Evaluating genetic capture‐recapture using a chimpanzee population of known size

Abstract

Genetic capture‐recapture (CR) estimates of population size have potential for aiding the conservation and management of rare or elusive animals. To date, few studies have explored the performance of genetic CR estimates by implementing them in a population of known size. We evaluated the accuracy and precision of genetic CR estimates by genotyping fecal samples collected opportunistically over the territory of a well‐studied group of approximately 190 previously identified and genotyped eastern chimpanzees (Pan troglodytes schweinfurthii) in Kibale National Park, Uganda. We compared the performance of genetic CR estimates based on 3‐month and 3‐year sampling periods to explore the impact of lengthened sample periods, which are expected to increase accuracy and precision of estimates but also increase the chances of violating population closure assumptions. We compared the effects of using spatial and non‐spatial models and equal or heterogeneous detection probabilities upon estimates. Over the 3‐year period, we detected 54% of the group members and produced population size estimates with more accuracy and narrower confidence intervals than the 3‐month sampling period. The population remained effectively closed over the 3 years and detection heterogeneity was linked to age but not sex. Non‐spatial methods estimated group size more accurately than spatially explicit methods, which had a stronger tendency to underestimate population size. This study suggests that genetic CR may produce accurate and precise population size estimates if substantial effort is allocated to sample collection and genotyping. © 2016 The Wildlife Society.

A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

“…Microsatellite genotyping is also necessary to identify unique individuals and thus should be considered a necessary part of the screening process. For example, our samples were first subjected to analysis at 15 microsatellite loci and categorized as individuals in the context of a long‐running project (Granjon et al., ; Langergraber, Mitani, & Vigilant, ; Langergraber, Watts, Vigilant, & Mitani, ). We could therefore be confident that our putative chimpanzee samples were indeed from chimpanzees.…”

“…As part of an on‐going population size monitoring project, DNA was extracted from these faecal samples using either the GeneMATRIX Stool DNA Purification Kit (Roboklon) according to the manufacturer's instructions or QIAmp Stool kit (Qiagen) with slight modifications from the manufacturer's protocol (Nsubuga et al., ). Microsatellite genotyping was performed to establish sex and individual identity as previously described (Arandjelovic et al., ; Granjon, Rowney, Vigilant, & Langergraber, ). We considered only extracts that were successfully genotyped at enough loci to confidently assign an ID (for details see Granjon et al., ) for exome sequencing.…”

“…Microsatellite genotyping was performed to establish sex and individual identity as previously described (Arandjelovic et al., ; Granjon, Rowney, Vigilant, & Langergraber, ). We considered only extracts that were successfully genotyped at enough loci to confidently assign an ID (for details see Granjon et al., ) for exome sequencing. Additionally, two tissue samples were collected from two deceased chimpanzees found within Kibale.…”

“…Other modifications to our protocol may also increase capture (Granjon et al, 2017;Langergraber, Mitani, & Vigilant, 2007;Langergraber, Watts, Vigilant, & Mitani, 2017). We could therefore be confident that our putative chimpanzee samples were indeed from chimpanzees.…”

An empirical evaluation of camera trapping and spatially explicit capture‐recapture models for estimating chimpanzee density

“…However, because chimpanzees recognize territory boundaries and rarely cross them, members of neighboring communities are detected less frequently than would be expected based on distance alone. We suspect similar effects contributed to the underestimation of chimpanzee density and population size reported by Granjon, Rowney, Vigilant, & Langergraber (), who also collected (genetic) SECR data within the known territory of a single community of known size.…”