En rouge les taxons pour lesquels l'arbre va plus loin :
Urochordés - Chondrichthyens - Actinoptérygiens - Lissamphibiens - Lépidosauriens - Oiseaux - Mammifères
Commentaires
Céphalochordés/Urochordés - Il fait désormais consensus que la position des Céphalochordés et des Urochordés est inversée par rapport à la systématique traditionnelle, i.e. que les Urochordés sont le véritable groupe frère des Craniates/Vertébrés.
Vertébrés - Du fait de la monophylie des Cyclostomes, le terme "Vertébrés" devient synonyme de "Craniates". Conformément à ce que cela suggère, il est apparu récemment que les myxines (Cyclostomes) possèdent bien des éléments vertébraux.
Cyclostomes - Il est désormais établi que les myxines et les lamproies forment bel et bien un groupe monophylétique.
Chéloniens - Les articles récents semblent s'accorder à placer les Chéloniens en groupe frère des Archosauriens. De fait le terme "Sauropsidés" devient synonyme de "Diapsides". Le clade formé par les Chéloniens et les Archosauriens a été récemment nommé Archélosauriens.
Références
Austin CM, Tan MH, Croft LJ, Hammer MP & Gan HM (2015) Whole genome sequencing of the Asian arowana (Scleropages formosus) provides insights into the evolution of ray-finned fishes. Genome Biology and Evolution, 7: 2885-2895
Chen M, Zou M, Yang L & He S (2012) Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing. PLoS ONE, 7: e36256
Chiari Y, Cachais V, Galtier N & Delsuc F (2012) Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biology, 10: 65
Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K & Glenn TC (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters, 8: 783-786
Donoghue PCJ & Keating JN (2014) Early vertebrate evolution. Palaeontology, 57: 879-893
Dunn CW, Giribet G, Edgecombe GD & Hejnol A (2014) Animal phylogeny and its evolutionary implications. Annual Reviews of Ecology Evolution, Evolution, and Systematics, 45: 371-395
Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR & Peterson KJ (2014) Toward consilience in reptile phylogeny: microRNAs support an archosaur, not a lepidosaur affinity for turtles. Evolution & Development, 16: 189-196
Fong JJ, Brown JM, Fujita MK & Boussau B (2012) A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PLoS ONE, 7: e48990
Gemell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH et al. (2020) The tuatara genome reveals ancient features of amniote evolution. Nature, 584: 403-409
Giribet G (2015) New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. Organisms Diversity & Evolution, 16: 419-426
Giribet G (2016) Genomics and the animal tree of life: conflicts and future prospects. Zoologica Scripta, 45: 14-21
Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanago M, Keeley SD, Tatsumi K, Tanaka K, Motone F, Kageyama Y et al. (2018) Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nature Ecology & Evolution, doi: 10.1038/s41559-018-0673-5
Heimberg AM, Cowper-Sallari R, Sémon M, Donoghue PCJ & Peterson KJ (2010) microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proceedings of the National Academy of Sciences of the United States of America, 107: 19379-19383
Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire JY, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M & Philippe H (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology & Evolution, 1: 1370-1378
Janvier P (2011) Comparative anatomy: all vertebrates do have vertebra. Current Biology, 21: R661-R663
Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M et al. (2019) Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nature Ecology & Evolution, 3: 1241-252
Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A et al. (2021) Giant lungfish genome elucidates the conquest of land by vertebrates. Nature, 590: 284-289
Ota KG, Oisi Y, Fujimoto S & Kuratani S (2014) The origin of developmental mechanisms underlying vertebral elements: implications from hagfish evo-devo. Zoology, 117: 77-80
Satoh N, Rokhsar D & Nishikawa T (2014) Chordate evolution and the three-phylum system. Proceedings of the Royal Society B, 281: 20141729
Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK et al. (2013) The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, 14: R28
Shen XX, Liang D, When JZ & Zhang P (2011) Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Molecular Biology and Evolution, 28: 3237-3252
Shen XX, Hittinger CT & Rokas A (2017) Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution, 1: 126
Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F et al. (2015) Hemichordate genomes and deuterostome origins. Nature, 527: 459-465
Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connelle MJ & Creevey CJ (2019) Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics. Molecular Biology and Evolution: msz067
Takezaki N & Nishihara H (2017) Support for lungfish as the closest relative of Tetrapods by using slowly evolving ray-finned fish as the outgroup. Genome Biology and Evolution, 9: 93-101
Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA et al. (2018) Comparative genomics reveals accelarated evolution in conserved pathways during the diversification of Anole lizards. Genome Biology and Evolution, 10: 489-506
Torres-Sánchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M & San Mauro D (2018) Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. Dna Research, doi: 10.1093/dnares/dsy034
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D et al. (2013) The draft genomes of softshell turtle and green sea turtle yield insights into the development and evolution of the turtlespecific body plan. Nature Genetics, 45: 701-706