Dispersal abilities play a crucial role in shaping the extent of
population genetic structure, with more mobile species being panmictic
over large geographic ranges and less mobile ones organized in
meta-populations exchanging migrants to different degrees. In turn,
population structure directly influences the coalescence pattern of the
sampled lineages, but the consequences on the estimated variation of the
effective population size (Ne) over time obtained by means of
unstructured demographic models remain poorly understood.
However, this knowledge is crucial for biologically interpreting the
observed Ne trajectory and further devising conservation strategies in
endangered species. Here we investigated the demographic history of four
shark species (Carharhinus melanopterus, Carharhinus limbatus,
Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of
endangered status and life history traits related to dispersal
distributed in the Indo-Pacific and sampled off New Caledonia. We
compared several evolutionary scenarios representing both
structured (meta-population) and unstructured models and
then inferred the Ne variation through time. By performing
extensive coalescent simulations, we provided a general framework
relating the underlying population structure and the observed Ne
dynamics. On this basis, we concluded that the recent decline observed
in three out of the four considered species when assuming
unstructured demographic models can be explained by the presence
of population structure. Furthermore, we also demonstrated the limits of
the inferences based on the sole site frequency spectrum and warn that
statistics based on linkage disequilibrium will be needed to exclude
recent demographic events affecting meta-populations.
The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History
