10e.treePL_config_dating

[General commands]
#Note that here we'll use the 1,000 bootstrapped trees and run treePL on each of them.
#We can then later summarize results and calculate confidence intervals (CIs) on the calibated nodes.
treefile = results_treePL_calibration/output_iqtree/iqtree_bootstrap_trees.tree
#Update numsites value when final supermatrix is ready for phylogeny inference; IQ-TREE logs this value in the file iqtree_bootstrap_logfile.log.
numsites = 13278
thorough
#For this run on the set of 1,000 bootstrap trees, use multiple threads to speed up the analyses.
#Note that this seems not to work on the Naturalis highmem cluster...
nthreads = 47

[Calibration]
#Set stem age of Brassicales using a representatative of sister family Malvaceae (here PAFTOL_014331 = Macrohasseltia macroterantha) and a random Brassicaceae (here S1408 = Eruca vesicaria)
#for use of fossil †Dressiantha bicarpellata dated @ 93.6–89.3 Ma (Gandolfo  et al., 1998).
mrca = BRASSICALES_STEM PAFTOL_014331 S1408
min = BRASSICALES_STEM 89.3
max = BRASSICALES_STEM 93.6

#Set crown age of Akaniaceae using two known family genera: Akania (here HYZL = Akania bidwillii) and Bretschneidera (here S1384 = Bretschneidera sinensis)
#for use of fossil †Akania sp. dated @ 62-61 Ma (Iglesias et al., 2007).
#mrca = AKANIACEAEA_CROWN S1384 HYZL
#min = AKANIACEAEA_CROWN 61
#max = AKANIACEAEA_CROWN 62

#Set stem age of Brassicaceae using a representative sister family Cleomaceae  (here PAFTOL_019361 = Cleome albescens) and a random Brassicaceae (here S1408 = Eruca vesicaria)
#for use of fossil †Palaeocleome lakensis @ 55.8 to 48.6 Ma (Chandler, 1962).
#mrca = BRASSICACEAE_STEM PAFTOL_019361 S1408
#min = BRASSICACEAE_STEM 48.6
#max = BRASSICACEAE_STEM 55.8

#Set stem are of tribe Thlaspideae using a representative of the tribe (here S1376 = Thlaspi arvense) and a representative of the sister tribe Eutremeae (here S0416 = Eutrema edwardsii)
#for use of fossil †Thlaspi primaevum dated @ ca. 32 Ma (Becker, 1961; Lielke et al., 2012).
#mrca = THLASPIDEAE_STEM S0416 S1376
#min = THLASPIDEAE_STEM 29
#max = THLASPIDEAE_STEM 33

#Note: so far excluded the use of fossil Capparidoxylon holleisii, because treePL seems unable to find a convergent solution when this calibration is included.
#mrca = CAPPARACEAEA_CROWN S1386 PAFTOL_019361
#min = CAPPARACEAEA_CROWN 16.3
#max = CAPPARACEAEA_CROWN 16.3

[Best optimization parameters]
#The following values were taken from the prime analysis ran before.
opt = 2
moredetail
optad = 1
moredetailad
optcvad = 1
moredetailcvad

[Best smoothing value]
#The following value was taken from the CV analysis ran before.
smooth = 10

[Output file of dating step]
outfile = results_treePL_calibration/output_treePL_dating/treePL_calibrated_phylogeny.tre