Eastern Box Turtle Genetics

RCN Topic: 
Job 5: Eastern Box Turtle Genetics
RCN PHASE 2; PROJECT 1 TURTLES; JOB 5 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 ftom The Turtle Survival Alliance (TSA). The TSA project to develop a barcoding
system using genetic samples collected across the range. The RCN fonds 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 constitate 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 ftom
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 asequencing run while maintaining the original identity.

 

Progress Reports

PDF icon 2022 3rd Qtr GSA 00046 Amend 3

Final Reports

PDF icon GSA 00046 Amend 3 INTERIM Report

GSA Information

GSA Number: GSA 00046 Amend 5

GSA Title: Eastern Box Turtle Genetics

GSA Contractor: The Mid-Atlantic Center for Herpetology and Conservation