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

Published: 17 August 2021| Version 1 | DOI: 10.17632/bgmg4rd2nw.1
, Christopher Kaelin,
, Jeremy Johnson,
, Dênis Sana, Laury Cullen,
, Edsel Moraes,
, Leandro Silveira, William Murphy,


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 an apex mammalian predator. We analyzed 13 jaguar ( Panthera onca ) whole genomes from individuals sampled in seven different biomes across the species’ range, including its northernmost extreme in the Mexico/USA border region. We used the pairwise sequentially Markovian coalescent (PSMC) method and screened the genomes for long runs of homozygosity (ROH) to characterize jaguar demographic history and detect signals of contemporary inbreeding. PSMC plots were consistent among individuals, suggesting that the jaguar lineage had an effective population size of up 100,000 individuals ca. 1 million years ago, then declined and rebounded during the Late Pleistocene, followed by a more recent decrease spanning the last 40,000 years. This recent 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 exhibited signals of inbreeding, and potentially recent bottlenecks, which indicates that this should be the focus of future in-depth research. Overall, our study illustrates the power of WGS data to survey and monitor genetic erosion in large carnivores triggered by anthropogenic habitat loss and fragmentation. Keywords: historical effective population size; runs of homozygosity; inbreeding; Felidae; carnivore conservation File 1: psmcfa file (bPon.jaguar_pantanal.noAmb.noX.zip) File 2: vcf file (jaguarGenomes.chrNum.bial.sorted.minQ20.noMiss.IDlabel.vcf.gz)



Mammalia, Evolutionary Genomics, Ecological Genomics