Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

Population genetic theory related to the consequences of rapid population
decline is well-developed, but there are very few empirical studies where
sampling was conducted before and after a known bottleneck event. Such
knowledge is of particular importance for species restoration, given links
between genetic diversity and the probability of long-term persistence. To
directly evaluate the relationship between current genetic diversity and
past demographic events, we collected genome-wide single nucleotide
polymorphism data from pre-bottleneck historical (c.1906) and
post-bottleneck contemporary (c.2014) samples of Pinzón giant tortoises
(Chelonoidis duncanensis; n=25 and 149 individuals, respectively) endemic
to a single island in the Galapagos. Pinzón giant tortoises had a
historically large population size that was reduced to just 150-200
individuals in the mid 20th century. Since then, Pinzón’s tortoise
population has recovered through an ex situ head-start program in which
eggs or pre-emergent individuals were collected from natural nests on the
island, reared ex situ in captivity until they were 4-5 years old, and
subsequently repatriated. We found that the extent and distribution of
genetic variation in the historical and contemporary samples was very
similar, with the latter group not exhibiting the characteristic genetic
patterns of recent population decline. No population structure was
detected either spatially or temporally. We estimated an effective
population size (Ne) of 58 (95% CI = 50-69) for the post-bottleneck
population; no pre-bottleneck Ne point estimate was attainable (95% CI =
39-infinity) likely due to the sample size being lower than the true Ne.
Overall, the historical sample provided a valuable benchmark for
evaluating the head-start captive breeding program, revealing high
retention of genetic variation and no skew in representation despite the
documented bottleneck event. Moreover, this work demonstrates the
effectiveness of head-starting in rescuing the Pinzón giant tortoise from
almost certain extinction.