DOI: 10.5061/dryad.h02h0
title: Data from: Genetics at the verge of extinction: insights from the Iberian lynx

description: 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.
description: Lyp_2002-2007-GENEPOPMicrosatellite genotypes for a sample of Iberian lynx individuals born in Doñana (first pop) and Andujar (second pop) between the years 2002-2007. Indivdiuals are identified by their year of birth. Data is in GenePop format.Lyp_1995-2007_UR-GENEPOPMicrosatellite genotypes for a sample of Iberian lynx individuals in which known pairs of closely related individuals were avoided. Individuals are identified by an internal lab code and were born in Doñana (first pop) and Andujar (second pop). Data is GenePop format.Lynx pardinus ATP8 haplotypesFasta file reporting the two partial ATP8 sequences found in Iberian lynx populations. The sequence was obtained by dideoxi sequencing of PCR products. Hapotype 1 was observed in all 23 individuals from Doñana population, while haplotype 2 was found in all 36 lynxes from Andújar population. Haplotypes 1 and 2 differ at a single site (site 42).LypATP8.fasIberian lynx cytochrome b, partial sequenceThe sequence was obtained by dideoxi sequencing of PCR products. All samples analysed (23 from Doñana and 36 from Andújar) yielded this same sequence.Iberian lynx control region, partial sequenceThe sequence was obtained by dideoxi sequencing of PCR products. All samples analysed (23 from Doñana and 36 from Andújar) yielded this same sequence.Concatenated mitochondrial haplotypesFasta file with the two mitochondrial haplotypes found for Iberian lynx. Here haplotypes are defined by the concatenation of the three mitochondrial fragments: partial mitochondrial control region (1-602), partial cytochrome b (603-1299) and partial APT8 (1300-1488). Haplotype 1 was found in all 23 samples from Doñana and haplotype 2 was found in all 36 samples from Andújar.ConcatenatedHaps.fas