The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions-6

Cates are shown on all nodes. The TPO primate clade appears here as a polytomy as the branch lengths are extremely short, however, this is in fact resolved with a low Bootstrap of 56%. The star symbol denotes those branches that were treated as foreground in the selection analysis. The analysis of the resolved phylogeny using gene tree species tree reconciliation method implemented in GeneTree. The large filled circles represent gene duplication events, and the red branches indicate gene losses.<p><b>Copyright information:</b></p><p>Taken from "The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions"</p><p>http://www.biomedcentral.com/1471-2148/8/101</p><p>BMC Evolutionary Biology 2008;8():101-101.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2315650.</p><p></p

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions-3

Ely selected in MPO, in blue is the heme binding site. Example of the affect on hydrogen bonding of one such mutation at positively selected position 496 in human MPO from Asparagine to Phenylalanine.<p><b>Copyright information:</b></p><p>Taken from "The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions"</p><p>http://www.biomedcentral.com/1471-2148/8/101</p><p>BMC Evolutionary Biology 2008;8():101-101.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2315650.</p><p></p

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions-5

He entire dataset. The bootstrap support values from 1000 replicates are shown on all nodes. (b) Resolved phylogeny following site stripping, the cow sequence for LPO can be seen to take an unusual place on the phylogeny.<p><b>Copyright information:</b></p><p>Taken from "The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions"</p><p>http://www.biomedcentral.com/1471-2148/8/101</p><p>BMC Evolutionary Biology 2008;8():101-101.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2315650.</p><p></p

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions-2

Cates are shown on all nodes. The TPO primate clade appears here as a polytomy as the branch lengths are extremely short, however, this is in fact resolved with a low Bootstrap of 56%. The star symbol denotes those branches that were treated as foreground in the selection analysis. The analysis of the resolved phylogeny using gene tree species tree reconciliation method implemented in GeneTree. The large filled circles represent gene duplication events, and the red branches indicate gene losses.<p><b>Copyright information:</b></p><p>Taken from "The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions"</p><p>http://www.biomedcentral.com/1471-2148/8/101</p><p>BMC Evolutionary Biology 2008;8():101-101.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2315650.</p><p></p

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions-4

Uences are outgroups to the MHP clade. The following are the species abbreviations used: Dog (D); Cow (C); Macaque (Ma); Human (H); Chimp (Ch); Rat (R); Mouse (M), Chicken (G), and Opossum (Op). This phylogeny was compared to each of the resultant site stripped phylogenies. Graph showing the RMSD nodal distance () between each site-stripped phylogeny () and the ideal phylogeny. : All: refers to the complete MSA; 8: site category 8 removed from the MSA; 8, 7: categories 8 and 7 removed from the MSA and so on up to the final column that contains only the most slowly evolving category of site. Values close to/zero correspond to complete agreement between the ideal and site stripped phylogeny.<p><b>Copyright information:</b></p><p>Taken from "The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions"</p><p>http://www.biomedcentral.com/1471-2148/8/101</p><p>BMC Evolutionary Biology 2008;8():101-101.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2315650.</p><p></p

Nucleotide_sequences_used_McCole_Evolution

Nucleotide sequences for genes used in the study, collected from UCSC, Ensembl genome broswers and the NCBI trace archive. File was created using word and saved as plain text. Abbreviated binomial nomenclature is used for each species, for example H. sapiens for humans