Abstract
In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.
Highlights
Turtles are among the most iconic of vertebrate lineages, yet the genomic basis for their unique adaptive evolutionary biology is just starting to be investigated with modern highthroughput DNA diagnostics, especially those species that have evolved fully pelagic marine life histories
Reference-based calling methods using Ch. mydas produced the greatest number of filtered loci (24,616–119,653) and Single-nucleotide polymorphisms (SNPs) (5,018–6,998) called compared with Chr. picta reference-based method with consideration of sea turtles as either a single group or two separate groups for population genetics analyses
We describe the application of a SNP calling pipeline to Atlantic loggerhead sea turtles that identifies loci in linkage disequilibrium and potentially sex-specific loci, calculates population genetics statistics, and assesses population structure
Summary
Turtles are among the most iconic of vertebrate lineages, yet the genomic basis for their unique adaptive evolutionary biology is just starting to be investigated with modern highthroughput DNA diagnostics, especially those species that have evolved fully pelagic marine life histories. Most species of sea turtle share similar lifecycles involving a juvenile pelagic phase and subadult neritic developmental phase (Luschi et al 2003).
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