DOI: 10.5061/dryad.gb5mkkwxv
title: Microsatellite loci genotypes dataset (N=121 unique individuals) from: Sex-mediated gene flow of grayfoot chacma baboons (Papio ursinus griseipes ) in a highly seasonal habitat of Gorongosa National Park, Mozambique

description: Investigating primates’ behavioral variation at the inter-population level
 is important for the advancement of biological anthropology and the
 understanding of the evolutionary processes leading to species-specific
 behavioral patterns. The study of behavioral diversity among populations
 also contributes to improve primates’ conservation efforts. Dispersal
 patterns tend to be similar among close phylogenetic lineages but may vary
 in response to individual-based responses to local demographic and
 environmental variation. Here, we investigate dispersal patterns of chacma
 baboons (Papio ursinus griseipes) living in Gorongosa National Park and
 the Catapu Forest Reserve in central Mozambique. The park consists of a
 mosaic landscape, located in a region of high seasonal variability. This
 area was the epicenter of a major war, which decimated most apex predators
 resulting in limited mammalian predation on baboons and a steep increase
 in groups number. Factors such as anthropogenic habitats disturbance,
 decreased interactions with predators, and increase in groups density have
 the potential for altering individual dispersal behaviour in primates,
 which may lead to lack of sex-bias in dispersal. We used a large genetic
 dataset of non-invasive DNA samples analyzed for uni- and bi-parentally
 inherited markers to characterize the spatial distribution of genetic
 variation and investigate the extent and direction of sex-mediated gene
 flow. We found high levels of genetic diversity and evidence for
 historical and very recent male-biased gene flow. Our study highlights the
 strong conservation of male-biased dispersal patterns in chacma baboon
 populations facing highly unpredictable environments and suggests that
 dispersal behaviors in Papio sp. are resilient to environmental
 variability and high seasonality.
description: <strong>Study site</strong> We
 carried out the study at Gorongosa National Park (GNP,
 18°43'56.54" S, 34°16'31.58" E, total area 3,770
 km<sup>2</sup>), which included the floodplain central area
 (GNP core), and the western entrance of the park (Boé-Maria, BM).The study
 also included samples collected in the Catapu Forest Reserve (CFR,
 16°50'54.11" S, 34°11'11.94" E, total area 250
 km<sup>2</sup>). <strong>DNA
 sampling</strong> Fecal samples from unidentified
 individuals were sampled opportunistically along unpaved roads and in
 areas usually frequented by baboons, such as the edge of drinking spots or
 foraging paths, during field expeditions carried out in the dry seasons of
 2017, 2018 and 2019. One tissue sample was retrieved from an individual
 who was the subject of infanticide, and one blood sample was collected
 during GPS collar placement as part of a different study (Lewis-Bevan
 <em>et al.</em>, in prep). Both samples have been analysed
 before (Santander <em>et al</em>., 2022). Fecal samples were
 collected in two main areas, GNP and CFR (Fig. 1). At GNP, sampling was
 carried out mainly at two locations – the core of GNP around Lake Urema
 and at Boé Maria- at a maximum distance of 30 km. BM is located
 approximately 11 km from the closest site at the core of GNP. At CFR,
 sampling was carried out at four sites located a maximum of 6 km apart
 (Fig. 1). Fecal samples were geo-referenced using a Global Positioning
 System (GPS) device (Garmin GPSMAP 64s). Notes were taken concerning
 samples’ preservation status and of the sex of individuals (when observed)
 and group size. Samples were collected at least 2 m apart to minimize the
 likelihood of sampling the same individuals. Gloves, facemasks, and
 hairnets were used during sampling to limit possible human
 cross-contamination. The collected fecal samples were preserved until DNA
 extraction using the “two-step protocol” (Roeder <em>et
 al.</em>, 2004), a procedure in which a 5 ml of fecal material is
 collected from the exterior part of the sample, by scraping the surface
 using a wooden stick, and immediately immersed in 99% ethanol for 24-48h.
 After that period, the samples were transferred to a tube containing 30g
 of Silica Gel (Type III, S-7625, indicating for desiccation,
 Sigma-Aldrich) and preserved as such until DNA extraction. The tissue and
 the blood sample were preserved in 99% ethanol at room temperature until
 DNA extraction. <strong>DNA
 extraction</strong> Fecal samples were
 transported to CIBIO laboratory facilities, Porto University, Portugal,
 for DNA extraction. Total genomic DNA was extracted using the QIAamp® DNA
 Stool Mini Kit (QIAGEN ®) with some modifications from the manufacturer’s
 protocol (Ferreira da Silva <em>et al.</em>, 2014). DNA
 extracts were eluted in 200ul Buffer AE and stored at -20ºC. Several
 precautions were taken to avoid contamination with exogenous DNA during
 sample extraction (Ferreira da Silva 2012). Negative controls were
 subjected to all the extraction procedures to test for the possible
 contamination with human DNA and/or cross-contamination between samples.
 Tissue and the blood DNA extraction was performed in GNP molecular lab,
 using the QIAGEN “DNeasy Blood & Tissue Kits” following the
 manufactures’ protocol. DNA extracts were eluted in 200ul Buffer AE and
 stored at -20ºC. <strong>DNA amplification and
 data production</strong> DNA samples were
 amplified via Polymerase Chain Reaction (PCR) to recover 490 base pairs
 (bp) of the mitochondrial control region (hypervariable region I) (mtDNA)
 (Hapke <em>et al.</em>, 2001), 14 autosomal microsatellite
 loci, and the Y chromosome-linked DYS576 locus. Microsatellite loci were
 human-derived with cross-amplification in other <em>Papio
 </em>sp. (Ferreira da Silva <em>et al.</em>, 2014). The
 Y-locus (DYS576) is one of the few human-derived markers showing variation
 in <em>Papio</em> sp. (<em>e.g.</em>, Jolly
 <em>et al.</em>, 2011). The sex of the individuals was
 identified using the molecular protocol developed by Di Fiore (2005) in
 which a fragment of the amelogenin X gene (~200 bp) and a fragment of the
 SRY gene (approximately 165 bp) are co-amplified in a multiplex PCR.
 Primer sequences and the PCR amplification cycling details are described
 in supplementary material: 1) procedures to limit cross-contamination
 between samples and by external DNA were implemented (supplementary
 material; 2) all PCRs were carried out in a T100TM BIO-RAD 96 Well Thermal
 Cycler at CTM/CIBIO. The set of fourteen autosomal
 microsatellite loci and the Y-chromosome locus were amplified using five
 multiplex PCR systems (Table S1, supplementary material 3). The range of
 amplified alleles sizes varies between approximately 123 and 270 bp. All
 markers were tetranucleotide repeats, except D7S503 and D5S1457 that were
 dinucleotides (Table S1, supplementary material 3). Successful PCR
 products were analysed using CTM fragment analysis service and run on an
 ABI3730XL capillary analyzer using a 16 GeneScanTM -500 LIZ ®
 size-standard. Microsatellite loci genotyping followed
 a modified version of the “multi-tubes” approach from (Taberlet
 <em>et al.</em>, 1996) in which the number of required
 repetitions across loci necessary to obtain reliable consensus genotypes
 was estimated on empirical data, following Ferreira da Silva <em>et
 al.</em>, (2014) (supplementary material 5). As a result, we carried
 out a minimum of four amplifications per locus per sample. The<em>
 </em>reliability of consensus genotypes was quantified using the
 mean “Quality Index” (QI, Miquel <em>et al.</em>, 2006) across
 loci. Genotypes with a QI below 0.55 were removed from the final dataset
 (Miquel <em>et al.</em>, 2006). The Probability of Identity
 (PI), which is the probability that two individuals sampled randomly from
 the population have the same genotype at all typed loci, and the PI
 between siblings (<em>PIsibs</em>) (Waits <em>et
 al.</em>, 2001) were estimated using GenAlEx v.6.503 (Peakall
 & Smouse, 2006). The minimum number of loci required to
 distinguish between different individuals using the study’s set of
 microsatellite loci was estimated using <em>poppr</em> 2.9.3
 package (Kamvar <em>et al.</em>, 2015) in R Studio v.1.3.1093.
 Samples with the same genotype (possibly belonging from re-sampled
 individuals) were removed from the dataset. Departure
 from Hardy-Weinberg equilibrium (HWE) was calculated per locus for the
 overall dataset and separately for GNP+BM and CFR using
 <em>PopGenReport</em> 2.2.2 R package (Adamack &
 Gruber, 2014). The p-value for significant deviations from HWE
 expectations was corrected using the Bonferroni adjustment for multiple
 comparisons. <em>Micro-Checker </em>version 2.2.3 (van
 Oosterhout <em>et al.</em>, 2006) was used to test
 locus-specific deficiency in heterozygotes due to null alleles, stutter
 band-related scoring errors and large-allele dropout, all three with a 95%
 confidence interval. An exact test for linkage disequilibrium (LD) between
 all pairs of loci was computed for each sampling area using Arlequin
 v.3.11 (Excoffier <em>et al.</em>, 2005). The significance of
 the association between pairs of loci was tested via a likelihood ratio
 test using 10,000 permutations. Percentage of missing data for the overall
 dataset and by sampling locations was estimated using
 <em>poppr</em> 2.9.3 R package.
description: # Microsatellite loci genotypes dataset (N=121 unique individuals) from
 the work: Sex-mediated gene flow of grayfoot chacma baboons (*Papio
 ursinus griseipes*) in a highly seasonal habitat of Gorongosa National
 Park, Mozambique
 [https://doi.org/10.5061/dryad.gb5mkkwxv](https://doi.org/10.5061/dryad.gb5mkkwxv) ## Description of the data and file structure Data is organized in an excel sheet, following Genelex software format. The first line has information on column information. First column is sample code, second column is the information of each sample on Quality Index (QI) estimated as in Miquel et al 2006, third column has the information on the population (Gorongosa or CFP), fourth and fifth column describes latitude and longitude coordinates (in decimal degrees), six column has information on the sex of sample (Male, Female or NA - Non identified), and next columns describe alleles size genotyped for each loci. Please note that DYS576 was only genotyped for males (samples identified as females are indicated by "female (NA - non applicable). Missing data (samples not reaching a consensus genotype) are indicated by "0" (zero).