Reynolds Lab Genotyping-By-Sequencing Protocol [download here]. This protocol is described in Quach, Reynolds, and Revell (in review).
1.1: 5’ ACACTCTTTCCCTACACGACGCTCTTCCGATCTAATGTGCA
[bc] [SBFI overhang]
1.2: 3’ TGTGAGAAAGGGATGTGCTGCGAGAAGGCTAGATTAC
[RC 1.1] [RC 1.1] [RC bc]
2.1: 5’ AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
2.2: 3’ ACGTTCTAGCCTTCTCGCCAAGTCGTCCTTACGGCTC
Please cite accordingly or contact me if these have been useful for you!
R Package Development
Collaborator: Ben Fitzpatrick (UTK)
Package DPR: Reynolds 2011; Reynolds and Fitzpatrick 2011
Conduct Decomposed Pairwise Regression analyses (Koizumi et al. 2006) for one or more datasets (multiple simulations) consisting of structured demes to identify outliers which are not in mutation-drift equilibrium.
Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology 3:91-99
Reynolds, R.G. (2011) Islands, metapopulations, and archipelagos: genetic equilibrium and non-equilibrium dynamics of structured populations in the context of conservation. Ph.D. Dissertation, University of Tennessee. [pdf]
Reynolds, R.G. and B.M. Fitzpatrick (2011) DPR- a package to implement decomposed pairwise regression in an isolation by distance framework. R package version 1.0.
Reynolds, R.G. and B.M. Fitzpatrick (2013) Tests of two methods for identifying founder effects in metapopulations reveal substantial type II error. Genetica 141: 119-131
Reynolds, R.G., M.L. Niemiller, and B.M. Fitzpatrick (2012) Genetic analysis of an endemic archipelagic lizard reveals sympatric cryptic lineages and taxonomic discordance. Conservation Genetics 13: 953-963
Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of relationship between degree of homoplasy and fragment size. Molecular Ecology 11:139-151.
Zhivotovsky L (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology 8:907-913.