Abstract
The phenetic analysis of non-nodulatingAcacia species by Harrier et al. (1997) was repeated to illustrate how different computer programs may generate alternative UPGMA trees for the very same data, even in the absence of data input order effects (ties). For example, all Harrier et al.'s UPGMA dendrograms produced by software from the Scottish Agricultural Statistics Service differed from those obtained by the packages NTSYS and MVSP87. Particularly, the positions ofA. albida, A. rovumae, andA. pentagona, as well as the relationships betweenDiacanthae andTriacanthae were affected by this phenomenon. Hence, whenever clustering techniques are used, care should be taken to consider possible software-dependent caveats and artefacts. Nevertheless, all programs provided clusterings that largely coincided with the subgeneric and sectional groupings proposed by Vassal (1972) although the positions of some species varied depending on whether morphological or molecular data were considered (e.g.A. albida andA. rovumae).
Similar content being viewed by others
References
Backeljau T., De Bruyn L., De Wolf H., Jordaens K., Van Dongen S., Winnepenninckx B. (1996) Multiple UPGMA and Neighbor-joining trees and the performance of some computer packages. Mol. Biol. Evol. 13: 309–313.
Bayer U. (1985) Lecture Notes in earth sciences. Volume 2. Pattern recognition problems in geology and paleontology. Springer, Berlin Heidelberg.
Bentham G. (1875) Revision of the suborderMimoseae. Trans. Linn. Soc. London 30: 335–664.
Blashfield R. (1977) The equivalence of three statistical packages for performing hierarchical cluster analysis. Psychometrika 42: 429–431.
Chalmers K. J., Newton A. C., Waugh R., Wilson J., Powell W. (1994) Evaluation of the extent of genetic variation in mahogonies (Meliaceae) using RAPD markers. Theor. Appl. Genet. 89: 504–508.
Chalmers K. J., Waugh R., Sprent J. I., Simons A. J., Powell W. (1992) Detection of genetic variation between and within populations ofGliricidia sepium andG. maculata using RAPD markers. Heredity 69: 465–472.
Dawson I. K., Chalmers K. J., Waugh R., Powell W. (1993) Detection and analysis of genetic variation inHordeum spontaneum populations from Israel using RAPD markers. Mol. Ecol. 2: 151–159.
Dawson I. K., Simons A. J., Waugh R., Powell W. (1995) Diversity and genetic differentiation among sub-populations ofGliricidia sepium revealed by PCR-based assays. Heredity 74: 10–18.
Dice L. R. (1945) Measures of the amount of ecological association between species. Ecology 26: 295–302.
Farris J. S., Albert V. A., Källersjö M., Lipscomb D., Kluge A. G. (1996) Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99–124.
Felsenstein J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
Harrier L. A., Whitty P. W., Sutherland J. M., Sprent, J. I. (1997) Phenetic investigation of non-nodulating African species ofAcacia (Leguminosae) using morphological and molecular markers. Plant Syst. Evol. 205: 27–51.
Hart G. (1983) The occurrence of multiple UPGMA phenograms. In: Felsenstein J. (ed.) Numerical taxonomy. Springer, Berlin Heidelberg, pp. 254–258.
Hilu K. W. (1994) Evidence from RAPD markers in the evolution ofEchinochloa millets (Poaceae). Plant Syst. Evol. 189: 247–257.
Kempton R., McNicol J. (1990) Graphical methods for multivariate data. Scottish Agricultural Statistics Service.
Kovach W. L. (1993) MVSP Plus: Multivariate statistical package, version 2.1. Pentraeth, Anglesey: Kovach Computing Services (distributed by Exeter Software, Setauket, New York).
Nei M. (1987) Molecular evolutionary genetics. Columbia University Press, New York.
Nei M., Li W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269–5273.
Orozco-Castillo C., Chalmers K. J., Waugh R., Powell W. (1994) Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theor. Appl. Genet. 87: 934–940.
Pankhurst R. J. (1991) Practical taxonomic computing. Cambridge University Press, Cambridge.
Podani J. (1994) Multivariate data analysis in ecology and systematics. A methodological guide to the SYN-TAX 5.0 package. SPB Academic Publishing bv, The Hague.
Rohlf F. J. (1993) NTSYS-pc: Numerical taxonomy and multivariate analysis system, version 1.80. Setauket, New York: Applied Biostatistics Inc. (distributed by Exeter Software, Setauket, New York).
Sneath P. H. A., Sokal, R. R. (1973) Numerical taxonomy. W. H. Freeman and Company, San Francisco.
Takezaki N. (1998) Tie trees generated by distance methods of phylogenetic reconstruction. Mol. Biol. Evol. 15: 727–737.
Vassal J. (1972) Apport des recherches ontogéniques et séminologiques à l'étude morphologique, taxonomique et phylogénique du genreAcacia. Bull. Soc. Hist. Nat. Toulouse 108: 125–247.
Wachira F. N., Powell W., Waugh R. (1997) An assessment of genetic diversity amongCamellia sinensis L. (cultivated tea) and its wild relatives based on randomly amplified polymorphic DNA and organelle-specific STS. Heredity 78: 603–611.
Whitty P. W., Powell, W., Sprent J. I. (1994) Molecular separation of genera in Cassiinae (Leguminosae), and analysis of variation in the nodulating species ofChamaecrista. Mol. Ecol. 3: 507–515.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Backeljau, T., Breugelmans, K., De Wolf, H. et al. Software dependent phenetic relationships of non-nodulating African species ofAcacia . Pl Syst Evol 220, 139–146 (2000). https://doi.org/10.1007/BF00985042
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00985042