Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning

Abstract

Translocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.

Disproportionate admixture improves reintroduction outcomes despite the use of low‐diversity source populations: population viability analysis for a translocation of the greater stick‐nest rat

“…These data were generated using ddRAD-seq (Poland et al, 2012) from ear or tail clips sampled from GSNRs trapped on the Franklin Islands in 1994 and on Salutation Island in 2016. SNPs with minor allele frequencies of <0.05 and more than 25% of missing data were removed (White et al, 2020b). Demultiplexed and adapter-trimmed sequencing data are available from NCBI's sequence read archive (accession number: PRJNA389954) and more detailed methodology regarding sampling, library preparation and bioinformatic processing can be found in White et al (2020b).…”

“…GSNRs were listed as ‘Endangered’ under the IUCN assessment criteria in 1996 but have since been downlisted to ‘Vulnerable’ due to successful translocations to a captive colony at Monarto Safari Park in the late 1980s and several conservation areas since 1990 (Short et al ., 2019). All five of the surviving translocated populations have lower genetic diversity than the Franklin Islands individuals (White et al ., 2020 b ), possibly due to founder effects in the Monarto captive population, over‐ and under‐representation of founders in translocated populations, and/or genetic drift after release. As the last remaining wild (and most genetically diverse) population, the Franklin Islands GSNRs represent both an important source for translocation harvesting and a critical population that must be conserved for the ongoing viability of the species.…”

“…As the last remaining wild (and most genetically diverse) population, the Franklin Islands GSNRs represent both an important source for translocation harvesting and a critical population that must be conserved for the ongoing viability of the species. Indeed, White et al (2020b) identified the Franklin Islands as the most appropriate source population for future GSNR translocations but suggested that other populations with lower diversity were good candidates for cross-translocations. We therefore aimed to use PVAs to determine an optimized harvesting strategy for a new reintroduction of GSNRs on Dirk Hartog Island, Western Australia, whereby natural Franklin Island stock is supplemented with individuals from an additional established translocated population in order to improve the translocation outcome while minimizing negative effects on source populations.…”

Genomic Approaches for Conservation Management in Australia under Climate Change

“…While there are still some uncertainties surrounding interpretation and uptake of genomic data in a management context [ 56 ], population genomics studies are increasingly being applied to conservation problems and management decision-making [ 65 ]. Genomic data have already been used to extensively study and characterise the genetic diversity of Australian wildlife, including quantifying the genetic effects of translocations in small mammal populations and identifying candidate genes associated with breeding success in marsupials [ 14 , 66 , 67 , 68 , 69 , 70 ].…”

“…Although many practitioners have been historically averse to admixture as a conservation strategy [ 131 ], a cultural shift has recently taken place. There have been a number of cases of successful collaboration between genetic researchers and conservation practitioners in Australia, such as the “devil tools & tech” umbrella framework implemented by the Save the Tasmanian Devil Program [ 126 ] and various provenance-related research projects to facilitate ecological restoration [ 69 , 132 , 133 ]. Indeed, the inclusion of non-academic co-authors in conservation genetics and genomics studies (e.g., [ 134 , 135 ]) has been shown to increase the likelihood of a specific solution- or policy-orientated outcome by up to 250% [ 136 ].…”