Skip to main content
SpringerLink
Log in

Analysis and Management of Gene and Allelic Diversity in Subdivided Populations Using the Software Program METAPOP

  • Protocol
  • First Online:
Data Production and Analysis in Population Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 888))

Abstract

METAPOP (http://webs.uvigo.es/anpefi/metapop/) is a desktop application that provides an analysis of gene and allelic diversity in subdivided populations from molecular genotype or coancestry data as well as a tool for the management of genetic diversity in conservation programs. A partition of gene and allelic diversity is made within and between subpopulations, in order to assess the contribution of each subpopulation to global diversity for descriptive population genetics or conservation purposes. In the context of management of subdivided populations in in situ conservation programs, the software also determines the optimal contributions (i.e., number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals in order to maintain the largest level of gene diversity in the whole population with a desired control in the rate of inbreeding. The partition of gene and allelic diversity within and between subpopulations is illustrated with microsatellite and SNP data from human populations.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  2. Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell Publishing, Malden, MA

    Google Scholar 

  3. Pérez-Figueroa A, Saura M, Fernández J, Toro MA, Caballero A (2009) METAPOP – a software for the management and analysis of subdivided populations in conservation programs. Conserv Genet 10:1097–1099

    Article  Google Scholar 

  4. Caballero A, Toro MA (2002) Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 3:289–299

    Article  CAS  Google Scholar 

  5. Caballero A, Rodríguez-Ramilo ST (2010) A new method for the partition of allelic differentiation within and between subpopulations and its application in conservation. Conserv Genet 11:2219–2229. doi:10.1007/s10592-010-0107-7

    Google Scholar 

  6. Fernández J, Toro MA, Caballero A (2008) Management of subdivided populations in conservation programs: development of a novel dynamic system. Genetics 179:683–692

    Article  PubMed  Google Scholar 

  7. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  PubMed  CAS  Google Scholar 

  8. Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biol 5:181–190

    Article  Google Scholar 

  9. Luikart G, Allendorf F, Cornuet JM, Sherwin W (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238–247

    Article  PubMed  CAS  Google Scholar 

  10. Santiago E, Caballero A (1998) Effective size and polymorphism of linked neutral loci in populations under selection. Genetics 149:2105–2117

    PubMed  CAS  Google Scholar 

  11. Wright S (1969) Evolution and the genetics of populations. The theory of gene frequencies, vol 2. University of Chicago Press, Chicago

    Google Scholar 

  12. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855

    Article  Google Scholar 

  13. Foulley JL, Ollivier L (2006) Estimating allelic richness and its diversity. Livest Sci 101:150–158

    Article  Google Scholar 

  14. Toro MA, Fernández J, Caballero A (2009) Molecular characterization of breeds and its use in conservation. Livest Sci 120: 174–195

    Article  Google Scholar 

  15. Eding H, Crooijmans PMA, Groenne MAM, Meuwissen THE (2002) Assessing the contribution of breeds to genetic diversity in conservation schemes. Genet Sel Evol 34:613–633

    Article  PubMed  Google Scholar 

  16. Ollivier L, Foulley JL (2005) Aggregate diversity: new approach combining within- and between-breed genetic diversity. Liv Prod Sci 95:247–254

    Article  Google Scholar 

  17. Ballou J, Lacy R (1995) Identifying genetically important individuals for management of genetic variation in pedigreed populations. In: Ballou JD, Gilpin M, Foose TJ (eds) Population management for survival and recovery. Columbia University Press, New York, pp 76–111

    Google Scholar 

  18. Meuwissen THE (2007) Operation of conservation schemes. In: Oldenbroek K (ed) Utilisation and conservation of farm animal genetic resources. Wageningen Academic Publishers, Wageningen, The Netherlands, pp 167–193

    Google Scholar 

  19. Fernández J, Toro MA, Caballero A (2001) Practical implementations of optimal management strategies in conservation programmes: a mate selection method. Anim Biodivers Conserv 24:17–24

    Google Scholar 

  20. Ávila V, Fernández J, Quesada H, Caballero A (2010) An experimental evaluation with Drosophila melanogaster of a novel dynamic system for the management of subdivided populations in conservation programs. Heredity 106: 765–774

    Google Scholar 

  21. 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 92:832–839

    Article  Google Scholar 

  22. Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671–680

    Article  PubMed  CAS  Google Scholar 

  23. Rosenberg NA, Pritchard JK, Weber JL et al (2002) Genetic structure of human populations. Science 298:2381–2385

    Article  PubMed  CAS  Google Scholar 

  24. Conrad DF, Jakobsson M, Coop G et al (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genet 38:1251–1260

    Article  PubMed  CAS  Google Scholar 

  25. Handley LJ, Manica A, Goudet J, Balloux F (2007) Going the distance: human population genetics in a clinal world. Trends Genet 23:432–439

    Article  PubMed  CAS  Google Scholar 

  26. Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1989) Numerical recipes. Cambridge University Press, Cambridge

    Google Scholar 

Download references

Acknowledgments

We thank Miguel Toro and Jesús Fernández for helpful discussions. This work was funded by the Ministerio de Ciencia e Innovación and Fondos Feder (CGL2009-13278-C02), and a grant for Consolidación e estruturación de unidades de investigación competitivas do sistema universitario de Galicia, Consellería de Educación e Ordenación Universitaria, Xunta de Galicia.

Author information

Authors and Affiliations

  1. Facultad de Biología, Departamento de Bioquímica, Genética e Inmunología Facultad de Biología, Universidad de Vigo, Vigo, Spain

    Andrés Pérez-Figueroa

  2. Departamento de Bioquímica, Genética e Inmunología Facultad de Biología, Universidad de Vigo, Vigo, Spain

    Silvia T. Rodríguez-Ramilo & Armando Caballero

Authors
  1. Andrés Pérez-Figueroa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Silvia T. Rodríguez-Ramilo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Armando Caballero
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Armando Caballero .

Editor information

Editors and Affiliations

  1. , Laboratoire d'Ecologie Alpine, Université Grenoble I, CNRS-UMR5553, rue de la Piscine 2233, Grenoble Cedex 09, 38041, France

    François Pompanon

  2. Laboratoire d'Ecologie Alpine, Université Grenoble 1, Rue de la Piscine 2233, Grenoble, 38041, France

    Aurélie Bonin

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media New York

About this protocol

Cite this protocol

Pérez-Figueroa, A., Rodríguez-Ramilo, S.T., Caballero, A. (2012). Analysis and Management of Gene and Allelic Diversity in Subdivided Populations Using the Software Program METAPOP. In: Pompanon, F., Bonin, A. (eds) Data Production and Analysis in Population Genomics. Methods in Molecular Biology, vol 888. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-870-2_15

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-869-6

  • Online ISBN: 978-1-61779-870-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation