Geology topics

Dean A. Bagley

Publications and source records attributed to Dean A. Bagley.

3 recordsLinked to original sources

USGS2026

Population structure and genetic stock identification in southeastern United States loggerhead sea turtles (Caretta caretta) using genome-wide SNPs

Characterizing the genetic structure and connectivity between populations of endangered species can be used to inform management actions. In vagile species with high gene flow or recently established populations, such characterizations can be difficult to undertake using traditional genetic markers, and genetic stock identification (GSI) may be confounded by allele-sharing between populations. Loggerhead sea turtles ( Caretta caretta ) in the southeastern United States comprise seven management units (MUs) based on female philopatry inferred via mitochondrial DNA sequences, yet nuclear microsatellite data do not reflect divergence. Further, loci for accurate GSI are not currently known. To address this, we generated genome-wide single nucleotide polymorphism (SNP) data from 146 females nesting at individual sites representative of each southeastern United States MU. We found weak (F ST =0.001–0.003) but significant divergence among all MUs, with more notable divergence between the Gulf Coast and Atlantic Ocean MUs, and amongst the Atlantic Ocean MUs. We then used an iterative leave-one-out approach to identify candidate loci for GSI. This approach identified loci that could assign individuals to natal ocean basins (i.e., to the Gulf Coast or to the Atlantic Ocean), and to individual MUs within the Atlantic Ocean, with high (≥90%) success and accuracy. Analyses of genome-wide SNPs refined our understanding of the magnitude and scale of population connectivity in loggerhead turtles in the southeastern United States, and provided a foundation for the development of SNP panels for accurate, fine-scale GSI in sea turtles.

Alabama, Florida, Georgia↗

USGS2020

Green turtle mitochondrial microsatellites indicate finer-scale natal homing to isolated islands than to continental nesting sites

In highly mobile philopatric species, defining the scale of natal homing is fundamental to characterizing population dynamics and effectively managing distinct populations. Genetic tools have provided evidence of regional natal philopatry in marine turtles, but extensive sharing of maternally inherited mitochondrial control region (CR) haplotypes within regions (<500 km) often impedes identification of population boundaries. Previous CR-based analyses of Florida (USA) green turtle Chelonia mydas nesting sites detected at least 2 populations, but the ubiquity of haplotype CM-A3.1 among southern rookeries decreased the power to detect differentiation. We reassessed population structure by sequencing the mitochondrial microsatellite (short tandem repeat, mtSTR) in 786 samples from 11 nesting sites spanning 700 km from Canaveral National Seashore through Dry Tortugas National Park. The mtSTR marker subdivided CM-A3.1 into 12 haplotypes that were structured among rookeries, demonstrating independent female recruitment into the Dry Tortugas and Marquesas Keys nesting populations. Combined haplotypes provided support for recognition of at least 4 management units in Florida: (1) central eastern Florida, (2) southeastern Florida, (3) Key West National Wildlife Refuge, and (4) Dry Tortugas National Park. Recapture data indicated female nesting dispersal between islands <15 km apart, but haplotype frequencies demonstrated discrete natal homing to island groups separated by 70 km. These isolated insular rookeries may be more vulnerable to climate change-mediated nesting habitat instability than those along continental coasts and should be monitored more consistently to characterize population status. Broader application of the mtSTR markers holds great promise in improving resolution of stock structure and migratory connectivity for green turtles globally.

Florida↗

USGS2014

Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

Green turtle ( Chelonia mydas ) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA ( mtDNA ) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

Florida↗