Data from: Genetics at the verge of extinction: insights from the Iberian lynx

Population viability might become compromised by the loss of genetic
diversity and the accumulation of inbreeding resulting from population
decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a
paradigmatic example of a species at the verge of extinction and, because
of the well-documented and different demographic histories of the two
remaining populations (Doñana and Andújar), it provides the opportunity to
evaluate the performance of analytical methods that are commonly applied
to detect genetic signatures of demographic decline. We used mitochondrial
sequences and a set of 36 microsatellite markers to evaluate the current
genetic status of the species and to assess the genetic signatures of its
past history. Mitochondrial diversity was extremely low with only two
haplotypes, alternatively fixed in each population. Both remnant
populations have low levels of genetic diversity at microsatellite
markers, particularly the population from Doñana, which has been isolated
and at small census sizes at least since the 1950s, and genetic
differentiation between the two populations is high. Bayesian
coalescent-based methods suggest an earlier decline starting hundreds of
years ago, while heterozygosity-excess and M-ratio tests did not provide
conclusive and consistent evidence for recent population size changes.
Also, a model of gene-flow received overwhelming support over a model of
pure drift. The discrepancies observed between some of our results and the
known recent history of the species call for caution in the interpretation
of the outcomes of some of these methods, especially when no information
on previous demographic history is available. Overall, our results suggest
that current genetic patterns in the Iberian lynx are mainly the result of
its recent decline and fragmentation and alerts on possible genetic risks
for its persistence. Conservation strategies should explicitly consider
this threat and incorporate an integrated genetic management of captive,
wild and reintroduced populations, including the genetic restoration of
wild populations through translocations.