Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 43-53

  Miller, Webb ^a   Wright, Stephen J ^b   Zhang, Yu ^a   Schuster, Stephan C ^a   Hayes, Vanessa M ^c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b University of Wisconsin Madison   (United States)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BREEDING PROGRAM; ENDANGERED SPECIES; GENETIC DIVERSITY; GENETIC VARIANTS; GENOME SEQUENCING; GENOMICS; GENOTYPING; MIXED-INTEGER LINEAR PROGRAMMING TECHNIQUES; OPTIMIZATION METHOD;

BIODIVERSITY; COMBINATORIAL OPTIMIZATION; DNA SEQUENCES; POPULATION STATISTICS;

CONSERVATION;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; BREEDING; ENDANGERED SPECIES; FOUNDER EFFECT; GENE FREQUENCY; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS; WILD ANIMAL;

ANIMALS; ANIMALS, WILD; BREEDING; COMPUTATIONAL BIOLOGY; ENDANGERED SPECIES; FOUNDER EFFECT; GENE FREQUENCY; GENETIC TECHNIQUES; GENETIC VARIATION; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77956815772     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (33)

1. R. Frankham, J. D. Ballou and D. A. Briscoe, Introduction to Conservation Genetics, Cambridge University Press (2002).
2. J. Höglund, Evolutionary Conservation Genetics, Oxford University Press (2009).
3. G. Bertorelle, M.W. Bruford, H. C. Hauffe, A. Rizzoli and C. Vernise, Population Genetics for Animal Conservation, Oxford University Press (2009).
4. D. R. Marshall and A. D. H. Brown, in Crop Genetics Resources for Today and Tomorrow (O. H. Frankel and J. G. Hawkes, eds.), Cambridge University Press, 53-80 (1975).
5. J. K. Pritchard, M. Stephens and P. Donnelly, Genetics 155, 945-959 (2000).
6. W. Miller, D. I. Drautz, A. Ratan, et al., Nature 456, 387-390 (2008).
7. W. Miller, D. I. Drautz, J. Janecka. et al., Genome Research 19, 213-220 (2009).
8. J. Slate, J.Gratten, D. Beraldi, et al., Genetica 136, 97-107 (2009).
9. N. Backström, N. Karaiskou, E. H. Leder et al., Genetics 179, 1479-1495 (2008).
10. The Bovine HapMap Consortium, Science 324, 528-532 (2009).
11. B. M. Kuehn, JAMA 300, 2715 (2008).
12. N. Siva, Nat. Biotech. 26, 256 (2008).
13. J. Czyzyk, M. Mesnier and J. J. Moré, IEEE Comp. Sci. Eng. 5, 68-75 (1998).
14. A. Brooke, D. Kendrick and A. Meeraus, GAMS: A User's Guide, The Scientific Press (1988).
15. T. Achterberg, Constraint Integer Programming, Ph. D. dissertation, TU Berlin (2007). Available at http://scip.zib.de/documentation.shtml.
16. H. V. Siddle, A. Kreiss, M. D. Eldridge et al., Proc. Natl. Acad. Sci. USA 104, 16221-16226 (2007).
17. B. Gouesnard, T. M. Bataillon, G. Decoux et al., J. Hered. 92, 93-94 (2001).
18. H. I. McKhann, C. Camilleri, A. Bérard, et al., Plant J. 38, 193-202 (2004).
19. C. S. Carlson, M. A. Eberly, M. J. Rieder et al., Nat. Genet. 33, 518-521 (2003).
20. P. Ng, S. Levy, J. Huang et al., PLoS Genetics 4, e1000160. doi:10.1371/journal.pgen.1000160 (2008).
21. P. I. Angermeier, Conserv. Biol.14, 373-381 (2000).
22. H. C. Rosenbaum, M. G. Egan, P. J. Clapham et al., Conserv. Biol. 14, 1837-1842 (2000).
23. A. Koblmüller, M. Nord, R. K. Wayne and J. A. Leonard, Mol. Ecol. 18, 2313-2326 (2009).
24. D. P. Faith, Biol. Conserv. 61, 1-10 (1992).
25. M. Steel, Syst. Biol. 54, 527-529 (2005).
26. F. Pardi and N. Goldman, Syst. Biol. 56, 431-444 (2007).
27. B. Q. Minh, F. Pardi, S. Klaere and A. von Haeseler, IEEE/ACM Trans. Comp, Biol. Bioinf. 6, 22-29 (2009).
28. D. J. Schoen and A. H. D. Brown, Proc. Natl. Acad. Sci. USA 90, 10623-10627 (1993).
29. R. Karp, Complexity of Computer Computations (R. E. Miller and J. W. Thatcher, eds), Plenum Press 85-103 (1972).
30. D. Hochbaum, Approximation Algorithms for NPHard Problems. PWS Publishing, Boston (1996).
31. M. Saura, A. Pérez-Figueroa, J. Fernándes et al., Conserv. Biol. 22, 1277-1287 (2008).
32. J. Vales-Alonso, J. Fernándes, F. J. Gonzáles-Castaño and A. Caballero, Math. Biosci 183, 161-173 (2003)
33. T. Y. Berger-Wolf, C. Moore and J. Saia, J. Theor. Biol. 244, 433-439 (2007).