#NEXUS

[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.


Generated on May 11, 2024; 20:44 GMT

TreeBASE (cc) 1994-2008

Study reference:
Hugall A., Foster R., & Lee M. 2007. Calibration Choice, Rate Smoothing, and the
Pattern of Tetrapod Diversification According to the Long Nuclear Gene RAG-1. Systematic
Biology, 56(4): 543-563.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1808]

BEGIN TAXA;
        TITLE  Codon_position_model_Bayesian_posterior_consensus;
        DIMENSIONS NTAX=88;
        TAXLABELS
            Alligator_mississipiensis
            Ambystoma_mexicanum
            Anas_strepera
            Anolis_paternus
            Apalone_spinifera
            Apomys_hylocoetes
            Aspidoscelis_tigris
            Asymblepharus_sikimmensis
            Basiliscus_plumifrons
            Bipes_biporus
            Brookesia_thieli
            Caiman_latirostris
            Calotes_calotes
            Carettochelys_insculpta
            Cercartetus_concinnus
            Chamaeleo_rudis
            Charadrius_vociferus
            Chelonia_mydas
            Coracias_caudata
            Crenadactylus_ocellatus
            Crocodylus_cataphractus
            Ctenophorus_salinarum
            Ctenotus_robustus
            Cylindrophis_ruffus
            Dermatemys_mawii
            Dibamus_sp.
            Dinodon_sp.
            Elephas_maximus
            Elgaria_panamintina
            Elseya_latisternum
            Eremias_sp.
            Eumeces_anthracinus
            Euprepis_auratus
            Gallus_gallus
            Gavia_immer
            Gavialis_gangeticus
            Gekko_gecko
            Geochelone_pardalis
            Grus_canadensis
            Heloderma_suspectum
            Homo_sapiens
            Hypogeophis_rostratus
            Ichthyophis_glutinosus
            Japalura_tricarinata
            Lama_glama
            Lanthanotus_borneensis
            Latimeria_menadoensis
            Leiocephalus_carinatus
            Leiolepis_belliana
            Lepidosiren_paradoxa
            Leposoma_parietale
            Lialis_jicari
            Lissemys_punctata
            Litoria_ewingii
            Megapodius_freycinet
            Monodelphis_domestica
            Mus_musculus
            Notoryctes_typhlops
            Ornithorhynchus_anatinus
            Oryctolagus_cuniculus
            Passer_montanus
            Pelusios_williamsi
            Physignathus_cocincinus
            Platysternon_megacephalum
            Pleurodeles_waltl
            Podocnemis_expansa
            Protopterus_dolloi
            Pseudothecadactylus_lindneri
            Ramphotyphlops_braminus
            Rattus_norvegicus
            Rhinatrema_bivittatum
            Rhineura_floridana
            Sarcophilus_harrisii
            Shinisaurus_crocodilurus
            Spheniscus_humboldti
            Sphenodon_punctatus
            Struthio_camelus
            Sus_scrofa
            Tachyglossus_aculeatus
            Tinamus_guttatus
            Tomistoma_schlegelii
            Typhlonectes_natans
            Typhlosaurus_lomii
            Varanus_griseus
            Xantusia_vigilis
            Xenopus_laevis
            Xenosaurus_grandis
            Zonosaurus_sp.
            ;
END;

BEGIN TREES;
      TITLE Tb8413;
      LINK TAXA = Codon_position_model_Bayesian_posterior_consensus;
      TREE nuc_MCMC_con = [&R] ((((((Monodelphis_domestica,(Sarcophilus_harrisii,(Notoryctes_typhlops,Cercartetus_concinnus))),((Elephas_maximus,(Homo_sapiens,(Oryctolagus_cuniculus,(Rattus_norvegicus,(Apomys_hylocoetes,Mus_musculus))))),(Sus_scrofa,Lama_glama))),(Tachyglossus_aculeatus,Ornithorhynchus_anatinus)),((Sphenodon_punctatus,((Dibamus_sp.,((((((Xenosaurus_grandis,(Elgaria_panamintina,Heloderma_suspectum)),(Shinisaurus_crocodilurus,(Varanus_griseus,Lanthanotus_borneensis))),(Ramphotyphlops_braminus,(Cylindrophis_ruffus,Dinodon_sp.))),((Leiocephalus_carinatus,(Basiliscus_plumifrons,Anolis_paternus)),(Leiolepis_belliana,((Brookesia_thieli,Chamaeleo_rudis),((Japalura_tricarinata,Calotes_calotes),(Physignathus_cocincinus,Ctenophorus_salinarum)))))),((Leposoma_parietale,Aspidoscelis_tigris),(Eremias_sp.,(Rhineura_floridana,Bipes_biporus)))),((Xantusia_vigilis,Zonosaurus_sp.),(Typhlosaurus_lomii,(Eumeces_anthracinus,(Euprepis_auratus,(Ctenotus_robustus,Asymblepharus_sikimmensis))))))),(Gekko_gecko,(Lialis_jicari,(Pseudothecadactylus_lindneri,Crenadactylus_ocellatus))))),((((Carettochelys_insculpta,(Lissemys_punctata,Apalone_spinifera)),((Chelonia_mydas,Dermatemys_mawii),(Geochelone_pardalis,Platysternon_megacephalum))),(Elseya_latisternum,(Podocnemis_expansa,Pelusios_williamsi))),((((Anas_strepera,(Gallus_gallus,Megapodius_freycinet)),((Gavia_immer,Charadrius_vociferus),((Spheniscus_humboldti,Grus_canadensis),(Coracias_caudata,Passer_montanus)))),(Tinamus_guttatus,Struthio_camelus)),((Alligator_mississipiensis,Caiman_latirostris),(Crocodylus_cataphractus,(Gavialis_gangeticus,Tomistoma_schlegelii))))))),(((Pleurodeles_waltl,Ambystoma_mexicanum),(Xenopus_laevis,Litoria_ewingii)),(Ichthyophis_glutinosus,(Rhinatrema_bivittatum,(Typhlonectes_natans,Hypogeophis_rostratus))))),(Protopterus_dolloi,Lepidosiren_paradoxa),Latimeria_menadoensis);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2784]


END;