Population genetics and phylogeography of the largest wild cat in the Americas: An analysis of the Jaguar by means of microsatellites and mitochondrial gene sequences

A total of 250 jaguars directly sampled in the wild (Guatemala, Costa Rica,Colombia, Venezuela, French Guiana, Peru, Bolivia and central and western BrazilianAmazon) were analyzed for 12 DNA microsatellite loci and for three mitochondrial genes(NADH5, 16S rRNA and ATP8). The main results were as follows: 1- The levels of genediversity were very high for microsatellites as well as for mt markers. These levels werehigher than those obtained in other studies by Eizirik's team. Explanations of why thisoccurred are herein discussed. 2- The highest gene diversity levels were found for thewestern Amazon areas for microsatellites as well as mt markers, with lower genediversity levels for areas far as away as central and eastern Brazil and Central America.3- The levels of genetic heterogeneity were small for the samples classified bymorphological subspecies, by countries and by considering the Amazon River as abarrier. Therefore, there is no clear evidence of the existence of "real" subspecies in thejaguars, especially, for the forms of South America. It was also clear that the AmazonRiver was not a geographical barrier for this large species, disagreeing with the claims of Eizirik et al., (2001). The levels of genetic heterogeneity by country were slightly higherthan by subspecies. This could have interesting repercussions in the conservation politicsof each Neotropical nation where jaguars live. Several AMOVAs showed that themajority of gene diversity was placed in individuals and that no other upper hierarchicalclusters have significant importance. The theoretical gene flow estimates were very highfor microsatellites as well as mt markers. However, the mt DNA gene flow estimateswere higher than for the microsatellites, disagreeing with the results of Eizirik et al.,(2001). 4- The assignment analyses with microsatellites as well as the spatial treeanalyses with mt DNA markers showed no significant geographical clusters for thejaguars analyzed. Even the percentage of first generation migration jaguars was elevated(10-20 %) showing the importance of gene flow in this species and, possibly, the nonexistenceof putative subspecies. 5- The overall jaguar sample analyzed at the mt NADH5locus showed a very significant population expansion from the western Amazon in threedifferent periods (500,000-600,000 YA; 150,000-250,000 YA and 10,000-55,000 YA).The climatologic changes in these periods are discussed in relationship with the jaguarpopulation expansions detected in this work.