title: Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).
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 co-amplify 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.
authors.affiliation: Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia.
authors.forename: Hugo B
authors.initials: HB
authors.lastname: Harrison
authors.affiliation: Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum 1400 S. Lake Shore Drive, Chicago, 60605, Illinois.
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Feldheim
authors.affiliation: Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia ; School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4811, Australia.
authors.forename: Geoffrey P
authors.initials: GP
authors.lastname: Jones
authors.affiliation: School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4811, Australia.
authors.forename: Kayan
authors.initials: K
authors.lastname: Ma
authors.affiliation: Biosciences Core Laboratory, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia.
authors.forename: Hicham
authors.initials: H
authors.lastname: Mansour
authors.affiliation: Biosciences Core Laboratory, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia.
authors.forename: Sadhasivam
authors.initials: S
authors.lastname: Perumal
authors.affiliation: Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia.
authors.forename: David H
authors.initials: DH
authors.lastname: Williamson
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Berumen
keywords: Plectropomus spp; coral trout; hybridization; microsatellite multiplex; parentage analysis