Conservation Genetics

, Volume 11, Issue 6, pp 2219–2229 | Cite as

A new method for the partition of allelic diversity within and between subpopulations

Research Article

Abstract

A method is proposed for the analysis of allelic diversity in the context of subdivided populations. The definition of an allelic distance between subpopulations allows for the partition of total allelic diversity into within- and between-subpopulation components, in a way analogous to the classical partition of gene diversity. A new definition of allelic differentiation, A ST , between subpopulations results from this partition, and is contrasted with the concept of allelic richness differentiation. The partition of allelic diversity makes it possible to establish the relative contribution of each subpopulation to within and between-subpopulation components of diversity with implications in priorisation for conservation. A comparison between this partition and that corresponding to allelic richness is illustrated with an example. Computer simulations are used to investigate the behaviour of the new statistic A ST in comparison with F ST for a finite island model under a range of mutation and migration rates. A ST has less dependence on migration rate than F ST for large values of migration rate, but the opposite occurs for low migration rates. In addition, the variance in the estimates of A ST is higher than that of F ST for low mutation rates, but the opposite for high mutation rates.

Keywords

Allelic diversity Gene diversity Heterozygosity Rarefaction Conservation priorities 

Notes

Acknowledgements

We thank L. Ollivier, J. L. Foulley, J. Fernández, M. A. Toro and three referees for useful comments on the manuscript. This work was funded by Ministerio de Ciencia y Tecnología and Fondos Feder (CGL2006-13445-C02/BOS and CGL2009-13278-C02), and Xunta de Galicia.

References

  1. Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biol 5:181–190CrossRefGoogle Scholar
  2. Barker JSF (2001) Conservation and management of genetic diversity: a domestic animal perspective. Can J For Res 31:588–595CrossRefGoogle Scholar
  3. Bataillon TM, David JL, Schoen DJ (1996) Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics 144:409–417PubMedGoogle Scholar
  4. Bennewitz J, Meuwissen THE (2005) Estimation of extinction probabilities of five german cattle breeds by population viability analysis. J Dairy Sci 88:2949–2961CrossRefPubMedGoogle Scholar
  5. Caballero A, Toro MA (2002) Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 3:289–299CrossRefGoogle Scholar
  6. Caballero A, Rodríguez-Ramilo ST, Ávila V, Fernández J (2010) Management of genetic diversity of subdivided populations in conservation programmes. Conserv Genet 11:409–419CrossRefGoogle Scholar
  7. Comps B, Gömöry D, Letouzey J, Thiébaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics 157:389–397PubMedGoogle Scholar
  8. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014PubMedGoogle Scholar
  9. Crow FJ, Kimura M (1970) An introduction to population genetics theory. Harper & Row, New YorkGoogle Scholar
  10. Eding H, Meuwissen THE (2001) Marker-based estimates of between and within population kinships for the conservation of genetic diversity. J Anim Breed Genet 118:141–159CrossRefGoogle Scholar
  11. Eding H, Crooijmans PMA, Groenne MAM, Meuwissen THE (2002) Assessing the contribution of breeds to genetic diversity in conservation schemes. Genet Sel Evol 34:613–633CrossRefPubMedGoogle Scholar
  12. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839CrossRefGoogle Scholar
  13. Ewens WJ (1964) The maintenance of alleles by mutation. Genetics 50:891–898PubMedGoogle Scholar
  14. Fabuel E, Barragán C, Silió L, Rodríguez MC, Toro MA (2004) Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 93:104–113CrossRefPubMedGoogle Scholar
  15. Fernández J, Toro MA, Caballero A (2004) Managing individuals’ contributions to maximize the allelic diversity maintained in small, conserved populations. Conserv Biol 18:1–10CrossRefGoogle Scholar
  16. Fernández J, Toro MA, Caballero A (2008) Management of subdivided populations in conservation programs: development of a novel dynamic system. Genetics 179:683–692CrossRefPubMedGoogle Scholar
  17. Foulley JL, Ollivier L (2006) Estimating allelic richness and its diversity. Liv Sci 101:150–158CrossRefGoogle Scholar
  18. Hill WG, Rasbash J (1986) Models of long term artificial selection in finite populations. Genet Res 48:41–50CrossRefPubMedGoogle Scholar
  19. Hulbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577–586CrossRefGoogle Scholar
  20. James JW (1970) The founder effect and response to artificial selection. Genet Res 16:241–250CrossRefPubMedGoogle Scholar
  21. Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5:539–543CrossRefGoogle Scholar
  22. Kimura M Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738Google Scholar
  23. Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Mol Ecol 11:2445–2449CrossRefPubMedGoogle Scholar
  24. Luikart G, Allendorf F, Cornuet JM, Sherwin W (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238–247CrossRefPubMedGoogle Scholar
  25. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323CrossRefPubMedGoogle Scholar
  26. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10CrossRefGoogle Scholar
  27. Notter DR (1999) The importance of genetic diversity in livestock populations of the future. J Anim Sci 77:61–69PubMedGoogle Scholar
  28. Ollivier L, Foulley JL (2005) Aggregate diversity: new approach combining within- and between-breed genetic diversity. Liv Prod Sci 95:247–254CrossRefGoogle Scholar
  29. Ollivier L, Foulley JL (2009) Managing genetic diversity, fitness and adaptation of farm animal genetic resources. In: van der Werf J, Graser H-U, Frankham R, Gondro C (eds) Adaptation and fitness in animal populations—evolutionary and breeding perspectives on genetic resource management. Springer, Dordrecht, pp 201–227Google Scholar
  30. Persson H, Widén B, Andersson S, Svensson L (2004) Allozyme diversity and genetic structure of marginal and central populations of Corylus avellana L. (Betulaceae). Plant Syst Evol 244:157–179CrossRefGoogle Scholar
  31. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855CrossRefGoogle Scholar
  32. Piyasatian N, Kinghorn BP (2003) Balancing genetic diversity, genetic gain and population viability in conservation programmes. J Anim Breed Genet 120:137–149CrossRefGoogle Scholar
  33. Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767–779PubMedGoogle Scholar
  34. Rodrigáñez J, Barragán C, Alves E, Cortázar C, Toro MA (2008) Genetic diversity and allelic richness in Spanish wild and domestic pig population estimated from microsatellite markers. Span J Agric Res 1:107–115Google Scholar
  35. Sanders HL (1968) Marine benthic diversity: a comparison study. Am Nat 102:243–282CrossRefGoogle Scholar
  36. Schoen DJ, Brown HD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc Natl Acad Sci USA 90:10623–10627CrossRefPubMedGoogle Scholar
  37. Simianer H (2005) Using expected allele number as objective function to design between and within breed conservation of farm animal biodiversity. J Anim Breed Genet 122:177–187CrossRefPubMedGoogle Scholar
  38. Stefenon VM, Gailing O, Finkeldey R (2008) Genetic structure of plantations and the conservation of genetic resources of Brazilian pine (Araucaria augustifolia). For Ecol Manag 255:2718–2725CrossRefGoogle Scholar
  39. Tapio M, Tapio I, Grislis Z, Holm LE, Jeppsson S, Kantanen J, Miceikiene I, Olsaker I, Viinalass H, Eythorsdottir E (2005) Native breeds demonstrate high contributions to the molecular variation in northern European sheep. Mol Ecol 14:3951–3963CrossRefPubMedGoogle Scholar
  40. Tapio I, Varv S, Bennewitz J, Maleviciute J, Fimland E, Grislis Z, Meuwissen THE, Miceikiene I, Olsaker I, Viinalass H, Vilkki J, Kantanen J (2006) Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data. Conserv Biol 20:1768–1779CrossRefPubMedGoogle Scholar
  41. Toro MA, Caballero A (2005) Characterization and conservation of genetic diversity in subdivided populations. Phil Trans R Soc B 360:1367–1378CrossRefPubMedGoogle Scholar
  42. Toro MA, Fernández J, Caballero A (2009) Molecular characterization of breeds and its use in conservation. Livest Sci 120:174–195CrossRefGoogle Scholar
  43. Tyler T (2002) Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology. Genome 45:1248–1256CrossRefPubMedGoogle Scholar
  44. Wang J (2004) Monitoring and managing genetic variation in group breeding populations without individual pedigrees. Conserv Genet 5:813–825CrossRefGoogle Scholar
  45. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  46. Weitzman ML (1998) The Noah’s Ark problem. Econometrica 66:1279–1298CrossRefGoogle Scholar
  47. Wilson A, Arcese P, Keller LF, Pruett CL, Winker K, Patten MA, Chan Y (2009) The contribution to island populations to in situ genetic conservation. Conserv Genet 10:419–430CrossRefGoogle Scholar
  48. Wright S (1969) Evolution and the genetics of populations. The theory of gene frequencies, vol 2. University of Chicago Press, ChicagoGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Armando Caballero
    • 1
  • Silvia T. Rodríguez-Ramilo
    • 1
  1. 1.Departamento de Bioquímica, Genética e Inmunología, Facultad de BiologíaUniversidad de VigoVigoSpain

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