Eastern Box Turtle Genetics

RCN Topic
Eastern Box Turtle Genetics

The Mid-Atlantic Center for Herpetology and Conservation will create a sub-contract with Tangled Bank Inc. to genotype approximately 500 individuals across the northeastern range using single nucleotide polymorphism (SNP) markers to add to samples collected as part of an existing grant from The Turtle Survival Alliance (TSA). The TSA project to develop a barcoding system using genetic samples collected across the range. The RCN funds will increase the number of samples analyzed from the Northeast region and support an assessment to identify conservation units. The northeast data will be analyzed using Bayesian clustering analyses to identify genetic demes that will constitute biological conservation units. Biological conservation units will identify populations and metapopulations that are interacting in a biologically meaningful way. In addition, traditional population genetics information (e.g. statistics on diversity, inbreeding, differentiation, etc.) will be generated for all biological conservation units. All participants in this action will follow equipment decontamination protocols (e.g. Miller and Gray 2009; NEPARC 2014). A relatively new technique will be employed, referred to as RADcap (Hoffterg et al. 2016). RADcap combines the best features of two commonly used NGS techniques: sequence capture (Gnirke et al. 2009; Оkou et al. 2007) and restriction-site associated DNA sequencing (RADseq; Baird et al. 2008; Davey & Blaxter 2010; Davey et al. 2011; Miller et al. 2007; Peterson et al. 2012). The melding of these approaches provides an ideal combination of sufficient genetic data (hundreds to thousands of data points) with extensive geographic representation (i.e. hundreds to thousands of individuals). RADcap requires the creation of biotinylated RNA probes, which are then used as “baits” for the target loci. To identify our genome targets, we must first sequence several representatives from each target region or species, using restriction-associated digest sequencing (RADseq). Designing the baits in this way also allows us to conveniently attach our own unique tags to the sheared ends of the DNA left by the restriction enzymes. Thus, we are able to “pool” several hundred samples on a sequencing run while maintaining the original identity.