DOI: 10.5061/dryad.15dv41p8p
title: Data from: Investigating anthropogenic and social influences on diet of semi-urban vervet monkeys using DNA metabarcoding

description: In human-dominated ecosystems, wildlife has been forced either to
 disappear or to adapt its behaviour in order to exploit the opportunities
 associated with anthropogenic activities. Vervet monkeys (Chlorocebus
 pygerythrus) are omnivorous primates whose natural habitats have been
 progressively encroached upon by expanding suburban development. Due to
 their generalist and opportunistic feeding behaviour, vervet monkeys have
 successfully adapted to semi-urban environments. Characterising the
 composition of their diet can therefore reveal how they exploit
 anthropogenic resources and uncover new foraging behaviours. However,
 accurately determining their diet through direct observation can be
 challenging, especially in semi-urban areas where numerous anthropogenic
 structures obstruct visibility. Environmental DNA (eDNA) has been proposed
 as a non-invasive complementary method to determine diet and foraging
 strategies by analysing the DNA mixtures present in faecal samples. In
 this study, we determined the dietary components of vervet monkeys using
 DNA metabarcoding of 447 faecal samples collected from two monkey groups
 over four months in a semi-urban neighbourhood in South Africa, and
 compared the results with observational foraging data to elucidate how
 vervet monkeys exploit anthropogenic resources. Subsequently, we evaluated
 whether dietary patterns can be distinguished between groups and within
 matrilineal levels. We found DNA metabarcoding data to be consistent with
 observational data, but the former revealed a broader diversity of
 consumed taxa. Additionally, we detected a difference in diet between the
 two groups, and a tendency for similar dietary patterns among matrilineal
 pairs compared to other group members. Our results support the use of the
 DNA metabarcoding methodology, both to determine the complex diet of
 omnivorous species in urbanised habitats and to address interindividual
 foraging behaviours.
description: DNA extraction: DNA was extracted from faecal samples using a
 phosphate buffer-based approach (Taberlet et al., 2018), based on the
 protocol from the NucleoSpin Soil Kit (Macherey-Nagel), with the following
 modifications. The faeces in the scintillation vials were directly
 transferred to 2 mL Eppendorf tubes with 1.3 mL of phosphate buffer. The
 samples were placed on a tube rotator for 15 minutes to facilitate DNA
 absorption and later homogenised by vortexing. The samples were then
 centrifuged for 5 minutes. The subsequent steps of the extraction required
 the use of QIAvac technology (Qiagen). DNA extractions were performed in a
 dedicated laboratory designed for handling low-template DNA samples
 (Laboratory for Conservation Biology, University of Lausanne). For
 subsequent analyses, all DNA extracts were dilutedfivefold.
 DNA metabarcoding assay: DNA extracts were amplified in
 triplicate using two sets of primers, one for plants and one for
 vertebrates. The first primer pair (Sper01) targets plant components of
 the diet by amplifying the P6 loop of the trnL (UAA) intron of chloroplast
 DNA (10-220 bp; Taberlet et al., 2018). The second primer pair (Vert01)
 amplifies a fragment of the mitochondrial rDNA 16S, and is highly specific
 for vertebrates (56-132 bp; Taberlet et al., 2018). For the latter, a
 blocking oligonucleotide
 (5'-CTATGCTTAGCCCTAAACCTCAGTAGTTAAACCAACAAAACTACT-C3-3') was
 added to specifically inhibit the amplification of vervet monkey DNA. PCR
 primers included 5? tags, consisting of an 8-nucleotide sequence with at
 least 3 nucleotide differences between each tag, are used for assigning
 sequences to their respective sample. PCR reactions were performed in a
 final volume of 20 µL in 96-well plates. For the Sper01 primers, the mix
 contained: 1× AmpliTaq Gold 360 (Applied Biosystems), 0.5 ?M of forward
 and reverse primers, 0.16 mg/mL of Bovine Serum Albumin (BSA; Roche
 Diagnostics), and 2 µL of template DNA. For the Vert01 primers, the mix
 contained 1 × AmpliTaq Gold 360 (Applied Biosystems), 0.2 ?M of forward
 and reverse primers, 0.16 mg/mL of Bovine Serum Albumin (BSA; Roche
 Diagnostics), 2 ?M of blocking oligonucleotide, and 2 µL of template DNA.
 PCR cycling conditions were 10 minutes at 95°C, followed by 40 cycles of
 30 seconds at 95°C, 30 seconds at 52°C or 49°C (for Sper01 and Vert01,
 respectively), and 60 seconds at 72°C, with a final extension of 7 minutes
 at 72°C and 10 minutes at 4°C. For each PCR plate, a negative extraction
 control, a negative PCR control (ultrapure water), positive controls, and
 blanks were included. Positive controls contained DNA of known
 concentration from plant or vertebrate species not expected at the study
 site, serving to validate the amplification success (Table S5).
 Amplification success was verified by 2% agarose gel electrophoresis for a
 subset of samples. Finally, PCR products for each primer pair were pooled
 for library preparation. DNA sequencing: Amplicons were
 purified using the MinElute PCR Purification Kit (Qiagen) and quantified
 with a Qubit 4 Fluorometer (Invitrogen). Fragment sizes and relative
 abundance of the amplicons were quantified using a Fragment Analyzer
 (Agilent Technologies). Libraries were then prepared using a protocol
 based on the TagSteady approach (Carøe & Bohmann, 2020). Library
 quantification was performed using a qPCR Real-Time System (Bio-Rad) to
 ensure accurate quantification. Following quantification, the size of the
 DNA fragments in the libraries was measured again using a Fragment
 Analyzer. Sequencing was performed on an Illumina MiniSeq System, using
 the Mid Output Kit, generating 8 million 150 bp paired-end
 reads. Local plant database: A list of plants present
 in the study area and potentially consumed by vervet monkeys was
 established based on input from local botanical experts. For each of these
 plants, we verified their presence in GenBank. Those that were missing or
 had low alignment scores to the targeted metabarcode (Identity
 &lt;98%, Coverage &lt;70%, E-value &gt;5) were identified
 morphologically in the field and collected for later sequencing, to create
 a custom database for the missing elements. In total, 37 plant species
 were sampled (Table S4). For each species, two pieces of one cm² leaf
 fragments were dried with silica gel beads in 20 mL HDPE scintillation
 vials (Carl Roth GmbH) and stored until DNA extraction, except for nine
 succulent plant species, which were preserved in 95% ethanol. DNA
 extraction was performed using the DNeasy Plant Mini Kit (Qiagen). PCR
 reactions were then carried out on the entire chloroplast trnL (UAA)
 intron region using primers c and d (Taberlet et al., 2007). They were
 performed in a total volume of 25 µL, containing: 1 × PCR Gold Buffer
 (Thermo Fisher Scientific), 2 mM of MgCl2, 0.2 mM of dNTPs, 0.5 ?M of
 forward and reverse primers, 1 U of AmpliTaq Gold 360 (Applied
 Biosystems), and 2 µL of template DNA diluted 250-fold. PCR cycling
 conditions consisted of an initial denaturation of 5 minutes at 95°C
 following by 45 cycles of 30 seconds at 95°C, 30 seconds at 5°C, and 60
 seconds at 72°C, with a final elongation of 5 minutes at 72°C.
 Subsequently, purification and Sanger sequencing were conducted at
 Microsynth AG (Balgach, Switzerland). The sequences were aligned using
 MEGA11 v. 11.0.13 (Tamura et al. 2021; Figure S1).
 Bioinformatics processing: Sequencing results from each library
 were handled separately using the OBITools package (Boyer et al., 2016).
 First, forward and reverse reads were assembled with a minimum quality
 score of 40 and assigned to each corresponding sample based on unique tags
 and primers. Identical sequences were then clustered. Sequences that could
 not be aligned, as well as those with fewer than 10 reads per library or
 those not meeting the appropriate primer length,h were removed. After
 correcting for PCR/sequencing errors, remaining clusters were reduced
 based on a 97% similarity threshold using the sumaclust algorithm (Mercier
 et al., 2013). Taxonomic assignment of sequences was based on three
 sources: the local plant database we created (see above), and two
 databases generated from in silico PCR simulations using our two sets of
 primers with a 95% similarity threshold. These simulations were queried
 against the GenBank database maintained by the National Center for
 Biotechnology Information (NCBI) using the ecoPCR software (Ficetola et
 al., 2010). Additionally, each operational taxonomic unit (OTU) identified
 for Sper01 and Vert01 was manually verified using BLAST on GenBank to
 confirm the results. Further sequence cleaning and analyses were conducted
 using the metabaR package (Zinger et al., 2021). In addition, because
 experiments involving peanuts as food rewards were conducted during the
 study period, we removed all DNA reads assigned to the o genus Arachis in
 the faecal samples collected the day after these experiments took
 place.
description: # Data from: Investigating anthropogenic and social influences on diet of
 semi-urban vervet monkeys using DNA metabarcoding ## Description of the
 data and file structure Date of data collection: August 2023 to December
 2023 Geographic location of data collection: Ballito, South Africa Funding
 sources that supported the collection of the data: Swiss National Science
 Foundation, Finnish KONE Foundation, and UZH Förderung des Akademischen
 Nachwuchses, Gebauer Stiftung #### DATA & FILE OVERVIEW 1\.
 Description of the dataset In human-dominated ecosystems, wildlife has
 been forced either to disappear or to adapt its behaviour in order to
 exploit the opportunities associated with anthropogenic activities. Vervet
 monkeys(Chlorocebus pygerythrus) are omnivorous primates whose natural
 habitats have been progressively encroached upon by expanding suburban
 development. Due to their generalist and opportunistic feeding behaviour,
 vervet monkeys have successfully adapted to semi-urban environments.
 Characterising the composition of their diet can therefore reveal how they
 exploit anthropogenic resources and uncover new foraging behaviours.
 However, accurately determining their diet through direct observation can
 be challenging, especially in semi-urban areas where numerous
 anthropogenic structures obstruct visibility. Thus, we determined the
 dietary components of vervet monkeys using DNA metabarcoding of faecal
 samples collected from three monkey groups between August and December
 2023 in a semi-urban neighbourhood in Ballito, South Africa. Then, we
 compared the results with observational foraging data to elucidate how
 vervet monkeys exploit anthropogenic resources. We evaluated whether
 dietary patterns can be distinguished between groups and within
 matrilineal levels. Sample collection Data for this study were collected
 at the Urban Vervet Project, located within the Simbithi Eco-Estate, a 4.7
 km2 private gated community in Ballito, South Africa. In total, 455 faecal
 samples were collected from 15 August 2023 to 22 December 2023 among three
 monkey groups (Acacia, Savanna, and Cats Whiskers). However, only 8
 samples belonged to the Cats Whiskers group. Each sample was collected
 within 15 minutes of defecation to limit the impact of external
 contaminants and then placed into 95% ethanol for 24-48 hours before being
 dried with silica gel beads and stored until DNA extraction. Faecal
 samples were not re-collected from individuals who had already been
 sampled on the same day. For the observational data, individuals were
 followed for 20 minutes, and their actions and interactions were recorded
 in a continuous way. If the focal individual was out of sight for a total
 of more than five minutes, the focal was aborted. Individuals were
 opportunistically chosen during three different time slots of the day
 (morning, noon, and afternoon) to achieve at least one successful focal
 sample per individual per time slot each month to have a balanced dataset
 through the day and a similar amount of observation for each individual.
 Monkeys were followed from sunrise to sunset, and GPS locations were
 obtained by the observers using a handheld GPS, which was set up to record
 locations continuously. Ad libitum data consist of spontaneous
 observations of behaviours related to anthropogenic interactions. We also
 collected some indigenous plant species to create a local database for the
 species not present in GenBank. The plants were either dried with silica
 gel beads or placed into 95% ethanol, depending on their morphology, and
 stored until DNA extraction. 2\. File List: File name:
 Sper01-1_S1_L001_R1_001.fastq Description: Forward reads of first-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-1_S1_L001_R2_001.fastq Description: Reverse reads of first-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-2_S2_L001_R1_001.fastq Description: Forward reads of second-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-2_S2_L001_R2_001.fastq Description: Reverse reads of second-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-3_S3_L001_R1_001.fastq Description: Forward reads of third-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-3_S3_L001_R2_001.fastq Description: Reverse reads of third-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-4_S4_L001_R1_001.fastq Description: Forward reads of fourth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-4_S4_L001_R2_001.fastq Description: Reverse reads of fourth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-5_S5_L001_R1_001.fastq Description: Forward reads of fifth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-5_S5_L001_R2_001.fastq Description: Reverse reads of fifth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-6_S6_L001_R1_001.fastq Description: Forward reads of sixth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-6_S6_L001_R2_001.fastq Description: Reverse reads of sixth-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-7_S7_L001_R1_001.fastq Description: Forward reads of seventh-plate
 sequences amplified using the Sper01 primer File name:
 Sper01-7_S7_L001_R2_001.fastq Description: Reverse reads of seventh-plate
 sequences amplified using the Sper01 primer File name:
 Vert01-1_S8_L001_R1_001.fastq Description: Forward reads of first-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-1_S8_L001_R2_001.fastq Description: Reverse reads of first-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-2_S9_L001_R1_001.fastq Description: Forward reads of second-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-2_S9_L001_R2_001.fastq Description: Reverse reads of second-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-3_S10_L001_R1_001.fastq Description: Forward reads of third-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-3_S10_L001_R2_001.fastq Description: Reverse reads of third-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-4_S11_L001_R1_001.fastq Description: Forward reads of fourth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-4_S11_L001_R2_001.fastq Description: Reverse reads of fourth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-5_S12_L001_R1_001.fastq Description: Forward reads of fifth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-5_S12_L001_R2_001.fastq Description: Reverse reads of fifth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-6_S13_L001_R1_001.fastq Description: Forward reads of sixth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-6_S13_L001_R2_001.fastq Description: Reverse reads of sixth-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-7_S14_L001_R1_001.fastq Description: Forward reads of seventh-plate
 sequences amplified using the Vert01 primer File name:
 Vert01-7_S14_L001_R2_001.fastq Description: Reverse reads of seventh-plate
 sequences amplified using the Vert01 primer File name: ngs_Sper01_1.txt
 Description: File to associate the first-plate sequences amplified using
 the Sper01 primer with each individual sample using the forward and
 reverse unique tag combinations File name: ngs_Sper01_2.txt Description:
 File to associate the second-plate sequences amplified using the Sper01
 primer with each individual sample using the forward and reverse unique
 tag combinations File name: ngs_Sper01_3.txt Description: File to
 associate the third-plate sequences amplified using the Sper01 primer with
 each individual sample using the forward and reverse unique tag
 combinations File name: ngs_Sper01_4.txt Description: File to associate
 the fourth-plate sequences amplified using the Sper01 primer with each
 individual sample using the forward and reverse unique tag combinations
 File name: ngs_Sper01_5.txt Description: File to associate the fifth-plate
 sequences amplified using the Sper01 primer with each individual sample
 using the forward and reverse unique tag combinations File name:
 ngs_Sper01_6.txt Description: File to associate the sixth-plate sequences
 amplified using the Sper01 primer with each individual sample using the
 forward and reverse unique tag combinations File name: ngs_Sper01_7.txt
 Description: File to associate the seventh-plate sequences amplified using
 the Sper01 primer with each individual sample using the forward and
 reverse unique tag combinations File name: ngs_Vert01_1.txt Description:
 File to associate the first-plate sequences amplified using the Vert01
 primer with each individual sample using the forward and reverse unique
 tag combinations File name: ngs_Vert01_2.txt Description: File to
 associate the second-plate sequences amplified using the Vert01 primer
 with each individual sample using the forward and reverse unique tag
 combinations File name: ngs_Vert01_3.txt Description: File to associate
 the third-plate sequences amplified using the Vert01 primer with each
 individual sample using the forward and reverse unique tag combinations
 File name: ngs_Vert01_4.txt Description: File to associate the
 fourth-plate sequences amplified using the Vert01 primer with each
 individual sample using the forward and reverse unique tag combinations
 File name: ngs_Vert01_5.txt Description: File to associate the fifth-plate
 sequences amplified using the Vert01 primer with each individual sample
 using the forward and reverse unique tag combinations File name:
 ngs_Vert01_6.txt Description: File to associate the sixth-plate sequences
 amplified using the Vert01 primer with each individual sample using the
 forward and reverse unique tag combinations File name: ngs_Vert01_7.txt
 Description: File to associate the seventh-plate sequences amplified using
 the Vert01 primer with each individual sample using the forward and
 reverse unique tag combinations File name: Metadata_UrbVer.csv
 Description: Metadata file related to the scat samples after lab
 manipulations. Provides on the ID for each replicate, the library number,
 the sample ID and the sample type. File name: Faecal_data.CSV Description:
 Metadata file of faecal samples, including individual information and
 field details related to the samples during the collection period. File
 name: Focal_data.CSV Description: Metadata file of focal data.Provides
 information on all observed behaviours and observer details over the
 course of each focal observation. File name: Adlibitum_data.CSV
 Description: Metadata file of monkeys' anthropogenic interactions.
 Provides specific details on the behaviour, interaction, conditions,
 consequences, and individuals. File name: 24PUVP_01_70120_C.fasta
 Description: Sequence for Albizia adianthifolia File name:
 24PUVP_03_70120_C.fasta Description: Sequence for Antidesma venosum File
 name: 24PUVP_04_70120_C.fasta Description: Sequence for Syzygium cordatum
 File name: 24PUVP_05_70120_C.fasta Description: Sequence for Mimusops
 caffra File name: 24PUVP_06_70120_C.fasta Description: Sequence for
 Garcinia gerrardii File name: 24PUVP_07_70120_C.fasta Description:
 Sequence for Xylotheca kraussiana File name: 24PUVP_15_Sper_g.fasta
 Description: Sequence for Aloe marlothii File name:
 24PUVP_16_70120_C.fasta Description: Sequence for Cussonia sphaerocephala
 File name: 24PUVP_17_70120_C.fasta Description: Sequence for Ficus
 burtt-davyi File name: 24PUVP_18_70120_C.fasta Description: Sequence for
 Sideroxylon inerme File name: 24PUVP_19_70120_C.fasta Description:
 Sequence for Leonotis leonurus File name: 24PUVP_21_70120_C.fasta
 Description: Sequence for Ficus lutea File name: 24PUVP_23_70120_C.fasta
 Description: Sequence for Ficus polita File name: 24PUVP_24_70120_C.fasta
 Description: Sequence for Cussonia zuluensis File name:
 24PUVP_25_70120_C.fasta Description: Sequence for Ficus trichopoda File
 name: 24PUVP_26_70120_C.fasta Description: Sequence for Macaranga capensis
 File name: 24PUVP_27_70120_C.fasta Description: Sequence for Syzygium
 gerrardii File name: 24PUVP_29_70120_C.fasta Description: Sequence for
 Carpobrotus dimidiatus File name: 24PUVP_30_70120_C.fasta Description:
 Sequence for Cordia caffra File name: 24PUVP_31_70120_C.fasta Description:
 Sequence for Dovyalis longipsina File name: 24PUVP_32_70120_C.fasta
 Description: Sequence for Dombeya rotundifolia File name:
 24PUVP_33_70120_C.fasta Description: Sequence for Eugenia capensis File
 name: 24PUVP_34_70120_C.fasta Description: Sequence for Hibiscus
 pedunculatus File name: 24PUVP_35_70120_C.fasta Description: Sequence for
 Teclea gerrardii File name: 24PUVP_36_70120_C.fasta Description: Sequence
 for Searsia gueinzii File name: 24PUVP_37_70120_C.fasta Description:
 Sequence for Mimusops obovata File name: 24PUVP_38_70120_C.fasta
 Description: Sequence for Ficus burkei File name: 24PUVP_39_70120_C.fasta
 Description: Sequence for Jasminum multipartitum DATA-SPECIFIC INFORMATION
 FOR: Faecal_data.csv 1\. Number of variables: 18 2\. Number of cases/rows:
 455 3\. Date: Date of sample collection * Time: Time of sample defecation
 * Group: Name of the monkey group for the sample * Data: Sample origin *
 IDFaecalSample: Name of the monkey for the sample * Sex: Sex of the monkey
 for the sample * Age: Age of the monkey for the sample * TimeCollected:
 Time of sample collection * Collector: Name of sample collector * ExpDay:
 States whether other experiments were done during sample defecation *
 DateProcessed: Date when the sample was dried with silica gel beads *
 TimeProcessed: Time when the sample was dried with silica gel beads *
 SampleNb: Sample number * Processor: Name of the person who dried the
 sample * Remarks: Remarks concerning the sample * Genetic: States whether
 a portion of the feces was also used for genetic analysis * DataInfo:
 Supplementary information about the data * DeviceId: ID of the device used
 to collect the data 4\. Missing data codes: None DATA-SPECIFIC INFORMATION
 FOR: Focal_data.csv 1\. Number of variable: 50 2\. Number of cases/rows:
 63946 3\. Variable list: * Date: Date of focal behaviour * Time: Time of
 focal behaviour * Group: Name of the monkey group for the focal behaviour
 * TimeZone: Time slots for focal behaviour. TimeZone1 is for morning
 period, TimeZone2 for noon period, and TimeZone3 for afternoon period *
 Data: Sample origin * Observer1: Name of the observer for the focal
 behaviour * Interobs: States whether a switch of observer occurred during
 the focal * IDFocal: Name of the monkey for focal behaviour * Behaviour:
 Category of behaviour. START and STOP indicate the beginning and the end
 of a focal, respectively * HabitatType: Habitat type during the focal *
 Baby: For a focal of a baby, indicates its situation with its mother *
 BehaviourType: Behaviour of the monkey * BehaviourFocal: Behaviour details
 during interaction between the focal monkey and another individual *
 IDIndividual2: Name of the monkey who interacts with the focal monkey *
 Interaction: Describes who started and ended the interaction * Complete:
 For sexual interaction, indicates whether the sexual behaviour was
 completed * AgonisticInteraction: For agonistic interaction, indicates
 whether support was given, and to whom * IDSupporters: For agonistic
 behaviour, indicates the name of the supporters if supporting *
 SupportersBehaviour: For agonistic behaviour, indicates behaviour details
 of the supporters if supporting * VictimSupResponse: For agonistic
 behaviour, indicates behaviour details of the supported victim *
 VictimRedResponse: For agonistic behaviour, indicates behaviour details of
 the redirected victim if redirection * IDInterruptor: Name of the
 interruptor during sexual behaviour * BehaviourInterruptor: Behaviour
 details of the interruptor * ResponseFocal: Behaviour details of the focal
 monkey * ResponsePartner: Behaviour details of the focal monkey’s partner
 * BehaviourFocal2: For affiliative behaviour, indicates behaviour details
 of the focal monkey with a second individual * IDIndividual3: Name of the
 second individual interacting with the focal monkey during affiliative
 behaviour * Interaction2: For affiliative behaviour, describes who started
 and ended the interaction between the focal monkey and the second
 individual * BehaviourFocal3: For affiliative behaviour, indicates
 behaviour details of the focal monkey with a third individual *
 IDIndividual4: Name of the third individual interacting with the focal
 monkey during affiliative behaviour * Interaction3: For affiliative
 behaviour, describes who started and ended the interaction between the
 focal monkey and the third individual * VPosture: For vigilant behaviour,
 indicates the posture of the focal monkey * VHeight: For vigilant
 behaviour, indicates the height of the focal monkey * VPosition: For
 vigilant behaviour, indicates the position of the focal monkey compared to
 the core of its group * FoodItem: For feeding behaviour, indicates the
 type of food consumed by the focal monkey * OtherFood: Indicates what food
 the focal monkey obtained from human interaction * Species: Indicates the
 species of natural plant consumed by the focal monkey * TreeItems:
 Indicates which part of the tree was consumed by the focal monkey *
 Object: Indicates which object the focal monkey was interacting with *
 Reason: Indicates the rare behaviour * CallType: For alarm behaviour,
 indicates the call type * Threat: For alarm behaviour, indicates what
 caused the focal monkey to give an alarm * ThreatMoving: States whether
 the threat was moving or not * PlayType: Indicates with what the focal
 monkey was playing * FocalBehav: For play behaviour, indicates behaviour
 details of the focal monkey (from 2024) * BehaviourIndiv1: For play
 behaviour, indicates behaviour details of the focal monkey (before 2024) *
 IDPartner: For play behaviour, indicates who the focal monkey interacts
 with * Remarks: Remarks for the focal behaviour * DataInfo: States whether
 the focal was aborted * DeviceId: ID of the device used to collect the
 data 4\. Missing data codes: None 5\. Abbreviations used: NA: not
 applicable pr: present gr: groom mc: muzzle contact pl: play pm: play
 mount wr: wrestle cw: chewing sg: sit in contact sw: sleep with to: touch
 em: embrace ca: carry infant ci: cling incorrectly cf: chew fingers gi:
 groom infant ii: infant inspect ih: infant handling lu: lift up nu: nurse
 pa: push away rb: retrieve baby rd: ride wt: walk on top ls: lipsmack tc:
 teeth-chattering fo: follow sm: smell li: lick ap: approach wb: walk by
 at: attack st: stare bd: broad side display bi: bite cr: crawl fm: feed
 from mouth gb: grab hb: head-bob hh: head-on-head hi: hit om: open-mouth
 threat sf: steal food so: sit on others tp: take place fl: flee ba: bark
 fh: frustration hop fi: fight ja: jump aside lo: look around ss:
 self-scratch le: leave rt: retreat av: avoid su: stand up sc: scream vo:
 vocalise ya: yawn bs: bite sexual hg: hip grab is: inspect sexual parts
 bb: bite balls mu: mount ma: masturbation rf: refuse ag: auto-groom as:
 auto-smell DATA-SPECIFIC INFORMATION FOR: Adlibitum_data.csv 1\. Number of
 variables: 29 2\. Number of cases/rows: 624 3\. Variable list: * Date:
 Date of the event * Time: Time when the event was registered * Group:
 Group of the monkey(s) involved in the event * Data: Name of the data *
 StartTime: Time when the event started * Location: Name of the place where
 the event happened * HabitatType: Type of the habitat where the event
 happened * DistanceBuilding: Distance between the monkey(s) and the
 closest building when the event happened * IDActors: Name of the monkey(s)
 involved in the event * Interactions: Type of interaction for the event *
 PositiveInteraction: If positive interaction, indicates how the monkey(s)
 obtained food for the event * FoodObtained: Type of food obtained by the
 monkey(s) for the event * FoodStatus: Status of the food for the event *
 FoodQuantity: Quantity of food obtained for the event * OtherFood: Details
 of food consumed by the monkey(s) for the event * MethodsUsed: If negative
 interaction, indicates how humans attempted to chase the monkey(s) *
 MonkeysResponse: If negative interaction, indicates the behaviour details
 of the monkey(s) * OtherResponse: If negative interaction, describes the
 other method used by humans to chase the monkey(s) * Interaction: If
 interaction with urbanisation, indicates the type of interaction specific
 to this category * ArtefactUsed: If interaction with an artefact,
 indicates the type of artefact * OtherArtefact: If interaction with an
 artefact, describes the other artefact * ObjectUsed: If interaction with
 an object, indicates the type of object * MonkeysBehav: Behaviour details
 of the monkey(s) for an event involving urbanisation * OtherObject: If
 interaction with an object, describes the other object * OtherBeahv: If
 urbanisation event, indicates the other behaviour the monkey(s) displayed
 * DurationHV: Approximate duration of the event * Remarks: Remarks of the
 event * DataInfo: Information concerning the data statement of the event *
 DeviceId: ID of the device used to collect the data 4\. Missing data
 codes: None 5\. Abbreviations used: NA; not applicable Rt; retreating Ag:
 auto-groom DATA-SPECIFIC INFORMATION FOR: Metadata_UrbVer.csv 1\. Number
 of variables: 4 2\. Number of cases/rows: 3648 3\. Variable list: *
 Sample_ID: Name of the sample replicate * library: Library number *
 sample: Sample name * sample_type: Type of the sample 4\. Missing data
 codes: None DATA-SPECIFIC INFORMATION FOR: ngs_Sper01_1.txt +
 ngs_Sper01_2.txt + ngs_Sper01_3.txt + ngs_Sper01_4.txt + ngs_Sper01_6.txt
 + ngs_Sper01_7.txt + ngs_Vert01_1.txt + ngs_Vert01_2.txt +
 ngs_Vert01_3.txt + ngs_Vert01_4.txt + ngs_Vert01_6.txt + ngs_Vert01_7.txt
 1\. Number of variables: 7 2\. Number of rows: 288 3\. Variable list: *
 Column1: Experiment name * Column2: Replicate name * Column3: Forward tag
 : Reverse tag * Column4: Forward primer * Column5: Reverse primer *
 Column6: “F” – needed to run Obitools * Column7: Position in the plate
 DATA-SPECIFIC INFORMATION FOR: ngs_Sper01_5.txt + ngs_Vert01_5.txt 1\.
 Number of variables: 7 2\. Number of rows: 96 3\. Variable list: *
 Column1: Experiment name * Column2: Replicate name * Column3: Forward tag
 : Reverse tag * Column4: Forward primer * Column5: Reverse primer *
 Column6: “F” – needed to run Obitools * Column7: Position in the plate
 INSTRUCTIONS TO PROCESS RAW SEQUENCING OUTPUT 28 sequencing files, 7
 libraries for 2 primers, 2 files for each library 1\. Join paired ends to
 have an aligned dataset 2. Use ngs_files for each library for a specific
 primer to assign sequences to each sample 3. Use the metadata files to
 assign samples to each individual. All empty cells and any cells
 containing NA represent missing data.