TreeBASE Search-Analyses for study 10908

@ARTICLE{TreeBASE2Ref19240, author = {John J. Wiens and Caitlin A. Kuczynski and Ted M. Townsend and Tod W. Reeder and Daniel G. Mulcahy and Jack W. Sites}, title = {Combining phylogenomics and fossils in higher level squamate reptile phylogeny: molecular data change the placement of fossil taxa. }, year = {2010}, keywords = {Combined analysis, fossils, lizards, morphology, phylogeny, snakes, squamates.}, doi = {}, url = {http://}, pmid = {}, journal = {Systematic Biology}, volume = {}, number = {}, pages = {}, abstract = {Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.} }

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Analyses for Study 10908

Citation title: "Combining phylogenomics and fossils in higher level squamate reptile phylogeny: molecular data change the placement of fossil taxa. ".

Study name: "Combining phylogenomics and fossils in higher level squamate reptile phylogeny: molecular data change the placement of fossil taxa. ".

This study is part of submission 10898 (Status: Published).

Analyses

Analysis 1

Analysis details

Input data

2 Input object(s)

Analysis step

Untitled --

Software used

Name
Algorithm
Commands
charset morph = 15795 -16157; partition type = 67 : BDNF_3rdpos , BDNF_1stpos , BDNF_2ndpos , BMP2_2ndpos , BMP2_3rdpos , BMP2_1stpos , DNAH3_3rdpos , DNAH3_1stpos , DNAH3_2ndpos , FSTL5_3rdpos , FSTL5_1stpos , FSTL5_2ndpos , RAG1_3rdpos , RAG1_1stpos , RAG1_2ndpos , NTF_1stpos , NTF_2ndpos , NTF_3rdpos , SLC30A1_1stpos , SLC30A1_2ndpos , SLC30A1_3rdpos , FSHR_1stpos , FSHR_2ndpos , FSHR_3rdpos , ZEB2_1stpos , ZEB2_2ndpos , ZEB2_3rdpos , TRAF6_1stpos , TRAF6_2ndpos , TRAF6_3rdpos , PNN_1stpos , PNN_2ndpos , PNN_3rdpos , SLC8A1_1stpos , SLC8A1_2ndpos , SLC8A1_3rdpos , VCPIP1_1stpos , VCPIP1_2ndpos , VCPIP1_3rdpos , ANDP_1stpos , ANDP_2ndpos , ANDP_3rdpos , CAND1_1stpos , CAND1_2ndpos , CAND1_3rdpos , DLL1_1stpos , DLL1_2ndpos , DLL1_3rdpos , ECEL_1stpos , ECEL_2ndpos , ECEL_3rdpos , ENC1_1stpos , ENC1_2ndpos , ENC1_3rdpos , GPR_1stpos , GPR_2ndpos , GPR_3rdpos , LRRN1_1stpos , LRRN1_2ndpos , LRRN1_3rdpos , NGFB_1stpos , NGFB_2ndpos , NGFB_3rdpos , SINCAIP_1stpos , SINCAIP_2ndpos , SINCAIP_3rdpos , morph; set partition = type; Prset applyto = ( 61 -63 ) statefreqpr = fixed ( equal ); Lset applyto = ( 1 , 2 , 3 , 28 , 29 , 30 , 52 , 53 , 54 , 58 , 59 , 60 , 64 , 65 , 66 ) Nst = 2 rates = invgamma; Lset applyto = ( 4 -27 ) Nst = 6 rates = invgamma; Lset applyto = ( 31 -33 ) Nst = 6 rates = invgamma; Lset applyto = ( 37 -51 ) Nst = 6 rates = invgamma; Lset applyto = ( 55 -57 ) Nst = 6 rates = invgamma; Lset applyto = ( 61 -63 ) Nst = 6 rates = invgamma; Lset applyto = ( 34 -36 ) Nst = 6 rates = gamma; Lset applyto = ( 67 ) coding = variable rates = gamma; unlink shape = ( all ) pinvar = ( all ) revmat = ( all ) statefreq = ( all ); Mcmc ngen = 20000000 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes;

Output data

1 Output object(s)