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RAPD problems in phylogenetics
Author(s) -
LANDRY PIERREALEXANDRE,
LAPOINTE FRANÇOISJOSEPH
Publication year - 1996
Publication title -
zoologica scripta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.204
H-Index - 64
eISSN - 1463-6409
pISSN - 0300-3256
DOI - 10.1111/j.1463-6409.1996.tb00167.x
Subject(s) - jaccard index , rapd , biology , jackknife resampling , phylogenetics , resampling , dice , phylogenetic tree , evolutionary biology , taxon , statistics , mathematics , genetics , cluster analysis , ecology , gene , genetic diversity , population , demography , estimator , sociology
This paper is intended to clarify some of the questions related with the application of RAPD for phylogenetic reconstruction purposes. Using different specimens of mammals selected across various taxonomic levels, we assessed the validity of RAPD to recover a known phylogeny, using four distance coefficients (simple matching, Russell & Rao, Jaccard, and Dice). We assessed the minimum number of primers required in the computations to obtain stable results in terms of distance estimates and/or topologies of the derived trees. These results based on distance methods were compared with those obtained with parsimony analyses of RAPD markers. Both approaches have shown to be equally problematic for comparing taxa above the family level. On the basis of these comparisons among various indices and methods, we recommend the use of Jaccard or Dice coefficients, with no less than twelve primers. We also suggest validation of any phylogeny based on RAPD data with a resampling procedure (i.e. the bootstrap or the jackknife) before any sound conclusion can be drawn.