title: Genetic censusing identifies an unexpectedly sizeable population of an endangered large mammal in a fragmented forest landscape.
abstract: BACKGROUND
  As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments.
  
  
  RESULTS
  From 2011 through 2013, we noninvasively collected 865 chimpanzee fecal samples across 633 km(2) and successfully genotyped 662 (77%) at up to 14 microsatellite loci. These genotypes corresponded to 182 chimpanzees, with a mean of 3.5 captures per individual. We obtained population size estimates of 256 (95% confidence interval 246-321) and 319 (288-357) chimpanzees using capture-with-replacement and spatially explicit capture-recapture models, respectively. The spatial clustering of associated genotypes suggests the presence of at least nine communities containing a minimum of 8-33 individuals each. Putative community distributions defined by the locations of associated genotypes correspond well with the distribution of 14 Y-chromosome haplotypes.
  
  
  CONCLUSIONS
  These census figures are more than three times greater than a previous estimate based on an extrapolation from small-scale nest count surveys that tend to underestimate population size. The distribution of genotype clusters and Y-chromosome haplotypes together indicate the presence of numerous male philopatric chimpanzee communities throughout the corridor habitat. Our findings demonstrate that, despite extensive habitat loss and fragmentation, chimpanzees remain widely distributed and exhibit distinct community home ranges. Our results further imply that elusive and rare species may adapt to degraded habitats more successfully than previously believed. Their long-term persistence is unlikely, however, if protection is not afforded to them and habitat loss continues unabated.
authors: Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 107, Los Angeles, CA, 90089-0371, USA. msmccart@usc.edu.|Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. msmccart@usc.edu.
authors: Maureen S
authors: MS
authors: McCarthy
authors: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. jack_lester@eva.mpg.de.
authors: Jack D
authors: JD
authors: Lester
authors: Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, Fife, KY16 9LZ, UK. ejh20@st-andrews.ac.uk.
authors: Eric J
authors: EJ
authors: Howe
authors: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. arandjel@eva.mpg.de.
authors: Mimi
authors: M
authors: Arandjelovic
authors: Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, 3616 Trousdale Parkway, AHF 107, Los Angeles, CA, 90089-0371, USA. stanford@usc.edu.
authors: Craig B
authors: CB
authors: Stanford
authors: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. vigilant@eva.mpg.de.
authors: Linda
authors: L
authors: Vigilant
mesh_terms: D000818:Animals; D056727:Endangered Species; D005243:Feces; D005260:Female; D065928:Forests; D005838:Genotype; D006239:Haplotypes; D008297:Male; D018895:Microsatellite Repeats; D008962:Models, Theoretical; D002679:Pan troglodytes / Q000235:genetics*; D011156:Population Density; D017422:Sequence Analysis, DNA; D014454:Uganda; D014998:Y Chromosome