Hostname: page-component-6bf8c574d5-b4m5d Total loading time: 0 Render date: 2025-02-20T09:23:49.588Z Has data issue: false hasContentIssue false
  • English
  • Français

Estimation of inbreeding coefficients from genotypic data on multiple alleles, and application to estimation of clonality in malaria parasites

Published online by Cambridge University Press:  14 April 2009

William G. Hill ,
Hamza A. Babiker ,
Lisa C. Ranford-Cartwright  and
David Walliker
William G. Hill*
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT
Hamza A. Babiker
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT
Lisa C. Ranford-Cartwright
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT
David Walliker
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT
*
* Corresponding author.
Rights & Permissions [Opens in a new window]

Summary

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

Methods for estimating probability of identity by descent (f) are derived for data on numbers of genotypes at single loci and at pairs of loci with many alleles at each locus. The methods are general, but are specifically applied to data on genotype frequencies in zygotes of the malaria parasite sampled from its mosquito host in order to find the extent of outcrossing in the parasite and the degree of clonality in populations. It is assumed that zygotes are the outcome either of gametes of the same clone, in which they are identical at all loci, or are products of two random, unrelated clones. From the estimate of f an effective number of clones per human host can also be derived. For Plasmodium falciparum from a Tanzanian village, estimates of f are 0·33 from data on zygote frequencies at two multiallelic loci, indicating that two-thirds of zygotes produce recombinant types.

Type
Research Article
Information
Genetics Research , Volume 65 , Issue 1 , February 1995 , pp. 53 - 61
Copyright
Copyright © Cambridge University Press 1995

References

Babiker, H. A., Creasey, A. M., Fenton, B., Bayoumi, R. A. L., Arnot, D. E., & Walliker, D., (1991). Genetic diversity of Plasmodium falciparum in a village in eastern Sudan. 1. Diversity of enzymes, 2D-PAGE proteins and antigens. Transactions of the Royal Society of Tropical Medicine and Hygiene 85, 572–577.CrossRefGoogle Scholar
Babiker, H. A., Ranford-Cartwright, L. C., Currie, D., Charlwood, J. D., Billingsley, P., Teuscher, T., & Walliker, D., (1994). Random mating in a natural population of the malaria parasite Plasmodium falciparum. Parasitology 109, 413–421.CrossRefGoogle Scholar
Boreham, P. F. L., Lenahan, J. K., Boulzaguet, R., Storey, J., Ashkar, T. S., Nambiar, R., & Matsushima, T., (1979). Studies on multiple feeding by Anopheles gambiae s.l. in a Sudan savanna area of north Nigeria. Transactions of the Royal Society of Tropical Medicine and Hygiene 73, 418–423.CrossRefGoogle Scholar
Burkot, T. R., Graves, P. M., Paru, R., & Lagog, M., (1988). Mixed blood feeding by the malaria vectors in the Anopheles punctulatus complex (Diptera: Culicidae). Journal of Medical Entomology 25, 205–213.CrossRefGoogle ScholarPubMed
Carter, R., & McGregor, I. A., (1973). Enzyme variation in Plasmodium falciparum in The Gambia. Transactions of the Royal Society of Tropical Medicine and Hygiene 67, 830–837.CrossRefGoogle ScholarPubMed
Conway, D. J., & McBride, J. S., (1991). Population genetics of Plasmodium falciparum within a malaria-hyperendemic area. Parasitology 103, 7–16.CrossRefGoogle ScholarPubMed
Creasey, A., Fenton, B., Walker, A., Thaithong, S., Oliveira, S., Matambu, S., & Walliker, D., (1990). Genetic diversity of Plasmodium falciparum shows geographical variation. American Journal of Tropical Medicine and Hygiene 42, 403–413.CrossRefGoogle ScholarPubMed
Curtis, C. F., & Otoo, L. N., (1986). A simple model of the build-up of resistance to mixtures of anti-malarial drugs. Transactions of the Royal Society of Tropical Medicine and Hygiene 80, 889–892.CrossRefGoogle ScholarPubMed
Dempster, A. P., Laird, N. M., & Rubin, D. B., (1977). Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society B39, 1–38.Google Scholar
Dye, C., & Godfray, H. C. F., (1993). On sex ratio and inbreeding in malaria parasite populations. Journal of Theoretical Biology 161, 131–134.CrossRefGoogle ScholarPubMed
Gokool, S., Curtis, C. F., & Smith, D. F., (1993). Analysis of mosquito bloodmeals by DNA profiling. Medical and Veterinary Entomology 7, 208–215.CrossRefGoogle ScholarPubMed
Guo, S. W., & Thompson, E. A., (1992). Performing the exact test for Hardy—Weinberg proportion for multiple alleles. Biometrics 48, 361–372.CrossRefGoogle ScholarPubMed
Hartl, D. L., & Clark, A. G., (1989). Principles of Population Genetics. Sunderland, MA: Sinauer.Google Scholar
Koehler, K. J., & Larntz, K., (1980). An empirical investigation of goodness-of-fit statistics for sparse multinomials. Journal of the American Statistical Association 75, 336–344.CrossRefGoogle Scholar
Levin, D. A., (1978). Genetic variation in annual Phlox: Self-compatible versus self-incompatible species. Evolution 32, 245–263.Google ScholarPubMed
Ranford-Cartwright, L. C., Balfe, P., Carter, R., & Walliker, D., (1991). Genetic hybrids of Plasmodium falciparum identified by amplification of genomic DNA from single oocysts. Molecular & Biochemical Parasitology 49, 239–244.CrossRefGoogle ScholarPubMed
Ranford-Cartwright, L. C., Balfe, P., Carter, R., & Walliker, D., (1993). Frequency of cross-fertilisation in the human malaria parasite Plasmodium falciparum. Parasitology 107, 11–18.CrossRefGoogle Scholar
Robertson, A., & Hill, W. G., (1984). Deviations from Hardy—Weinberg proportions: sampling variances and use in estimation of inbreeding coefficients. Genetics 107, 703–718.CrossRefGoogle ScholarPubMed
Simonoff, J. S., (1985). An improved goodness-of-fit statistic for sparse multinomials. Journal of the American Statistical Association 80, 671–677.CrossRefGoogle Scholar
Smith, C. A. B., (1957). Counting methods in genetical studies. Annals of Human Genetics 21, 254–276.CrossRefGoogle Scholar
Smith, T., Charlwood, J. D., Kihonda, J., Mwankusye, S., Billingsley, P., Meuwissen, J., Lyimo, E., Takken, W., Teuscher, T., & Tanner, M., (1993). Absence of seasonal variation in malaria parasitaemia in an area of intense seasonal transmission. Acta Tropica 54, 55–72.CrossRefGoogle Scholar
Read, A. F., Nabara, A., Nee, S., Keymer, A. E., & Day, K. P., (1992). Gametocyte sex ratios as indirect measures of outcrossing rates in malaria. Parasitology 104, 387–395.CrossRefGoogle ScholarPubMed
Tait, A., & Turner, C. M. R., (1990). Genetic exchange in Trypanosoma brucei. Parasitology Today 6, 70–75.CrossRefGoogle ScholarPubMed
Thaithong, S., Beale, G. H., Fenton, B., McBride, J., Rosario, V., Walker, A., & Walliker, D., (1984). Clonal diversity in a single isolate of the malaria parasite Plasmodium falciparum. Transactions of the Royal Society of Tropical Medicine and Hygiene 78, 242–245.CrossRefGoogle Scholar
Tibayrenc, M., Kjellberg, F., Araaud, J., Oury, B., Breniere, S. F., Darde, M.-L., & Ayala, F. J., (1991). Are eukaryotic microorganisms clonal or sexual? A population genetics vantage. Proceedings of the National Academy of Sciences USA 88, 5129–5133.CrossRefGoogle ScholarPubMed
Triglia, T., Wellems, T. E., & Kemp, D. J., (1992). Towards a high resolution map of the Plasmodium falciparum genome. Parasitology Today 8, 225–229.CrossRefGoogle ScholarPubMed
Walliker, D., (1989). Implications of genetic exchange in the study of protozoan infections. Parasitology 99, S49–S58.CrossRefGoogle Scholar
Weir, B. S., (1990). Genetic Data Analysis. Sunderland, MA: Sinauer.Google Scholar
Weir, B. S., & Cockerham, C. C., (1973). Mixed self and random mating at two loci. Genetical Research 21, 247–262.CrossRefGoogle ScholarPubMed
Wright, S., (1921). Systems of mating. Genetics 6, 111–178.CrossRefGoogle ScholarPubMed