User:Manudouz/sandbox/CAT Model

CAT is a model of DNA and protein sequence evolution.^[1]

Construction of the model

Reduction of long-branch attraction

CAT reduces long-branch attraction artefacts.^[2]

Applications

Acoelomorphs

Symsagittifera : Parsimony versus CAT^[3].

Xenacoelomorpha^[4] sister group to Nephrozoa^[5].

Turtles

Elucidation of the phylogenetic position of turtles among sauropsids^[6].

Ciliates

Unravelling the deep phylogenetic relationships among major ciliate lineages + the position of Protocruzia.^[7]

Convergent evolution in ciliates.^[8]

Mitochondria origin

Phylogenomic analyses indicate that mitochondria evolved from a proteobacteria lineage that branched off before the divergence of all sampled alphaproteobacteria.^[9]

Archaea

Supermatrix of proteins.^[10]

2D Tree of life

Concatenation of 35 core protein-coding genes.^[11] "We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data".

Redirect

Phylobayes

REDIRECT CAT model

References

^ Lartillot, Nicolas; Philippe, Hervé (2004-06-01). "A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process". Molecular Biology and Evolution. 21 (6): 1095–1109. doi:10.1093/molbev/msh112. ISSN 0737-4038. PMID 15014145.
^ Lartillot, Nicolas; Brinkmann, Henner; Philippe, Hervé (2007-01-01). "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model". BMC Evolutionary Biology. 7 (1): S4. doi:10.1186/1471-2148-7-S1-S4. ISSN 1471-2148. PMC 1796613. PMID 17288577.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Philippe, Hervé; Brinkmann, Henner; Martinez, Pedro; Riutort, Marta; Baguñà, Jaume (2007-08-08). "Acoel Flatworms Are Not Platyhelminthes: Evidence from Phylogenomics". PLOS ONE. 2 (8): e717. doi:10.1371/journal.pone.0000717. ISSN 1932-6203. PMC 1933604. PMID 17684563.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Philippe, Hervé; Brinkmann, Henner; Copley, Richard R.; Moroz, Leonid L.; Nakano, Hiroaki; Poustka, Albert J.; Wallberg, Andreas; Peterson, Kevin J.; Telford, Maximilian J. (2011-02-10). "Acoelomorph flatworms are deuterostomes related to Xenoturbella". Nature. 470 (7333): 255–258. doi:10.1038/nature09676. PMC 4025995. PMID 21307940.
^ Cannon, Johanna Taylor; Vellutini, Bruno Cossermelli; Smith, Julian; Ronquist, Fredrik; Jondelius, Ulf; Hejnol, Andreas (2016-02-04). "Xenacoelomorpha is the sister group to Nephrozoa". Nature. 530 (7588): 89–93. doi:10.1038/nature16520.
^ Chiari, Ylenia; Cahais, Vincent; Galtier, Nicolas; Delsuc, Frédéric (2012-01-01). "Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)". BMC Biology. 10: 65. doi:10.1186/1741-7007-10-65. ISSN 1741-7007. PMC 3473239. PMID 22839781.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Gentekaki, E.; Kolisko, M.; Boscaro, V.; Bright, K. J.; Dini, F.; Di Giuseppe, G.; Gong, Y.; Miceli, C.; Modeo, L. (2014-09-01). "Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages". Molecular Phylogenetics and Evolution. 78: 36–42. doi:10.1016/j.ympev.2014.04.020.
^ Lynn, Denis H.; Kolisko, Martin (2017-09-01). "Molecules illuminate morphology: phylogenomics confirms convergent evolution among 'oligotrichous' ciliates". International Journal of Systematic and Evolutionary Microbiology. 67 (9): 3676–3682. doi:10.1099/ijsem.0.002060. ISSN 1466-5026.
^ Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ (April 2018). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. doi:10.1038/s41586-018-0059-5. PMID 29695865.
^ Adam, Panagiotis S; Borrel, Guillaume; Brochier-Armanet, Céline; Gribaldo, Simonetta (2017-08-04). "The growing tree of Archaea: new perspectives on their diversity, evolution and ecology". The ISME Journal. 11 (11): 2407–2425. doi:10.1038/ismej.2017.122. ISSN 1751-7362. PMC 5649171. PMID 28777382.{{cite journal}}: CS1 maint: PMC format (link)
^ Williams, Tom A.; Cox, Cymon J.; Foster, Peter G.; Szöllősi, Gergely J.; Embley, T. Martin (2020). "Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution. 4 (1): 138–147. doi:10.1038/s41559-019-1040-x. ISSN 2397-334X. PMC 6942926. PMID 31819234.{{cite journal}}: CS1 maint: PMC format (link)

[1] Lartillot, Nicolas; Philippe, Hervé (2004-06-01). "A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process". Molecular Biology and Evolution. 21 (6): 1095–1109. doi:10.1093/molbev/msh112. ISSN 0737-4038. PMID 15014145.

[2] Lartillot, Nicolas; Brinkmann, Henner; Philippe, Hervé (2007-01-01). "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model". BMC Evolutionary Biology. 7 (1): S4. doi:10.1186/1471-2148-7-S1-S4. ISSN 1471-2148. PMC 1796613. PMID 17288577.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[3] Philippe, Hervé; Brinkmann, Henner; Martinez, Pedro; Riutort, Marta; Baguñà, Jaume (2007-08-08). "Acoel Flatworms Are Not Platyhelminthes: Evidence from Phylogenomics". PLOS ONE. 2 (8): e717. doi:10.1371/journal.pone.0000717. ISSN 1932-6203. PMC 1933604. PMID 17684563.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[4] Philippe, Hervé; Brinkmann, Henner; Copley, Richard R.; Moroz, Leonid L.; Nakano, Hiroaki; Poustka, Albert J.; Wallberg, Andreas; Peterson, Kevin J.; Telford, Maximilian J. (2011-02-10). "Acoelomorph flatworms are deuterostomes related to Xenoturbella". Nature. 470 (7333): 255–258. doi:10.1038/nature09676. PMC 4025995. PMID 21307940.

[5] Cannon, Johanna Taylor; Vellutini, Bruno Cossermelli; Smith, Julian; Ronquist, Fredrik; Jondelius, Ulf; Hejnol, Andreas (2016-02-04). "Xenacoelomorpha is the sister group to Nephrozoa". Nature. 530 (7588): 89–93. doi:10.1038/nature16520.

[6] Chiari, Ylenia; Cahais, Vincent; Galtier, Nicolas; Delsuc, Frédéric (2012-01-01). "Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)". BMC Biology. 10: 65. doi:10.1186/1741-7007-10-65. ISSN 1741-7007. PMC 3473239. PMID 22839781.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[7] Gentekaki, E.; Kolisko, M.; Boscaro, V.; Bright, K. J.; Dini, F.; Di Giuseppe, G.; Gong, Y.; Miceli, C.; Modeo, L. (2014-09-01). "Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages". Molecular Phylogenetics and Evolution. 78: 36–42. doi:10.1016/j.ympev.2014.04.020.

[8] Lynn, Denis H.; Kolisko, Martin (2017-09-01). "Molecules illuminate morphology: phylogenomics confirms convergent evolution among 'oligotrichous' ciliates". International Journal of Systematic and Evolutionary Microbiology. 67 (9): 3676–3682. doi:10.1099/ijsem.0.002060. ISSN 1466-5026.

[MartijnVosseberg2018-9] Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ (April 2018). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. doi:10.1038/s41586-018-0059-5. PMID 29695865.

[Adam2017-10] Adam, Panagiotis S; Borrel, Guillaume; Brochier-Armanet, Céline; Gribaldo, Simonetta (2017-08-04). "The growing tree of Archaea: new perspectives on their diversity, evolution and ecology". The ISME Journal. 11 (11): 2407–2425. doi:10.1038/ismej.2017.122. ISSN 1751-7362. PMC 5649171. PMID 28777382.{{cite journal}}: CS1 maint: PMC format (link)

[11] Williams, Tom A.; Cox, Cymon J.; Foster, Peter G.; Szöllősi, Gergely J.; Embley, T. Martin (2020). "Phylogenomics provides robust support for a two-domains tree of life". Nature Ecology & Evolution. 4 (1): 138–147. doi:10.1038/s41559-019-1040-x. ISSN 2397-334X. PMC 6942926. PMID 31819234.{{cite journal}}: CS1 maint: PMC format (link)

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