Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
Thornhill, Andrew et al. (2017), Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology), v3, UC Berkeley, Dataset, https://doi.org/10.6078/D1VD4P
This is the DNA sequence alignment for the 1083 OTUs used in Thornhill et al. 2017. We defined monophyletic OTUs at the finest scale possible given data availability and current understanding of the evolutionary relationships of Californian plant lineages. Using all 5258 species described in The Jepson eFlora (http://ucjeps.berkeley.edu/eflora/) as a starting point, a thorough literature search was undertaken to find molecular phylogenetic studies that had included California taxa. Genera were split into finer level OTUs if robust evidence existed for monophyly of subclades and representative DNA data either were available in GenBank or could be generated within the scope of the project. Genera were lumped in a few cases if recent evidence showed that one is nested in another. In total, 1083 OTUs were defined to include the 5258 binomials (Table S2 in Thornhill et al. 2017 details the OTU to which each binomial was assigned).
This Nexus file contains the concatenated 26,993 base pair sequence alignment and the phylogenetic trees used in A.H. Thornhill, B.G. Baldwin, W.A. Freyman, S. Nosratinia, M.M. Kling, N. Morueta-Holme, T.P Madsen, D.D. Ackerly, and B.D. Mishler. 2017. Spatial phylogenetics of the native California flora. BMC Biology 15:96
Use with the other Thornhill et al. (2017) data sets linked below.
National Science Foundation, Award: DEB-1354552