#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; 7:50 GMT

TreeBASE (cc) 1994-2008

Study reference:
Simmons M., & Freudenstein J. 2002. Uninode coding vs. gene-tree parsimony for phylogenetic
reconstruction using duplicate genes. Molecular Phylogenetics and Evolution,
23(3): 481-498.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S875]

BEGIN TAXA;
        TITLE  TaxonLabelSet10876;
        DIMENSIONS NTAX=73;
        TAXLABELS
            Alligator_mississippiensis
            Alopias_vulpinus
            Ambystoma_tigrinum
            Anas_platyrhynchos
            Anguilla_anguilla
            Anolis_carolinensis
            Anser_sp
            Astyanax_fasciatus
            Balaenoptera_sp
            Bos_taurus
            Brachiostoma_sp
            Brachydanio_rerio
            Bufo_japonicus
            Callithrix_jacchus
            Canis_familiaris
            Capra_hircus
            Carassius_auratus
            Catostomus_commersoni
            Cavia_porcellus
            Ciona_sp
            Columba_livia
            Coregonus_autumnalis
            Coturnix_coturnix
            Crocodylus_novaeguineae
            Cyprinus_carpio
            Dicentrarchus_labrax
            Dipnoi_sp
            Eptatretus_burgeri
            Eptatretus_stouti
            Equus_caballus
            Felis_silvestris_catus
            Fundulus_heteroclitus
            Gadus_morhua
            Gallus_gallus
            Gambusia_affinis
            Gecko_gecko
            Homo_sapiens
            Ictalurus_punctatus
            Lampetra_japonica
            Macacca_mulatta
            Meleagris_gallopavo
            Mesocricetus_auratus
            Mus_musculus
            Naja_naja
            Oncorhynchus_masou
            Oncorhynchus_mykiss
            Oncorynchus_keta
            Oreochromis_mossambicensis
            Oryctolagus_cuniculus
            Oryzias_latipes
            Ovis_aries
            Petromyzon_marinus
            Plethodon_jordani
            Pleurodeles_waltl
            Pleuronectes_platessa
            Poecilia_reticulata
            Pomatoschistus_minutus
            Raja_erinacea
            Rana_catesbeiana
            Rana_sp
            Rattus_norvegicus
            Salmo_salar
            Scleropus_sp
            Sparus_aurata
            Sphoeroides_nephelus
            Squalus_acanthias
            Struthio_camelus
            Sus_scrofa
            Takifugu_rubripes
            Testudines_sp
            Torpedo_marmorata
            Vulpes_vulpes
            Xenopus_laevis
            ;
END;

BEGIN TREES;
      TITLE Tb6230;
      LINK TAXA = TaxonLabelSet10876;
      TREE 'Table 1 and appendices 1-8' = [&R] (Ciona_sp,(((((((((((((((Vulpes_vulpes,Felis_silvestris_catus,Canis_familiaris),Equus_caballus),(Sus_scrofa,(((Ovis_aries,Capra_hircus),Bos_taurus),Balaenoptera_sp))),((Homo_sapiens,Macacca_mulatta),Callithrix_jacchus)),Cavia_porcellus),((Mus_musculus,Rattus_norvegicus),Mesocricetus_auratus)),Oryctolagus_cuniculus),(((((Gallus_gallus,Coturnix_coturnix),Meleagris_gallopavo),(Anas_platyrhynchos,Anser_sp)),Columba_livia,Struthio_camelus),(Alligator_mississippiensis,Crocodylus_novaeguineae),Testudines_sp)),(((Rana_sp,Rana_catesbeiana),Xenopus_laevis,Bufo_japonicus),(Ambystoma_tigrinum,Pleurodeles_waltl,Plethodon_jordani))),((Scleropus_sp,Anolis_carolinensis),(Gecko_gecko,Naja_naja))),((Torpedo_marmorata,Raja_erinacea),Squalus_acanthias,Alopias_vulpinus)),Dipnoi_sp),((((((((Sparus_aurata,Dicentrarchus_labrax),Oreochromis_mossambicensis),(Sphoeroides_nephelus,Takifugu_rubripes),Pleuronectes_platessa),Fundulus_heteroclitus,Poecilia_reticulata,Gambusia_affinis,Pomatoschistus_minutus,Oryzias_latipes),((Salmo_salar,Oncorhynchus_mykiss,Coregonus_autumnalis,Oncorynchus_keta,Oncorhynchus_masou),Gadus_morhua)),((Carassius_auratus,Cyprinus_carpio),Catostomus_commersoni,Ictalurus_punctatus,Brachydanio_rerio,Astyanax_fasciatus)),Anguilla_anguilla),(Eptatretus_burgeri,Eptatretus_stouti))),(Petromyzon_marinus,Lampetra_japonica)),Brachiostoma_sp));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4031]


END;