Abstract
We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.
Full Text
The Full Text of this article is available as a PDF (3.4 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Cavalli-Sforza L. L., Edwards A. W. Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet. 1967 May;19(3 Pt 1):233–257. [PMC free article] [PubMed] [Google Scholar]
- Crandall K. A., Templeton A. R. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics. 1993 Jul;134(3):959–969. doi: 10.1093/genetics/134.3.959. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Excoffier L., Smouse P. E., Quattro J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992 Jun;131(2):479–491. doi: 10.1093/genetics/131.2.479. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988;22:521–565. doi: 10.1146/annurev.ge.22.120188.002513. [DOI] [PubMed] [Google Scholar]
- Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
- Hedges S. B., Kumar S., Tamura K., Stoneking M. Human origins and analysis of mitochondrial DNA sequences. Science. 1992 Feb 7;255(5045):737–739. doi: 10.1126/science.1738849. [DOI] [PubMed] [Google Scholar]
- Hudson R. R., Slatkin M., Maddison W. P. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992 Oct;132(2):583–589. doi: 10.1093/genetics/132.2.583. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lake J. A. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 1987 Mar;4(2):167–191. doi: 10.1093/oxfordjournals.molbev.a040433. [DOI] [PubMed] [Google Scholar]
- Li W. H., Gouy M. Statistical tests of molecular phylogenies. Methods Enzymol. 1990;183:645–659. doi: 10.1016/0076-6879(90)83042-8. [DOI] [PubMed] [Google Scholar]
- Long J. C. The allelic correlation structure of Gainj- and Kalam-speaking people. I. The estimation and interpretation of Wright's F-statistics. Genetics. 1986 Mar;112(3):629–647. doi: 10.1093/genetics/112.3.629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Merriwether D. A., Clark A. G., Ballinger S. W., Schurr T. G., Soodyall H., Jenkins T., Sherry S. T., Wallace D. C. The structure of human mitochondrial DNA variation. J Mol Evol. 1991 Dec;33(6):543–555. doi: 10.1007/BF02102807. [DOI] [PubMed] [Google Scholar]
- Nei M., Tajima F. Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics. 1983 Sep;105(1):207–217. doi: 10.1093/genetics/105.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pamilo P., Nei M. Relationships between gene trees and species trees. Mol Biol Evol. 1988 Sep;5(5):568–583. doi: 10.1093/oxfordjournals.molbev.a040517. [DOI] [PubMed] [Google Scholar]
- Quattro J. M., Avise J. C., Vrijenhoek R. C. Molecular evidence for multiple origins of hybridogenetic fish clones (Poeciliidae:Poeciliopsis). Genetics. 1991 Feb;127(2):391–398. doi: 10.1093/genetics/127.2.391. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Slatkin M., Maddison W. P. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics. 1989 Nov;123(3):603–613. doi: 10.1093/genetics/123.3.603. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Templeton A. R. Human origins and analysis of mitochondrial DNA sequences. Science. 1992 Feb 7;255(5045):737–737. doi: 10.1126/science.1590849. [DOI] [PubMed] [Google Scholar]
- Thompson E. A., Neel J. V., Smouse P. E., Barrantes R. Microevolution of the Chibcha-speaking peoples of lower Central America: rare genes in an Amerindian complex. Am J Hum Genet. 1992 Sep;51(3):609–626. [PMC free article] [PubMed] [Google Scholar]
- Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
- Watterson G. A., Guess H. A. Is the most frequent allele the oldest? Theor Popul Biol. 1977 Apr;11(2):141–160. doi: 10.1016/0040-5809(77)90023-5. [DOI] [PubMed] [Google Scholar]