title: Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited.
abstract: We investigated the basal phylogeny of eukaryotes through analyses of sequences from the ADP-ATP mitochondrial carrier, a transmembrane protein that is stable in function across eukaryote kingdoms. The ADP-ATP data strongly suggest the grouping of Plantae and Fungi to the exclusion of Metazoa. We implemented several procedures to avoid pervasive analytical artifacts such as erroneous alignment, random rooting, long branch attraction, and misidentification of noisy characters. The quest of an eukaryote tree that would be largely consistent across multiple loci might be essentially illusory because of differential lineage sorting, horizontal gene transfer, and the chimeric nature of early eukaryotes. Better understanding of these evolutionary parameters, requiring separate phylogenetic analyses of multiple independent loci, is fundamental for resolution of the modes of emergence and evolution of the major eukaryote lineages.
authors.affiliation: Unit of Evolutionary Genetics, Free University of Brussels (ULB), C.P. 300, Institute of Molecular Biology and Medicine, Rue Jeener and Brachet 12, B-6041 Gosselies, Belgium.
authors.forename: A
authors.initials: A
authors.lastname: Löytynoja
authors.forename: M C
authors.initials: MC
authors.lastname: Milinkovitch
mesh_terms: D000818:Animals; D005057:Eukaryotic Cells; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics*; D000226:Mitochondrial ADP, ATP Translocases / Q000235:genetics*; D010802:Phylogeny; D010944:Plants / Q000235:genetics / Q000378:metabolism
chemical_list: D000226:Mitochondrial ADP, ATP Translocases