Using multi-objective artificial immune systems to find core collections based on molecular markers

Shana Schlottfeldt, André C.P.L.F. Carvalho, Maria Emilia M.T. Walter, Mariana P.C. Telles, Jon Timmis, José Alexandre F. Diniz-Filho

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)

Abstract

Germplasm collections are an important strategy for conservation of diversity, a challenge in ecoinformatics. It is common to select a core to represent the genetic diversity of a germplasm collection, aiming to minimize the costs of conservation, while ensuring the maximization of genetic variation. For the problem of finding a core for a germplasm collection, we proposed the use of a constrained multi-objective artificial immune algorithm (MAIS), based on principles of systematic conservation planning (SCP), and incorporating heterozygosity information. Therefore, optimization takes genotypic diversity and variability patterns into account. As a case study, we used Dipteryx alata molecular marker information. We were able to identify within several accessions, the exact entries that should be chosen to preserve species diversity. MAIS presented better performance measure results when compared to NSGA-II. The proposed approach can be used to help construct cores with maximal genetic richness, and also be extended to in situ conservation. As far as we know, this is the first time that an AIS algorithm is applied to the problem of finding a core for a germplasm collection using heterozygosity information as well.

Original languageEnglish
Title of host publicationGECCO 2015 - Proceedings of the 2015 Genetic and Evolutionary Computation Conference
EditorsSara Silva
PublisherAssociation for Computing Machinery
Pages1271-1278
Number of pages8
ISBN (Electronic)9781450334723
DOIs
Publication statusPublished - 11 Jul 2015
Event16th Genetic and Evolutionary Computation Conference, GECCO 2015 - Madrid, Spain
Duration: 11 Jul 201515 Jul 2015

Publication series

NameGECCO 2015 - Proceedings of the 2015 Genetic and Evolutionary Computation Conference

Conference

Conference16th Genetic and Evolutionary Computation Conference, GECCO 2015
Country/TerritorySpain
CityMadrid
Period11 Jul 201515 Jul 2015

Keywords

  • Artificial immune systems
  • Biodiversity
  • Core collection
  • Genetic variability
  • Germplasm
  • Multi-objective optimization
  • Systematic conservation planning

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