African Journal of Biotechnology Vol. 6 (6), pp. 639-649, 19 March 2007   

ISSN 1684–5315 © 2007 Academic Journals        

Review

Phylogenetics in plant biotechnology: principles, obstacles and opportunities for the resource poor

Joel W. Ochieng^1*, Anne W. T. Muigai² and George N. Ude³

¹Sections of Genetics, College of Agriculture and Veterinary Sciences, University of Nairobi, P.O. Box 29053 Nairobi, 00625 Kenya.

²Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000 Nairobi, 00200 Kenya.

³Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, MD 20715, USA.

*Corresponding author. E-mail: j.ochieng.10@scu.edu.au,  Tel: +61 2 6620 3961, Fax: +61 2 6622 2080.

Accepted 5 February, 2007

Phylogenetic inference has become routine for most studies of genetic variation among plant taxa. However, inferring phylogenies can be confounded by both biological and computational or statistical complexities, resulting in misleading evolutionary hypotheses. This is particularly critical because the “true tree” can only truly be known in exceptional circumstances. Moreover, selecting appropriate marker(s), characters, sample sizes and the appropriate reconstruction methods offers a challenge to most evolutionary geneticists. Textbooks are generic (and sometimes outdated), and in resource poor labs, they may altogether be inaccessible. In this review, we take the worker through the low-down on reconstructing a phylogeny, review the enigmatic biological and computational problems, and examine cases where cheaper markers and extremely small sample sizes can recover a reliable phylogeny.

Key words: Phylogeny, tree incongruence, homoplasy, lineage sorting, molecular markers.