. The Biological bulletin. Biology; Zoology; Biology; Marine Biology. IOIKI 'i»ii' 4000 5000 Number of Sites 8000. 2000 3000 4000 5000 6000 Number of Sites Figure 2. Proportion of trees identical to the whole-genome tree in- ferred from different sampling schemes. Data points represent mean of 1024 samples of the indicated size, error bars denote 95% confidence intervals for the mean, diamonds represent maximum likelihood, triangles represent parsimony, and squares represent neighbor-joining. (A) Samples of contiguous sites beginning at random locations. (B) Samples of sites individual
. The Biological bulletin. Biology; Zoology; Biology; Marine Biology. IOIKI 'i»ii' 4000 5000 Number of Sites 8000. 2000 3000 4000 5000 6000 Number of Sites Figure 2. Proportion of trees identical to the whole-genome tree in- ferred from different sampling schemes. Data points represent mean of 1024 samples of the indicated size, error bars denote 95% confidence intervals for the mean, diamonds represent maximum likelihood, triangles represent parsimony, and squares represent neighbor-joining. (A) Samples of contiguous sites beginning at random locations. (B) Samples of sites individually and independently chosen without replacement from random locations throughout the genome. that are individually and independently chosen. The obser- vation that the two sampling schemes produce different results is evidence that contiguous sequence data do not meet the assumption. Taken over the entire study, the principal conclusions are that individual gene sequences are not sufficient samples from which to infer the phytogeny of these taxa; and that contiguous DNA sequence data are not and hence do not meet the basic assumption of the bootstrap. More detail and elaboration of these and other points can be found in references 4 and 5. Literature Cited 1. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376. 2. Fitch, W. M. 1971. Toward defining the course of evolution: minima] change for a specific tree topology. Syst. Biol. 20: 406-416. 3. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406- 425. 4. Cummings, M. P., S. P. Otto, and J. Wakeley. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12: 814-822. 5. Otto, S. P., M. P. Cummings, and J. Wakeley. 1996. Inferring phytogenies from DNA sequence data: the effects of sampling. Pp. 103-115 in New Uses for New Phytogenies.
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