6 June 2022

This directory contains analytical files that were assembled for the article:

Speonastes gen. nov. from Northeastern Andhra Predesh: evidence for early Mesozoic diversification of Phreatoicidea (Isopoda, Crustacea) in Gondwana

George D. F. Wilson 1,2 and Shabuddin Shaik 3

1 Saugatuck Natural History Laboratory, Saugatuck, MI, USA; 

3 Department of Life Science, Central University of Karnataka, Kadaganchi, Aland Road, Kalaburagi Dist. - 585 367, India; shabu.biologist@gmail.com

2 Corresponding author: George D. F. Wilson, P. O. Box 714, Saugatuck, Michigan 49453, USA. e-mail: gdfw@snhlab.com 

File List:

Phreatoi20220525.nex 
	Mesquite data file that contains all data from the DELTA taxonomic database that were used for data presentation, organization, analysis, as well as trees resulting from all analyses. For Mesquite version 3.70; Maddison WP, Maddison DR. 2021. Mesquite: a modular system for evolutionary analysis.  Version 3.6 University of British Columbia & Oregon State University., http://www.mesquiteproject.org/ 
	DOI: 10.5281/zenodo.6617910
The DELTA database is still be expanded and changed so it is not included here
	For DELTA, see website https://www.delta-intkey.com/
	publications:
Dallwitz MJ. 1980. A general system for coding taxonomic descriptions. TAXON 29: 41-46.
Dallwitz MJ, Paine TA, Zurcher EJ. 2000. User's guide to the DELTA system: a general system for processing taxonomic descriptions. CSIRO: Canberra.

		
Phreatoi20220525.tnt -  the TNT data file generated by Mesquite
Analyses were performed using TNT-64bit, version 1.5, Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.
Note: TNT counts zero as a number so the first tree, taxon or k paramter is 0, the second is 1, the third is 2 and so on  

TNT Scripts were written or modified for this project by George D. F. Wilson. They were run using the console in Ubuntu 20.04 but should work using the console version of TNT in other operating systems available from http://www.lillo.org.ar/phylogeny/tnt/. I recommend using the console because it allows you do to multiple analysis with one script. 

Each script has a banner that explains what is being done. If this fails to appear the first time, enter n and restart the script

These are easily modified in a text editor to change the analysis
 -- tnt.run : standard run of tnt. 
 -- tnt-jacK.run :  symmetric jackknife analysis with concavity parameter, select file, concavity and prob parameter  
 -- piwe_rangeK.run : A range of concavity parameters are selected at the beginning and run sequentially
 -- setk_trans.run : Modified from setk.run by Salvador Arias, Instituto Miguel Lillo, San Miguel de Tucuman, Argentina
 -- aquickie_bt1000.run : Modified from the standard script distributed with TNT with more iterations of jackknifing
 
 If you are new to using TNT, see the information available on http://www.lillo.org.ar/phylogeny/tnt/ as well as these articles:
Goloboff PA. 1993. Estimating character weights during tree search. Cladistics 9: 83-91.
Goloboff PA. 1997. Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs. Cladistics 13: 225-245.
Goloboff PA, Carpenter JM, Arias JS, Esquivel DRM. 2008. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24: 758-773.
Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.
Goloboff PA, Farris JS. 2001. Methods for Quick Consensus Estimation. Cladistics 17: S26-S34.
Goloboff PA, Farris JS, Källersjö M, Oxelman B, Ramírez MJ, Szumik CA. 2003. Improvements to resampling measures of group support. Cladistics 19: 324-332.
Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.