Data from: Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

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 unstructureddemographic 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.