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

Cite this dataset

Austin, James et al. (2021). Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus) [Dataset]. Dryad.


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.


Genotypes were generated from 22 loci, 21 of which were designed specifically from Eumops floridanus. We used PacBio sequences on size selected fragments then search for repeat motifs with sufficient flanking regions to design primers. Methods followed those in Saaranin and Austin 2010 (J Hered 101:784–788

Usage notes

Multilocus genotypes are provided in a simple text file in Genepop format.

Populations are in order of names in heading line, and correspond to the abbreviations given in the manuscript. Missing genotypes are presented as 000000.


Florida Fish and Wildlife Conservation Commission

National Institute of Food and Agriculture, Award: 1018767