Skip to main content
SpringerLink
Log in

Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract.

A method is presented for estimating the transition/transversion ratio (TI/TV), based on phylogenetically independent comparisons. TI/TV is a parameter of some models used in phylogeny estimation intended to reflect the fact that nucleotide substitutions are not all equally likely. Previous attempts to estimate TI/TV have commonly faced three problems: (1) few taxa; (2) nonindependence among pairwise comparisons; and (3) multiple hits make the apparent TI/TV between two sequences decrease over time since their divergence, giving a misleading impression of relative substitution probabilities. We have made use of the time dependency, modeling how the observed TI/TV changes over time and extrapolating to estimate the ``instantaneous'' TI/TV—the relevant parameter for phylogenetic inference. To illustrate our method, TI/TV was estimated for two mammalian mitochondrial genes. For 26 pairs of cytochrome b sequences, the estimate of TI/TV was 5.5; 16 pairs of 12s rRNA yielded an estimate of 9.5. These estimates are higher than those given by the maximum likelihood method and than those obtained by averaging all possible pairwise comparisons (with or without a two-parameter correction for multiple substitutions). We discuss strengths, weaknesses, and further uses of our method.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Allard MW, Miyamoto MM, Jarecki L, Kraus F, Tennant MR (1992) DNA systematics and evolution of the artiodactyl family Bovidae. Proc Natl Acad Sci USA 89:3972–3976

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Archer M (1984) The Australian marsupial radiation. In: Archer M, Clayton G (eds) Vertebrate zoogeography and evolution in Australia. Hesperian Press, Perth, pp 633–809

    Google Scholar 

  • Baverstock PR, Archer M, Adams M, Richardson BJ (1982) Genetic relationships among 32 species of Australian dasyurid marsupials. In: Arch M (ed) Carnivorous marsupials. Royal Zoological Society of New South Wales, Sydney, pp 641–650

    Google Scholar 

  • Bromham LD, Rambaut AE, Harvey PH (1996) Determinants of rate variation in mammalian DNA sequence evolution. J Mol Evol 43 (in press)

  • Brownell E (1983) DNA/DNA hybridization studies of muroid rodents: symmetry and rates of molecular evolution. Evolution 37:1034–1051

    Article  Google Scholar 

  • Burt A (1989) Comparative methods using phylogenetically independent contrasts. Oxf Surv Evol Biol 6:33–53

    Google Scholar 

  • Butler PM (1988) Phylogeny of the insectivores. In: Benton MJ (ed) The phylogeny and classification of tetrapods, volume 2: mammals. Clarendon Press, Oxford, pp 117–142

    Google Scholar 

  • Carroll RC (1989) Vertebrate paleontology and evolution. WH Freeman, New York

    Google Scholar 

  • Catzeflis FM, Nevo E, Ahlquist JE, Sibley CG (1989) Relationships of the chromosomal species in the Eurasian mole rates of the Spalax ehrenbergi group as determined by DNA-DNA hybridization, and an estimate of the spalacid-murid divergence time. J Mol Evol 29:223–232

    Article  PubMed  CAS  Google Scholar 

  • Catzeflis FM, Aguilar J-P, Jaeger J-J (1992) Muroid rodents: phylogeny and evolution. Trends Ecol Evol 7:122–126

    Article  PubMed  CAS  Google Scholar 

  • Corbet GB, Hill JE (1991) A world list of mammalian species. Oxford University Press, Oxford

    Google Scholar 

  • Eisenberg JF (1981) The mammalian radiations. The Athlone Press, London

    Google Scholar 

  • Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1–15

    Article  Google Scholar 

  • Felsenstein J (1988) Phylogenies from molecular data: inference and reliability. Annu Rev Genet 22:521–565

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1992) Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet Res Camb 59:139–147

    Article  CAS  Google Scholar 

  • Felsenstein J (1993) PHYLIP. Version 3.5c. University of Washington, Seattle

    Google Scholar 

  • Forstén A (1992) Mitochondrial-DNA time-table and the evolution of Equus: comparison of molecular and paleontological evidence. Ann Zool Fennici 28:301–309

    Google Scholar 

  • Garland TJ, Janis CM (1993) Does metatarsal/femur ratio predict maximal running speed in cursorial mammals? J Zool Lond 229:133–151

    Article  Google Scholar 

  • Garland TJ, Dickerman AW, Janis CW, Jones JA (1993) Phylogenetic analysis of covariance by computer simulation. Syst Biol 42:265–292

    Article  Google Scholar 

  • Georgiadis NJ, Kat PW, Oketch H, Patton J (1990) Allozyme divergence within the Bovidae. Evolution 44:2135–2149

    Article  Google Scholar 

  • Geraads D (1992) Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla). Zool J Linn Soc 104:193–207

    Article  Google Scholar 

  • Hafner DJ (1984) Evolutionary relationships of the Nearctic Sciuridae. In: Murie JO, Michener GR (eds) The biology of ground-dwelling squirrels: annual cycles, behavioural ecology, and sociality. pp 3–23

    Google Scholar 

  • Hafner MS, Sudman PD, Villablanca FX, Spradling TA, Demastes JW, Nadler SA (1994) Disparate rates of molecular evolution in cospeciating hosts and parasites. Science 265:1087–1090

    Article  PubMed  CAS  Google Scholar 

  • Hartl GB, Göltenboth R, Grillitsch M, Willing R (1988) On the biochemical systematics of the Bovini. Biochem Syst Ecol 16:575–579

    Article  CAS  Google Scholar 

  • Hartl GB, Burger H, Willing R, Suchentrunk F (1990) On the biochemical systematics of the Caprini and Rupicaprini. Biochem Syst Ecol 18:175–182

    Article  CAS  Google Scholar 

  • Honeycutt RL, Williams SL (1982) Genic differentiation in pocket gophers of the genus Pappogeomys with comments on intergeneric relationships in the subfamily Geomyinae. J Mamm 63:208–217

    Article  Google Scholar 

  • Janis CM (1988) New ideas in ungulate phylogeny and evolution. Trends Ecol Evol 3:291–297

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Kingdon J (1982) East African mammals: an atlas of evolution. Academic Press, London

    Google Scholar 

  • Kumar S, Tamura K, Nei M (1993) MEGA: molecular evolutionary genetics analysis. The Pennsylvania State University, University Park

    Google Scholar 

  • Li WH, Gouy M, Sharp PM, O’hUigin C, Yang YY (1990) Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla and Carnivora and molecular clocks. PNAS 87:6703–6707

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Macdonald DW (ed) (1984) The encyclopaedia of mammals. Unwin Hyman, London

    Google Scholar 

  • Novacek MJ (1992) Mammalian phylogeny: shaking the tree. Nature 356:121–125

    Article  PubMed  CAS  Google Scholar 

  • Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) Fast DNAml a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:4148

    Google Scholar 

  • Pagel MD, Harvey PH (1992) On solving the correct problem: wishing does not make it so. J Theor Biol 156:425–430

    Article  Google Scholar 

  • Purvis A (1995) A composite estimate of primate phylogeny. Philos Trans R Soc Lond Biol 348:405–421

    Article  PubMed  CAS  Google Scholar 

  • Randi E, Fusco G, Lorenzini R, Tosco S, Tosi G (1991) Allozyme divergence and phylogenetic relationships among Capra, Ovis and Rupicapra (Artiodactyla, Bovidae). Heredity 67:281–286

    Article  PubMed  Google Scholar 

  • Reeder TW (1995) Phylogenetic relationships among phrynosomatid lizards as inferred from mitochrondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions. Mol Phylogenet Evol 4:203–222

    Article  PubMed  CAS  Google Scholar 

  • Reig OA, Kirsch JAW, Marshall LG (1987) Systematic relationships of the living and Neocenozoic American “opossum-like” marsupials (suborder Didelphimorphia), with comments on the classification of these and of the Cretaceous and Paleogene New World and European metatherians. In: Archer M (ed) Possums and opossums: studies in evolution. Surrey Beatty and the Royal Zoological Society of New South Wales, Sydney, pp 1–89

    Google Scholar 

  • Sarich VM (1986) Rodent macromolecular systematics. In: Luckett WP, Hartenberger J-L (eds) Evolutionary relationships among rodents; a multidisciplinary analysis. pp 423–452

    Google Scholar 

  • She JX, Bonhomme F, Boursot P, Thaler L, Catzeflis F (1990) Molecular phylogenies in the genus Mus: comparative analysis of electrophoretic, scnDNA hybridization, and mtDNA RFLP data. Biol J Linn Soc 41:83–103

    Article  Google Scholar 

  • Stanley HF, Kadwell M, Wheeler JC (1994) Molecular evolution of the family Camelidae: a mitochondrial DNA study. Proc R Soc Lond [Biol] 256:1–6

    Article  CAS  Google Scholar 

  • Wakeley J (1996) The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. Trends Ecol Evol 11:158–163

    Article  PubMed  CAS  Google Scholar 

  • Wayne RK, Benveniste RE, Janczewski DN, O’Brien SJ (1989) Molecular and biochemical evolution of the Carnivora. In: Gittleman JL (ed) Carnivore behavior, ecology, and evolution. Chapman and Hall, London, pp 465–494

    Chapter  Google Scholar 

  • Wheeler WC, Honeycutt RL (1988) Paired sequence difference in ribosomal RNAs evolutionary and phylogenetic implications. Mol Biol Evol 5:90–96

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom, GB

    Andy Purvis & Lindell Bromham

Authors
  1. Andy Purvis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lindell Bromham
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Received: 22 August 1995 / Accepted: 26 July 1996

Rights and permissions

Reprints and permissions

About this article

Cite this article

Purvis, A., Bromham, L. Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny. J Mol Evol 44, 112–119 (1997). https://doi.org/10.1007/PL00006117

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/PL00006117

Search

Navigation