Monitoring a Puma (Puma concolor) Population in a Fragmented Landscape in Southeast Brazil Renata A. Miotto 1,3 , Marcelo Cervini 1 , Rodrigo A. Begotti 2 , and Pedro M. Galetti Jr. 1 1 Laborato ´rio de Biodiversidade Molecular e Citogene ´tica, Departamento de Gene ´ tica e Evoluc ¸a ˜o, Universidade Federal de Sa ˜o Carlos— UFSCar, Rodovia Washington Luı ´s, km 235, CEP 13565‐905, Monjolinho, Sa ˜ o Carlos—SP, Brazil 2 Escola Superior de Agricultura ‘Luiz de Queiroz’—ESALQ/USP, Departamento de Cie ˆ ncias Florestais, Avenida Pa ´dua Dias, 11, CEP 13418‐ 900, Agronomia, Piracicaba‐SP, Brazil ABSTRACT The northeast area of São Paulo state has been intensively deforested, resulting in a highly fragmented landscape composed of a few large patches and several small patches of natural vegetation surrounded by sugarcane, eucalyptus, and citrus plantations. In this sce- nario, we investigated the puma (Puma concolor) population size, sex ratio, and relatedness in two of the last, and largest, natural refuges in the area using a noninvasive method during 2004–2008. By collecting and individualizing fecal samples by microsatellites, we identi- fied 17 individuals, 13 females (76.4%) and 4 males (23.6%) in these areas. Five females were sampled in distinct years and over an extended time and probably represented resident adults. By investigating the relatedness among individual pumas inhabiting the area, we found that only three animals were not related to each other. We also found evidence that young females might establish an adjacent or overlapping territory to their mothers (phylopatry). Moreover, we registered 11 road‐killed individuals nearby the study area, ten males and one female, and six human–puma conflicts. The study area may act as a source of individuals that disperse across the matrix to occupy new home ranges, maintaining some degree of gene flow in a source–sink metapopulation structure. Finally, we recommend that puma management should be conducted at the landscape level to provide effective puma conservation in northeastern São Paulo state. Abstract in Portuguese is available in the online version of this article. Key words : fecal DNA; metapopulation; microsatellites; noninvasive sampling; relatedness; road kills; sex ratio. THE NORTHEAST AREA OF SÃO PAULO STATE WAS ORIGINALLY COV- ERED BY CERRADO (South American savanna) and semideciduous forest (one of Atlantic Forest phytophysiognomy), but for the last three centuries, it has experienced distinct cycles of human exploitation of its fertile soils. During this period, coffee planta- tions, sugarcane crops, and the increasing urban population have led to an intensive deforestation of the original cover (Dean 1996). This occupation resulted in a disturbed landscape com- posed of few large native vegetation patches (>1000 ha) and diverse small patches (<50 ha), few of which protected by the government (Ribeiro et al. 2009). In this scenario, natural habitats were reduced or eliminated, forcing large carnivores to adapt to a new fragmented landscape. How these carnivores have adapted in the northeast area of São Paulo state is poorly investigated. Sensitive species like the jaguar (Panthera onca) went extinct, but more plastic species, such as the puma (Puma concolor) and the maned wolf (Chrysocyon brachyurus), still inhabit small patches of natural vegetation in the area (Talamoni et al. 2000, Mantovani 2001, Miotto et al. 2007, Lyra‐ Jorge et al. 2008). In this context, populational, ecological, and behavioral information are necessary for effective species man- agement, to measure the success of this action, and to determine whether protected or remnant areas are maintaining viable popu- lations (Caughley 1994). Puma genetics, ecology, social organization, and population dynamics have been extensively studied in North America (e.g ., Ross & Jalkotzy 1992, Beier 1993, Roelke et al. 1993, Beier et al. 1995, Sweanor et al. 2000, Logan & Sweanor 2001), but there are few studies in South America. In Brazil, studies have focused on food habits, habitat use (Emmons 1987, Ciocheti 2007, Lyra‐ Jorge et al. 2008), and puma–human conflicts (Mazzolli et al. 2002, Conforti & Azevedo 2003, Azevedo 2008). Counting and identifying individual pumas is extremely diffi- cult because they are elusive and occur at low densities. Usually, estimates of puma population sizes, sex ratios, or population dynamics are based on capture–recapture methods that track individuals through telemetry data (Beier et al. 1995, Sweanor et al. 2000) or on camera‐trapping methods (Kelly et al. 2008, Paviolo et al. 2009). As an alternative, organic materials that indi- viduals leave behind can be used to demographically monitor elusive species (Wayne & Morin 2004). New molecular techniques of DNA extraction applied to materials such as hair and feces allow us to analyze organisms in a noninvasive way (Morin & Woodruff 1996) and offer an alternative to identify and count individuals, in addition to giving information on sex ratio and dispersers (Kohn & Wayne 1997). Received 16 June 2010; revision accepted 11 January 2011. 3 Corresponding author; e‐mail: remiotto@yahoo.com.br 98 ª 2011 The Author(s) Journal compilation ª 2011 by The Association for Tropical Biology and Conservation BIOTROPICA 44(1): 98–104 2012 10.1111/j.1744-7429.2011.00772.x