Protocols and Data

Here are links to validated exon-primed, intron-spanning (EPIC) single copy nuclear loci for bryophytes, details about making GBS libraries in the lab, several protocols that we routinely use (written for training undergrads and new graduate students), protocols and media recipes from the CSH Emerging Model Organisms chapter on Physcomitrella patens, and a few data matrices from published papers.

EPIC primers for bryophytes

These primers work well for Ceratodon purpureus and closely related species (see McDaniel et al. 2013 and Norrell et al. 2014), and the majority are variable within species. They have also been tested on a wide variety of other mosses, including Atrichum, Bryum, Timmia, Plagiothecium, Pleurozium, Hylocomium, Orthotrichum, among others (see Patino et al. 2015) – check with Stuart for the latest on what loci work best with your taxon. Its time to move beyond ITS and chloroplast markers!

Primer sequences from McDaniel et al. 2013, Applications in Plant Sciences

GBS in the McDaniel lab

McDaniel lab standard protocols

Moss protocols (designed for P. patens but generally work on C. purpureus, and probably others)

Data matrices (see Publications for full citation)

  • Sequence alignment for McDaniel et al. 2013, Evolution
  • Sequence alignment for McDaniel et al. 2010, Evolution
  • Sequence alignment for McDaniel Shaw 2005, Molecular Ecology
  • Data matrix for McDaniel 2005, Evolution
  • Sequence alignment for McDaniel et al. 2003, Evolution