Live Oaks Phylogeography Data Management
Introduction
Documentation of important data files that were collected from live oaks for a phylogeography project. Also, documented are spectral measurements of dried leaves that were taken in spring 2021 from leaf samples that were collected as herbariums for the phylogeography project. Not all individuals in each file were successfully matched. There are many copies of one excel file in the Live Oaks folder. The matched files are not limited to the files mentioned below. The most recent files were chosen. Also, there are some variations of the sample ID between different types of data e.g. MX-MB3030 and MXMB3030.
Spectra
Files
There are 3 files created on Fulcrum App that document metadata and storage location of the spectra of dried live oaks taken in spring 2021. The README.txt has column definitions. The fulcrum_id in file 1 links to the fulcrum_parent_id in file 2. The files are linked from the shared google drive and are also stored in the University shared drive. Please refer to the SVC leaf measurements protocol for instrument settings.
- Path of University Shared Drive: Lab-cavender\4_Project_Folders\Live Oaks\Spectra of Dried Specimen\
- Spectra in .sig files that can be opened as text files.
File 1:
live_oaks_leaf_spectra.csv
File 2:
live_oaks_leaf_spectra_spectral_measurements.csv
File 3:
README.txt
Notes
- Files ending in WR, means white reference.
- If the file name ends with _BAD.sig, the spectra are unusable because of either poor quality or low reflectance.
- Structure of a .sig file follows:
- Several lines of metadata, e.g. instrument name and type, scan time, etc.
- 4 columns of data:
- wavelength (nm)
- reference radiance
- target radiance
- percent reflectance
Molecular Data
Microsatellite Sequences
-
File 1: LAB-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Molecular Data\Structure\All live oak microsats_Structure1.8.14.xls
-
Raw sequences: LAB-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Molecular Data\Structure\All live oak microsats_Structure.xls
Chloroplast DNA
- Path: LAB-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Molecular Data\Cp DNA
Notes
Path includes few folders containing full sequences.
RAD seqences
- Path: LAB-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Molecular Data\RAD\
Notes
RAD-seq was processed on a few individuals of each live oak species.
NIA-i3
- Path: LAB-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Molecular Data\NIA\
Morphology
Foliar area of leaf scans.
- File 1: Lab-cavender\4_Project_Folders\Live Oaks\Live oak phylogeography II\Morphology documentation\Anne's Shape Results\All together\All_Virentes.xlsx
Products
| Year | Citation | DOI | UMN shared drive | Data | Code |
|---|---|---|---|---|---|
| 2015 | Cavender-Bares J., et al. 2015. Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach. Molecular Ecology 24: 3668-3687 | 10.1111/mec.13269 | !Path: Lab-cavender > 4_Project_Folders > Live Oaks > Live oak phylogeography II | RADseq, Accession #s on GenBank, Dryad | |
| 2011 | Cavender-Bares J., et al. 2011. Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone. Journal of Biogeography 38(5): 962-981 | 10.1111/j.1365-2699.2010.02451.x | !Path: Lab-cavender > 4_Project_Folders > Live Oaks > Live oak phylogeography II | ||
| 2009 | Cavender-Bares J. and Pahlich A. 2009. Molecular, morphological, and ecological niche differentiation of sympatric sister oak species, Quercus virginiana and Q. geminata (Fagaceae). American Journal of Botany 96(9): 1690-1702. | 10.3732/ajb.0800315 | !Path: Lab-cavender > 4_Project_Folders > Live Oaks > | ||
| 2015 | Deacon N.J. and Cavender-Bares J. 2015. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica. PLoS ONE, 10(9): e0138783. doi:10.1371/journal.pone.013878 | 10.1371/journal.pone.0138783 | !Path: Lab-cavender > 4_Project_Folders > Live Oaks > | ||
| 2011 | Guggar P.F. and Cavender-Bares J. 2011. Molecular and morphogical support for a Florida origin of the Cuban oak. Journal of Biogeography. | 10.1111/j.1365-2699.2011.02610.x | !Path: Lab-cavender > 4_Project_Folders > Live Oaks > |