Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae)

The jaguar (Panthera onca), the largest felid in the American Continent, is currently threatened by habitat loss, fragmentation and human persecution. We have investigated the genetic diversity, population structure and demog raphic history of jaguars across their geographical range by analysing 715 base pairs of the mitochondrial DNA (mtDNA) control region and 29 microsate llite loci in approximate to 40 individuals sampled from Mexico to southern Brazil. Jaguars display low to moderate levels of mtDNA diversity and medi um to high levels of microsatellite size variation, and show evidence of a recent demographic expansion. We estimate that extant jaguar mtDNA lineages arose 280 000-510 000 years ago (95% CI 137 000-830 000 years ago), a youn ger date than suggested by available fossil data. No strong geographical st ructure was observed, in contrast to previously proposed subspecific partit ions. However, major geographical barriers such as the Amazon river and the Darien straits between northern South America and Central America appear t o have restricted historical gene flow in this species, producing measurabl e genetic differentiation. Jaguars could be divided into four incompletely isolated phylogeographic groups, and further sampling may reveal a finer pa ttern of subdivision or isolation by distance on a regional level. Operatio nal conservation units for this species can be defined on a biome or ecosys tem scale, but should take into account the historical barriers to dispersa l identified here. Conservation strategies for jaguars should aim to mainta in high levels of gene flow over broad geographical areas, possibly through active management of disconnected populations on a regional scale.