Assessing the power of informative subsets of loci for population assignment: Standard methods are upwardly biased

Molecular Ecology Resources

Volumn 10, Issue 4, 2010, Pages 701-710

  Anderson, E C ^a,b  

^a SOUTHWEST FISHERIES SCIENCE CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Assignment test; Cross validation; Holdout data; Training data

Indexed keywords

EID: 77954260692     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02846.x     Document Type: Article

References (17)

1. Anderson EC, Waples RS, Kalinowski ST. An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 2008, 65:1475-1486.
2. Banks MA, Eichert W, Olsen JB. Which genetic loci have greater population assignment power? Bioinformatics 2003, 19:1436-1438.
3. Bromaghin JF. BELS: backward elimination locus selection for studies of mixture composition or individual assignment. Molecular Ecology Resources 2008, 8:568-571.
4. Eguchi S, Copas J. Interpreting Kullback-Leibler divergence with the Neyman-Pearson lemma. Journal of Multivariate Analysis 2006, 97:2034-2040.
5. Guinand B, Scribner K, Topchy A, Page K, Punch W, Burnham-Curtis M. Sampling issues affecting accuracy of likelihood-based classification using genetical data. Environmental Biology of Fishes 2004, 69:245-259.
6. Guyon I, Elisseeff A. An introduction to variable and feature selection. Journal of Machine Learning Research 2003, 3:1157-1182.
7. Hansen MM, Kenchington E, Nielsen EE. Assigning individual fish to populations using microsatellite DNA markers. Fish and Fisheries 2001, 2:93-112.
8. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics (Oxford) 2002, 18:337-338.
9. Jain AK, Duin RPW, Mao J. Statistical pattern recognition: a review. IEEE Transactions on Pattern Analysis and Machine Intelligence 2000, 22:4-37.
10. Kalinowski ST. Genetic polymorphism and mixed-stock fisheries analysis. Canadian Journal of Fisheries and Aquatic Sciences 2004, 61:1075-1082.
11. Manel S, Gaggiotti OE, Waples RS. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution 2005, 20:136-142.
12. Mosteller F, Tukey JW. Data Analysis and Regression 1977, Addison-Wesley, Menlo Park
13. Novembre J, Johnson T, Bryc K. Genes mirror geography within Europe. Nature 2008, 456:98-101.
14. Rannala B, Mountain JL. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the USA 1997, 94:9197-9201.
15. Topchy A, Scribner K, Punch W. Accuracy-driven loci selection and assignment of individuals. Molecular Ecology Notes 2004, 4:798-800.
16. Trunk GV. A problem of dimensionality: a simple example. IEEE Transactions on Pattern Analysis and Machine Intelligence 1979, 1:306-307.
17. Weir BS. Genetic Data Analysis II 1996, Sinauer Associates, Sunderland, MA