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

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 Textbooks are generic (and sometimes outdated), and in resource poor labs, they may altogether be inaccessible.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.