Solution of the generalized noah's ark problem

Systematic Biology

Volumn 62, Issue 1, 2013, Pages 147-156

  Billionnet, Alain ^a  

^a ENSIIE   (France)

Author keywords

Biodiversity conservation; experiments; integer programming; Noah's Ark Problem; Phylogenetic diversity; taxon selection

Indexed keywords

ANIMAL; ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; PHYLOGENY; SURVIVAL;

ANIMALS; BIODIVERSITY; MODELS, BIOLOGICAL; PHYLOGENY; SURVIVAL;

EID: 84871823066     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys081     Document Type: Article

References (32)

1. Billionnet A. 2011a. Solving the probabilistic reserve selection problem. Ecol. Modell. 222:546-554.
2. Billionnet A. 2011b. Spatial optimization of wildlife populations with probabilistic habitat connections. For. Sci. 57:336-342.
3. Bordewich M., Rodrigo A., Semple C. 2008. Selecting taxa to save or sequence: desirable criteria and a greedy solution. Syst. Biol. 57: 825-834.
4. Bordewich M., Semple C. 2008. Nature reserve selection problem: a tight approximation algorithm. IEEE/ACM Trans. Comput. Biol. Bioinform. 5:275-280.
5. Bradley S. P., Hax A. C., Magnanti T. L. 1977. Applied mathematical programming. Reading (MA): Addison-Wesley. 539 p.
6. Camm J. D., Norman S. K., Polasky S., Solow A. R. 2002. Nature reserve site selection to maximize expected species covered. Oper. Res. 50:946-955.
7. CPLEX. 2007. ILOG CPLEX 10. 2. 0 reference manual. Gentilly (France): ILOG CPLEX Division.
8. Faith D. P. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1-10.
9. Faith D. P. 1994. Phylogenetic pattern and the quantification of organismal biodiversity. Philos. Trans. R. Soc. Lond. B 345:45-58.
10. Faith D. P. 2008a. Phylogenetic diversity and conservation. In: Carroll S. P., Fox C. W., editors. Conservation biology, evolution in action. New York: Oxford University Press, p. 99-115.
11. Faith D. P. 2008b. Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conserv. Biol. 22:1461-1470.
12. Faith D. P., Baker A. M. 2006. Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol. Bioinform. Online 2:121-128.
13. Faith D. P., Carter G., Cassis G., Ferrier S., Wilkie L. 2003. Complementarity, biodiversity viability analysis, and policy-based algorithms for conservation. Environ. Sci. Policy 6:311-328.
14. Fourer R., Gay D. M., Kernighan B. W. 1993. AMPL, a modeling language for mathematical programming. Danvers (MA): Boyd & Fraser Publishing Company.
15. Garey M. R., Johnson D. S. 1979. Computers and intractability: a guide to the theory of NP-Completeness. New York: W. H. Freeman and Company.
16. Hartmann K., Steel M. 2006. Maximizing phylogenetic diversity in biodiversity conservation: greedy solutions to the Noah's Ark Problem. Syst. Biol. 55:644-651.
17. Hickey G., Blanchette M., Carmi P., Maheshwari A., Zeh N. 2011. An approximation algorithm for the Noah's Ark Problem with randomfeatures loss. IEEE/ACMTrans. Comput. Biol. Bioinform. 8: 551-556.
18. Hickey G., Carmi P., Maheshwari A., Zeh N. 2008. NAPX: a polynomial time approximation scheme for the Noah's Ark Problem. WABI Proceedings of the 8th international workshop on Algorithms in Bioinformatics. Springer-Verlag: Berlin Heidelberg, p. 76-86.
19. Minh B. Q., Klaere S., Von Haeseler A. 2006. Phylogenetic diversity within seconds. Syst. Biol. 55:769-773.
20. Moulton V., Semple C., Steel M. 2007. Optimizing phylogenetic diversity under constraints. J. Theor. Biol. 246:186-194.
21. Nemhauser G. L., Wolsey L. A. 1988. Integer and combinatorial optimization. New York: Wiley, 763 p.
22. Pardi F. 2009. Algorithms on phylogenetic trees [Ph. D. Thesis]. Cambridge: University of Cambridge, St Catharine's College.
23. Pardi F., Goldman N. 2005. Species choice for comparative genomics: no need for cooperation. PLoS Genet. 1:e71.
24. Pardi F., Goldman N. 2007. Resource-aware taxon selection for maximizing phylogenetic diversity. Syst. Biol. 56:431-444.
25. Perry N. 2010. The ecological importance of species and theNoah's Ark problem. Ecol. Econ. 69:478-485.
26. Purvis A., Hector A. 2000. Getting the measure of biodiversity. Nature 405:212-219.
27. Simianer H., Marti S. B., Gibson J., Hanotte O., Rege J. E. O. 2003. An approach to the optimal allocation of conservation funds to minimize loss of genetic diversity between livestock breeds. Ecol. Econ. 45:377-392.
28. Steel M. 2005. Phylogenetic diversity and the greedy algorithm. Syst. Biol. 54:527-529.
29. Van Dyke F. 2008. Conservation biology, foundations, concepts, applications, ch. 4. New York: Springer.
30. Weitzman M. L. 1992. On diversity. Q. J. Econ. 107:363-406.
31. Weitzman M. L. 1998. The Noah's Ark problem. Econometrica 66: 1279-1298.
32. Witting L., Loeschcke V. 1995. The optimization of biodiversity conservation. Biol. Conserv. 71:205-207.