Data and R code for: Linking climate variability to demography in cooperatively breeding meerkats
Data files
Apr 10, 2025 version files 6.24 MB
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README.md
7.47 KB
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Thorley_2025_EcologicalMonographs.zip
6.23 MB
Abstract
This dryad repository contains data sets and R scripts for our Ecological Monographs (2025) paper: Linking climate variability to demography in cooperatively breeding meerkats. The aim of our study was to develop a mechanistic understanding of how variation in rainfall and temperature affect meerkat demography. Specifically, we:
- Identified the critical period during which rainfall influences vegetation productivity at the field site.
- Investigated how vegetation productivity and temperature influence meerkat foraging performance.
- Examined how these climatic variables impact daily weight fluctuations and overall body condition.
- Analyzed conditions under which meerkats fail to accumulate enough mass during foraging to offset overnight losses.
- Explored the influence of body condition on reproduction and survival.
- Projected future temperature trends and their implications for meerkat populations up to the mid and end of the century.
To achieve these aims, our study included numerous data sets and analyses which we detail in the README.
Please note that the individual, group, and litter identities have been anonymised for this study. This is to prevent anyone from trying to link different studies carried out by the Kalahari Meerkat Project, and using the data to conduct their own analyses without knowledge of how the data have been processed, or of the system from which they derive. Within our specific study, the identities are relationally-linked, so that, for example, Individual "4" is consistent across data sets.
📁 Thorley_2025_EcologicalMonographs.zip
Dataset DOI: 10.5061/dryad.2ngf1vj11
Each analysis is provided in a separate R script, with the data sets needed for each script explained in detail.
(1) Part1_RainfallNDVI_Climwin.R
- MeerkatNDVIMasked.csv
Average NDVI across the ranges of all meerkat groups (MODIS MOD13Q1).
- date
– dd/mm/yyyy
- mean_ndvi_masked
– NDVI is provided every 16 days
- MeerkatRainReserve.csv
Daily rainfall at the field site.
- date
– dd/mm/yyyy
- rain_method
– Indicates how the daily value was collected (Manual / NOAA / Station)
- rain_reserve
– Total daily rainfall (mm)
(2) Part2_ForagingPerformance.R
- MeerkatForagingData.csv
Historical data set of focal observations (1996–2001).
- IndividID
– Individual identity
- GroupRef
– Group identity
- Focal_ID
– Unique identifier for the observations
- FocalDate
– dd/mm/yyyy
- FocalYear
– Year in which the focal was conducted
- FocalMonth
– Month in which the focal was conducted
- BehavObsDuration
– Duration of the focal observation (minutes)
- numAvgHour
– Mid-point of the focal, as the hour of the day
- tempmax
– Maximum temperature on the day of the focal (°C)
- ndvi
– NDVI at the field site (GIMMS NDVI3g)
- SuccForageBoutCount
– Number of successful prey pursuits (prey captures)
- TotalDigDuration
– Time spent digging for prey (seconds)
- DigProp
– Proportion of focal time spent digging
(3) Part3_DWGandOML.R
- MeerkatWeeklyPopulationLevelDWG.csv
Population-level average daily weight gain, averaged per week.
- date
– dd/mm/yyyy
- uniqueinds
– Number of unique individuals averaged
- mean_morningmass
– Mean morning body mass (g)
- mean_massresid
– Mean residual body mass (g), referred to as body condition in the paper (i.e., deviation from individual lifetime mass trajectories)
- mean_percentmassgain
– % daily body mass gain (morning to evening), averaged over all individuals in the week
- mean_absmassgain
– Absolute daily body mass gain (g), averaged over all individuals
- ConditionChange_t_t1
– Change in average body condition from one week to the next (g)
- MeerkatIndividualDailyWeightGain.csv
Individual daily body mass gain data.
- date
– dd/mm/yyyy
- Season
– Early summer / Late summer / Winter
- IndividID
– Individual identity
- GroupRef
– Group identity
- Sex
– M / F
- DomStatus
– Dominant or subordinate individual
- BirthDate
– Date of birth (dd/mm/yyyy)
- Age_year
– Age in years
- MorningWeightTime
– Time of morning measurement (dd/mm/yyyy hh:ss)
- EveningWeightTime
– Time of evening measurement (dd/mm/yyyy hh:ss)
- MorningWeight
– Morning body mass (g)
- EveningWeight
– Evening body mass (g)
- WeightGain
– Daily body mass gain (g)
- TimeDifference
– Time between measurements (hours)
- percentmassgain
– % body mass gain (evening / morning × 100)
- GroupSize_1moavg
– Average group size in the preceding month
- tempmax
– Maximum daily temperature (°C)
- ndvi_group
– Average NDVI within the home range (MODIS MOD13Q1)
- mass_resid
– Residual body mass (g)
- MeerkatOvernightMassLoss.csv
Individual overnight body mass loss.
Combines daily weight gain (DWG) and overnight mass loss (OML) for estimating day-to-day mass changes. Columns as for MeerkatIndividualDailyWeightGain.csv
, but also:
- OvernightMassLoss_g
– Change in body mass from previous evening to morning (g)
- OvernightMassLoss_percent
– % change in body mass from previous evening to morning
- WeightChangeMorningToMorning
– Body mass change from one morning to the next (g)
(4) Part4_DistributedLagModels.R
- MeerkatDailyTemp.csv
Long-term daily temperatures from the Kuruman River Reserve.
Data collected either at the field site (_station
) or from the NOAA Climate Prediction Center (_noaa
).
- date
– dd/mm/yyyy
- tempmin_noaa
– Minimum daily temperature (°C), NOAA
- tempmax_noaa
– Maximum daily temperature (°C), NOAA
- tempmid_noaa
– Mid-range daily temperature (°C), NOAA
- tempmin_station
– Minimum daily temperature (°C), onsite
- tempmax_station
– Maximum daily temperature (°C), onsite
- MeerkatNDVIMasked.csv
(As described in Part (1))
- MeerkatWeeklyConditionAllAdults.csv
Average weekly body condition of all adults contributing data.
- week
– Week of the year
- date
– dd/mm/yyyy
- uniqueinds
– Number of distinct individuals
- weeklyresid
– Mean weekly body condition (g)
- weeklyreldev
– Proportional deviation in condition
- n_weeklyresid
– Number of weight measurements used
- Groupsize
– Average group size (incl. pups)
- Groupsize_ExcPups
– Average group size (excl. pups)
- MeerkatWeeklyCondition[SubFemales|SubMales|DomFemales|DomMales].csv
Same structure as above, separated by sex and dominance status.
(5) Part5_VitalRates.R
- MeerkatPregnancySurvival.csv
Pregnancy status and survival of individuals.
- IndividID
– Individual identity
- MonthStart
– Start of the month
- Age
– Age at month start (days)
- avgCondition
– Average monthly body condition (g); similar to mass_resid
. NA indicates that an individual is missing body mass information for that month.
- TB
– Did the female have TB? (Y / N)
- Dominant
– Was the female dominant? (Y / N)
- Died
– Did the female die during the month? (0 / 1)
- Diss
– Did the female disappear? (0 / 1)
- Preg
– Did the female fall pregnant in the month? (0 / 1). NA indicates months where the female was pregnant, thus neither 0/1.
- MeerkatLitterSuccess.csv
Weaning success of litters.
- FemaleID
– Female identifier (same as IndividID
)
- ReprodRef
– Litter identifier
- BirthDate
– Date of birth (dd/mm/yyyy)
- Age
– Age of the mother at pregnancy start (days)
- Cond7Day
– Average maternal condition (g) during week around pregnancy. NA indicates that an individual is missing body mass information for that week.
- TB
– Did the mother have TB? (Y / N)
- Dominant
– Was the mother dominant? (Y / N)
- LitterSuccess
– Were any pups weaned? (0 / 1)
(6) Part6_FutureWarmingKalahari.R
- MeerkatCMIP6Tmax.csv
Climate projections from CMIP6 EC-Earth3-CC model: number of days exceeding temperature thresholds.
- year
– Year of model output
- experiment
– historical / ssp245 (medium-risk) / ssp585 (high-risk)
- model
– Model used (EC-Earth3-CC)
- Longitude
, Latitude
– Coordinates (°)
- tmax35
– Days exceeding 35°C
- tmax37
– Days exceeding 37°C
- MeerkatCMIP6ConsecutiveTmax.csv
Same structure as above, but includes:
- Maximum number of consecutive days exceeding 35°C (maxstreak35
) and 37°C (maxstreak37
) thresholds
- data_0.cpg
,data_0.dbf
, data_0.prj
, data_0.shp
, data_0.shx
Shape files for the meerkat IUCN distribution used in plotting.
Access information
Other publicly accessible locations of the data:
The data was collected as part of a long-term study of meerkats in the southern Kalahari Desert. All methods of data collection are outlined in the paper and are also summarised in Clutton-Brock and Manser (2016). The project's data is stored on a centralised SQL database and was processed for analyses by the lead author using R.
All of the analyses are tied, directly or indirectly, to the effects of climate and/or vegetation productivity. Climate data included daily rainfall measured on-site, and temperature data taken from the NOAA Climate Prediction Centre. We also extracted future temperatures from the Coupled Model Intercomparison Project 6 (CMIP6) for two future pathways: a medium-risk scenario (SSP2-4.5) and a high-risk scenario (SSP5-8.5), which we obtained from the Copernicus Climate Change service (https://cds.climate.copernicus.eu/). We selected the EC-EARTH3-CC model from CMIP6. Vegetation productivity was assessed using NDVI from the MODIS MOD13Q1 product the GIMMS NDVI3g product.
Clutton-Brock, T.H., & Manser, M.B. (2016) Meerkat: cooperative breeding in the Kalahari. In Cooperative breeding in vertebrates. (eds, W.D. Koenig, & J.L. Dickinson), pp. 294-317. Cambridge University Press, Cambridge, UK. https://doi.org/10.1017/CBO9781107338357.018