Data from: Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

Long-term population history can influence the genetic effects of recent
bottlenecks. Therefore, for threatened or endangered species, an
understanding of the past is relevant when formulating conservation
strategies. Levels of variation at neutral markers have been useful for
estimating local effective population sizes (Ne) and inferring whether
population sizes increased or decreased over time. Furthermore, analyses
of genotypic, allelic frequency, and phylogenetic information can
potentially be used to separate historical from recent demographic
changes. For 15 populations of Galápagos giant tortoises (Chelonoidis
sp.), we used 12 microsatellite loci and DNA sequences from the
mitochondrial control region and a nuclear intron, to reconstruct
demographic history on shallow (past ~100 generations, ~2500 years) and
deep (pre-Holocene, >10 thousand years ago) timescales. At the deep
timescale, three populations showed strong signals of growth, but with
different magnitudes and timing, indicating different underlying causes.
Furthermore, estimated historical Ne of populations across the archipelago
showed no correlation with island age or size, underscoring the complexity
of predicting demographic history a priori. At the shallow timescale, all
populations carried some signature of a genetic bottleneck, and for 12
populations, point estimates of contemporary Ne were very small (i.e.,
< 50). On the basis of the comparison of these genetic estimates
with published census size data, Ne generally represented ~0.16 of the
census size. However, the variance in this ratio across populations was
considerable. Overall, our data suggest that idiosyncratic and
geographically localized forces shaped the demographic history of tortoise
populations. Furthermore, from a conservation perspective, the separation
of demographic events occurring on shallow versus deep timescales permits
the identification of naturally rare versus newly rare populations; this
distinction should facilitate prioritization of management action.