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Molecular scatology as a conservation tool. (Felid Conservation).


The threat of predation on livestock by large carnivores represents a major impediment to the conservation of intact ecosystems throughout the world. Although it has taken nearly a century to learn the truth about predation on livestock in North America, advanced technologies now exist to greatly expedite similar findings elsewhere. By examining the dietary ecology of puma and jaguar on a cattle ranch in the Venezuelan llanos, it is possible to help identify simple, effective methods to reduce livestock predation. In my study, dietary habits of the puma and jaguar were defined from feces (scats), kills, and ranch records. Scats were assigned to predator species through analysis of mitochondrial DNA from feces of wild carnivores. Based on dietary and ecological data of these two large carnivores, recommendations on livestock husbandry are made.

The puma (Puma concolor) and the jaguar (Panthera onca) are large sympatric carnivores trying to survive in increasingly fragmented habitats of the Neotropics. Much of the range of these endangered animals has been converted to ranchlands, which now hold some of the last remaining natural habitats in Latin America. In much of the Neotropics, the major cause of mortality for large felids is persecution by cattle ranchers for alleged predation on livestock. To conserve viable populations of large cats it is necessary to find some resolution to this problem. This study attempts to accurately identify the predator species involved in livestock depredation, and to provide a clearer understanding of carnivore interactions with livestock.

Dietary habits can be accurately determined noninvasively only by a thorough analysis of scats--the end product of predation. Unfortunately, accurate analysis has eluded scientists until recently. Scats have traditionally been sorted to donor species by diameter. In 1980 thin layer chromatography analysis of bile acids was introduced (Major et al.), and for more than a decade it was the most accurate method for determining donor species. But bile acid assays can give misleading results for closely related carnivores. The identity of puma and jaguar scats is based on the presence of one bile acid that appears in only 71% of jaguar scats, leaving a 29% possibility of mistaking jaguars for pumas (Taber et al. 1997). Nevertheless, diameter of puma and jaguar feces in Taber's study overlapped in almost all size ranges. The need for a more definitive analysis is apparent.

The advent of polymerase chain reaction (PCR) has enabled scientists to acquire information through molecular analysis. Hoss et al. (1992) used genetic techniques to analyze mitochondrial DNA (mtDNA) from sloughed off colon cells found in wild scat in order to identify Italian bears. By isolating DNA from scats and checking it against reference samples, it is now possible to accurately determine which species, and sometimes even which individual left the sample (Kohn et al. 1995; Kohn et al. 1999; Ernst et al. 2000).

Molecular scatology can provide new insights into the carnivore diet, and help lead to solutions for a range of conservation problems (Kohn and Wayne 1997). With the use of scat-sniffing dogs, non-biased recovery of samples from multiple target species is now feasible (Wasser et al. 1999), making population estimates for similar-sized sympatric species possible. By analyzing the prey content of scats from undisturbed habitats, we can determine the preferred prey of carnivores. If we manage this prey appropriately, attacks on livestock by hungry carnivores can be reduced.

The molecular method is completely noninvasive, though removing all scats may confuse animals by removing territorial markers, which also signal reproductive status (Brown et al. 1994). The field collection methods for this study were simple and effective; samples were collected, air-dried, and then stored at room temperature. Using these collection and storage methods, a recent lab run produced positive identifications from scats that were seven to ten years old (in preparation). Samples were transported without freezing or excess bulk, hazardous chemicals, or cumbersome permit restrictions. Scats are the only item from Appendix I species exempt from CITES controls (Gerloff et al. 1995), although other restrictions, such as those imposed by the USDA, may apply.

Carnivore scats were collected opportunistically from roads and trails on Hato Pinero, a cattle ranch in the llanos, the seasonally flooding savanna of western Venezuela. Samples were dried and a small portion of each scat was stored for genetic analysis (Farrell et al. 2000). Samples were then analyzed for prey contents; remains were visually identified to the lowest taxon possible by examining teeth, claws, bones, fur, feathers, and scales. For this study, all mammals less than one kilogram were considered small--mostly rodents, but including small marsupial mouse opossums (Marmosa sp.). Medium mammal prey ranged from 1 to 15 kilograms, including armadillo (Dasypus novemcinctus), rabbit, sloth (Bradypus variegatus), opossum (Didelphis marsupialis), juvenile peccary, and newborn calves (Bos bos). Large mammals were anything over 15 kilograms, such as adult capybara (Hydrochaeris hydrochaeris) and peccary, deer, giant anteater (Myrmecophaga tridactyla), and juvenile and adult cows.

In the llanos, the ocelot (Leopardus pardalis) and crab-eating fox (Cerdocyon thous) each average about six to 10 kg in body weight, the puma about 40 to 50 kg, and the jaguar up to 100 kg (Figure 1). But, body size is not necessarily indicative of scat size. Puma scats have been identified down to 19mm in diameter, and ocelot scats up to 27 mm. Because of this overlap, it was necessary to define prey contents of almost all size predator scats to accurately define the dietary habits of puma and jaguar. Frequency of occurrence of prey types were separated into small and large predator categories--first based on size of scat (traditional method) and then based on DNA identification.


For the preliminary analysis by scat size, scats were split into large, assumed to be puma and jaguar, and small, assumed to be ocelot and fox. Based on previous studies (L. Emmons, personal communication; Fernandez et al. 1997), 25 mm dry diameter was chosen as an arbitrary breaking point large enough so that it was beyond the range of most fox and ocelots.

For the molecular analysis, a portion of the mitochondrial cytochrome b gene was chosen as the DNA marker to assign unknown scats to predator species. Samples were washed, and DNA extracted from the isolate and amplified using PCR (Farrell et al. 2000). The resulting strands of DNA were sequenced and compared to samples extracted from blood of the carnivore species at the study site. Even this test wasn't perfect at first--one sample that could not be matched to a known carnivore was compared to sequences posted in GenBank using the BLAST program (National Center for Biotechnology Information (NCBI), to find a cytochrome b sequence with the closest match. When that came back as a fruitfly (Drosophila melanogaster; likely apprehended while the scat was collected), primers that targeted carnivores were designed. The sample was reamplified with these new primers and found to be a perfect match with our ocelot reference. Targeting a shortened fragment of 147 base pairs also increased the percentage of successful samples, because fecal DNA is often degraded. Twenty of 34 samples (59%) were successfully sequenced.

Three jaguar and two fox scats were identical to control samples, as were five puma scats (one puma scat differed by one base pair). The sequences from 10 ocelots showed more variation, which makes sense in light of a study by Eizerick et al. (1998) showing a relatively high degree of intraspecific variation among the smaller Neotropical felids.

Puma, ocelot, and fox scat sizes overlap in a narrow range around 25mm diameter, and puma and jaguar overlap at larger diameters between 32 and 37 mm (Figure 2). One individual can leave scats of various sizes, and the range of body sizes can vary greatly within species. For example, male jaguars in the llanos average about 100 kilograms, whereas males in the Central American rain forest average 55 kg.


Using size to define dietary analyses, smaller carnivores appear to ingest solely mammalian prey (Table 1, left side). They even appear to take large prey, though the thought of an ocelot or fox subduing and killing an 18 kg collared peccary (Tayassu tajacu) may seem unusual. Large predators appear to take prey from all categories, predominantly small mammals.

DNA analysis of samples shows that almost the inverse is true. Large carnivores prey exclusively on medium and large mammals, and small carnivores take a wide range of prey, including everything except large mammals (Table 1, right side). Analysis of one scat with a size indicative of a small ocelot (19.25mm), clarified that it was a puma who ate the peccary.

McNemar's test (Harrison 1996) showed the difference between identification of scat donor by size and by genetic analysis to be highly significant (X_ = 7.36, p<0.01, ldf). With differentiation by size, 83% of ocelot and fox scats were misclassified as large predator scats, and 12% of puma and jaguar scats were misclassified as small predator scats. These findings are preliminary and the sample size is small, dietary results may change when scats from the last two years of the three year project are analyzed.

With DNA analysis, predators are discernable to the species level (Table 2). The biomass of each prey type is then calculated to learn its relative importance in each carnivore's diet (Farrell et al. 2000). Dietary resources are divided more between large and small carnivores than between same size sympatric carnivores; puma and jaguar versus fox and ocelot. Jaguar scats contained a peccary and a cottontail rabbit (Sylvilagus floridanus). A third was disqualified from the dietary analysis because it contained a wild pig set as bait while trapping cats for radio-telemetry. Five puma scats contained a couple of juvenile peccaries, an armadillo, one deer (Odocoileus virginianus), and a domestic guard dog (Canis familiarus), confirming the suspicion of ranch workers that their missing tag-along dog had been consumed by a puma. The samples containing dog and pig bait illustrate that this method can be used to pinpoint problem predators.

Dietary data derived from the genetic analysis, along with information from kills recovered during this study and ranch records, can offer suggestions to help decrease livestock predation. Livestock and wild kills were examined when located (n = 15) and habitat conditions were recorded to discern where cats kill, and what conditions are conducive to predation. Seven verifiable incidences of livestock predation were examined, and six of these confirmed as pumas (Farrell 1999). Frequency and location of predation by cats on cattle was determined from 10 years of ranch records that reported causes of livestock mortality (Table 3; Hato Pinero, unpublished data). When observations of livestock killed during my study are combined with evidence from ranch records and molecular data, the preference for different sizes of prey between the two cats becomes clearer. Jaguars select for very large adult prey. They took only a very small percentage of the total cattle lost (<1% according to ranch records), yet these cows were typically full grown and a greater financial loss per head. As the more endangered of the two felids, perhaps jaguars should be allowed to keep practicing business as usual, and a compensation program for ranchers be initiated. Pumas are pinpointed as a greater problem; they are more general in prey selection and concentrate on medium and large size prey--often in the form of newborn and juvenile calves. Their preference for calves and juveniles when preying on livestock corroborates data from genetic identification of puma scats that revealed no prey item larger than a juvenile calf.

While jaguars prefer moister habitats of lower elevations; the pumas preference for dry habitat types is significant. Pumas move to dryer, nonflooding ranges for the wet season. Unfortunately cattle are also moved to these areas at the same time. The birthing of inseminated cows (each representing an investment of over $100 US) is timed as well for the beginning of the wet season in pastures along the edges of the ranch, In these areas humans harvest much of the natural prey, so it is no surprise that these pastures exhibit the greatest incidences of livestock predation. Pumas arriving thin and hungry from desolate ranges at the end of the dry season are greeted by a landscape flush with naive, newborn prey that are just learning to walk.

It is important to incorporate different types of data and the views of different parties to create solutions that will be effective in helping both predators and local ranchers. This study verified that pumas are a greater problem than jaguars on Hato Pinero. By determining which prey carnivores favor through scat analysis, management of the preferred prey can help reduce predation problems. To test deterrence, electric fencing was used in one of the hardest hit maternity pastures during a later phase of this study, and found to curtail predation by 100% (Scognamillo et al. 1999). One noteworthy finding of my study is that when water buffalo (Bubalis bubalis) were placed with cattle, predation mortalities in one long-suffering maternity pasture decreased close to zero (Andres Rodriguez, personal communication). Water buffalo are already being raised on this and other ranches throughout the llanos for meat and cheese and mix well with cattle, while apparently affording them some protection from predation (Farrell 1998).

Vast portions of puma and jaguar ranges are dedicated to livestock production--often on ranches of 80,000 to 120,000 hectares that contain large areas of natural habitat. Owners who are confident that their stock is safe are less likely to go hunting for these elusive cats. Reducing the threat of felid predation on livestock will have broad implications for future conservation of jaguar and puma in the Neotropics.
Table 1. A comparison of prey frequencies with scats separated by
size and molecular analysis. One jaguar scat was disqualified from
the dietary analysis for containing bait (from Farrell et al. 2000).
Small predators = Fox and ocelot. Large predators = Puma and jaguar.

 Frequency (%) of Prey Types

 Scat size mtDNA

 Small Large
 predators Predators Small Large
 [less than [greater than Predators Predators
 or equal or equal
 to] 25mm to] 25mm

mammals 75 46 64 --

mammals 12.5 12 3 50

mammals 12.5 9 -- 50

Reptiles -- 9 9 --

Birds -- 12 12 --

Fish -- 3 3 --

Crabs -- 9 9 --

 n=3 n=16 n=12 n=7
Table 2. Frequency of prey biomass with predator scats identified
using molecular analysis (from Farrell 1999).

 Jaguar Puma Ocelot Fox
 n = 2 n = 5 n = 10 n = 2

mammals -- -- 26 34

mammals 28 45 22 --

mammals 72 54 -- --

Reptiles -- -- 43 --

Birds -- -- 7 23

Fish -- -- -- 31

Crabs -- -- 2 12
Table 3. Predation on cattle (calves and adults) by puma
and jaguar on Hato Pinero from January 1987 through October
1996, as reported by ranch workers (Hato Pinero, unpublished
data; from Farrell 1999). * There was found to be
a discrepancy of 27% between causes of livestock mortality
reported by ranch workers and evidence at the site when
reported incidences of predation were investigated in 1999.

 Total Puma Jaguar

Number of mortalities attributed
to predation * 310 275 35

% Predation 89 11

% of total cattle mortalities from
all causes (n=3672) 8.4 7.5 <1


I would like to thank Sam Wasser and Chris Clarke, who generously allowed me to learn in the Center for Wildlife Conservation's molecular lab, Joe Roman who helped with many facets of this study, Brian Bowen who encouraged this along, and Mel Sunquist, without whom this would not have been possible. Martin Smith reviewed earlier versions of the manuscript and his suggestions improved the paper. Many others helped as well, special thanks to the llaneros on Hato Pinero. This study was part of work done for a Masters thesis at the University of Florida, Gainesville, with Dr. Mel Sunquist, who put together the field project.

Literature cited

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Eizirick E., S.L. Bonato, W.E. Johnson, P.G. Crawshaw Jr., J.C. Vie, D.M. Brousset, S.J. O'Brien, F.M Salzano. 1998. Phylogeographic patterns and evolution of the mitochondrial DNA control region in two Neotropical cats (Mammalia, Felidae). Journal of Molecular Evolution 47:613-624.

Ernest HB, M.C.T. Penedo, B.P. May, M. Syvanen and W,M. Boyce. 2000. Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA. Molecular Ecology 9:433-441.

Farrell L.E. 1998. Water buffalo as a conservation tool. Water Buffalo Newsletter 10(4):2 The American Water Buffalo Association, Gainesville, FL.

Farrell L.E. 1999. The ecology of the puma and the jaguar in the Venezuelan llanos. MS thesis. University of Florida, Gainesville.

Farrell, L.E., J. Roman and M.E. Sunquist. 2000. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Molecular Ecology 9:1583-1590.

Fernandez G.J., J.C. Corley and A.F. Capurro. 1997. Identification of cougar and jaguar feces through bile acid chromatography. Journal of Wildlife Management 61:506-510.

Gerloff U, C. Schlotterer, K. Rassmann, I. Rambold, G. Hohmann, B. Fruth and D. Tautz. 1995. Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Molecular Ecology 4:515-518.

Harrison, J.M. 1996. Categorical Data Analysis. Jay M. Harrison, IFAS Dept. of Statistics. University of Florida, Gainesville, FL.

Hoss M., M. Kohn, S. Paabo, F. Knauer and W. Schroder. 1992. Excrement analysis by PCR. Nature 359:199.

Kohn M., F. Knauer, A. Stoffella, W. Schroder and S. Paabo. 1995. Conservation genetics of the European brown bear--a study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology 4:95-103.

Kohn M.H. and R.K. Wayne. 1997. Facts from feces revisited. Trends in Ecology and Evolution 12:223-227.

Kohn M.H., E.C. York, D.A. Kamradt, G. Haught, R.M. Sauvajot and R.K. Wayne. 1999. Estimating population size by genotyping faeces. Proceedings of the Royal Society of London B 266:657-663.

Linares, O.J. 1998. Mamiferos de Venezuela. Sociedad Conservationista Audubon de Venezuela, Caracas.

Major M., M.K. Johnson, W.S. Davis and T.F. Kellog. 1980. Identifying scats by recovery of bile acids. Journal of Wildlife Management 44:290-293.

Scognamillo, D., I.E. Maxit, M. Sunquist, and L. Farrell. In press. Ecologia del jaguar y el problema de la depredacion sobre ganado en Hato Pinero, Venezuela. Manuscript submitted for publication in El Jaguar en el nuevo milenio. Una evaluacion de su estado, deteccion de prioridades y recomendaciones para la conservacion de los jaguares en America. Medellin, R. A., C. Chetkiewicz, A. Rabinowitz, K. H. Redford, J. G. Robinson, E.W. Sanderson, y A. Taber, eds. Universidad Nacional Autonoma de Mexico/Wildlife Conservation Society. Mexico D. F.

Taber A.B., A.J. Novaro, N. Neris and F.H. Colman. 1997. The food habits of sympatric jaguar and puma in the Paraguayan Chaco. Biotropica 29:204-213.

Wasser S., M. Parker and B. Davenport. 1999. Noninvasive DNA sampling using scat sniffing dogs. Society for Conservation Biology Abstracts. Thirteenth Annual Meeting, College Park, Maryland.
Laura E. Farrell
Museum of Comparative Zoology, Harvard University. 26 Oxford Street,
Cambridge, MA 02138;
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Author:Farrell, Laura E.
Publication:Endangered Species Update
Date:Jul 1, 2001
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