Whole-genome sequences shed light onto demographic history and
contemporaneous genetic erosion of free-ranging jaguar (Panthera onca)
populations
Abstract
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.