Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. We empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in small samples of five jaguar (Panthera onca) demes. Given their intrinsic properties as a targeted capture, WES allowed for a more straightforward reconstruction of loci compared to GBS, which in turn facilitated the identification of true polymorphisms across individuals. In contrast, GBS data showed a recurrent miscalling of heterozygous sites. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, varying the values of parameters for locus assembly, genotype calling and SNP filtering in the latter technique. Changes in parameterization induced measurable differences in summary statistics, both between approaches and among distinct batches of GBS data. The application of post-processing genotype filters based on mean depth of reads had major effects on the consistency between approaches. Overall, we observed that the direct empirical comparison of GBS and WES for estimating population genetic attributes from the same set of individuals provided an interesting opportunity to assess the consistency of these approaches, revealing relevant aspects that should be considered in such analyses. Our results highlight the importance of thorough data filtering in genomic approaches to obtain robust genetic diversity and differentiation estimates.

The vast amount of data contained in a single genome represents a detailed record of past events in that lineage and may forecast its evolutionary potential in the face of environmental changes. Here we employed whole-genome sequence (WGS) data to infer the demographic history and assess signals of recent inbreeding in jaguar (Panthera onca) populations. We analyzed whole genomes from 13 individuals (nine of which are reported here for the first time) sampled in seven different biomes across the species’ range, including its northernmost extreme in the Mexico/USA border region. We modelled demographic history using the PSMC method, and analyzed long runs of homozygosity (ROH) to assess signals of population bottlenecks and inbreeding. PSMC plots were very consistent among individuals, indicating that the jaguar lineage had an effective population size of up 100,000 individuals ca. 1 million years ago, then sharply declined and rebounded during the Late Pleistocene, followed by a more gradual decline in the last 40,000 years. This decline was more pronounced in the North/Central American genomes, likely reflecting population bottlenecks during the south-north colonization towards the edge of the species’ current range. The ROH analysis revealed a relatively small burden for most jaguars, indicating a recent history of outbreeding and large-scale connectivity among regional populations. However, northern range-edge individuals and those from severely fragmented populations showed signals of recent bottlenecks and, in the latter case, inbreeding. Our results illustrate the power of WGS data to survey and monitor the genetic erosion triggered by anthropogenic habitat fragmentation.