Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)

Knowledge of genetic structure is essential for the long-term management
and conservation of endangered species. We report the results from a
genetic examination of the federally endangered Florida bonneted bat
(Eumops floridanus) sampled from its range in southern Florida, USA.
Bonneted bats are primarily found in four regions separated by
approximately 100 to 250 kms, including three western natural areas (BW,
PC, and CC) and one urban population on the east coast [Miami-Dade County
(MD)]. We used 22 microsatellite loci and cytochrome b sequences to assess
the extent of connectivity and levels of genetic diversity. Regional
populations were highly differentiated (FST = 0.178) and model-based and
multivariate analyses showed that MD was the most distinct among pairwise
comparisons. Regional populations are small (i.e., Ne < 100) but
demographically stable. Estimates of contemporary migration and historic
gene flow suggest that regional populations do not frequently exchange
migrants, but simulations suggest that the divergence among western
regions is likely a result of recent genetic drift rather than long-term
isolation. Significantly, mitochondrial DNA revealed that haplotypes from
MD were similar or shared with those recognized as Eumops ferox from Cuba
and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in
Florida. Our data support the management of each of the four populations
as distinct population segments, and that BW, PC and CC combined are on an
independent evolutionary trajectory from bats in MD. Critically, bonneted
bats in Florida appear to harbor cryptic diversity that will require a
reassessment of their taxonomy.