Hostname: page-component-cd9895bd7-fscjk Total loading time: 0 Render date: 2024-12-28T03:22:15.717Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity of Philippine Rubus moluccanus L. (Rosaceae) populations examined with VNTR DNA probes

Published online by Cambridge University Press:  10 July 2009

Daniel T. Busemeyer ,
Stephan Pelikan ,
Robert S. Kennedy  and
Steven H. Rogstad
Daniel T. Busemeyer
Affiliation:
Department of Biological Sciences ML6, University of Cincinnati, Cincinnati, Ohio 45221–0006, U.S.A.
Stephan Pelikan
Affiliation:
Department of Mathematical Sciences ML25, University of Cincinnati, Cincinnati, Ohio 45221–0025, U.S.A.
Robert S. Kennedy
Affiliation:
Museum of Natural History & Science, Cincinnati Museum Center, 1720 Gilbert Ave., Cincinnati, Ohio 45202, U.S.A.
Steven H. Rogstad
Affiliation:
Department of Biological Sciences ML6, University of Cincinnati, Cincinnati, Ohio 45221–0006, U.S.A.
Get access Rights & Permissions [Opens in a new window]

Abstract

Two synthetic DNA probes composed of tandemly repeated ‘core’ sequences (GACA and GATA) were used to examine genetic diversity at multiple variable-number-tandem-repeat (VNTR) loci within and among four spatially isolated Philippine populations of Rubus moluccanus L. (Rosaceae), an uncultivated bramble widely distributed throughout southeast Asia – Malesia. Central goals were to determine whether apomictic propagation was detectable in R. moluccanus and to examine whether populations isolated on separate islands, or on mountain tops on a single island, were genetically differentiated. Sampling 22 individuals per population, the findings include: (1) no two individuals shared identical VNTR band profiles and thus apomictic propagation was not detected; (2) the mean number of bands scored per individual was 24.3 (SD = 3.91) and the proportion of polymorphic loci within populations ranged from 0.69 to 1.00 (mean = 0.86 ± SD = 0.085); (3) the average proportion of bands shared between individuals within populations ranged from 0.39 to 0.67 (0.50 ± 0.067), while average interpopulation similarity ranged from 0.21 to 0.50 (0.32 ± 0.092); and (4) estimated heterozygosity within populations ranged from 0.42 to 0.79 (0.62 ± 0.083), while interpopulation heterozygosity ran from 0.62 to 0.81 (0.74 ± 0.062). Permutation tests were used to estimate the statistical significance of differences in similarity between populations. A Luzon population isolated by 1200 km was always significantly different in similarity tests when compared with each of the other three populations, all located on Mindanao (and separated by at least 100 km but less than 250 km). Of the latter three, only one population differed significantly from the other two in the degree of VNTR markers shared, possibly reflecting biogeographic partitioning suggested for the island. Across all populations, average estimated Fst was 0.154, although mean inter-island Fst (0.224) was significantly higher than mean intra-island Fst (0.085). These results suggest that, while intra-island gene flow is relatively high, significant differentiation of tropical species may occur even over short distances on individual islands. Preservation of only a limited number of populations may result in a significant loss of genetic diversity in such species.

Keywords

conservation biologyDNA fingerprintingminisatellite DNApopulation geneticsrflp analysis
Type
Research Article
Information
Journal of Tropical Ecology , Volume 13 , Issue 6 , November 1997 , pp. 867 - 884
Copyright
Copyright © Cambridge University Press 1997

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

LITERATURE CITED

Antonius, K. & Nybom, H. 1994. DNA fingerprinting reveals significant amounts of genetic variation in a wild raspberry (Rubus idaeus) population. Molecular Ecology 3:177–180.CrossRefGoogle Scholar
Arens, P., Odinot, P., Van Heusden, A. W., Lindhout, P. & Vosman, B. 1995. GATA- and GACA-repeats are not evenly distributed throughout the tomato genome. Genome 38:84.CrossRefGoogle Scholar
Backer, C. A. & Backhuizen Van Den Brink, R. C. Jr. 1963. Flora of Java. NVP Noordhoff. Groningen. Netherlands. 1240 pp.Google Scholar
Baker, C. S., Gilbert, D. A., Weinrich, M. T., Lambertsen, R., Calambokidis, J., Mcardle, B., Chambers, G. K. & O'Brien, S. J. 1993. Population characteristics of DNA fingerprints in humpback whales (Megaptera novaeangliae). Journal of Heredity 84:281–290.CrossRefGoogle ScholarPubMed
Britten, R. J. 1994. Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes. Proceedings of the National Academy of Sciences USA 91:5992–5996.CrossRefGoogle ScholarPubMed
Brown, W. H. 1951. Useful plants of the Philippines. Dept of Agriculture and Natural Resources, Philippine Bureau of Science Technical Bulletin 10. Bureau of Printing, Manila. 187 pp.Google Scholar
Busemeyer, D. T. 1995. Comparative genetic diversity of Philippine Rubus moluccanus L. (Rosaceae) populations detected with synthetic VNTR loci probes. M.Sc. Thesis. University of Cincinnati, Cincinnati. 82 pp.Google Scholar
Crane, M. B. & Thomas, P. T. 1939. Segregation in asexual (apomictic) offspring in Rubus. Nature 143:684.CrossRefGoogle Scholar
Czapik, R. 1981. Elementary apomictic processes in Rubus L. Acta Societatis Botanicorum Poloniae 50:201–204.CrossRefGoogle Scholar
Epplen, J. T. 1988. On simple repeated GATA-GACA sequences in animal genomes: a critical reappraisal. Journal of Heredity 79:409–417.CrossRefGoogle Scholar
Eriksson, O. & Bremer, B. 1993. Genet dynamics of the clonal plant Rubus saxatilis. Journal of Ecology 81:533–542.CrossRefGoogle Scholar
Flint, J., Boyce, A. J., Martinson, J. J. & Clegg, J. B. 1989. Population bottlenecks in Polynesia revealed by minisatellites. Human Genetics 83:257–263.CrossRefGoogle ScholarPubMed
Focke, W. O. 1910. Species Ruborum. Bibliotheca botanica 72:1–233. E. Schweizerbartsche Verlagsbuchhandlung, Stuttgart.Google Scholar
Focke, W. O. 1914. Species Ruborum. Bibliotheca botanica 83:1–274. E. Schweizerbartsche Verlagsbuchhandlung, Stuttgart.Google Scholar
Geyer, C. J., Ryder, O. A., Chemnick, L. G. & Thompson, E. A. 1993. Analysis of relatedness in the California condors from DNA fingerprints. Molecular Biology and Evolution 10:571–589.Google Scholar
Gilbert, D. A., Lehman, N., O'Brien, S. J. & Wayne, R. K. 1990. Genetic fingerprinting reflects population differentiation in the California Channel Island fox. Nature 344:764–767.CrossRefGoogle ScholarPubMed
Gilbert, D. A., Packer, C., Pusey, A. W., Stephens, J. C. & O'Brien, S. J. 1991. Analytical DNA fingerprinting in lions: parentage, genetic diversity, and kinship. Journal of Heredity 82:378–386.CrossRefGoogle ScholarPubMed
Good, P. 1994. Permutation tests: a practical guide to resampling methods for testing hypotheses. Springer-Verlag New York, Inc. 228 pp.CrossRefGoogle Scholar
Grant, V. 1981. Plant speciation (2nd edition). Columbia University Press. New York. 563 pp.CrossRefGoogle Scholar
Hamrick, J. L. & Godt, M. J. W. 1990. Allozyme diversity in plant species. Pp. 43–63 in Brown, H. D., Clegg, M. T., Kahler, A. L. & Weir, B. S. (eds). Plant population genetics, breeding, and genetic resources. Sinauer Associates, Sunderland.Google Scholar
Jarman, A. P. & Wells, R. A. 1989. Hypervariable minisatellites: recombinators or innocent bystanders? Trends in Genetics 5:367–371.CrossRefGoogle ScholarPubMed
Jeffreys, A. J., Wilson, V. & Thein, S. L. 1985. Individual-specific ‘fingerprints’ of human DNA. Nature 316:76–79.CrossRefGoogle ScholarPubMed
Jeffreys, A. J., Wilson, V., Thein, S. L., Weatherall, D. J. & Ponder, B. A. J. 1986. DNA ‘fingerprints’ and segregation analysis of multiple markers in human pedigrees. American Journal of Human Genetics 39:11–24.Google ScholarPubMed
Jeffreys, A. J., Royle, N. J., Wilson, V. & Wong, Z. 1988. Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature 332:278–281.CrossRefGoogle ScholarPubMed
Jennings, D. L. 1988. Raspberries and blackberries: their breeding, diseases and growth. Academic Press, Harcourt Brace Jovanovich, London. 230 pp.Google Scholar
Jin, L. & Chakraborty, R. 1993. A bias-corrected estimate of heterozygosity for single-probe multilocus DNA fingerprints. Molecular Biology and Evolution 10:1112–1114.Google ScholarPubMed
Kennedy, R. S., Gonzales, P. C. & Miranda, H. C. Jr., 1997. New Aethopyga sunbirds (Aves: Nectariniidae) from the island of Mindanao, Philippines. Auk 114:1–10.CrossRefGoogle Scholar
Kimura, M. & Ohta, T. 1971. Theoretical aspects of population genetics. Princeton University Press, Princeton. 219 pp.Google ScholarPubMed
Knight, R. L. & Keep, E. 1960. The genetics of suckering and tip rooting in the raspberry. Pp. 57–62 in Report of East Malling Research Station for 1959.Google Scholar
Kuhnlein, U., Zadworny, D., Dawe, Y., Fairfull, R. W. & Gavora, J. S. 1990. Assessment of inbreeding by DNA fingerprinting development of a calibration curve using defined strains of chickens. Genetics 125:161–165.CrossRefGoogle ScholarPubMed
Lynch, M. 1990. The similarity index and DNA fingerprinting. Molecular Biology and Evolution 7:478–484.Google ScholarPubMed
Lynch, M. 1991. Analysis of population genetic structure by DNA fingerprinting. Pp. 113–126 in Burke, T., Dolf, G., Jeffreys, A. J. & Wolff, R. (eds). DNA fingerprinting: approaches and applications. Birkhauser Verlag, Basel, Switzerland. 400 pp.CrossRefGoogle Scholar
Milgroom, M. G., Lipari, S. E. & Powell, W. A. 1992. DNA fingerprinting and analysis of population structure in the chestnut blight fungus, Cryphonectria parasitica. Genetics 131:297–306.CrossRefGoogle ScholarPubMed
Nakamura, T., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E. & White, R. 1987. Variable number of tandem-repeat (VNTR) markers for human gene mapping. Science 235:1616–1622.CrossRefGoogle ScholarPubMed
Nei, M. 1973, Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Science U.S.A. 70:3321–3323.CrossRefGoogle ScholarPubMed
Nybom, H. 1988. Apomixis versus sexuality in blackberries (Rubus subgen. Rubus, Rosaceae). Plant Systematics and Evolution 160:207–218.CrossRefGoogle Scholar
Nybom, H. 1993. Applications of DNA fingerprinting in plant population studies. Pp. 294–309 in Pena, S. J., Chakraborty, R., Epplen, J. T. & Jeffreys, A. J. (eds). DNA fingerprinting: state of the science. Birkhauser Verlag, Basel, Switzerland. 466 pp.Google Scholar
Nybom, H. 1995. Evaluation of interspecific crossing experiments in facultatively apomictic blackberries (Rubus subgen. Rubus) using DNA fingerprinting. Hereditas 122:57–65.CrossRefGoogle Scholar
Nybom, H. & Schaal, B. A. 1990. DNA ‘fingerprints’ reveal genotypic distributions in natural populations of blackberries and raspberries (Rubus, Rosaceae). American Journal of Botany 77:883–888.CrossRefGoogle Scholar
Parent, J.-G., & Page, D. 1992. Identification of raspberry cultivars by nonradioactive DNA fingerprinting. Hortscience 27:1108–1110.CrossRefGoogle Scholar
Powell, J. M. 1976. Ethnobotany. Pp. 106–183 in Paijmans, K. (ed.). New Guinea vegetation. Australian National University Press, Canberra.Google Scholar
Proctor, M. & Yeo, P. 1973. The pollination of flowers. W. Collins & Sons, London. 418 pp.Google Scholar
Prodohl, P. A., Taggart, J. B. & Ferguson, A. 1994. Single locus inheritance and joint segregation analysis of minisatellite (VNTR) DNA loci in brown trout (Salmo trutta L.). Heredity 73:556–564.CrossRefGoogle Scholar
Richards, A. J. 1986. Plant breeding systems. George Allen & Unwin, London. 529 pp.Google Scholar
Rogstad, S. H. 1992. Saturated NaCl-CTAB Solution as a means of field preservation of leaves for DNA analyses. Taxon 41:701–708.CrossRefGoogle Scholar
Rogstad, S. H. 1993. Surveying plant genomes for variable number of tandem-repeat loci. Methods in Enzymology 224:278–294.CrossRefGoogle ScholarPubMed
Rogstad, S. H. 1994. Inheritance in turnip of variable-number tandem-repeat genetic markers revealed with synthetic repetitive DNA probes. Theoretical and Applied Genetics 89:824–830.CrossRefGoogle ScholarPubMed
Rogstad, S. H. 1996. Assessing genetic diversity in plants with synthetic tandem repetitive DNA probes. Pp. 1–14 in Gustafson, J. P. & Flavell, R. B. (eds). Genomes of plants and animals. Plenum Press, New York.Google Scholar
Rogstad, S. H., Nybom, H. & Schaal, B. A. 1991a. The tetrapod ‘DNA fingerprinting’ M13 repeat probe reveals genetic diversity and clonal growth in quaking aspen (Populus tremuloides). Plant Systematics and Evolution 175:115–123.CrossRefGoogle Scholar
Rogstad, S. H., Wolff, K. & Schaal, B. A. 1991b. Geographical variation in Asimina triloba Dunal (Annonaceae) revealed by the M13 ‘DNA fingerprinting’ probe. American Journal of Botany 78:1391–1396.CrossRefGoogle Scholar
Rogstad, S. H. & Pelikan, S. 1996. GELSTATS: a computer program for population genetics analyses using VNTR multilocus probe data. BioTechniques 21:1128–1131.CrossRefGoogle ScholarPubMed
Sambrook, J., Fritsch, E. F. & Maniatis, T. 1989. Molecular cloning: a laboratory manual (2nd edition). Cold Spring Harbor Laboratory Press, New York. 978 pp.Google Scholar
Scribner, K. T., Arntzen, J. W. & Burke, T. 1994. Comparative analysis of intra- and interpopulation genetic diversity in Bufo bufo, using allozyme, single-locus microsatellite, minisatellite, and multilocus minisatellite data. Molecular Biology and Evolution 11:737–748.Google ScholarPubMed
Stephens, J. C., Gilbert, D. A., Yuhki, N. & O'Brien, S. J. 1992. Estimation of heterozygosity for single-probe multilocus DNA fingerprints. Molecular Biology and Evolution 9:729–743.Google ScholarPubMed
Taylor, E. B. 1995. Genetic variation at minisatellite DNA loci among North Pacific populations of steelhead and rainbow trout (Oncorhynchus mykiss). Journal of Heredity 86:354–363.CrossRefGoogle Scholar
Thomas, L. & Ballou, J. 1983. Equations and population management (Appendix 2). Pp. 474–484 in Schonewald-Cox, C. M., Chambers, S. M., MacBryde, B. & Thomas, L. (eds). Genetics and conservation. Benjamin/Cummings Publishing Co., Menlo Park.Google Scholar
Weir, B. S. 1990. Genetic data analysis. Sinauer Associates, Inc., Sunderland, Mass. 375 pp.Google Scholar
Weising, K., Nybom, H., Wolff, K. & Meyer, W. 1995. DNA fingerprinting in plants and fungi. CRC Press, Boca Raton. 322 pp.Google Scholar
Westneat, D. P., Noon, W. A., Reeve, R. K. & Aquadro, C. F. 1988. Improved hybridization conditions for DNA ‘fingerprints’ probed with M13. Nucleic Acids Research 16:4161.CrossRefGoogle ScholarPubMed
Wetton, J. H., Carter, R. C., Parkin, D. T. & Walters, D. 1987. Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 327:147–149.CrossRefGoogle ScholarPubMed
Wilkinson, L. 1990. SYSTAT statistics manual. SYSTAT Inc., Evanston. 676 pp.Google Scholar
Wolff, K., Rogstad, S. H. & Schaal, B. A. 1994. Population and species variation of minisatellite DNA in Plantago. Theoretical and Applied Generics 87:733–740.CrossRefGoogle ScholarPubMed
Wright, S. 1969. Evolution and the genetics of populations. II. The theory of gene frequencies. University of Chicago Press, Chicago. 511 pp.Google Scholar
Wright, S. 1978. Evolution and the genetics of populations. IV. Variability within and among populations. University of Chicago Press, Chicago. 580 pp.Google Scholar