Conservation genomics of the endangered Seychelles magpie robin (Copsychus sechellarum)

  • Emily L Cavill

Student thesis: Master's ThesisMaster of Science by Research (MScR)


‘Threatened’ species often exist as small, isolated populations, such as those on islands. Characteristic consequences of this are inbreeding – the mating of closely related individuals – which can result in reduced heterozygosity and increased risk of inbreeding depression. These species sometimes undergo ‘rescue’, whereby well–intentioned parties translocate individuals from a healthy (or sometimes the last remaining) population to a new destination to help the species recover. Repeated translocations resulting in repeated founder effects can potentially lead to a decrease in genetic diversity in the new populations. Translocations have been an integral factor in the recovery of the Seychelles magpie robin (Copsychus sechellarum), an endangered species endemic to Seychelles, but the potential genetic consequences of their translocation history have not yet been explored.

For this project, 110 Seychelles magpie robin genomes, representing the five islands within the Seychelles Archipelago on which the species currently exists, were re–sequenced and mapped against a reference genome which was constructed de novo for the species. Mapping the re–sequenced genomes against the species–specific reference allowed for identification of the genetic variation in the form of single nucleotide polymorphisms (SNPs). These SNPs were used to identify patterns of heterozygosity, homozygosity and autozygosity in each individual to investigate inbreeding and genetic diversity across the islands.

With minimal genetic research previously undertaken on the Seychelles magpie robin, this project offered the first analysis of the genetic profile of this endangered species. A very low level of heterozygosity was observed, coupled with long homozygous segments that suggest recent inbreeding, probably a consequence of the most recent population bottleneck experienced. Three of the four translocated populations displayed less genetic diversity than the founder population from which they were taken – the familiar pattern observed as a result of the evolutionary force of genetic drift following founder events. Furthermore, and perhaps surprising given the recent time since the new populations were established, population structure was observed among translocated populations.

New awareness of this inbreeding and continued monitoring of the population will allow for genetically informed management decisions, particularly concerning the future translocations planned for this species.
Date of Award1 Oct 2019
Original languageEnglish
Awarding Institution
  • University of Bristol
SupervisorGareth Jones (Supervisor), Martin J Genner (Supervisor) & Tom Gilbert (Supervisor)


  • conservation genomics
  • endangered species
  • bottleneck
  • translocations
  • whole genome re-sequencing

Cite this