# Main · The Equations

## Work in a nutshell

I love numbers. There is something magical about them: one can represent almost anything with numbers or mathematical symbols. Luckily, most of my work deals with applications of mathematics and statistics to biological problems.

I was born in Chile, grew up in Chile, Venezuela and Argentina. I studied forestry in Chile and after that I worked for the Chilean Tree Breeding Cooperative. I lived four years in New Zealand while doing my PhD and then moved to Hobart, Tasmania, Australia. There I was leader of the breeding strategies project at the CRC for Sustainable Production Forestry for three years. After that I worked as Forest Biometrician in Forestry Tasmania for another three years. Now I am again in New Zealand, working as Senior Lecturer for the School of Forestry, University of Canterbury.

## Work

I am Senior Lecturer in Tree Breeding and Forest Genetics for the School of Forestry, University of Canterbury in Christchurch, New Zealand. I also am a consultant working on applied tree breeding and genetics. I teach an elective course on ‘Applied tree breeding’ (FORE436), the tree breeding component of ‘Introduction to silviculture’ (FORE219), part of ‘Regression modelling’ (STAT224) and ‘Trees, Forests and the Environment’ (FORE111, for which I am coordinator). I am the coordinator for ‘Forests and People’ (FORE121).

My main research interests are:

• Genetics of wood properties. This is my current obsession, where I am starting from scratch trying to quickly learn the basics.
• Design of breeding strategies, especially on terms of progeny testing.
• Multivariate analysis of progeny tests, including variance components estimations and prediction of breeding values. This includes analysis of longitudinal data and the genetic control of wood properties. For this I use mosly ASReml, for which the best reference—modestly—is the ASReml Cookbook. There are still lots of people using SAS out there, and I have started compiling information on Quantitative Genetics in SAS.
• System integration, using ASReml, R, Python, SAS, Fortran and whatever else gets the job done.
• Combining genetics/breeding with other parts of production systems (e.g. silviculture, growth modeling).
• Large scale level genetic evaluation (e.g., national level). What are the compromises that we need to accept when working with huge data sets?
• Definition of breeding objectives, especially of forest systems with multiple end-products. I am particularly interested in alternative economic approaches for valuing wood quality.

I am the Coordinator of the IUFRO Working Group 2.04.02: Breeding theory and progeny testing. (that is a mouthful!). You can see my curriculum vitae in PDF format (file size around 130 KB, and in need of a cleanup).

### Past lives

Before working in Canterbury I was Forest Biometrician in Forestry Tasmania. There I worked mostly in growth modelling and statistical consulting. Even before, I was a post-doctoral research fellow at the School of Plant Science (University of Tasmania) and the Cooperative Research Centre for Sustainable Production Forestry. Apart of being leader of the Breeding Strategies project, 25% of my time went to the Genetics and Reproductive Biology project. I also interacted with the Molecular Genetics of Eucalypts, and Wood Quality projects.

### Odds and ends

In May 2005 I have started to write down Research Notes—very draft ideas I am playing with—on a few topics that I find interesting. My work involves a fair amount of interaction with students and industry, for which I use the following presentation guidelines.

## Education

Between 1996 and early 2000 I did my PhD in quantitative genetics and tree breeding at Massey University (New Zealand) under the supervision of Prof. Dorian Garrick, who is now Jay Lush Endowed Chair in Animal Breeding and Genetics at Iowa State University. My animal breeding pedigree is Dorian Garrick ← Dale van Vleck ← Charles Henderson ← Lanoy Hazel ← Jay Lush. In June 2009 I completed my first pilgrimage to Ames, Iowa, so I am a practicing breeder ;-).

My PhD topic was ‘Multiple trait improvement of radiata pine’, which included the analysis of longitudinal data and the development of breeding objectives for radiata pine. I finished my thesis on January 21, 2000. My studies were supported by the NZ Ministry of Foreigns Affairs and Trade, and the NZ Forest Research Institute.

I did my B. For. Sci. (Hons) degree and got my Forest Engineer title at the School of Forest Sciences, Universidad de Chile, with a thesis analyzing the early performance of progeny tests of Eucalyptus camaldulensis. My first job was working for the Chilean Tree Improvement Cooperative in data analysis and planning of breeding strategies, mostly working with Pinus radiata and Eucalyptus globulus.

## Publications

The following list includes papers in scientific journals, book chapters and written papers in conferences. A most comprehensive list, separated by type of publication and including other activities, can be found in my CV here (<130 KB in PDF format, readable using Adobe Acrobat).

My papers published in the Canadian Journal of Forest Research are available here subject to these copyright and author rights notices. Papers published in the Australian Journal of Botany are subject to this copyright notice. In summary, you are entitled to download the papers and abstracts for your personal use, but you can not modify or republish this material somewhere else. Capice? Preprints represent the state of the article just before publication, and do not contain any ammendments. I scanned some papers for which I do not have the original electronic file; they are indicated as PDF image, and are large(ish) files.

I am making as many publications as possible available as PDFs in this site. Eventually I hope to make them all available, with the exception of recently submitted papers (only until they are accepted for publication). Many of these publications are also stored in the University of Canterbury Research Repository.

[43]
Alzamora, R.M. and Apiolaza, L.A. 2010. A hedonic price analysis of radiata pine logs for appearance timber. Forest Science. In press.
* Using a hedonic approach for the estimation of economic weights to breed for appearance timber.
[42]
McDonald, T.M. and Apiolaza, L.A. 2009. Genotype by Environment interaction of Pinus radiata In New Zealand. Australasian Forest Genetics Conference. 20–22 April, Perth, Western Australia, Australia.
* Figuring out what is driving GxE for dbh in New Zealand.
[41]
Alzamora, R.M. and Apiolaza, L.A. 2009. Hedonic prices for structural wood attributes of radiata pine logs in New Zealand. Australasian Forest Genetics Conference. 20–22 April, Perth, Western Australia, Australia (PDF 308KB).
* Estimating the economic values of small end diameter, wood stiffness, basic density and branches for structural grades production.
[40]
Apiolaza, L.A. 2009. Modeling wood quality using random regression splines. Australasian Forest Genetics Conference. 20–22 April, Perth, Western Australia, Australia (PDF 140KB).
* Using random regression splines to justify early screening for wood dimensional stability.
[39]
Apiolaza, L.A., Chauhan, S. and Walker, J.C.F. 2009. Revisiting Eucalypts Workshop, Wood Technology Research Centre. 155 p. ISBN 978 0 473 14703.
* I co-edited the proceedings and coauthored three papers.
[38]
Apiolaza, L.A. 2009. Exploiting different scales of variability in a generic Eucalyptus species. Revisiting Eucalypts Workshop, Wood Technology Research Centre. 12 February, Christchurch, New Zealand. pp 83–89 (PDF 168KB).
* Making use of between population, within population and within tree variability to breed for niche species and products.
[37]
Apiolaza, L.A. 2009. Very early selection for wood quality: screening for early winners. Annals of Forest Science 66(6): 1 (PDF 168KB).. The original publication is freely available at http://www.afs-journal.org/.
* Developing the idea of first-past-the-post selection for wood quality.
[36]
Warren, E., Smith, R.G.B., Apiolaza, L.A. and Walker, J.C.F. 2009. Effect of stocking on juvenile wood stiffness for three Eucalyptus species. New Forests 37(3): 241–250. DOI 10.1007/s11056–008–9120–9.
* On how increasing stocking improves stiffness (for E. cloeziana, E. pilularis and E. dunnii) up to around 1,250 trees/ha.
[35]
Apiolaza, L.A., Walker, J.C.F., Nair, H. and Butterfield, B.G. 2008. Very early screening of wood quality for radiata pine: pushing the envelope. Society of Wood Science and Technology 51st annual convention. 10–11 November, Concepción, Chile. WQ-1 (PDF 416KB).
* Forcing trees to express differences on wood quality under one year of age for selection purposes.
[34]
Laffan, M., Rees, S. and Apiolaza, L.A. 2008. Effects of cultivation method on the early growth of Pinus radiata on a low quality site in north-eastern Tasmania. Tasforests 17: 9–14 (PDF image 550KB).
* The title says it all.
[33]
Apiolaza, L.A. 2008. Improvement objectives for short rotation forestry. New Zealand Journal of Forestry 52(4): 26–28 (PDF galley proofs 84KB).
* Opinion piece on why we should change our improvement objectives in New Zealand forestry.
[32]
Li, Y., Dutkowski, G.W., Apiolaza, L.A., Pilbeam, D.J., Costa e Silva, J. and Potts, B.M. 2007. The genetic architecture of a Eucalyptus globulus full-sib breeding population in Australia. Forest Genetics. 12: 167–179 (PDF galley proof 152 KB).
* Attempting to estimate non-additive effects from small(ish) trials.
[31]
Whittock, S.P., Dutkowski, G.W., Greaves, B.L. and Apiolaza, L.A. 2007. Integrating revenues from carbon sequestration into economic breeding objectives for Eucalyptus globulus pulpwood production. Annals of Forest Science 64: 239–246 (PDF paper 236 KB). The original publication is available at http://www.afs-journal.org/.
* Confirmed common sense (the least common of the senses) result showing a high correlation between traditional breeding objectives and the ones including carbon revenues.
[30]
Alzamora, R.M. and Apiolaza, L.A. 2007. Economic approaches for valuing wood quality. Australasian Forest Genetics Conference—Breeding for Wood quality. 11–14 April, Hobart, Tasmania, Australia.
* Having a look at alternative economic frameworks for valuing wood quality traits.
[29]
Apiolaza, L.A. 2007. Breeding wood quality: from average corewood value to early bloomers. Proceedings of Australasian Forest Genetics Conference — Breeding for Wood Quality. 11–14 April, Hobart, Tasmania, Australia. (PDF of abstract and presentation in conference web site)
* Pushing for selection of trees that quickly reach a threshold of wood quality rather than of trees with the best average value.
[28]
Currie, A., Langford, G., McGhie, T., Apiolaza, L.A., Snelling, C., Braithewaite, B. and Vather, R. 2006. Inheritance of antioxidants in a New Zealand blackcurrant (Ribes nigrum L.) population. 13th Australasian Plant Breeding Conference, 18–21 April, Christchurch, New Zealand: 218–225. (PDF paper 328 KB)
* Blackcurrants are good for you.
[27]
Sinn, D.L., Apiolaza, L.A. and Moltschaniwskyj, N.A. 2006. Genetic analysis and reproductive consequences of squid personality traits. Journal of Evolutionary Biology 19(5): 1437–1447. (PDF paper 584 KB).
* Yes, you read correctly: a paper on the genetics of personality of dumpling squid. David did a great job rearing squid, assessing them and trying to make sense of everything that was going on. A full electronic copy of his Ph.D. thesis is available, and the story made the news.
[26]
MacDonald, M.A., Apiolaza, L.A. and Grove, S. 2005. The birds of retained vegetation corridors: a pre- and post-logging comparison in dry sclerophyll forest in Tasmania. Forest Ecology and Management 218: 277–290. (Abstract) (PDF paper 345 KB).
* Using generalised linear models (Poisson distribution, log link, autoregressive error structure fitted using generalised estimating equations) to study the effect of logging on bird populations.
[25]
Apiolaza, L.A., Raymond, C.A. and Yeo, B. 2005. Genetic variation of physical and chemical wood properties of Eucalyptus globulus. Silvae Genetica 54: 160–166. (Abstract) (PDF galley proof 386 KB)
* Studying the degree of genetic variation for diameter, basic density, predicted pulp yield, fibre length, microfibril angle and cellulose content amongst eight subraces of Eucalyptus globulus.
[24]
Potts, B.M., Vaillancourt, R.E., Jordan, G., Dutkowski, G.W. , Costa e Silva, J., McKinnon, G., Steane, D., Volker, P., Lopez, G.A., Apiolaza, L.A., Li, Y., Marques, C. and Borralho, N.M.G. 2004. Exploration of the Eucalyptus globulus gene pool. In: Eucalyptus in a changing world, IUFRO Symposium. Aveiro, Portugal. 11–15 October 2004. (PDF paper 347 KB).
* Badly breaking my ‘no more than four authors per paper’ policy. A review paper that included part of my work on economic value of different subraces, presented with much more detail in publication [25].
[23]
Whittock, S.P., Apiolaza, L.A., Dutkowski, G.W., Greaves, B.L. and Potts, B.M. 2004. Carbon revenues and economic breeding objectives in Eucalyptus globulus pulpwood plantations. In: Eucalyptus in a changing world, IUFRO Symposium. Aveiro, Portugal. 11–15 October 2004. (PDF paper 164 KB).
* Integration of carbon revenues into production system models used to define economic breeding objectives for the genetic improvement of pulp-wood plantations.
[22]
Whittock, S.P., Greaves, B.L. and Apiolaza, L.A. 2004. The comparative economics of genetically improved seedling and coppice crops in Eucalyptus globulus plantations. Forest Ecology and Management 191: 267–274. (Abstract) (PDF paper 187 KB).
* Facing your second rotation? So what do you do? Go for replanting with genetically improved stock of just coppice what you already have? It certainly depends on how well is your breeding program doing..
[21]
Raymond, C.A. and Apiolaza, L.A. 2004. Incorporating wood quality and deployment traits in Eucalyptus globulus and Eucalyptus nitens. In ‘Plantation Forest Biotechnology for the 21st Century’. pp 87–99. (PDF preprint 397 KB)
* Book chapter reviewing work on breeding objectives, sampling methods and strategies for wood quality traits, and the role of propagation traits in breeding and deployment strategies.
[20]
McRae T.A., Apiolaza L.A., Dutkowski G.W., Kerr R.J., Pilbeam, D.J., Powell, M.B. and Tier, B. 2003. TREEPLAN® - A genetic evaluation system for forest trees. Proceedings of the 27th Southern Forest Tree Improvement Conference, Stillwater, Oklahoma, USA. July 2003. (PDF preprint 65 KB)
* A more detailed version of 16 pitched for a different audience, in an attempt to sell the idea of TREEPLAN to breeders in the US. However, please see note for paper [16].
[19]
Whittock, S.M., Apiolaza, L.A., Kelly, C.M. and Potts, B.M. 2003. Genetic control of coppice and lignotuber development in Eucalyptus globulus. Australian Journal of Botany 51(1): 57–67. (PDF paper 346 KB)
* Using quantitative genetics data (from progeny tests) to explore the relationship between coppicing, lignotubers and vigour, with evolutionary implications.
[18]
Lopez, G.A., Potts, B.M., Vaillancourt, R.E. and Apiolaza, L.A. 2003. Maternal and carryover effects on early growth of Eucalyptus globulus. Canadian Journal of Forest Research 33(11): 2108–2115. (PDF paper 99 KB)
* Importance of maternal effects through germination, nursery and early growth. Some neat models for full diallel analyses.
[17]
Lopez, G.A., Potts, B.M., Dutkowski, G.W., Apiolaza, L.A. and Gelid, P. 2002. Genetic variation and inter-trait correlations in Eucalyptus globulus base population trials in Argentina. Forest Genetics 9(3): 223–237.
* Large multivariate analyses, confirming results for the CSIRO collection in Argentina.
[16]
Kerr, R.J., Dutkowski, G.W., Apiolaza, L.A., McRae, T.A., and Tier, B. 2002. Developing a genetic evaluation system for forest tree breeding - the making of TREEPLAN. Proceedings of the 7th World Congress of Genetics Applied to Livestock Production. Montpellier, France 07–10. CD-ROM communication No 07–10. (PDF paper 175 KB)
* Discussion of the application of BLUP in tree breeding at a large scale (national evaluation). What this paper does not mention is that ASReml is fundamental for the use of TREEPLAN. All (co)variance components used by TREEPLAN are obtained from individual-site analysis using ASReml.
[15]
Alzamora, R.M., Apiolaza, L.A. and Ide, S. 2002. Evaluación física y económica de pérdidas en volumen debido al daño de Rhyacionia buoliana (Shiff.) en plantaciones de Pinus radiata D. Don en la Novena y Décima Regiones de Chile. [Physical and economic evaluation of volume losses due to Rhyacionnia buoliana (Shiff.) damage in Pinus radiata D. Don plantations in southern Chile]. Bosque 23(2): 29–42. (Unformatted web version)
* A bit of a side track working with my friend Ramy with growth models, insect damage and economic evaluation.
[14]
Kerr, R.J., Tier, B., McRae, T.A., Dutkowski, G.W. and Apiolaza, L.A. 2001. TREEPLAN - A genetic evaluation system for forest tree improvement. In ‘Developing the Eucalypt of the Future’. 10–15 September, Valdivia, Chile.(PDF preprint 35 KB)
* Introducing TREEPLAN to the forest genetics world.
[13]
McRae, T.A., Pilbeam, D.J., Gore, P.L., Dutkowski, G.W. and Apiolaza, L.A. 2001. Australian cooperative tree improvement strategy for Eucalyptus globulus. In ‘Developing the Eucalypt of the Future’. 10–15 September, Valdivia, Chile. (PDF abstract 18 KB)
* A brief description of our work revamping STBA’s (Southern Tree Breeding Association) breeding strategy.
[12]
Apiolaza, L.A. and Greaves, B.L. 2001. Why are most breeders not using economic breeding objectives? In: Developing the eucalypt of the future, IUFRO Symposium. Valdivia, Chile. 10–15 September 2001. (PDF preprint 152 KB)
* Why?
[11]
Apiolaza, L.A. and Garrick, D.J. 2001. Breeding objectives for three silvicultural regimes of radiata pine. Canadian Journal of Forest Research 31: 654–662. (Abstract) (PDF paper 106 KB)
* My first attempt at developing simple breeding objectives for a vertically integrated industry with multiple end-products.
[10]
Apiolaza, L.A. and Garrick, D.J. 2001. Analysis of longitudinal data from progeny tests: some multivariate approaches. Forest Science 47: 129–140. (PDF paper 121 KB)
* The aleph: integrating most models for longitudinal data analysis in a tree (‘animal’) model framework. A nice introduction to multivariate genetic evaluation.
[09]
Apiolaza, L.A. 2000. Multiple trait improvement of radiata pine. PhD Thesis, Massey University, Palmerston North, New Zealand.
* Hard four years. It has been published as papers [6], [7], [8], [10] and [11].
[08]
Apiolaza, L.A., Garrick, D.J. and Burdon, R.D. 2000. Optimising early selection using longitudinal data. Silvae Genetica 49: 195–200. (Abstract) (PDF paper 579 KB)
* Yet another early-selection paper but with a twist.
[07]
Apiolaza, L.A., Gilmour, A.R. and Garrick, D.J. 2000. Variance modelling of longitudinal data from progeny tests. Canadian Journal of Forest Research 30: 645–654. (Abstract) (PDF paper 133 KB)
* A beautiful (for me) paper. It was hard to stop Arthur to keep trying models ;-)
[06]
Apiolaza, L.A., Burdon, R.D. and Garrick, D.J. 1999. Effect of univariate subsampling on the efficiency of bivariate parameter estimation and selection using half-sibs progeny tests. Forest Genetics 9:79–87. (PDF preprint 113 KB)
* My first publication as a senior author.
[05]
Burdon, R.D. and Apiolaza, L.A. 1998. Short note: more generalised estimation of between-trait genetic correlations using data from collateral relatives. Silvae Genetica 47:174–175. (Abstract) (PDF paper 73 KB)
* A ‘mathematical divertimento’. One day we should extend this work with some ‘real-life’ application.
[04]
Apiolaza, L.A., Burdon, R.D. and Garrick, D.J. 1998. Effects of subsampling on open-pollinated progeny tests. 6th World Congress of Genetics Applied to Livestock Production (Tree Breeding Session). Volume 27: 491–494. Armidale, Australia. (PDF paper 132 KB)
* Early results of the For Genet 9:79–87 paper.
[03]
Shelbourne, C.J.A., Apiolaza, L.A., Jayawickrama, K. and Sorenssen, C. 1997. Developing breeding objectives for Radiata Pine in New Zealand. IUFRO Conference. Rotorua, New Zealand. pp 160–168. (PDF image, Danger Will Robinson: 2.4MB!)
* A very detailed list of potential breeding objective traits and selection criteria for radiata pine.
[02]
Ipinza, R.H., Garcia, X., Apiolaza, L.A., Molina, M.P., Chung, P. and Parra, P. 1994. Variación juvenil de un ensayo de procedencias y familias de Eucalyptus globulus subsp. globulus Labill, en la séptima región, Chile. (Juvenile variation in a provenance and family test of Eucalyptus globulus subsp. globulus Labill, in the VII Region, Chile). Ecología 8: 259–270. (Abstract)
* An early genetic evaluation paper published in Spain. All models used in the papers were developed in my Forest Engineer’s thesis.
[01]
Apiolaza, L.A. 1994. Evaluación genética de la fase juvenil de Eucalyptus camaldulensis Dehnh. en Mel-Mel y Longotoma, V Región. (Genetic evaluation of the juvenile stage of Eucalyptus camaldulensis Dehnh. in Mel-Mel and Longotoma, V Region, Chile). Escuela de Ingeniería Forestal, Universidad de Chile. (Abstract)
* My first steps in quantitative genetics, using family models and Henderson’s methods to estimate variance components. First registered use of cluster and discriminant analysis to create “macroprovenances” (now called subraces) to simplify the genetic analysis.