Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

Harrison, Hugo B., Feldheim, Kevin A., Jones, Geoffrey P., Ma, Kayan, Mansour, Hicham, Perumal, Sadhasivan, Williamson, David H., and Berumen, Michael L. (2014) Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecology and Evolution, 4 (11). pp. 2046-2057.

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View at Publisher Website: http://dx.doi.org/10.1002/ece3.1002
 
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Abstract

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that coamplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

Item ID: 34561
Item Type: Article (Refereed Research - C1)
Keywords: coral trout, hybridization, microsatellite multiplex, parentage analysis, Plectropomus spp
Additional Information:

© 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Supplemental information for this paper is available from the publisher website (see related URL).

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ISSN: 2045-7758
Funders: King Abdullah University of Science and Technology (KAUST), National Environmental Research Program (NERP), Australian Research Council (ARC)
Projects and Grants: KAUST CRG-1-2012-BER-002 and OCRF-SPCF-2011-BER-001
Date Deposited: 11 Mar 2015 23:20
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8302 Fisheries - Wild Caught > 830204 Wild Caught Fin Fish (excl. Tuna) @ 100%
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