Cladistic revision of Cretaceous Brachylepadomorpha and Verrucomorpha dataset
Andy S. Gale & Steven U. Vidovic
2023-06-28
Read me: TNT script, Nexus file, R scripts and results
Read me
Citing this document
Please cite the published papers and underpinning data separately when appropriate. A BibTex reference is provided below:
@misc{Gale_&_Vidovic_2023_Brachylepadomorpha_and_Verrucomorpha_dataset,
title={Cladistic revision of Cretaceous Brachylepadomorpha and Verrucomorpha dataset},
author={Gale, Andy S and Vidovic, Steven U},
howpublished={\url{https://doi.org/10.5258/SOTON/D2700}},
doi={10.5258/SOTON/D2700},
timestamp={2023.06.29},
year={2023},
publisher={ePrints Soton}
}This dataset comprises the TNT (Goloboff & Catalano 2016) script to run a cladistic analysis of sessile cirripede groups and bootstrap resampling with 1000 replicates; the output files from TNT; the supporting Nexus file; and an R script for post-analysis of the tree to calculate the Gap Excess Ratio (GER; Wills 1999).
The cladistic analysis comprises 48 characters, one of which is continuous, all others were treated as unordered with equal weights. The TNT script also contains instructions to run an implied weights analysis.
To successfully execute the TNT script, the user will need to include the correct file path to their own copy of Stats.run, a TNT script for calculating the ensemble consistency index and retention index.
TNT scripts can be given a .tnt extension and can be read by TNT and Mesquite. Nexus files can be given a .nex extension and can be read by Mesquite and TNT. R files can be given a .r extension and can be run in RStudio. The output log can be read in plain text, .tre and .nex output files can be opened by all the software used in this study.
Contributions to this dataset:
Gale made intellectual contributions with respect to the anatomy, systematics and stratigraphic occurrence of sessile cirripede groups. Gale: co-designed the analysis; wrote the characters; coded the matrix.
Addresses: School of the Environment, Geography and Geosciences, University of Portsmouth, Burnaby Building, Burnaby Road, Portsmouth PO13QL, UK; Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW75BD, UK.
Vidovic made intellectual contributions with respect to cladistic analysis and post-analysis. Vidovic: wrote the dataset; co-designed and executed the analysis; wrote the scripts and functions; created the files; edited the characters; coded the matrix.
Address: Open Research & Publication Practice, University of Southampton, Hartley Library, University Road, Southampton SO17 1BJ, UK.
References
Bell, M. A. and Lloyd, G. T. 2014. Strap: Stratigraphic Tree Analysis for Palaeontology [Computer software].
Goloboff, P.A. and Catalano, S.A., 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics, 32, pp.221-238. https://doi.org/ 10.1111/cla.12160
Revell, L. J. 2012. Phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution *3**, 217–223. https://doi.org/10.1111/j.2041-210X.2011.00169.x
Wills, M. A. 1999. Congruence between phylogeny and stratigraphy: Randomization tests and the Gap Excess Ratio. Systematic Biology, 48, 559-580. https://doi.org/10.1080/106351599260148
Scripts & Outputs
TNT script
mxram 10000;
Log Gale_&_Vidovic_2023_Log;
nstates 32;
MXRAM;
quote 'Equal weights analysis';
xread
48 18
&[cont]
Capitulum 15
Pollicipes 15
Etcheslepas 15
Pedupycnolepas 8
Pycnolepas 8
Faxelepas 8
Eoverruca 6
Gibbosaverruca 6
Rostratoverruca 6
Verruca 6
Fallaxlepas 8
Brachylepas 8
Parabrachylepas 10
Epibrachylepas 10
Octomeris 12
Catophragmus 12
B.guascoi 8
Priscoverruca 6
&[num]
Capitulum 0002000000000000000000000-0-0000000---00-000000
Pollicipes 0002000000000000000000000-0-0000000---00-000000
Etcheslepas 0000000000000000000000000-0-0000000---00-000000
Pedupycnolepas 0000100001111110010000100-0-0000000---00-000000
Pycnolepas 0010100001111110010000100-0-0000000---00-000000
Faxelepas 1010100011111110010100100-0-0000000---00-000000
Eoverruca 1010100011111111--010111----0000000---00-000000
Gibbosaverruca 201--21121111111--020111----000110000-00-000000
Rostratoverruca 211--21121111111--020111----111110011000-000000
Verruca 211--21121111111--020111----111110011100-000000
Fallaxlepas 0?111010011111100100001010100000000---00-000000
Brachylepas 01111110011111100100001010100000000---00-000000
Parabrachylepas 011111100111111011101-1010110000000---010001000
Epibrachylepas 011111100111111001101-2011110000011---110111000
Octomeris 0112-11001111111--101-2011110000011---111111111
Catophragmus 0112111001111111--000-2010100000011---111111111
B.guascoi 0111111021111111--0000100-0-0000000---00-000000
Priscoverruca 211--21121111111--020111----111110011100-000000
;
RSEED*;
IENUM;
taxname=;
tplot;
Proc /Users/stevenvidovic/Desktop/TNT/stats.run;
Macro -;
export = Gale_&_Vidovic_2023_out.nex;
export - Gale_&_Vidovic_2023_tree_out.tre;
resample boot replications 1000;
export - Gale_&_Vidovic_2023-bs1000.nex ;
MXRAM;
quote 'Implied weights analysis';
xread
48 18
&[cont]
Capitulum 15
Pollicipes 15
Etcheslepas 15
Pedupycnolepas 8
Pycnolepas 8
Faxelepas 8
Eoverruca 6
Gibbosaverruca 6
Rostratoverruca 6
Verruca 6
Fallaxlepas 8
Brachylepas 8
Parabrachylepas 10
Epibrachylepas 10
Octomeris 12
Catophragmus 12
B.guascoi 8
Priscoverruca 6
&[num]
Capitulum 0002000000000000000000000-0-0000000---00-000000
Pollicipes 0002000000000000000000000-0-0000000---00-000000
Etcheslepas 0000000000000000000000000-0-0000000---00-000000
Pedupycnolepas 0000100001111110010000100-0-0000000---00-000000
Pycnolepas 0010100001111110010000100-0-0000000---00-000000
Faxelepas 1010100011111110010100100-0-0000000---00-000000
Eoverruca 1010100011111111--010111----0000000---00-000000
Gibbosaverruca 201--21121111111--020111----000110000-00-000000
Rostratoverruca 211--21121111111--020111----111110011000-000000
Verruca 211--21121111111--020111----111110011100-000000
Fallaxlepas 0?111010011111100100001010100000000---00-000000
Brachylepas 01111110011111100100001010100000000---00-000000
Parabrachylepas 011111100111111011101-1010110000000---010001000
Epibrachylepas 011111100111111001101-2011110000011---110111000
Octomeris 0112-11001111111--101-2011110000011---111111111
Catophragmus 0112111001111111--000-2010100000011---111111111
B.guascoi 0111111021111111--0000100-0-0000000---00-000000
Priscoverruca 211--21121111111--020111----111110011100-000000
;
RSEED*;
PIWE=3;
IENUM;
taxname=;
tplot;
Quit
cnames
{0 'The_number_of_plates_comprising_the_capitulum;
{1 'Capitulum bilaterally symmetrical (0); slight asymmetry (1); strong asymmetry (2) ';
{2 'Capitulum tall, laterally compressed (0); low, broad as high (1) ';
{3 'Peduncle present (0); absent (1) ';
{4 'Peduncular plates bear inner shelf (0); ball and socket articulation (1); no shelf, smooth interior (2) ';
{5 'Peduncular plates small (0); large, form alternating rows around capitulum (1) ';
{6 'Tall carina 2-3x breadth (0); low, hemiconical (1); low, asymmetrical (2)';
{7 'Rostrum half height of carina (0); equal height (1) ';
{8 'Rostrum and carina do not articulate (0); articulate on one side only (1) ';
{9 'Rostrum and carina symmetrical (0); slanted (1); strongly asymmetrical (2) ';
{10 'Carinolatera present (0); absent (1) ';
{11 'Rostrolatera_present_(0)_absent_(1) ';
{12 'Inframedian_latera_present_(0)_absent_(1) ';
{13 'Subrostrum_present_(0)_absent_(1) ';
{14 'Subcarina_present_(0)_absent_(1) ';
{15 'Minor_latera_present_(0)_absent_(1) ';
{16 'Upper latus present (0); absent (1) ';
{17 'Upper latus tall, triangular (0); low, equilaterally triangular (1) ';
{18 'Upper latus with angled basal margin (0); straight basal margin (1) ';
{19 'Scuta taller than broad (0); broader than tall (1) ';
{20 'Scuta and terga symmetrical (0); weakly asymmetrical (1); strongly asymmetrical (2) ';
{21 'Terga rhombic (0); kite-shaped (1) ';
{22 'Scuta and terga possess narrow apicobasal ridges (0); broad apicobasal ridge on FT and FS ';
{23 'Scuta and terga with weak articulation (0); scutal auricle fits into tergal notch (1); articulation interpenetrant (2) ';
{24 'No secondary ribs on scuta and terga (0); interpenetrant ribs present (1) ';
{25 'Articular ridge absent on scuta (0); present (1) ';
{26 'Articular ridge on scuta: weakly developed (0); strongly developed (1) ';
{27 'Articular furrow absent on scuta (0); present (1) ';
{28 'Articular furrow on scuta: weakly developed (0); strongly developed (1) ';
{29 'Occludent regions of F scuta and F terga not differentiated (0); occludent wing present (1) ';
{30 'Occludent margin at acute angle to FS margin of FT (0); right angles (1) ';
{31 'Tergal notch shallow (0); deeply inset (1) ';
{32 'Carina-FT contact simple (0); with interpenetrant ribs (1) ';
{33 'Rostrum-FS contact simple (0); interpenetrant (1) ';
{34 'Scutum and tergum of pair in same plane (0); strongly angled (1) ';
{35 'Pairs of scuta and terga parallel (0); splayed, to form operculum (1) ';
{36 'Scutal adductor on FS indistinct (0); sharply defined, impressed (1) ';
{37 'Myophore absent (0); present (1)';
{38 'Myophore forms tongue (0); forms horizontal sheet (1) ';
{39 'Depressor muscle insertion in band on basal margins of scuta and terga (0); discrete insertion sites on basal margins (1) ';
{40 'Tergal depressor insertion absent (0); present (1) ';
{41 'Tergal depressor insertion weak, set on mid-lower carinal margin (0); strong, toothed, set on summit of carinal margin (1) ';
{42 'Rostroscutal depressor insertion absent (0); present (1) ';
{43 'Lateral scutal depressor insertion absent (0)?; present (1) ';
{44 'Marginals absent (0)?; marginals present (1) ';
{45 'Rostromarginals_absent_(0)_present_(1) ';
{46 'Carinomarginals_absent_(0)_present_(1) ';
{47 'Marginals do not articulate with rostrum and carina (0); articulate (1) ';
;Gale_&_Vidovic_2023_out.nex
(Capitulum ,(Pollicipes ,(Etcheslepas ,(Pedupycnolepas ,(Pycnolepas ,((Faxelepas ,(Eoverruca ,(Gibbosaverruca ,(Rostratoverruca ,(Verruca ,Priscoverruca ))))),(B.guascoi ,(Fallaxlepas ,(Brachylepas ,(Parabrachylepas ,(Epibrachylepas ,(Octomeris ,Catophragmus ))))))))))));library(phytools)
GVTree<-read.tree("/Users/stevenvidovic/Gale_&_Vidovic_2023_out.nex")
plotTree(GVTree)
Gale_&_Vidovic_2023_tree_out.tre
#NEXUS
begin trees ;
tree tnt_1 = [&U]
(Capitulum ,(Pollicipes ,(Etcheslepas ,(Pedupycnolepas ,(Pycnolepas ,((Faxelepas ,(Eoverruca ,(Gibbosaverruca ,(Rostratoverruca ,(Verruca ,Priscoverruca ))))),(B.guascoi ,(Fallaxlepas ,(Brachylepas ,(Parabrachylepas ,(Epibrachylepas ,(Octomeris ,Catophragmus ))))))))))));
end ; Gale_&_Vidovic_2023-bs1000.nex
#NEXUS
begin trees ;
tree tnt_1 = [&U]
(Capitulum ,(Pollicipes ,(Etcheslepas ,(Pedupycnolepas ,(Pycnolepas ,(Faxelepas ,(Eoverruca ,(Gibbosaverruca ,(Rostratoverruca ,Verruca ,Priscoverruca )))),(B.guascoi ,(Fallaxlepas ,Brachylepas ,(Parabrachylepas ,(Epibrachylepas ,(Octomeris ,Catophragmus ))))))))));
end ; TNT output log file
Matrices will be read as alpha-numeric data
Matrix space: allocate for up to 32 states
TNT - max. ram = 10000.00 Mbytes
No ram used yet
'Equal weights analysis'
Matrix (48x18, 32 states). Memory required for data: 0.24 Mbytes
Data were read as mixed types: numeric, and continuous
Random seed is 5758
Implicit enumeration, 1 trees found, score 77.000.
Taxon names is ON
Tree 0:
,-- Capitulum
| ,-- Pollicipes
|--| | ,-- Etcheslepas
`--| | ,-- Pedupycnolepas
`--| | ,-- Pycnolepas
`--| | ,-- Faxelepas
| | ,--| ,-- Eoverruca
`--| | `--| ,-- Gibbosaverruca
| | `--| ,-- Rostratoverruca
`--| `--| ,-- Priscoverruca
| `----- Verruca
| ,-- B.guascoi
`--| ,-- Fallaxlepas
`--| ,-- Brachylepas
`--| ,-- Parabrachylepas
`--| ,-- Epibrachylepas
`--| ,-- Catophragmus
`----- Octomeris
Reading from /Users/stevenvidovic/Desktop/TNT/stats.run
Macro language is ON
Macros: 50.5 Kb in use, 51.8 Kb free
Report is ON
Floating point printing uses 3 digits
Consistency index
0
0 0.805
Retention index
0
0 0.909
Again reading from /Users/stevenvidovic/Desktop/TNT/Gale_&_Vidovic_2023_analysis_script.txt
Macro language is OFF
WARNING:
File "Gale_&_Vidovic_2023_out.nex" already exists. It will be overwritten.
WARNING:
File "Gale_&_Vidovic_2023_tree_out.tre" already exists. It will be overwritten.
Saved trees (Nexus format) to file Gale_&_Vidovic_2023_tree_out.tre
GC values, 1000 replicates, cut=0 (tree 0) - Standard Bootstrap
,-- Capitulum
| ,-- Pollicipes
|--| | ,-- Etcheslepas
`--100| | ,-- Pedupycnolepas
`--60| | ,-- Pycnolepas
| | | ,-- Faxelepas
`--100| |--41| ,-- Eoverruca
| | `--51| ,-- Gibbosaverruca
| | `--98| ,-- Priscoverruca
`--52| `--97+-- Verruca
| `-- Rostratoverruca
| ,-- B.guascoi
| | ,-- Brachylepas
`--33| |-- Fallaxlepas
`--38| ,-- Parabrachylepas
`--92| ,-- Epibrachylepas
`--92| ,-- Catophragmus
`--97--- Octomeris
Average group support: 59.7
WARNING:
File "Gale_&_Vidovic_2023-bs1000.nex" already exists. It will be overwritten.
Saved trees (Nexus format) to file Gale_&_Vidovic_2023-bs1000.nex
TNT - max. ram = 9999.10 Mbytes
9999.48 Mbytes unused
0.52 Mbytes in use:
0.50 Mbytes for data matrix (48 chars., 18 taxa)
0.03 Mbytes for 100 trees
'Implied weights analysis'
WARNING:
Data from:
/Users/stevenvidovic/Desktop/TNT/Gale_&_Vidovic_2023_analysis_script.txt
will be replaced with data from:
/Users/stevenvidovic/Desktop/TNT/Gale_&_Vidovic_2023_analysis_script.txt
Matrix (48x18, 32 states). Memory required for data: 0.24 Mbytes
Data were read as mixed types: numeric, and continuous
Random seed is 6441
Implied Weighting is ON
Implicit enumeration, 1 trees found, score 3.22143.
Taxon names is ON
Tree 0:
,-- Capitulum
| ,-- Pollicipes
|--| | ,-- Etcheslepas
`--| | ,-- Pedupycnolepas
`--| | ,-- Pycnolepas
`--| | ,-- Faxelepas
| | ,--| ,-- Eoverruca
`--| | `--| ,-- Gibbosaverruca
| | `--| ,-- Verruca
`--| `--| ,-- Priscoverruca
| `----- Rostratoverruca
| ,-- B.guascoi
`--| ,-- Fallaxlepas
`--| ,-- Brachylepas
`--| ,-- Parabrachylepas
`--| ,-- Epibrachylepas
`--| ,-- Catophragmus
`----- OctomerisR script for calculating GER
library(phytools)
library(strap)
Tree<-read.tree("/Users/stevenvidovic/Gale_&_Vidovic_2023_out.nex") # Select the nexus tree output from the TNT script Gale_&_Vidovic_2023_out.nex
Tree[["edge"]]
Tree[["Nnode"]]
Tree[["tip.label"]]
NAME<-c("Capitulum","Pollicipes","Etcheslepas","Pedupycnolepas","Pycnolepas","Faxelepas","Eoverruca","Gibbosaverruca","Rostratoverruca","Verruca","Fallaxlepas","Brachylepas","Parabrachylepas","Epibrachylepas","Octomeris","Catophragmus","B.guascoi","Priscoverruca") # Creates names for a lookup table of stratigraphic occurrences
FAD<-c(94, 80, 149, 132, 110, 65, 107, 2.6, 2.6, 67, 93, 100, 80, 80, 0, 0, 80, 80) # Adds first known occurrence to the lookup table
LAD<-c(0, 0, 132, 100, 70, 2.6, 75, 0, 0, 0, 66, 66, 80, 66, 0, 0, 66, 60) # Adds last known occurrence to the lookup table
Strat1 <- data.frame(row.names=NAME, FAD, LAD) # Creates a data frame out of the FAD and LAD, giving the taxon names to the row names
tree_l <- DatePhylo(Tree, Strat1, method="equal", rlen=1) #converts the tree to have timed branch lengths
geoscalePhylo(tree_l, Strat1, units = c("Eon","Era","Period","Epoch","Age"),boxes="Age", cex.tip=0.4,tick.scale="Age",direction="upwards",vers="ICS2013") #Plots chronostratigraphic tree
GER<-StratPhyloCongruence(tree_l, Strat1, rlen=0, method="basic", samp.perm=1000, rand.perm=1000, hard=TRUE, randomly.sample.ages=FALSE, fix.topology=TRUE, fix.outgroup=TRUE, outgroup.taxon = "Capitulum" ) # calculate Gap Excess Ratio,other metrics and P values
GER$input.tree.results #reports the results of the analyses
# The following repeats the previous script after removing the outgroup taxa
Treeingroup<-Tree
Treeingroup<-drop.tip(Treeingroup,"Capitulum") # Removing the younger outgroup
Treeingroup<-drop.tip(Treeingroup,"Pollicipes") # ditto
Nameingroup<-c("Etcheslepas","Pedupycnolepas","Pycnolepas","Faxelepas","Eoverruca","Gibbosaverruca","Rostratoverruca","Verruca","Fallaxlepas","Brachylepas","Parabrachylepas","Epibrachylepas","Octomeris","Catophragmus","B.guascoi","Priscoverruca")
FADingroup<-c(149, 132, 110, 65, 107, 2.6, 2.6, 67, 93, 100, 80, 80, 0, 0, 80, 80)
LADingroup<-c(132, 100, 70, 2.6, 75, 0, 0, 0, 66, 66, 80, 66, 0, 0, 66, 60)
Stratig <- data.frame(row.names=Nameingroup, FADingroup, LADingroup)
colnames(Stratig)[2]="LAD"
colnames(Stratig)[1]="FAD"
tree_lig <- DatePhylo(Treeingroup, Stratig, method="equal", rlen=1)
geoscalePhylo(tree_lig, Stratig, units = c("Eon","Era","Period","Epoch","Age"),boxes="Age", cex.tip=0.4,tick.scale="Age",direction="upwards",vers="ICS2013")
GERig<-StratPhyloCongruence(tree_lig, Stratig, rlen=0, method="basic", samp.perm=1000, rand.perm=1000, hard=TRUE, randomly.sample.ages=FALSE, fix.topology=TRUE, fix.outgroup=TRUE, outgroup.taxon = "Etcheslepas" )
GERig$input.tree.results 
Cladogram redrawn from r analysis to calculate the GER
Nexus file - built in Mesquite 3.11
#NEXUS
[written Wed Jun 28 23:26:49 BST 2023 by Mesquite version 3.11 (build 766) at MacBook-Pro.local/192.168.1.22]
BEGIN TAXA;
DIMENSIONS NTAX=18;
TAXLABELS
Capitulum Pollicipes Etcheslepas Pedupycnolepas Pycnolepas Faxelepas Eoverruca Gibbosaverruca Rostratoverruca Verruca Fallaxlepas Brachylepas Parabrachylepas Epibrachylepas Octomeris Catophragmus B.guascoi Priscoverruca
;
END;
BEGIN CHARACTERS[!MATRIX];
TITLE Categorical_states_matrix;
DIMENSIONS NCHAR=47;
FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A B C D E F G H J K M N P Q R S T U V W X Y Z a b c d e f";
CHARSTATELABELS
1 'Capitulum bilaterally symmetrical (0); slight asymmetry (1); strong asymmetry (2) ', 2 'Capitulum tall, laterally compressed (0); low, broad as high (1) ', 3 'Peduncle present (0); absent (1) ', 4 'Peduncular plates bear inner shelf (0); ball and socket articulation (1); no shelf, smooth interior (2) ', 5 'Peduncular plates small (0); large, form alternating rows around capitulum (1) ', 6 'Tall carina 2-3x breadth (0); low, hemiconical (1); low, asymmetrical (2)', 7 'Rostrum half height of carina (0); equal height (1) ', 8 'Rostrum and carina do not articulate (0); articulate on one side only (1) ', 9 'Rostrum and carina symmetrical (0); slanted (1); strongly asymmetrical (2) ', 10 'Carinolatera present (0); absent (1) ', 11 'Rostrolatera present (0) absent (1) ', 12 'Inframedian latera present (0) absent (1) ', 13 'Subrostrum present (0) absent (1) ', 14 'Subcarina present (0) absent (1) ', 15 'Minor latera present (0) absent (1) ', 16 'Upper latus present (0); absent (1) ', 17 'Upper latus tall, triangular (0); low, equilaterally triangular (1) ', 18 'Upper latus with angled basal margin (0); straight basal margin (1) ', 19 'Scuta taller than broad (0); broader than tall (1) ', 20 'Scuta and terga symmetrical (0); weakly asymmetrical (1); strongly asymmetrical (2) ', 21 'Terga rhombic (0); kite-shaped (1) ', 22 'Scuta and terga possess narrow apicobasal ridges (0); broad apicobasal ridge on FT and FS ', 23 'Scuta and terga with weak articulation (0); scutal auricle fits into tergal notch (1); articulation interpenetrant (2) ', 24 'No secondary ribs on scuta and terga (0); interpenetrant ribs present (1) ', 25 'Articular ridge absent on scuta (0); present (1)', 26 'Articular ridge on scuta: weakly developed (0); strongly developed (1) ', 27 'Articular furrow absent on scuta (0); present (1)', 28 'Articular furrow on scuta: weakly developed (0); strongly developed (1) ', 29 'Occludent regions of F scuta and F terga not differentiated (0); occludent wing present (1) ', 30 'Occludent margin at acute angle to FS margin of FT (0); right angles (1) ', 31 'Tergal notch shallow (0); deeply inset (1) ', 32 'Carina-FT contact simple (0); with interpenetrant ribs (1) ', 33 'Rostrum-FS contact simple (0); interpenetrant (1) ', 34 'Scutum and tergum of pair in same plane (0); strongly angled (1) ', 35 'Pairs of scuta and terga parallel (0); splayed, to form operculum (1) ', 36 'Scutal adductor on FS indistinct (0); sharply defined, impressed (1) ', 37 'Myophore absent (0); present (1)', 38 'Myophore forms tongue (0); forms horizontal sheet (1) ', 39 'Depressor muscle insertion in band on basal margins of scuta and terga (0); discrete insertion sites on basal margins (1) ', 40 'Tergal depressor insertion absent (0); present (1) ', 41 'Tergal depressor insertion weak, set on mid-lower carinal margin (0); strong, toothed, set on summit of carinal margin (1) ', 42 'Rostroscutal depressor insertion absent (0); present (1) ', 43 'Lateral scutal depressor insertion absent (0)†; present (1) ', 44 'Marginals absent (0)†; marginals present (1) ', 45 'Rostromarginals absent (0) present (1) ', 46 'Carinomarginals absent (0) present (1) ', 47 'Marginals do not articulate with rostrum and carina (0); articulate (1) ' ;
MATRIX
Capitulum 0002000000000000000000000-0-0000000---00-000000
Pollicipes 0002000000000000000000000-0-0000000---00-000000
Etcheslepas 0000000000000000000000000-0-0000000---00-000000
Pedupycnolepas 0000100001111110010000100-0-0000000---00-000000
Pycnolepas 0010100001111110010000100-0-0000000---00-000000
Faxelepas 1010100011111110010100100-0-0000000---00-000000
Eoverruca 1010100011111111--010111----0000000---00-000000
Gibbosaverruca 201--21121111111--020111----000110000-00-000000
Rostratoverruca 211--21121111111--020111----111110011000-000000
Verruca 211--21121111111--020111----111110011100-000000
Fallaxlepas 0?111010011111100100001010100000000---00-000000
Brachylepas 01111110011111100100001010100000000---00-000000
Parabrachylepas 011111100111111011101-1010110000000---010001000
Epibrachylepas 011111100111111001101-2011110000011---110111000
Octomeris 0112-11001111111--101-2011110000011---111111111
Catophragmus 0112111001111111--000-2010100000011---111111111
B.guascoi 0111111021111111010000100-0-0000000---00-000000
Priscoverruca 211--21121111111--020111----111110011100-000000
;
END;
BEGIN CHARACTERS;
TITLE Continuous_states_matrix;
DIMENSIONS NCHAR=1;
FORMAT DATATYPE = CONTINUOUS GAP = - MISSING = ?;
CHARSTATELABELS
1 The_number_of_plates_comprising_the_capitulum ;
MATRIX
Capitulum 15.0
Pollicipes 15.0
Etcheslepas 15.0
Pedupycnolepas 8.0
Pycnolepas 8.0
Faxelepas 8.0
Eoverruca 6.0
Gibbosaverruca 6.0
Rostratoverruca 6.0
Verruca 6.0
Fallaxlepas 8.0
Brachylepas 8.0
Parabrachylepas 10.0
Epibrachylepas 10.0
Octomeris 12.0
Catophragmus 12.0
B.guascoi 8.0
Priscoverruca 6.0
;
END;
BEGIN ASSUMPTIONS;
TYPESET * UNTITLED (CHARACTERS = Categorical_states_matrix) = unord: 1 - 47;
TYPESET * UNTITLED (CHARACTERS = Continuous_states_matrix) = Squared: 1;
END;
BEGIN NOTES;
CHARACTERS = Categorical_states_matrix TAXA = Taxa;
TEXT CHARACTER = 1 TEXT = 'Capitulum bilaterally symmetrical (0); slight asymmetry (1); strong asymmetry (2)^nCapitulum tall, laterally compressed (0); low, broad as high (1)^nCapitulum composed of >8 plates (0); 8 plates (1); 6 plates (2); 10 plates (3) 4^nPeduncle present (0); absent (1)^nPeduncular plates bear inner shelf (0); ball and socket articulation (1); no shelf, smooth interior (2)^nPeduncular plates small (0); large, form alternating rows around capitulum (1)^nTall carina 2-3x breadth (0); low, hemiconical (1)^nRostrum half height of carina (0); equal height (1)^nRostrum and carina do not articulate (0); articulate on one side only (1)^nRostrum and carina symmetrical (0); slanted (1); strongly asymmetrical (2)^nCarinolatera present (0); absent (1)^nRostrolatera present (0) absent (1)^nInframedian latera present (0) absent (1)^nSubrostrum present (0) absent (1)^nSubcarina present (0) absent (1)^nMinor latera present (0) absent (1)^nUpper latus present (0); absent (1)^nUpper latus tall, triangular (0); low, equilaterally triangular (1)^nUpper latus with angled basal margin (0); straight basal margin (1)^nScuta taller than broad (0); broader than tall (1)^nScuta and terga symmetrical (0); weakly asymmetrical (1); strongly asymmetrical (2)^nTerga rhombic (0); kite-shaped (1)^nScuta and terga possess narrow apicobasal ridges (0); broad apicobasal ridge on FT and FS^nScuta and terga with weak articulation (0); scutal auricle fits into tergal notch (1); articulation interpenetrant (2)^nNo secondary ribs on scuta and terga (0); interpenetrant ribs present (1)^nArticular ridge absent on scuta (0); weakly developed (1); strongly developed (2)^nArticular furrow absent on scuta (0); weakly developed (1); strongly developed (2)^nOccludent regions of F scuta and F terga not differentiated (0); occludent wing present (1)^nOccludent margin at acute angle to FS margin of FT (0); right angles (1)^nTergal notch shallow (0); deeply inset (1)^nCarina-FT contact simple (0); with interpenetrant ribs (1)^nRostrum-FS contact simple (0); interpenetrant (1)^nScutum and tergum of pair in same plane (0); strongly angled (1)^nPairs of scuta and terga parallel (0); splayed, to form operculum (1)^nScutal adductor on FS indistinct (0); sharply defined, impressed (1)^nMyophore absent (0); forms tongue (1); forms horizontal sheet (2)^nDepressor muscle insertion in band on basal margins of scuta and terga (0); discrete insertion sites on basal margins (1)^nTergal depressor insertion absent (0); Tergal depressor insertion weak, set on mid-lower carinal margin (1); strong, toothed, set on summit of carinal margin (2)^nRostroscutal depressor insertion absent (0); present (1)^nLateral scutal depressor insertion absent (0)†; present (1)^nMarginals absent (0)†; marginals present (1)^nRostromarginals absent (0) present (1)^nCarinomarginals absent (0) present (1)^nMarginals do not articulate with rostrum and carina (0); articulate (1)Capitulum bilaterally symmetrical (0); slight asymmetry (1); strong asymmetry (2)^nCapitulum tall, laterally compressed (0); low, broad as high (1)^nCapitulum composed of >8 plates (0); 8 plates (1); 6 plates (2); 10 plates (3) 4^nPeduncle present (0); absent (1)^nPeduncular plates bear inner shelf (0); ball and socket articulation (1); no shelf, smooth interior (2)^nPeduncular plates small (0); large, form alternating rows around capitulum (1)^nTall carina 2-3x breadth (0); low, hemiconical (1)^nRostrum half height of carina (0); equal height (1)^nRostrum and carina do not articulate (0); articulate on one side only (1)^nRostrum and carina symmetrical (0); slanted (1); strongly asymmetrical (2)^nCarinolatera present (0); absent (1)^nRostrolatera present (0) absent (1)^nInframedian latera present (0) absent (1)^nSubrostrum present (0) absent (1)^nSubcarina present (0) absent (1)^nMinor latera present (0) absent (1)^nUpper latus present (0); absent (1)^nUpper latus tall, triangular (0); low, equilaterally triangular (1)^nUpper latus with angled basal margin (0); straight basal margin (1)^nScuta taller than broad (0); broader than tall (1)^nScuta and terga symmetrical (0); weakly asymmetrical (1); strongly asymmetrical (2)^nTerga rhombic (0); kite-shaped (1)^nScuta and terga possess narrow apicobasal ridges (0); broad apicobasal ridge on FT and FS^nScuta and terga with weak articulation (0); scutal auricle fits into tergal notch (1); articulation interpenetrant (2)^nNo secondary ribs on scuta and terga (0); interpenetrant ribs present (1)^nArticular ridge absent on scuta (0); weakly developed (1); strongly developed (2)^nArticular furrow absent on scuta (0); weakly developed (1); strongly developed (2)^nOccludent regions of F scuta and F terga not differentiated (0); occludent wing present (1)^nOccludent margin at acute angle to FS margin of FT (0); right angles (1)^nTergal notch shallow (0); deeply inset (1)^nCarina-FT contact simple (0); with interpenetrant ribs (1)^nRostrum-FS contact simple (0); interpenetrant (1)^nScutum and tergum of pair in same plane (0); strongly angled (1)^nPairs of scuta and terga parallel (0); splayed, to form operculum (1)^nScutal adductor on FS indistinct (0); sharply defined, impressed (1)^nMyophore absent (0); forms tongue (1); forms horizontal sheet (2)^nDepressor muscle insertion in band on basal margins of scuta and terga (0); discrete insertion sites on basal margins (1)^nTergal depressor insertion absent (0); Tergal depressor insertion weak, set on mid-lower carinal margin (1); strong, toothed, set on summit of carinal margin (2)^nRostroscutal depressor insertion absent (0); present (1)^nLateral scutal depressor insertion absent (0)†; present (1)^nMarginals absent (0)†; marginals present (1)^nRostromarginals absent (0) present (1)^nCarinomarginals absent (0) present (1)^nMarginals do not articulate with rostrum and carina (0); articulate (1)';
CHARACTERS = Continuous_states_matrix TAXA = Taxa;
END;
BEGIN MESQUITECHARMODELS;
ProbModelSet * UNTITLED (CHARACTERS = Categorical_states_matrix) = 'Mk1 (est.)': 1 - 47;
ProbModelSet * UNTITLED (CHARACTERS = Continuous_states_matrix) = Brownian_default: 1;
END;
BEGIN TREES;
Title 'Trees from "GALE_&_Vidovic_2023_tree_out.tre"';
ID 0189041d36ad8;
LINK Taxa = Taxa;
TRANSLATE
[0] 1 Capitulum,
[1] 2 Pollicipes,
[2] 3 Etcheslepas,
[3] 4 Pedupycnolepas,
[4] 5 Pycnolepas,
[5] 6 Faxelepas,
[6] 7 Eoverruca,
[7] 8 Gibbosaverruca,
[8] 9 Rostratoverruca,
[9] 10 Verruca,
[10] 11 Fallaxlepas,
[11] 12 Brachylepas,
[12] 13 Parabrachylepas,
[13] 14 Epibrachylepas,
[14] 15 Octomeris,
[15] 16 Catophragmus,
[16] 17 B.guascoi,
[17] 18 Priscoverruca;
TREE tnt_1 = (1,(2,(3,(4,(5,((6,(7,(8,(9,(10,18))))),(17,(11,(12,(13,(14,(15,16))))))))))));
END;
Begin MESQUITE;
MESQUITESCRIPTVERSION 2;
TITLE AUTO;
tell ProjectCoordinator;
timeSaved 1687991214851;
linkFile '../GALE_&_Vidovic_2023_tree_out.tre';
linkFile '../GALE_&_Vidovic_2023_tree_out.tre';
linkFile '../GALE_&_Vidovic_2023_tree_out.tre';
getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
tell It;
setID 0 4033909454505056158;
tell It;
setDefaultOrder 16 17 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15;
attachments ;
endTell;
endTell;
getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
tell It;
setID 0 3747491882715114200;
tell It;
setDefaultOrder 1 2 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 32 26 31 28 31 32 33 34 35 36 37 40 41 38 43 44 41 44 45 46 47 48 49;
attachments ;
endTell;
mqVersion 311;
checksumv 0 3 2303381834 null getNumChars 47 numChars 47 getNumTaxa 18 numTaxa 18 short false bits 7 states 7 sumSquaresStatesOnly 1906.0 sumSquares 1906.0 longCompressibleToShort true usingShortMatrix false NumFiles 4 NumMatrices 2;
mqVersion;
setID 1 7709094195914369840;
mqVersion 311;
checksumv 1 3 4240696501 null numChars 1 numItems 1 min 6.0 max 15.0 sumSquares 1727.0 NumFiles 4 NumMatrices 2;
mqVersion;
endTell;
getWindow;
tell It;
suppress;
setResourcesState false false 100;
setPopoutState 452;
setExplanationSize 0;
setAnnotationSize 0;
setFontIncAnnot 0;
setFontIncExp 0;
setSize 1440 754;
setLocation 0 25;
setFont SanSerif;
setFontSize 10;
getToolPalette;
tell It;
endTell;
desuppress;
endTell;
getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
tell It;
makeTreeWindow #4033909454505056158 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
tell It;
suppressEPCResponse;
setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
tell It;
setTreeBlock 1;
setTreeBlockID 0189041d36ad8;
toggleUseWeights off;
endTell;
setAssignedID 1129.1687991177403.7242900836017181817;
getTreeWindow;
tell It;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
setSize 1340 682;
setLocation 0 25;
setFont SanSerif;
setFontSize 10;
getToolPalette;
tell It;
endTell;
setActive;
getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
tell It;
suppress;
setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree;
tell It;
setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
tell It;
branchLengthsToggle off;
toggleScale on;
toggleBroadScale off;
toggleCenter on;
toggleEven on;
setFixedTaxonDistance 0;
endTell;
setEdgeWidth 4;
showEdgeLines on;
orientUp;
endTell;
setBackground White;
setBranchColor Black;
showNodeNumbers off;
showBranchColors on;
labelBranchLengths off;
centerBrLenLabels on;
showBrLensUnspecified on;
showBrLenLabelsOnTerminals on;
setBrLenLabelColor 0 0 255;
setNumBrLenDecimals 6;
desuppress;
getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
tell It;
setColor Black;
toggleColorPartition off;
toggleColorAssigned on;
toggleShadePartition off;
toggleShowFootnotes on;
toggleNodeLabels on;
toggleCenterNodeNames off;
toggleShowNames on;
namesAngle ?;
endTell;
endTell;
setTreeNumber 1;
setDrawingSizeMode 0;
toggleLegendFloat on;
scale 0;
toggleTextOnTree off;
togglePrintName on;
showWindow;
endTell;
desuppressEPCResponse;
getEmployee #mesquite.trees.ColorBranches.ColorBranches;
tell It;
setColor Red;
removeColor off;
endTell;
getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
tell It;
setAlwaysOn off;
endTell;
getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
tell It;
colorByPartition off;
endTell;
getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;
tell It;
setOn on;
setDigits 4;
writeAsPercentage off;
toggleCentred off;
toggleHorizontal on;
toggleWhiteEdges on;
toggleShowOnTerminals on;
setFontSize 10;
setOffset 0 0;
endTell;
getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings;
tell It;
setOn on;
toggleCentred on;
toggleHorizontal on;
setFontSize 10;
setOffset 0 0;
toggleShowOnTerminals on;
endTell;
getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
tell It;
panelOpen false;
endTell;
endTell;
endTell;
getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
tell It;
showDataWindow #3747491882715114200 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
tell It;
getWindow;
tell It;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
setSize 1340 682;
setLocation 0 25;
setFont SanSerif;
setFontSize 10;
getToolPalette;
tell It;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
endTell;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
colorCells #mesquite.charMatrices.ColorCells.ColorCells;
tell It;
setColor Dark Gray;
removeColor on;
endTell;
colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor;
colorText #mesquite.charMatrices.NoColor.NoColor;
setBackground White;
toggleShowNames on;
toggleShowTaxonNames on;
toggleTight off;
toggleThinRows off;
toggleShowChanges on;
toggleSeparateLines off;
toggleShowStates on;
toggleAutoWCharNames on;
toggleAutoTaxonNames off;
toggleShowDefaultCharNames off;
toggleConstrainCW on;
toggleBirdsEye off;
toggleShowPaleGrid off;
toggleShowPaleCellColors off;
toggleShowPaleExcluded off;
togglePaleInapplicable on;
toggleShowBoldCellText off;
toggleAllowAutosize on;
toggleColorsPanel off;
toggleDiagonal on;
setDiagonalHeight 80;
toggleLinkedScrolling on;
toggleScrollLinkedTables off;
endTell;
showWindow;
getWindow;
tell It;
forceAutosize;
endTell;
getEmployee #mesquite.charMatrices.AlterData.AlterData;
tell It;
toggleBySubmenus off;
endTell;
getEmployee #mesquite.charMatrices.ColorByState.ColorByState;
tell It;
setStateLimit 9;
toggleUniformMaximum on;
endTell;
getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
tell It;
showStrip off;
endTell;
getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
tell It;
togglePanel off;
endTell;
getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
tell It;
showStrip off;
endTell;
getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
tell It;
autotabOff;
endTell;
getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
tell It;
showStrip off;
endTell;
getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;
tell It;
panelOpen true;
endTell;
endTell;
showDataWindow #7709094195914369840 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
tell It;
getWindow;
tell It;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
setSize 1340 682;
setLocation 0 25;
setFont SanSerif;
setFontSize 10;
getToolPalette;
tell It;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
endTell;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
colorCells #mesquite.charMatrices.NoColor.NoColor;
colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor;
colorText #mesquite.charMatrices.NoColor.NoColor;
setBackground White;
toggleShowNames on;
toggleShowTaxonNames on;
toggleTight off;
toggleThinRows off;
toggleShowChanges on;
toggleSeparateLines off;
toggleShowStates on;
toggleAutoWCharNames on;
toggleAutoTaxonNames off;
toggleShowDefaultCharNames off;
toggleConstrainCW on;
toggleBirdsEye off;
toggleShowPaleGrid off;
toggleShowPaleCellColors off;
toggleShowPaleExcluded off;
togglePaleInapplicable on;
toggleShowBoldCellText off;
toggleAllowAutosize on;
toggleColorsPanel off;
toggleLinkedScrolling on;
toggleScrollLinkedTables off;
endTell;
showWindow;
getWindow;
tell It;
forceAutosize;
endTell;
getEmployee #mesquite.charMatrices.AlterData.AlterData;
tell It;
toggleBySubmenus off;
endTell;
getEmployee #mesquite.charMatrices.ColorByState.ColorByState;
tell It;
setStateLimit 9;
toggleUniformMaximum on;
endTell;
getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
tell It;
setColor Red;
removeColor off;
endTell;
getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
tell It;
togglePanel off;
endTell;
getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
tell It;
showStrip off;
endTell;
getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
tell It;
showStrip off;
endTell;
getEmployee #mesquite.cont.ItemsEditorForInfoPanel.ItemsEditorForInfoPanel;
tell It;
panelOpen false;
endTell;
endTell;
endTell;
getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
tell It;
showCharacters #3747491882715114200 #mesquite.lists.CharacterList.CharacterList;
tell It;
setData 0;
getWindow;
tell It;
newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder;
newAssistant #mesquite.lists.CharListInclusion.CharListInclusion;
newAssistant #mesquite.lists.CharListPartition.CharListPartition;
newAssistant #mesquite.parsimony.CharListParsModels.CharListParsModels;
newAssistant #mesquite.lists.CharacterStats.CharacterStats;
tell It;
toggleSelectedOnly off;
endTell;
getTable;
tell It;
rowNamesWidth 796;
endTell;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
setSize 1340 682;
setLocation 0 25;
setFont SanSerif;
setFontSize 10;
getToolPalette;
tell It;
setTool mesquite.lists.CharacterList.CharacterListWindow.arrow;
endTell;
endTell;
showWindow;
getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel;
tell It;
togglePanel off;
endTell;
endTell;
endTell;
endTell;
end;Character mapping
Character 1: The number of plates comprising the capitulum (continuous)
Continuous character mapping
Node map for categorical character state mapping