The Scramble for Africa in the late 1800s marked the beginning of increased human population growth in Africa. Here, we determined the genetic architecture of both historical and modern lions to identify changes in genetic diversity that occurred during this period of landscape and anthropogenic change. We surveyed microsatellite and mitochondrial genetic variation from 143 high-quality museum specimens of known provenance and combined them with data from recently published nuclear and mitochondrial studies. Analysis of variation at 9 microsatellites and 280 polymorphic mitogenome SNPs indicate the presence of male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd=0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of fine structure in modern populations, able to detect most sampling locations. Mitochondrial analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as subpopulations became more differentiated, while mitochondrial structure and diversity was maintained over time.
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