CAT News Special Issue 4 - The Jaguar in Brazil 31 Jaguar Conservation Genetics Eduardo Eizirik 1,2 , Taiana Haag 1,3 , Anelisie S. Santos 1 , Francisco M. Salzano 3 , Leandro Silveira 4 , Fernando C. C. Azevedo 2 and Mariana M. Furtado 4,5 1 Centro de Biologia Genômica e Molecular, Faculdade de Biociências, PUCRS; Av. Ipiranga 6681, prédio 12. Porto Alegre – RS 90619-900, Brazil, eduardo.eizirik@pucrs.br 2 Instituto Pró-Carnívoros, Av. Horácio Neto, Parque Edmundo Zanoni, CEP: 12945-010, Atibaia – SP, Brazil 3 Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, UFRGS, Caixa Postal 15053, Porto Alegre - RS 91501-970, Brazil 4 Jaguar Conservation Fund; P.O. Box 193, CEP: 75830-000, Mineiros – GO, Brazil 5 Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508-270, Brazil Information on genetic aspects of jaguar populations is still scarce. Initial studies have surveyed genetic diversity para- meters and assessed the geographic differentiation among individuals on a continental or sub-continental scale, but so far little has been accomplished with respect to investigating regional or local jaguar populations. Moreover, different studies have employed different sets of molecular markers, posing potential problems for the future development of comparative analyses across study sites and ecosystems. Here we review the current status of jaguar genetic studies, present a new set of microsatellite markers that may be useful for jaguar population genetic studies, and survey the molecular diversity of two adjacent wild jaguar populations, sampled in the Brazilian Pantanal region. Our results suggest that this set of mar- kers is highly efficient for jaguar genetic studies, and that moderate to high levels of variability are present in wild jaguar populations, at least in the surveyed areas of the Pantanal. This contribution may be useful as a review of jaguar genetics, as well as a baseline empirical work that might support future in-depth investigations of these and other free-ranging populations of this felid. The use of molecular tools to inves- tigate genetic, ecological and behav- ioral aspects of wildlife populations has gained immense popularity in recent years, allowing unprecedented probing into multiple components of organis- mal biology which were previously inaccessible. In addition to its scientific relevance, knowledge of such aspects is often a critical component for the de- sign of adequate conservation strategies on behalf of species and ecosystems. Genetic data are required to understand long-term demographic history and dynamics, and to characterize social structure and patterns of dispersal and territoriality. They are also useful for assessing evolutionary potential and in- ferring census and effective population sizes, which are important components of Population Viability Analyses. The field of Conservation Genetics encom- passes a diverse array of methodologi- cal approaches involving the use of genetic information to tackle these and other issues of conservation concern. Jaguars (Fig. 1) are an elusive spe- cies whose population biology has been historically difficult to study, and only recently has been the focus of in-depth investigation made possible by tech- nological and analytical innovations. If ecological investigations of jaguars are now the focus of multiple studies at various field sites, genetic analyses of this species are still in their infancy, having been severely limited by the practical difficulty in sampling biologi- cal materials representative of natural populations. A range-wide assessment of genetic diversity and evolutionary history has been performed, and studies addressing regional or local-level issues are starting to become feasible, as im- proved methods for biological sampling become incorporated in this scientific discipline. Here we (i) review the his- tory of jaguar conservation genetics and the current state of the field, (ii) discuss the advantages and prospects of developing a set of molecular mark- ers that can become standardized for jaguar population genetics, and (iii) pre- sent novel preliminary data describing the levels of microsatellite diversity in a natural jaguar population, that of the southern Brazilian Pantanal. Although the jaguar had been in- cluded in previous genetic studies ad- dressing phylogenetic questions with the use of molecular markers (e.g. Johnson & O’Brien 1997), its intra- specific levels of diversity had not been investigated until 2001. In that year, a study employing mitochondrial DNA (mtDNA) sequences encompassing a segment of the control region (CR) and 29 nuclear microsatellite loci addressed the genetic diversity and demographic history of jaguars, based on 44 indivi- duals sampled from Mexico to southern Brazil (Eizirik et al. 2001). That study revealed that this species exhibits a shallow mtDNA structure, compared to other felids, with low differentiation among geographic regions. The shal- low structure, with low inter-regional differentiation, was inferred to have been caused by a rather recent popula- tion expansion, ca. 300,000 years ago, followed by a history of demographic connectivity over a continental scale. No support was observed for the clas- sically recognized jaguar subspecies, a finding that had also been reported on the basis of morphological data (Larson 1997). The major pattern that emerged from that data set was a phylogeogra- phic partition between the northern and southern portions of the range, likely a function of reduced historical gene flow across the Amazon River. The levels of diversity detected in the hypervariable microsatellite loci were quite high and also indicative of large scale gene flow across the range of the species. No ma-