Genetic assessment of ex situ populations to aid species conservation and maintain heterozygosity in non-model species

  • Graeme Fox Manchester Metropolitan University
  • Iulia Darolti The University of Manchester
  • Jean-Denis Hibbitt SEA LIFE Global, Merlin Animal Welfare and Development
  • Richard F Preziosi Manchester Metropolitan University
  • John L Fitzpatrick
  • Jennifer K Rowntree Manchester Metropolitan University
Keywords: Raja undulata, microsatellite markers, population genetic structure, elasmobranchii, Next Generation Sequencing


The number of species classified by the IUCN as endangered or critically endangered is predicted to increase dramatically in the coming decades. During this time, we will also see a parallel rise in the number of captive populations of endangered species. Appropriate genetic management strategies must be implemented to avoid inbreeding depression and heterozygosity loss in these small ex situ populations. Despite strong conservation concern, genetic markers are typically unavailable for threatened species and must be developed, often as a new captive population is being established. These novel markers can then be used to assess the relatedness and diversity of the founding population, inform breeding programmes and make routine assessments after each captive generation; processes which should be standard practice when managing ex situ populations. Here we present a case study in the assessment of genetic health of a captive population of the endangered undulate ray (Raja undulata). Novel microsatellite markers were designed using a next-generation sequencing workflow and primer pairs amplifying eight polymorphic microsatellite loci characterised in 35 captive individuals. Sampling of live individuals used a minimally invasive method and the genotypes determined were used to evaluate the overall genetic diversity of the captive population, predict the relatedness of each pair of individuals and to monitor for changes in the rate of heterozygosity after the first captive generation. Our approach offers a useful roadmap for the rapid assessment of genetic health of ex situ elasmobranch populations, and is also applicable to any captive or wild population requiring genetic management.