Summary
The statistical properties of three molecular tree construction methods—the unweighted pair-group arithmetic average clustering (UPG), Farris, and modified Farris methods—are examined under the neutral mutation model of evolution. The methods are compared for accuracy in construction of the topology and estimation of the branch lengths, using statistics of these two aspects. The distribution of the statistic concerning topological construction is shown to be as important as its mean and variance for the comparison.
Of the three methods, the UPG method constructs the tree topology with the least variation. The modified Farris method, however, gives the best performance when the two aspects are considered simultaneously. It is also shown that a topology based on two genes is much more accurate than that based on one gene.
There is a tendency to accept published molecular trees, but uncritical acceptance may lead one to spurious conclusions. It should always be kept in mind that a tree is a statistical result that is affected strongly by the stochastic error of nucleotide substitution and the error intrinsic to the tree construction method itself.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Daniels GR, Deininger PL (1985) Repeated sequence families derived from mammalian tRNA genes. Nature 317:819–822
Dayhoff MO (ed) (1972) Atlas of protein sequence and structure. National Biomedical Research Foundation, Washington, D.C.
Dekio S, Yamasaki R, Jidoi J, Hori H, Osawa S (1984) Secondary structure and phylogeny ofStaphylococcus andMicrococcus 5S rRNAs. J Bacteriol 159:233–237
Faith DP (1985) Distance methods and approximation of mostparsimonious trees. Syst Zool 34:312–325
Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668
Gojobori T, Nei M (1984) Concerted evolution of the immunoglobulin VH gene family. Mol Biol Evol 1:195–212
Hasegawa M, Yano T (1984) Phylogeny and classification ofHominoidea as inferred from DNA sequence data. Proc Japan Acad 60:389–392
Hori H, Osawa S (1979) Evolutionary change in 5S RNA secondary structure and a phylogenetic tree of 54 5S RNA species. Proc Natl Acad Sci USA 76:381–385
Jukes TH, Cantor CH (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–123
Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624–626
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England
Küntzel H, Köchel HG (1981) Evolution of rRNA and origin of mitochondria. Nature 293:751–755
Miyata T, Yasunaga T, Nishida T (1980) Nucleotide sequence divergence and functional constraint in mRNA evolution. Proc Natl Acad Sci USA 77:7328–7332
Nei M (1975) Molecular population genetics and evolution. North Holland, Amsterdam
Nei M, Stephens JC, Saitou N (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol Biol Evol 2:66–85
Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53:131–147
Schwartz RM, Dayhoff MO (1978) Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts. Science 199:359–403
Sibley CG, Ahlquist JE (1984) The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J Mol Evol 20:2–15
Sokal RR, Sneath PHA (1963) Principles of numerical taxonomy. Freeman, San Francisco
Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460
Tateno Y (1985) Theoretical aspects of molecular tree estimation. In: Ohta T, Aoki K (eds) Population genetics and molecular evolution. Japan Sci Soc Press, Tokyo/Springer-Verlag, Berlin, pp 293–312
Tateno Y, Nei M, Tajima F (1983) Accuracy of estimated phylogenetic trees from molecular data, I. Distantly related species. J Mol Evol 18:387–404
Templeton AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and the apes. Evolution 37:221–244
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Tateno, Y., Tajima, F. Statistical properties of molecular tree construction methods under the neutral mutation model. J Mol Evol 23, 354–361 (1986). https://doi.org/10.1007/BF02100645
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF02100645