimal alphabets for an RNA world Proceedings of the Royal Society of London. Series B, Biological Science 270 1177-1182
  • Hendy M. D., Holland B. R., (2003) Upper bounds on maximum likelihood for phylogenetic trees Bioinformatics 19 Oxford University Press Oxford, England, UK
  • Holland, B. R., Moulton, V. (2003). Consensus networks: A method for visualising incompatibilities in collections of trees (pp. 165-176). InG. Benson & R. Page (Eds.) (ed(s).). Third International Workshop, WABI 2003, September 15 - 20, Budapest, Hungary. New York, NY: Springer-Verlag.
  • Holland, B. R., Penny, D., Hendy, D. (2003). Outgroup misplacement and phylogenetic inaccuracy under a molecular clock: A simulation study Systematic Biology 52 (2), 229-238
  • Salemi, M., Oliveira, T. D., Courgnaud, V., Moulton, V., Holland, B. R., Cassol, S., Switzer, W. M., Vandamm, A. M. (2003). Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses Journal of Virology 77 7202-7213
  • Strimmer, K., Forslund, K., Holland, B. R., Moulton, V. (2003). A novel exploratory method for visual recombination detection Genome Biology 4 (5), R33.1-R33.12
  • Wagele, J., Holland, B. R., Dreyer, H., Hackethal, B. (2003). Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats Molecular Phylogenetics and Evolution 28 536-551
  • Zhang, N., Harrex, A. L., Holland, B. R., Fenton, L. E., Cannon, R. D., Schmid, J. (2003). Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus Genome Research 13 2005-2017
  • Holland, B. R., Huber, K. T., Dress, A., Moulton, V. (2002). ä plots: A tool for analyzing phylogenetic distance data Molecular Biology and Evolution 19 (12), 2051-2059
  • Ritchie, P. A., Lambert, D. M., Millar, C. D., Holland, B. R., Drummond, A. J., Baroni, C. (2002) Rates of evolution in ancient DNA from Adelie penguins Science 295 (5563) 4514 2270-2273 March
  • Zhang, N., Harrex, A. L., Holland, B. R., Cannon, R. D., Schmid, J. (2002). Sixty-one alleles of the ALS7 open reading frame in sixty-six Candida albicans strains: ALS7 is a hypermutable contingency locus Poster at 7th International Mycological Congress August 11-17, RichText, Oslo, Norway
  • Zhang, N., Harrex, A. L., Holland, B. R., Cannon, R. D., Schmid, J. (2001). Genomic Markers of Pathogenicity of Candida albicans In NZMS Annual Meeting, Wellington: New Zealand
  • Chor B., Hendy M. D., Holland B. R., Penny D. D., (2000) Multiple maxima of likelihood in phylogenetic trees: An analytic approach 4th International Conference on Computational Molecular Biology 108-117
  • Holland, B. R., Schmid, J. (1999). Choosing meaningful model strains for microbiological research in NZMS Annual Meeting, Dunedin, New Zealand

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