Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program
Jensen, Evelyn (2022), Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program, Dryad, Dataset, https://doi.org/10.5061/dryad.rfj6q57dt
Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017 – 2020) of the genetically-informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, Chelonoidis becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.
Small tissue biopsies were obtained from the 98 successfully hatched offspring (20 hatched 2017/2018, 43 hatched 2018/2019, 35 hatched 2019/2020) and stored at ambient temperature in Longmire Lysis buffer (Longmire et al. 1997) until arrival in the lab, after which they were stored at 4 °C. DNA was extracted from the tissues using Qiagen DNeasy kits following the manufacturer’s protocol. PCR products were separated by electrophoresis using an Applied Biosystems (AB) 3730xl capillary sequencer, with allele peaks identified in GeneMarker (Hulce et al. 2011). Genotypes for both the breeders and offspring were called using bins through the R package MsatAllele (Alberto 2009), R version 3.6.2 (R Development Core Team 2019) and then manually verified by eye. All DNA samples were genotyped at the same 21 loci as Quinzin et al. (2019). However, since 4 loci did not perform consistently across samples, they were excluded from downstream analyses which were based on 17 loci (Supplementary Table 2).