Journal
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
Volume 370, Issue 1678, Pages -Publisher
ROYAL SOC
DOI: 10.1098/rstb.2014.0335
Keywords
gene tree-species tree; genomics; statistics; birth-death models; gene transfer; gene duplication
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Funding
- French Agence Nationale de la Recherche (ANR) [ANR-10-BINF-01-01]
- FP7-PEOPLE-CIG grant 'GENESTORY'
- PRACE project [2013081661]
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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.
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