Mandrills (Mandrillus sphinx) are endemic to the tropical forests of Central Africa and are threatened by habitat loss and hunting. Mandrills exist in “hordes” that are some of the largest groups observed for non-human primates, at times including close to one thousand individuals. Yet the population dynamics and connectivity between hordes in the wild remain poorly understood. This dataset includes microsatellite data from biological samples, primarily feces, collected from three wild mandrill hordes (SEGC, ECOFAC, and Mikongo) in Lopé National Park, Gabon. These data were used to examine connectivity between the three hordes, in particular male-biased dispersal, and to test for historical population bottlenecks that may have occurred during past periods of environmental change. Our findings show that these three hordes constitute an admixed metapopulation with frequent dispersal between hordes that is likely male-biased, although the lack of inter-horde genetic differentiation limits estimation of migration rates. The effective population size of the three hordes appears to be historically stable, with no evidence of past population bottlenecks, despite mandrills’ recent declining numbers.

This dataset contains processed genotypes for an estimated 368 mandrills: 232 from the SEGC horde, 80 from the ECOFAC horde, and 56 from the Mikongo horde. These genotypes were PCR-amplified from samples collected between the years of 2016 and 2019. 348 of these genotypes originate from non-invasively collected fecal samples, while 14 originate from blood and six from hair. Each genotype contains 13 microsatellite loci (disregarding missing data), with duplicate genotypes removed. Genotype files of males only and females only are also available.

Fecal samples were collected from the SEGC herd during three successive summer dry seasons in 2016, 2017, and 2018. Sampling was conducted during July or August, when adult males and females are both present in the horde (Abernethy et al., 2002). Radio telemetry was used to locate the SEGC horde daily, and researchers then followed the mandrills and opportunistically collected fresh (<6 hours old) fecal samples. In 2019, samples were collected from the Mikongo and ECOFAC hordes, which have not been radio-collared. Samples were stored in 50mL Falcon tubes with ~25mL silica gel since this is an effective method for preserving nuclear DNA (Soto-Calderón et al., 2009). After storage at ambient temperature in the field for one to four weeks, samples were transferred to a -20°C freezer. DNA was extracted using QIAmp DNA Stool Mini Kits (Qiagen, California). In addition to the non-invasive samples of feces, some samples of blood and plucked hair were also collected from SEGC individuals anesthetized for radio collaring for an unrelated project. DNA was extracted from these blood and hair samples using the DNeasy Blood & Tissue Kit (Qiagen, CA).

Each sample was genotyped for a set of 16 highly polymorphic microsatellite markers (Benoit et al., 2014). Full details on genotyping methods can be found in the related publications, but, briefly, the 16 markers were assembled into four multiplex PCRs of four microsatellite loci each (Guibinga Mickala et al., 2022). The markers were amplified using fluorolabeled primers and sized on an ABI3130xl sequencer (Applied Biosystems, CA). Three replicates of each PCR were performed, and each sample was considered heterozygous if two alleles appeared in at least two replicates, and homozygous if a single allele appeared alone in all three replicates. Any genotypes not satisfying either condition were treated as missing data. Samples with consensus genotypes at fewer than seven loci were discarded, since they did not contain sufficient information for individual identification. Three loci were ultimately discarded from the final dataset due to poor amplification or possible null alleles.

The sex of sampled individuals was determined using markers on the X and Y chromosomes, which were also included in the multiplex PCRs and amplified with fluorolabeled primers. The X marker was a 193-base fragment of the amelogenin gene, and the Y chromosome marker was a 163-base section of the sex-determining region (SRY) (Di Fiore, 2005). To identify cases where multiple samples were collected from the same individual, microsatellite genotypes from all samples were compared pairwise. In a pilot study, the probability of identity was calculated to illustrate the probability of two individuals sharing a genotype at a single locus by chance (Waits et al., 2001), thus informing the number of microsatellite loci required to differentiate individuals. Based on these results, a pair of samples was considered to have originated from the same individual if the genotypes matched at a minimum of six loci (probability of identical genotypes by chance at six loci <0.01), with no more than two mismatches allowed. Sex markers were used as additional verification. 

• Abernethy, K., White, L. J. T., & Wickings, E. J. (2002). Hordes of mandrills (Mandrillus sphinx): Extreme group size and seasonal male presence. Journal of Zoology, Proceedings of the Zoological Society of London, 258, 131–137. https://doi.org/10.1017/S0952836902001267
• Benoit, L., Mboumba, S., Willaume, E., Kappeler, P. M., & Charpentier, M. (2014). Using next-generation sequencing methods to isolate and characterize 24 simple sequence repeat loci in mandrills (Mandrillus sphinx). Conservation Genetics Resources, 6(4), 903–905. https://doi.org/10.1007/s12686-014-0237-1
• Di Fiore, A. (2005). A rapid genetic method for sex assignment in non-human primates. Conservation Genetics, 6, 1053–1058. https://doi.org/10.1007/s10592-005-9086-5
• Guibinga Mickala, A., Weber, A., Ntie, S., Gahlot, P., Lehmann, D., Mickala, P., Abernethy, K., & Anthony, N. (2022). Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lope National Park, Gabon, using a non-invasive genetic approach. Conservation Genetics, 23, 871-883. https://doi.org/10.1007/s10592-022-01458-2
• Soto-Calderón, I. D., Ntie, S., Mickala, P., Maisels, F., Wickings, E. J., & Anthony, N. M. (2009). Effects of storage type and time on DNA amplification success in tropical ungulate faeces. Molecular Ecology Resources, 9(2), 471–479. https://doi.org/10.1111/j.1755-0998.2008.02462.x
• Waits, L. P., Luikart, G., & Taberlet, P. (2001). Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology, 10(1), 249–256. https://doi.org/10.1046/j.1365-294x.2001.01185.x.