Aardvark microsatellite data for southern and east Africa

Aim: As climate change accelerates, assessing how climate shapes
gene flow and neutral and adaptive genetic differentiation on landscapes
is increasingly important. Aardvarks (Orycteropus afer) are ecologically
important in sub-Saharan Africa but are sensitive to human pressures and
increasing aridity. We used individual, population, and landscape genetic
approaches to infer the influence of landscape, climate, and potential
adaptive differences on gene flow. Location: We surveyed 8 protected and 4
privately owned areas in South Africa, 2 protected areas in Eswatini, and
one location in Kenya during 2016–2018. Methods: We developed
microsatellite markers and methods for DNA extraction from feces,
collected and genotyped fecal samples from focal areas, and estimated
genetic structure. We inferred space use from individual redetections,
tested for close relatives, and estimated genetic neighborhood distance.
We applied individual-based landscape genetic analyses at multiple scales
across South Africa to test hypotheses about genetic differentiation by
landscape resistance and potential adaptive differences. Results: We
developed 19 variable microsatellite loci and collected 253 fecal samples
from 13 focal areas. We genotyped 104 samples successfully at ≥8 loci as
needed for individual identification. Genetic structure suggested 3
regional divisions in South Africa. We detected individuals at locations
≤7.3 km distant and closely related individuals at ≤44 km; genetic
neighborhood distance was <55 km. Lower precipitation increased
landscape resistance and strongly predicted genetic differentiation at
most spatial scales. Temperature differences at sampling sites also
influenced structure, suggesting climate-associated adaptive differences.
Main Conclusions: Genetic structure of aardvarks in South Africa and
Eswatini is strongly shaped by climate, with arid areas limiting gene
flow, and reflects apparent isolation by adaptation associated with
temperature. Dispersal distances likely are <45 km. The markers we
developed will facilitate studies of space use, dispersal, population
density, or survival. Aridification will increase fragmentation and we
recommend monitoring aardvark presence as an indicator of ecosystem change
associated with aridification.