title: Phylogenetic analysis of genome rearrangements among five mammalian orders.
abstract: Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Luo
authors.forename: William
authors.initials: W
authors.lastname: Arndt
authors.forename: Yiwei
authors.initials: Y
authors.lastname: Zhang
authors.forename: Guanqun
authors.initials: G
authors.lastname: Shi
authors.forename: Max A
authors.initials: MA
authors.lastname: Alekseyev
authors.forename: Jijun
authors.initials: J
authors.lastname: Tang
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
authors.forename: Robert
authors.initials: R
authors.lastname: Friedman
mesh_terms: D000818:Animals; D001188:Artiodactyla / Q000145:classification / Q000235:genetics; D005075:Biological Evolution; D002335:Carnivora / Q000145:classification / Q000235:genetics; D023061:Gene Order; D016678:Genome; D008322:Mammals / Q000145:classification* / Q000235:genetics; D008957:Models, Genetic; D010527:Perissodactyla / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D011323:Primates / Q000145:classification / Q000235:genetics; D020543:Proteome / Q000032:analysis; D012377:Rodentia / Q000145:classification / Q000235:genetics; D012984:Software
chemical_list: D020543:Proteome