Spatiotemporal Genetic Diversity of Lions

Abstract

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 finescale nuclear genetic structure and loss of genetic diversity as subpopulations became more differentiated, while mitochondrial structure and diversity was maintained over time.

A kingdom in decline: Holocene range contraction of the lion (Panthera leo) modelled with global environmental stratification

“…Our modelling indicates that through the pluvial/interpluvial cycles of the Holocene the sub-Saharan range of lions has always been contiguous, and so we have no evidence for any significant gaps between populations caused by depopulated zones of climatically unfavourable terrestrial habitat. An analysis of nuclear DNA from historical samples of lions ( Curry et al, 2020 ) supports contiguity amongst modern lion populations (but not amongst present day fragmented populations), but mitochondrial DNA (mtDNA) suggests regional subdivisions. This reflects sex-biased dispersal amongst lions, with males dispersing from natal prides while females remain resident.…”

“…Sex-biased dispersal implies that something else has created barriers to female lion dispersal between Western African and Eastern/Southern African populations. This is significant given the pre-Holocene mtDNA divergence amongst these lion populations ( Antunes et al, 2008 ; Barnett et al, 2014 ; Bertola et al, 2016 ; De Manuel et al, 2020 ; Curry et al, 2020 ), and numerous other large mammalian grassland/savanna species ( Bertola et al, 2016 ). Thus, patterns of regional climate alone are not able to explain longer-term genetic divergence between populations.…”

“…The position of major rivers through Africa, in addition to contractions of suitable habitat driven by climate change, are the likely causes of vicariance over 100ka. Suture zones and parapatric (sub)speciation are likely important in maintaining genetic variation ( Bertola et al, 2016 ; Curry et al, 2020 ; Curry, White & Derr, 2019 ; Dures et al, 2020 ). The persistence of major river barriers/corridors in the region, appears to have major biogeographical legacies in terms of defining boundaries between populations and linkage between areas.…”