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Analyses for Study 19738

Citation title: "Redescription of the skull of ?Trionyx? kyrgyzensis and improved phylogenetic taxon sampling of Cretaceous and Paleogene soft-shelled turtles (Trionychidae) of Asia, including the oldest crown trionychids".

Study name: "Redescription of the skull of ?Trionyx? kyrgyzensis and improved phylogenetic taxon sampling of Cretaceous and Paleogene soft-shelled turtles (Trionychidae) of Asia, including the oldest crown trionychids".

This study is part of submission 19738 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

P. kyrgyzensis only, Parsimony --

Step details

Name

Software used

Name
Algorithm
Commands
set autoclose=yes maxtrees=10000 increase=no; set criterion=parsimony; outgroup outgroup; delete Amyda_gregaria Ulutrionyx_ninae Trionyx_kansaiensis Khunnuchelys_kizylkumensis Gobiapalone_breviplastra Gobiapalone_orlovi Kuhnemys_maortuensis Perochelys_lamadongensis; hsearch addseq=random swap=TBR nreps=1000 enforce=no; condense collapse=minbrlen deldupes=yes; savetrees file=FILENAME.tre; contree all /strict=yes adams=yes majrule=yes file=FILENAME_con.tre; describetrees all; gettrees file=FILENAME_con.tre; describetrees all;

Output data

3 Output object(s)

Input data

1 Input object(s)

Analysis step

All fossils, Parsimony --

Step details

Name

Software used

Name
Algorithm
Commands
set autoclose=yes maxtrees=10000 increase=no; set criterion=parsimony; outgroup outgroup; loadconstr file=trionychid_scaffold_khunnuchelys-scaffold.tre asbackbone; hsearch addseq=random swap=TBR nreps=1000 constraints=allconstr enforce=yes; condense collapse=minbrlen deldupes=yes; savetrees file=kyrggrp160105allconstr-pars.tre; contree all /strict=yes adams=yes majrule=yes file=kyrggrp160105allconstr_con.tre; describetrees all; gettrees file=kyrggrp160105allconstr_con.tre; describetrees all

Output data

4 Output object(s)

Input data

1 Input object(s)

Analysis step

All Fossils, Bayesian --

Step details

Name

Software used

Name
Algorithm
Commands
BEGIN MRBAYES; [run with constraint] log start file=FILENAME_log.txt replace; set autoclose=yes nowarn=yes; constraint khunkan hard = Trionyx_kansaiensis Khunnuchelys_kizylkumensis; constraint bb01 partial = Cycloderma_aubryi Cycloderma_frenatum Cyclanorbis_elegans Cyclanorbis_senegalensis Lissemys_punctata : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb02 partial = Cycloderma_aubryi Cycloderma_frenatum Lissemys_punctata: Cyclanorbis_elegans Cyclanorbis_senegalensis; constraint bb03 partial = Cycloderma_aubryi Cycloderma_frenatum: Cyclanorbis_elegans Cyclanorbis_senegalensis Lissemys_punctata; constraint bb04 partial = Trionyx_triunguis Pelochelys_bibroni Chitra_indica : Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb05 partial = Apalone_ferox Apalone_mutica Apalone_spinifera : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb06 partial = Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; LSET coding=informative; PRSET symdirihyperpr=fixed(infinity) topologypr=constraints(khunkan, bb01, bb02, bb03, bb04, bb05, bb06); mcmc ngen=10000000 samplefreq=100 printfreq=10000 nchains=1 nruns=1; ss alpha=0.3 nsteps=10; sumt burnin=25000 contype=allcompat; sump burnin=25000; END;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

P. kyrgyzensis only, Bayesian --

Step details

Name

Software used

Name
Algorithm
Commands
BEGIN MRBAYES; [run with constraint] log start file=FILENAME.txt replace; set autoclose=yes nowarn=yes; constraint bb01 partial = Cycloderma_aubryi Cycloderma_frenatum Cyclanorbis_elegans Cyclanorbis_senegalensis Lissemys_punctata : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb02 partial = Cycloderma_aubryi Cycloderma_frenatum Lissemys_punctata: Cyclanorbis_elegans Cyclanorbis_senegalensis; constraint bb03 partial = Cycloderma_aubryi Cycloderma_frenatum: Cyclanorbis_elegans Cyclanorbis_senegalensis Lissemys_punctata; constraint bb04 partial = Trionyx_triunguis Pelochelys_bibroni Chitra_indica : Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb05 partial = Apalone_ferox Apalone_mutica Apalone_spinifera : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; constraint bb06 partial = Amyda_cartilaginea Nilssonia_formosa Nilssonia_gangeticus Nilssonia_hurum : Trionyx_triunguis Pelochelys_bibroni Chitra_indica Rafetus_euphraticus Apalone_ferox Apalone_mutica Apalone_spinifera Pelodiscus_sinensis Palea_steindachneri Dogania_subplana; LSET coding=informative; PRSET symdirihyperpr=fixed(infinity) topologypr=constraints(bb01, bb02, bb03, bb04, bb05, bb06); mcmc ngen=10000000 samplefreq=100 printfreq=10000 nchains=1 nruns=1; ss alpha=0.3 nsteps=10; sumt burnin=25000 contype=allcompat; sump burnin=25000; END;

Output data