Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.
ELTE-MTA 'Lendület' Biophysics Research Group, Pázmány P. stny. 1A, 1117 Budapest, Hungary.
Gergely J
GJ
Szöllősi
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69000 Lyon, France.
Adrián Arellano
AA
Davín
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69000 Lyon, France Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, 38334 Montbonnot, France.
Eric
E
Tannier
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69000 Lyon, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, 69622 Villeurbanne, France.
Vincent
V
Daubin
Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69000 Lyon, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, 69622 Villeurbanne, France bastien.boussau@univ-lyon1.fr.
Bastien
B
Boussau
D003198:Computer Simulation; D000458:Cyanobacteria / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D008957:Models, Genetic; D010802:Phylogeny
birth–death models; gene duplication; gene transfer; gene tree-species tree; genomics; statistics