Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): A software for choosing the appropriate number of markers and samples

Methods in Ecology and Evolution

Volumn 4, Issue 3, 2013, Pages 299-303

  Hoban, Sean ^a   Gaggiotti, Oscar ^b   Bertorelle, Giorgio ^a  

^a UNIVERSITY OF FERRARA   (Italy)

^b Universitàe Josef Fourier   (France)

Author keywords

Conservation interventions; Data analysis; Management; Molecular ecology; Monitoring; Simulation; Statistical power

Indexed keywords

EID: 84875237706     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210x.12025     Document Type: Article

References (20)

1. Balding, D.J. & Nichols, R.A. (1997) Significant genetic correlations among Caucasians at forensic DNA loci. Heredity, 78, 583-589.
2. Excoffier, L. & Foll, M. (2011) Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics, 27, 1332-1334.
3. Excoffier, L. & Lischer, H.E.L. (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
4. Gaggiotti, O.E., Brooks, S.P., Amos, W. & Harwood, J. (2004) Combining demographic, environmental and genetic data to test hypotheses about colonization events in metapopulations. Molecular Ecology, 13, 811-825.
5. Garza, J.C. & Williamson, E.G. (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10, 305-318.
6. Girod, C., Vitalis, R., Leblois, R. & Freville, H. (2011) Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the Msvar method. Genetics, 188, 165-179.
7. Heled, J. & Drummond, A.J. (2008) Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology, 8, 289.
8. Hoban, S., Bertorelle, G. & Gaggiotti, O.E. (2012a) Computer simulations: tools for population and evolutionary genetics. Nature Reviews Genetics, 73, 2-14.
9. Hoban, S., McCleary, T., Schlarbaum, S., Anagnostikas, S. & Romero-Severson, J. (2012b) Human impacted landscapes facilitate hybridization between a native and an introduced tree species. Evolutionary Applications. 5, 720-731.
10. Kalinowski, S.T. (2005) Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity, 94, 62-65.
11. Laval, G. & Excoffier, L. (2004) SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20, 2485-7.
12. Luikart, G. & Cornuet, J. (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology, 12, 228-237.
13. Manel, S., Berthier, P. & Luikart, G. (2002) Detecting wildlife poaching: identifying the origin of multilocus genotypes. Conservation Biology, 16, 650-659.
14. Marjoram, P. & Tavare, S. (2006) Modern computational approaches for analysing molecular genetic variation data. Nature Reviews Genetics, 7, 759-770.
15. Morin, P.A., Martien, K.K. & Taylor, B.L. (2009) Assessing statistical power of SNPs for population structure and conservation studies. Molecular Ecology Resources, 9, 66-73.
16. Paetkau, D., Calvert, W., Stirling, I. & Strobeck, C. (1995) Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology, 4, 347-354.
17. Peterman, R.M. (1990) Statistical power analysis can improve fisheries research and management. Canadian Journal of Fisheries and Aquatic Sciences, 47, 2-15.
18. Ryman, N. & Palm, S. (2006) POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology, 6, 600-602.
19. Swatdipong, A., Primmer, C. & Vasemägi, A. (2010) Historical and recent genetic bottlenecks in European grayling, Thymallus thymallus. Conservation Genetics, 11, 279-292.
20. Ward, S.M. & Jasieniuk, M. (2009) Review: sampling weedy and invasive plant populations for genetic diversity analysis. Weed Science, 57, 593-602.