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International Journal of Genomics
Volume 2016 (2016), Article ID 2374610, 12 pages
Review Article

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

1College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
2The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
3Danforth Center, 975 N. Warson Road, St. Louis, MO 63132, USA

Received 24 December 2015; Revised 19 March 2016; Accepted 21 March 2016

Academic Editor: Ettore Randi

Copyright © 2016 Kristopher J. L. Irizarry et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.