Phylogenomics in the Hard Pines (Pinus subsection Ponderosae; Pinaceae) Confirms Paraphyly in Pinus ponderosa, and Places Pinus jeffreyi with the California Big Cone Pines
Ann Willyard, David S. Gernandt, Blake Cooper, Connor Douglas, Kristen Finch, Hassan Karemera, Erik Lindberg, Stephen K. Langer, Julia Lefler, Paula Marquardt, Dakota L. Pouncey, and Frank Telewski
Corresponding author: Ann Willyard, Hendrix College, Biology Department, 1600 Washington Avenue, Conway, Arkansas, USA, willyard@hendrix.edu
Files archived at Dryad (legends are included inside each file):
Appendix S1. Maps of sample locations.
Appendix S2. Sequencing results by sample.
Appendix S3. Alignment of nuclear sequences (.fas).
Appendix S4. Alignment of plastid sequences (.fas).
Appendix S5. Low copy nuclear gene results by gene.
Appendix S6. The 50% majority rule consensus tree using low copy nuclear genes in RAxML without I. Numbers are bootstrap support. This tree shows branch lengths.
Appendix S7. The 50% majority rule consensus tree using low copy nuclear genes and maximum parsimony. Numbers are nodes with bootstraps 70% and higher. 
Appendix S8. The 50% majority rule consensus tree using plastomes and maximum parsimony. Numbers are nodes with bootstraps 70% and higher. 
Appendix S9. Monophyly results