title: Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees.
abstract: As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland christophe.praz@unine.ch jonathan.romiguier@gmail.com Laurent.Keller@unil.ch.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Romiguier
authors.affiliation: Department of Entomology, University of Illinois, Urbana.
authors.forename: Sydney A
authors.initials: SA
authors.lastname: Cameron
authors.affiliation: Department of Entomology, University of California, Riverside.
authors.forename: S Hollis
authors.initials: SH
authors.lastname: Woodard
authors.affiliation: Department of Biology, Hobart and William Smith Colleges, Geneva, NY.
authors.forename: Brielle J
authors.initials: BJ
authors.lastname: Fischman
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland christophe.praz@unine.ch jonathan.romiguier@gmail.com Laurent.Keller@unil.ch.
authors.forename: Laurent
authors.initials: L
authors.lastname: Keller
authors.affiliation: Institute of Biology, University of Neuchatel, Neuchatel, Switzerland christophe.praz@unine.ch jonathan.romiguier@gmail.com Laurent.Keller@unil.ch.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Praz
mesh_terms: D000818:Animals; D001482:Base Composition; D001516:Bees / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D017344:Genes, Insect; D018740:Genetic Heterogeneity; D049750:Genome, Insect; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny
keywords: GC-biased gene conversion; base composition; bees; eusociality; phylogenomics